diff --git a/.github/workflows/python-testing.yml b/.github/workflows/python-testing.yml
index c5ab746a..e411ba21 100644
--- a/.github/workflows/python-testing.yml
+++ b/.github/workflows/python-testing.yml
@@ -77,5 +77,11 @@ jobs:
     - name: Test cropseg bids, with path override, left hemi
       run: | 
         $HIPPUNFOLD - test_out participant -np --modality cropseg --path_cropseg test_data/data_cropseg_1hemi/sub-{subject}_hemi-{hemi}_dseg.nii.gz --hemi L
+    - name: Test T2w with T1w template registration
+      run: |
+        $HIPPUNFOLD test_data/bids_singleT2w test_out participant -np --modality T2w --t1_reg_template
+    - name: Test T2w with additional T1w output space 
+      run: |
+        $HIPPUNFOLD test_data/bids_singleT2w test_out participant -np --modality T2w --output_space T1w
 
 
diff --git a/docs/tutorials/standardBIDS.md b/docs/tutorials/standardBIDS.md
index daeae7b4..f307b104 100644
--- a/docs/tutorials/standardBIDS.md
+++ b/docs/tutorials/standardBIDS.md
@@ -20,18 +20,19 @@ prefixing the command with `singularity run`. This will expect
     └── sub-002/
     ...
 
+The `--modality` flag is required to specify which input image type should be used and in most cases, T1w should be most robust (though other types are supported!).
+
 The T1w image is used to register to a standardized
 template (CITI168), making it possible to reorient, upsample, and crop
 around the left and right hippocampi (this is referred to within
-HippUnfold as `space-corobl`). Note that only the T1w image needs to
-have a whole-brain field of view. By default, any additional input images
-are coregistered and preprocessed, but this can be skipped with the
-flags `--skip_coreg` and `--skip_preproc`, repsectively.
+HippUnfold as `space-corobl`). Note that the T1w image should 
+have a whole-brain field of view. 
 
 More examples of possible BIDS-compliant datasets can be found in
 [hippunfold/test\_data/](https://github.com/khanlab/hippunfold/tree/master/test_data).
 
 ## Different input modalities 
+
 By default, HippUnfold expects the `PATH_TO_BIDS_DIR` to contain at least
 one T1w file for segmenting intrahippocampal
 structures like the SRLM. However, we have
@@ -39,18 +40,20 @@ also provided models trained with T1w, T2w, or DWI data, or, users can input
 their own custom manual segmentations for unfolding, which can be
 specified with the `--modality` flag. For example:
 
-    hippunfold  PATH_TO_BIDS_DIR PATH_TO_OUTPUT_DIR participant --modality T1w
+    hippunfold  PATH_TO_BIDS_DIR PATH_TO_OUTPUT_DIR participant --modality T2w
 
-would work for a dataset with only T1w images, like this one:
+would work for a dataset with only T2w images, like this one:
 
     PATH_TO_BIDS_DIR/
     └── sub-001/
         └── anat/
-            └── sub-001_T1w.nii.gz
+            └── sub-001_T2w.nii.gz
     ...
 
-Note that specifying a manual segmentation (eg. `--modality segT1w`)
-expects to additionally find a file with the suffix `_dseg` which should
+Note that in this case, registration to a T2w CITI168 template will be performed with the input T2w image. In some cases it may be preferrable to use a T1w image for registration to the standard CITI168 template. A T1w image can be registered to both the input T2w and T1w CITI168 template with the `--t1_reg_template` flag. This is typically most robust as long as a full brain FOV T1w image is available. If this registering is still failing then it may be improved with the `--rigid-reg-template` flag.
+
+Specifying a manual segmentation (eg. `--modality segT1w`)
+expects to additionally find an input file with the suffix `_dseg` which should
 contain labels following the protocol outlined
 [here](https://ars.els-cdn.com/content/image/1-s2.0-S1053811917309977-mmc1.pdf).
 More details are provided on using manual segmentations on the following
@@ -84,17 +87,4 @@ This will search for any any files following the naming scheme and fill
 in `{subject}` IDs for any files it can. Alternatively, `{subject}` IDs
 can be provided in a list with the `--participant_label` flag.
 
-## No T1w images
-
-It is difficult to automatically reorient and crop images appropriately
-without a whole-brain T1w image, which we recommend collecting as a part
-of any acquisition protocol when possible. However, if this is not
-possible, the T2w image may be used instead by specifying it as the T1w
-with the `--path_T1w` flag. This registration may fail, and is
-especially likely to fail if the T2w images are not whole-brain. This
-can sometimes be ameliorated with the `--rigid_reg_template` flag.
 
-Alternatively, if you do not have a standard T1w scan, consider manually
-orienting and/or cropping your data and following the examples outlined
-in the [Specialized scans
-tutorial](specializedScans.md).
diff --git a/hippunfold/config/snakebids.yml b/hippunfold/config/snakebids.yml
index 731529f3..2bb38929 100644
--- a/hippunfold/config/snakebids.yml
+++ b/hippunfold/config/snakebids.yml
@@ -134,7 +134,6 @@ parse_args:
       - segT1w
       - segT2w
       - cropseg
-      - neonateT1w
       
   --derivatives:
     help: 'Path to the derivatives folder (e.g. for finding manual segs) (default: %(default)s) '
@@ -179,7 +178,10 @@ parse_args:
     default: 'CITI168'
     help: 'Set the template to use for registration to coronal oblique. (default: %(default)s)'
 
-
+  --t1_reg_template:
+    help: 'Use T1w to register to template space, instead of the segmentation modality. Note: this was the default behavior prior to v1.0.0.  (default: %(default)s)'
+    default: false
+    action: store_true
 
   --use_gpu:
     help: 'Enable gpu for inference by setting resource gpus=1 in run_inference rule (default: %(default)s)'
@@ -193,12 +195,9 @@ parse_args:
 
   --output_spaces:
     choices: 
-      - 'cropT1w'
-      - 'corobl'
-    default:
-      - 'cropT1w'
+      - 'T1w'
     nargs: '+'
-    help: 'Sets the output space for results (default: %(default)s)'
+    help: 'Sets additional output spaces for results (default: %(default)s)'
 
   --output_density:
     choices:
@@ -261,10 +260,11 @@ singularity:
   ants: 'docker://kaczmarj/ants:2.3.4'
 
 xfm_identity: resources/identity_xfm.txt
-template: dHCP
+template: CITI168
 template_files:
   CITI168:
     T1w: resources/CITI168/T1w_head_700um.nii.gz
+    T2w: resources/CITI168/T2w_head_700um.nii.gz
     xfm_corobl: resources/CITI168/CoronalOblique_rigid.txt
     crop_ref: resources/CITI168/T2w_300umCoronalOblique_hemi-{hemi}.nii.gz
     crop_refT1w: resources/CITI168/T1w_300umCoronalOblique_hemi-{hemi}.nii.gz
@@ -399,7 +399,6 @@ laplace_labels:
 
 
 output_spaces:
-  - cropT1w
 
 participant_label:
 exclude_participant_label:
@@ -418,4 +417,5 @@ skip_coreg: False
 keep_work: False
 skip_inject_template_labels: False
 force_nnunet_model: False
-root: results
\ No newline at end of file
+t1_reg_template: False
+root: results
diff --git a/hippunfold/resources/CITI168/T2w_head_700um.nii.gz b/hippunfold/resources/CITI168/T2w_head_700um.nii.gz
new file mode 100644
index 00000000..022c4d34
Binary files /dev/null and b/hippunfold/resources/CITI168/T2w_head_700um.nii.gz differ
diff --git a/hippunfold/workflow/Snakefile b/hippunfold/workflow/Snakefile
index a3af7346..97efe6fa 100644
--- a/hippunfold/workflow/Snakefile
+++ b/hippunfold/workflow/Snakefile
@@ -7,21 +7,63 @@ from snakebids import bids
 configfile: "config/snakebids.yml"
 
 
-# make adjustments to input params:
-# right now hippb500 or cropseg cannot use T1w output space
-if config["modality"] == "hippb500" or config["modality"] == "cropseg":
-    config["output_spaces"] = ["corobl"]
+# consider moving this logic to another smk file to clean-up
 
-if config["skip_inject_template_labels"]:
-    config["autotop_labels"] = ["hipp"]
-
-# get list of inputs to limit to (T1w + modalities)
 limit_to_list = set()
-if "cropT1w" in config["output_spaces"]:
+ref_spaces = []
+crop_ref_spaces = []
+template_modality = False
+
+# if no additional output spaces chosen, then empty list:
+if config["output_spaces"] == None:
+    config["output_spaces"] = []
+
+# set the lists used for output spaces
+if (
+    config["modality"] == "T1w"
+    or config["modality"] == "segT1w"
+    or "T1w" in config["output_spaces"]
+):
+    ref_spaces.append("T1w")
+    crop_ref_spaces.append("cropT1w")
     limit_to_list.add("T1w")
+if (
+    config["modality"] == "T2w"
+    or config["modality"] == "segT2w"
+    or "T2w" in config["output_spaces"]
+):
+    ref_spaces.append("T2w")
+    crop_ref_spaces.append("cropT2w")
+    limit_to_list.add("T2w")
+if (
+    config["modality"] == "hippb500"
+    or config["modality"] == "cropseg"
+    or "corobl" in config["output_spaces"]
+):
+    ref_spaces.append("corobl")
+    crop_ref_spaces.append("corobl")
+
+
+# set the modality to use for template registration
+if "T2w" in config["modality"]:
+    if config["t1_reg_template"]:
+        limit_to_list.add("T1w")
+        template_modality = "T1w"
+    else:
+        template_modality = "T2w"
+
+elif "T1w" in config["modality"]:
+    template_modality = "T1w"
+
+
+# only generate hipp surface if skipping template injection
+#   i.e. drop dentate
+if config["skip_inject_template_labels"]:
+    config["autotop_labels"] = ["hipp"]
 
 
-if config["modality"][:3] == "seg":  # if modality is segT2w, then add seg and T2w
+# add seg (if chosen) and the modality to the inputs
+if config["modality"][:3] == "seg":  # if modality is segT2w, then add seg
     limit_to_list.add("seg")
     limit_to_list.add(config["modality"][3:])
 else:
@@ -95,7 +137,7 @@ include: "rules/warps.smk"
 include: "rules/shape_inject.smk"
 include: "rules/gifti.smk"
 include: "rules/subfields.smk"
-include: "rules/resample_final_to_crop_t1.smk"
+include: "rules/resample_final_to_crop_native.smk"
 
 
 rule all:
diff --git a/hippunfold/workflow/rules/common.smk b/hippunfold/workflow/rules/common.smk
index 1d1d1cd9..4eeeaf1b 100644
--- a/hippunfold/workflow/rules/common.smk
+++ b/hippunfold/workflow/rules/common.smk
@@ -24,11 +24,6 @@ def get_modality_suffix(modality):
 
 
 def get_final_spec():
-    surf_spaces = []
-    if "cropT1w" in config["output_spaces"]:
-        surf_spaces.append("T1w")
-    if "corobl" in config["output_spaces"]:
-        surf_spaces.append("corobl")
 
     if len(config["hemi"]) == 2:
         specs = expand(
@@ -42,7 +37,7 @@ def get_final_spec():
                 **config["subj_wildcards"],
             ),
             density=config["output_density"],
-            space=surf_spaces,
+            space=ref_spaces,
             autotop=config["autotop_labels"],
             allow_missing=True,
         )
@@ -59,7 +54,7 @@ def get_final_spec():
                 **config["subj_wildcards"],
             ),
             density=config["output_density"],
-            space=surf_spaces,
+            space=ref_spaces,
             hemi=config["hemi"],
             autotop=config["autotop_labels"],
             allow_missing=True,
@@ -79,7 +74,7 @@ def get_final_subfields():
             **config["subj_wildcards"],
         ),
         hemi=config["hemi"],
-        space=config["output_spaces"],
+        space=crop_ref_spaces,
         allow_missing=True,
     )
 
@@ -109,7 +104,7 @@ def get_final_coords():
             dir=["AP", "PD", "IO"],
             autotop=config["autotop_labels"],
             hemi=config["hemi"],
-            space=config["output_spaces"],
+            space=crop_ref_spaces,
             allow_missing=True,
         )
     )
@@ -129,7 +124,7 @@ def get_final_coords():
             desc=[desc_io],
             dir=["IO"],
             hemi=config["hemi"],
-            space=config["output_spaces"],
+            space=crop_ref_spaces,
             allow_missing=True,
         )
     )
@@ -137,11 +132,6 @@ def get_final_coords():
 
 
 def get_final_transforms():
-    if "cropT1w" in config["output_spaces"]:
-        output_ref = "T1w"
-    else:
-        output_ref = "corobl"
-
     xfms = []
 
     xfms.extend(
@@ -157,7 +147,7 @@ def get_final_transforms():
                 to="unfold",
                 mode="image",
             ),
-            space=output_ref,
+            space=ref_spaces,
             autotop=config["autotop_labels"],
             hemi=config["hemi"],
             allow_missing=True,
@@ -177,31 +167,13 @@ def get_final_transforms():
                 to="{space}",
                 mode="image",
             ),
-            space=output_ref,
-            autotop=config["autotop_labels"],
-            hemi=config["hemi"],
-            allow_missing=True,
-        )
-    )
-    xfms.extend(
-        expand(
-            bids(
-                root=root,
-                datatype="seg",
-                **config["subj_wildcards"],
-                label="{autotop}",
-                suffix="xfm.nii.gz",
-                hemi="{hemi}",
-                from_="{space}",
-                to="unfold",
-                mode="image",
-            ),
-            space=output_ref,
+            space=ref_spaces,
             autotop=config["autotop_labels"],
             hemi=config["hemi"],
             allow_missing=True,
         )
     )
+
     xfms.extend(
         expand(
             bids(
@@ -223,7 +195,7 @@ def get_final_transforms():
 def get_final_anat():
     anat = []
 
-    if "cropT1w" in config["output_spaces"]:
+    if "T1w" in ref_spaces or "T2w" in ref_spaces:
         anat.extend(
             expand(
                 bids(
@@ -237,7 +209,7 @@ def get_final_anat():
                     hemi="{hemi}",
                     **config["subj_wildcards"],
                 ),
-                space=config["output_spaces"],
+                space=crop_ref_spaces,
                 hemi=config["hemi"],
                 allow_missing=True,
             )
@@ -247,19 +219,26 @@ def get_final_anat():
 
 def get_final_qc():
     qc = []
+
     # right now can only do qc from cropT1w space
-    if "cropT1w" in config["output_spaces"]:
+    #    output_ref = []
+    #    if "cropT1w" in config["output_spaces"]:
+    #        output_ref.append("T1w")
+    #    if "cropT2w" in config["output_spaces"]:
+    #        output_ref.append("T2w")
 
+    if not template_modality == False:
         qc.extend(
             expand(
                 bids(
                     root=root,
                     datatype="qc",
                     suffix="regqc.png",
-                    from_="subject",
+                    from_="{native_modality}",
                     to=config["template"],
                     **config["subj_wildcards"],
                 ),
+                native_modality=template_modality,
                 allow_missing=True,
             )
         )
@@ -271,11 +250,13 @@ def get_final_qc():
                     datatype="qc",
                     suffix="dseg.png",
                     desc="subfields",
-                    space="cropT1w",
+                    #                   space="crop{native_modality}",
+                    space="{native_modality}",
                     hemi="{hemi}",
                     **config["subj_wildcards"],
                 ),
                 hemi=config["hemi"],
+                native_modality=crop_ref_spaces,
                 allow_missing=True,
             )
         )
@@ -287,7 +268,8 @@ def get_final_qc():
                     suffix="midthickness.surf.png",
                     den="{density}",
                     desc="subfields",
-                    space="cropT1w",
+                    #                    space="crop{native_modality}",
+                    space="{native_modality}",
                     hemi="{hemi}",
                     label="{autotop}",
                     **config["subj_wildcards"],
@@ -295,38 +277,41 @@ def get_final_qc():
                 hemi=config["hemi"],
                 autotop=config["autotop_labels"],
                 density=config["output_density"],
+                native_modality=crop_ref_spaces,
                 allow_missing=True,
             )
         )
-        if len(config["hemi"]) == 2:
-            qc.extend(
-                expand(
-                    bids(
-                        root=root,
-                        datatype="qc",
-                        desc="subfields",
-                        suffix="volumes.png",
-                        **config["subj_wildcards"],
-                    ),
-                    allow_missing=True,
-                )
+    if len(config["hemi"]) == 2:
+        qc.extend(
+            expand(
+                bids(
+                    root=root,
+                    datatype="qc",
+                    desc="subfields",
+                    space="{native_modality}",
+                    suffix="volumes.png",
+                    **config["subj_wildcards"],
+                ),
+                native_modality=ref_spaces,
+                allow_missing=True,
             )
+        )
 
-        if (config["modality"] == "T1w") or (config["modality"] == "T2w"):
-            qc.extend(
-                expand(
-                    bids(
-                        root=root,
-                        datatype="qc",
-                        desc="unetf3d",
-                        suffix="dice.tsv",
-                        hemi="{hemi}",
-                        **config["subj_wildcards"],
-                    ),
-                    hemi=config["hemi"],
-                    allow_missing=True,
-                )
+    if (config["modality"] == "T1w") or (config["modality"] == "T2w"):
+        qc.extend(
+            expand(
+                bids(
+                    root=root,
+                    datatype="qc",
+                    desc="unetf3d",
+                    suffix="dice.tsv",
+                    hemi="{hemi}",
+                    **config["subj_wildcards"],
+                ),
+                hemi=config["hemi"],
+                allow_missing=True,
             )
+        )
     return qc
 
 
diff --git a/hippunfold/workflow/rules/gifti.smk b/hippunfold/workflow/rules/gifti.smk
index ad4cfbed..5b39f20c 100644
--- a/hippunfold/workflow/rules/gifti.smk
+++ b/hippunfold/workflow/rules/gifti.smk
@@ -306,8 +306,8 @@ rule unflip_gii_unfolded:
         "cp {input.gii} {output.gii}"
 
 
-# warp from corobl to T1w
-rule warp_gii_to_T1w:
+# warp from corobl to native
+rule warp_gii_to_native:
     input:
         gii=bids(
             root=work,
@@ -324,7 +324,7 @@ rule warp_gii_to_T1w:
             datatype="anat",
             **config["subj_wildcards"],
             suffix="xfm.txt",
-            from_="T1w",
+            from_="{native_modality}",
             to="corobl",
             desc="affine",
             type_="ras"
@@ -335,7 +335,7 @@ rule warp_gii_to_T1w:
             datatype="surf",
             den="{density}",
             suffix="{surfname}.surf.gii",
-            space="T1w",
+            space="{native_modality}",
             hemi="{hemi}",
             label="{autotop}",
             **config["subj_wildcards"]
@@ -348,7 +348,7 @@ rule warp_gii_to_T1w:
         "wb_command -surface-apply-affine {input.gii} {input.xfm} {output.gii}"
 
 
-# morphological features, calculated in T1w space:
+# morphological features, calculated in native space:
 rule calculate_surface_area:
     input:
         gii=bids(
diff --git a/hippunfold/workflow/rules/preproc_t1.smk b/hippunfold/workflow/rules/preproc_t1.smk
index 8add34da..1e3672e1 100644
--- a/hippunfold/workflow/rules/preproc_t1.smk
+++ b/hippunfold/workflow/rules/preproc_t1.smk
@@ -125,14 +125,16 @@ rule reg_to_template:
 
 rule qc_reg_to_template:
     input:
-        ref=os.path.join(
-            workflow.basedir, "..", config["template_files"][config["template"]]["T1w"]
+        ref=lambda wildcards: os.path.join(
+            workflow.basedir,
+            "..",
+            config["template_files"][config["template"]][wildcards.native_modality],
         ),
         flo=bids(
             root=work,
             datatype="anat",
             **config["subj_wildcards"],
-            suffix="T1w.nii.gz",
+            suffix="{native_modality}.nii.gz",
             space=config["template"],
             desc="affine"
         ),
@@ -143,7 +145,7 @@ rule qc_reg_to_template:
                 datatype="qc",
                 **config["subj_wildcards"],
                 suffix="regqc.png",
-                from_="subject",
+                from_="{native_modality}",
                 to=config["template"]
             ),
             caption="../report/t1w_template_regqc.rst",
@@ -162,7 +164,7 @@ rule convert_template_xfm_ras2itk:
             datatype="anat",
             **config["subj_wildcards"],
             suffix="xfm.txt",
-            from_="T1w",
+            from_="{reg_suffix}",
             to=config["template"],
             desc="affine",
             type_="ras"
@@ -173,7 +175,7 @@ rule convert_template_xfm_ras2itk:
             datatype="anat",
             **config["subj_wildcards"],
             suffix="xfm.txt",
-            from_="T1w",
+            from_="{reg_suffix}",
             to=config["template"],
             desc="affine",
             type_="itk"
@@ -230,7 +232,7 @@ rule invert_template_xfm_itk2ras:
             datatype="anat",
             **config["subj_wildcards"],
             suffix="xfm.txt",
-            from_="T1w",
+            from_="{native_modality}",
             to="corobl",
             desc="affine",
             type_="itk"
@@ -241,7 +243,7 @@ rule invert_template_xfm_itk2ras:
             datatype="anat",
             **config["subj_wildcards"],
             suffix="xfm.txt",
-            from_="T1w",
+            from_="{native_modality}",
             to="corobl",
             desc="affineInverse",
             type_="ras"
@@ -261,7 +263,7 @@ rule template_xfm_itk2ras:
             datatype="anat",
             **config["subj_wildcards"],
             suffix="xfm.txt",
-            from_="T1w",
+            from_="{native_modality}",
             to="corobl",
             desc="affine",
             type_="itk"
@@ -272,7 +274,7 @@ rule template_xfm_itk2ras:
             datatype="anat",
             **config["subj_wildcards"],
             suffix="xfm.txt",
-            from_="T1w",
+            from_="{native_modality}",
             to="corobl",
             desc="affine",
             type_="ras"
diff --git a/hippunfold/workflow/rules/preproc_t2.smk b/hippunfold/workflow/rules/preproc_t2.smk
index e49a74f9..9eec9f2f 100644
--- a/hippunfold/workflow/rules/preproc_t2.smk
+++ b/hippunfold/workflow/rules/preproc_t2.smk
@@ -240,29 +240,110 @@ rule reg_t2_to_t1:
         "c3d_affine_tool  {output.xfm_ras} -oitk {output.xfm_itk}"
 
 
-# now have t2 to t1 xfm, compose this with t1 to corobl xfm
-rule compose_t2_xfm_corobl:
+rule reg_t2_to_template:
+    """register t2 directly to template, instead of using t1"""
     input:
-        t2_to_t1=bids(
+        flo=bids(
             root=work,
             datatype="anat",
             **config["subj_wildcards"],
-            suffix="xfm.txt",
-            from_="T2w",
-            to="T1w",
-            desc="rigid",
-            type_="itk"
+            suffix="T2w.nii.gz",
+            desc="preproc"
+        ),
+        ref=os.path.join(
+            workflow.basedir, "..", config["template_files"][config["template"]]["T2w"]
+        ),
+        xfm_identity=os.path.join(workflow.basedir, "..", config["xfm_identity"]),
+    params:
+        cmd=reg_to_template_cmd,
+    output:
+        warped_subj=bids(
+            root=work,
+            datatype="anat",
+            **config["subj_wildcards"],
+            suffix="T2w.nii.gz",
+            space=config["template"],
+            desc="affine"
         ),
-        t1_to_cor=bids(
+        xfm_ras=bids(
             root=work,
             datatype="anat",
             **config["subj_wildcards"],
             suffix="xfm.txt",
-            from_="T1w",
-            to="corobl",
+            from_="T2w",
+            to=config["template"],
             desc="affine",
-            type_="itk"
+            type_="ras"
         ),
+    container:
+        config["singularity"]["autotop"]
+    group:
+        "subj"
+    shell:
+        "{params.cmd}"
+
+
+def get_inputs_compose_t2_xfm_corobl(wildcards):
+    if config["t1_reg_template"]:
+        # xfm0: t2 to t1
+        # xfm1: t1 to corobl
+        t2_to_t1 = (
+            bids(
+                root=work,
+                datatype="anat",
+                **config["subj_wildcards"],
+                suffix="xfm.txt",
+                from_="T2w",
+                to="T1w",
+                desc="rigid",
+                type_="itk"
+            ),
+        )
+        t1_to_cor = (
+            bids(
+                root=work,
+                datatype="anat",
+                **config["subj_wildcards"],
+                suffix="xfm.txt",
+                from_="T1w",
+                to="corobl",
+                desc="affine",
+                type_="itk"
+            ),
+        )
+        return {"t2_to_t1": t2_to_t1, "t1_to_cor": t1_to_cor}
+
+    else:
+
+        # xfm0: t2 to template
+        t2_to_std = (
+            bids(
+                root=work,
+                datatype="anat",
+                **config["subj_wildcards"],
+                suffix="xfm.txt",
+                from_="T2w",
+                to=config["template"],
+                desc="affine",
+                type_="itk"
+            ),
+        )
+
+        # xfm1: template to corobl
+        std_to_cor = (
+            os.path.join(
+                workflow.basedir,
+                "..",
+                config["template_files"][config["template"]]["xfm_corobl"],
+            ),
+        )
+        return {"t2_to_std": t2_to_std, "std_to_cor": std_to_cor}
+
+
+# now have t2 to t1 xfm, compose this with t1 to corobl xfm
+rule compose_t2_xfm_corobl:
+    input:
+        unpack(get_inputs_compose_t2_xfm_corobl),
     output:
         t2_to_cor=bids(
             root=work,
diff --git a/hippunfold/workflow/rules/resample_final_to_crop_t1.smk b/hippunfold/workflow/rules/resample_final_to_crop_native.smk
similarity index 89%
rename from hippunfold/workflow/rules/resample_final_to_crop_t1.smk
rename to hippunfold/workflow/rules/resample_final_to_crop_native.smk
index 6b5f2310..14b92207 100644
--- a/hippunfold/workflow/rules/resample_final_to_crop_t1.smk
+++ b/hippunfold/workflow/rules/resample_final_to_crop_native.smk
@@ -7,19 +7,19 @@ rule create_native_crop_ref:
             datatype="seg",
             suffix="dseg.nii.gz",
             desc="subfields",
-            space="T1w",
+            space="{native_modality}",
             hemi="{hemi}",
             **config["subj_wildcards"]
         ),
     params:
         resample="400%",
-        pad_to="192x256x256vox",
+        pad_to="256x256x256vox",
     output:
         ref=bids(
             root=work,
             datatype="seg",
             suffix="cropref.nii.gz",
-            space="T1w",
+            space="{native_modality}",
             hemi="{hemi}",
             **config["subj_wildcards"]
         ),
@@ -47,7 +47,7 @@ rule resample_unet_native_crop:
             datatype="anat",
             **config["subj_wildcards"],
             suffix="xfm.txt",
-            from_="T1w",
+            from_="{native_modality}",
             to="corobl",
             desc="affine",
             type_="itk"
@@ -56,7 +56,7 @@ rule resample_unet_native_crop:
             root=work,
             datatype="seg",
             suffix="cropref.nii.gz",
-            space="T1w",
+            space="{native_modality}",
             hemi="{hemi}",
             **config["subj_wildcards"]
         ),
@@ -66,7 +66,7 @@ rule resample_unet_native_crop:
             datatype="seg",
             suffix="dseg.nii.gz",
             desc="unet",
-            space="cropT1w",
+            space="crop{native_modality}",
             hemi="{hemi}",
             **config["subj_wildcards"]
         ),
@@ -95,7 +95,7 @@ rule resample_postproc_native_crop:
             datatype="anat",
             **config["subj_wildcards"],
             suffix="xfm.txt",
-            from_="T1w",
+            from_="{native_modality}",
             to="corobl",
             desc="affine",
             type_="itk"
@@ -104,7 +104,7 @@ rule resample_postproc_native_crop:
             root=work,
             datatype="seg",
             suffix="cropref.nii.gz",
-            space="T1w",
+            space="{native_modality}",
             hemi="{hemi}",
             **config["subj_wildcards"]
         ),
@@ -114,7 +114,7 @@ rule resample_postproc_native_crop:
             datatype="seg",
             suffix="dseg.nii.gz",
             desc="postproc",
-            space="cropT1w",
+            space="crop{native_modality}",
             hemi="{hemi}",
             **config["subj_wildcards"]
         ),
@@ -143,7 +143,7 @@ rule resample_subfields_native_crop:
             datatype="anat",
             **config["subj_wildcards"],
             suffix="xfm.txt",
-            from_="T1w",
+            from_="{native_modality}",
             to="corobl",
             desc="affine",
             type_="itk"
@@ -152,7 +152,7 @@ rule resample_subfields_native_crop:
             root=work,
             datatype="seg",
             suffix="cropref.nii.gz",
-            space="T1w",
+            space="{native_modality}",
             hemi="{hemi}",
             **config["subj_wildcards"]
         ),
@@ -162,7 +162,7 @@ rule resample_subfields_native_crop:
             datatype="seg",
             suffix="dseg.nii.gz",
             desc="subfields",
-            space="cropT1w",
+            space="crop{native_modality}",
             hemi="{hemi}",
             **config["subj_wildcards"]
         ),
@@ -193,7 +193,7 @@ rule resample_coords_native_crop:
             datatype="anat",
             **config["subj_wildcards"],
             suffix="xfm.txt",
-            from_="T1w",
+            from_="{native_modality}",
             to="corobl",
             desc="affine",
             type_="itk"
@@ -202,7 +202,7 @@ rule resample_coords_native_crop:
             root=work,
             datatype="seg",
             suffix="cropref.nii.gz",
-            space="T1w",
+            space="{native_modality}",
             hemi="{hemi}",
             **config["subj_wildcards"]
         ),
@@ -213,7 +213,7 @@ rule resample_coords_native_crop:
             dir="{dir}",
             suffix="coords.nii.gz",
             desc="{desc}",
-            space="cropT1w",
+            space="crop{native_modality}",
             hemi="{hemi}",
             label="{autotop}",
             **config["subj_wildcards"]
@@ -227,20 +227,20 @@ rule resample_coords_native_crop:
         "antsApplyTransforms -d 3 --interpolation NearestNeighbor -i {input.nii} -o {output.nii} -r {input.ref}  -t [{input.xfm},1]"
 
 
-rule resample_t1_to_crop:
+rule resample_native_to_crop:
     input:
         nii=bids(
             root=root,
             datatype="anat",
             **config["subj_wildcards"],
             desc="preproc",
-            suffix="T1w.nii.gz"
+            suffix="{native_modality}.nii.gz"
         ),
         ref=bids(
             root=work,
             datatype="seg",
             suffix="cropref.nii.gz",
-            space="T1w",
+            space="{native_modality}",
             hemi="{hemi}",
             **config["subj_wildcards"]
         ),
@@ -249,8 +249,8 @@ rule resample_t1_to_crop:
             root=root,
             datatype="seg",
             desc="preproc",
-            suffix="T1w.nii.gz",
-            space="cropT1w",
+            suffix="{native_modality}.nii.gz",
+            space="crop{native_modality}",
             hemi="{hemi}",
             **config["subj_wildcards"]
         ),
@@ -273,7 +273,7 @@ def get_xfm_t2_to_t1():
             **config["subj_wildcards"],
             suffix="xfm.txt",
             from_="T2w",
-            to="T1w",
+            to="{native_modality}",
             desc="rigid",
             type_="itk"
         )
@@ -293,7 +293,7 @@ rule resample_t2_to_crop:
             root=work,
             datatype="seg",
             suffix="cropref.nii.gz",
-            space="T1w",
+            space="{native_modality}",
             hemi="{hemi}",
             **config["subj_wildcards"]
         ),
@@ -308,7 +308,7 @@ rule resample_t2_to_crop:
             datatype="seg",
             desc="preproc",
             suffix="T2w.nii.gz",
-            space="cropT1w",
+            space="crop{native_modality}",
             hemi="{hemi}",
             **config["subj_wildcards"]
         ),
diff --git a/hippunfold/workflow/rules/subfields.smk b/hippunfold/workflow/rules/subfields.smk
index 4f81bbb5..f4eb724d 100644
--- a/hippunfold/workflow/rules/subfields.smk
+++ b/hippunfold/workflow/rules/subfields.smk
@@ -93,8 +93,8 @@ rule combine_tissue_subfield_labels_corobl:
         "c3d {input.tissue} -dup {params.remap_dg} -dup {params.remap_srlm} {params.remap_cyst} {input.subfields} -push dg -max -push srlm -max -push cyst -max -type uchar -o {output}"
 
 
-rule resample_subfields_to_T1w:
-    """Resampling to T1w native space"""
+rule resample_subfields_to_native:
+    """Resampling to native space"""
     input:
         nii=bids(
             root=work,
@@ -110,13 +110,17 @@ rule resample_subfields_to_T1w:
             datatype="anat",
             **config["subj_wildcards"],
             suffix="xfm.txt",
-            from_="T1w",
+            from_="{native_modality}",
             to="corobl",
             desc="affine",
             type_="itk"
         ),
         ref=bids(
-            root=work, datatype="anat", **config["subj_wildcards"], suffix="T1w.nii.gz"
+            root=root,
+            datatype="anat",
+            **config["subj_wildcards"],
+            desc="preproc",
+            suffix="{native_modality}.nii.gz"
         ),
     output:
         nii=bids(
@@ -124,7 +128,7 @@ rule resample_subfields_to_T1w:
             datatype="seg",
             suffix="dseg.nii.gz",
             desc="subfields",
-            space="T1w",
+            space="{native_modality,T1w|T2w}",
             hemi="{hemi}",
             **config["subj_wildcards"]
         ),
@@ -137,8 +141,8 @@ rule resample_subfields_to_T1w:
         "antsApplyTransforms -d 3 --interpolation MultiLabel -i {input.nii} -o {output.nii} -r {input.ref}  -t [{input.xfm},1]"
 
 
-rule resample_postproc_to_T1w:
-    """Resample post-processed tissue seg to T1w"""
+rule resample_postproc_to_native:
+    """Resample post-processed tissue seg to native"""
     input:
         nii=bids(
             root=work,
@@ -154,13 +158,17 @@ rule resample_postproc_to_T1w:
             datatype="anat",
             **config["subj_wildcards"],
             suffix="xfm.txt",
-            from_="T1w",
+            from_="{native_modality}",
             to="corobl",
             desc="affine",
             type_="itk"
         ),
         ref=bids(
-            root=work, datatype="anat", **config["subj_wildcards"], suffix="T1w.nii.gz"
+            root=root,
+            datatype="anat",
+            **config["subj_wildcards"],
+            desc="preproc",
+            suffix="{native_modality}.nii.gz"
         ),
     output:
         nii=bids(
@@ -168,7 +176,7 @@ rule resample_postproc_to_T1w:
             datatype="seg",
             suffix="dseg.nii.gz",
             desc="postproc",
-            space="T1w",
+            space="{native_modality,T2w|T2w}",
             hemi="{hemi}",
             **config["subj_wildcards"]
         ),
@@ -181,8 +189,8 @@ rule resample_postproc_to_T1w:
         "antsApplyTransforms -d 3 --interpolation MultiLabel -i {input.nii} -o {output.nii} -r {input.ref}  -t [{input.xfm},1]"
 
 
-rule resample_unet_to_T1w:
-    """Resample unet tissue seg to T1w"""
+rule resample_unet_to_native:
+    """Resample unet tissue seg to native"""
     input:
         nii=bids(
             root=work,
@@ -198,13 +206,17 @@ rule resample_unet_to_T1w:
             datatype="anat",
             **config["subj_wildcards"],
             suffix="xfm.txt",
-            from_="T1w",
+            from_="{native_modality}",
             to="corobl",
             desc="affine",
             type_="itk"
         ),
         ref=bids(
-            root=work, datatype="anat", **config["subj_wildcards"], suffix="T1w.nii.gz"
+            root=root,
+            datatype="anat",
+            **config["subj_wildcards"],
+            desc="preproc",
+            suffix="{native_modality}.nii.gz"
         ),
     output:
         nii=bids(
@@ -212,7 +224,7 @@ rule resample_unet_to_T1w:
             datatype="seg",
             suffix="dseg.nii.gz",
             desc="unet",
-            space="T1w",
+            space="{native_modality,T1w|T2w}",
             hemi="{hemi}",
             **config["subj_wildcards"]
         ),
@@ -234,7 +246,7 @@ rule get_subfield_vols_subj:
                 **config["subj_wildcards"],
                 datatype="seg",
                 hemi="{hemi}",
-                space="cropT1w",
+                space="{native_modality}",
                 desc="subfields",
                 suffix="dseg.nii.gz"
             ),
@@ -250,6 +262,7 @@ rule get_subfield_vols_subj:
         tsv=bids(
             root=root,
             datatype="seg",
+            space="{native_modality}",
             desc="subfields",
             suffix="volumes.tsv",
             **config["subj_wildcards"]
@@ -263,6 +276,7 @@ rule plot_subj_subfields:
         tsv=bids(
             root=root,
             datatype="seg",
+            space="{native_modality}",
             desc="subfields",
             suffix="volumes.tsv",
             **config["subj_wildcards"]
@@ -272,6 +286,7 @@ rule plot_subj_subfields:
             bids(
                 root=root,
                 datatype="qc",
+                space="{native_modality}",
                 desc="subfields",
                 suffix="volumes.png",
                 **config["subj_wildcards"]
@@ -297,7 +312,7 @@ def get_bg_img_for_subfield_qc(wildcards):
         datatype="seg",
         desc="preproc",
         suffix=f"{bg_modality}.nii.gz",
-        space="cropT1w",
+        space="crop{native_modality}",
         hemi="{hemi}",
         **config["subj_wildcards"],
     )
@@ -311,7 +326,7 @@ rule qc_subfield:
             datatype="seg",
             suffix="dseg.nii.gz",
             desc="subfields",
-            space="cropT1w",
+            space="crop{native_modality}",
             hemi="{hemi}",
             **config["subj_wildcards"]
         ),
@@ -322,7 +337,7 @@ rule qc_subfield:
                 datatype="qc",
                 suffix="dseg.png",
                 desc="subfields",
-                space="cropT1w",
+                space="crop{native_modality}",
                 hemi="{hemi}",
                 **config["subj_wildcards"]
             ),
@@ -342,7 +357,7 @@ rule qc_subfield_surf:
             datatype="surf",
             suffix="midthickness.surf.gii",
             den="{density}",
-            space="T1w",
+            space="{native_modality}",
             hemi="{hemi}",
             label="{autotop}",
             **config["subj_wildcards"]
@@ -355,7 +370,7 @@ rule qc_subfield_surf:
                 suffix="midthickness.surf.png",
                 den="{density}",
                 desc="subfields",
-                space="cropT1w",
+                space="crop{native_modality}",
                 hemi="{hemi}",
                 label="{autotop}",
                 **config["subj_wildcards"]
diff --git a/hippunfold/workflow/rules/warps.smk b/hippunfold/workflow/rules/warps.smk
index 6f1959d2..ec2246e4 100644
--- a/hippunfold/workflow/rules/warps.smk
+++ b/hippunfold/workflow/rules/warps.smk
@@ -451,8 +451,8 @@ rule compose_warps_unfold2corobl_lhemi:
         "antsApplyTransforms -o [{output.unfold2corobl},1] -r {input.ref} -t {input.flipLR_xfm} -t {input.unfold2native} -i {input.unfold_ref} -v"
 
 
-rule compose_warps_t1_to_unfold:
-    """ Compose warps from T1w to unfold """
+rule compose_warps_native_to_unfold:
+    """ Compose warps from native to unfold """
     input:
         corobl2unfold=bids(
             root=work,
@@ -473,12 +473,12 @@ rule compose_warps_t1_to_unfold:
             suffix="refvol.nii.gz",
             **config["subj_wildcards"]
         ),
-        t1w2corobl=bids(
+        native2corobl=bids(
             root=work,
             datatype="anat",
             **config["subj_wildcards"],
             suffix="xfm.txt",
-            from_="T1w",
+            from_="{native_modality}",
             to="corobl",
             desc="affine",
             type_="itk"
@@ -491,7 +491,7 @@ rule compose_warps_t1_to_unfold:
             label="{autotop}",
             suffix="xfm.nii.gz",
             hemi="{hemi}",
-            from_="T1w",
+            from_="{native_modality}",
             to="unfold",
             mode="image"
         ),
@@ -500,11 +500,11 @@ rule compose_warps_t1_to_unfold:
     group:
         "subj"
     shell:
-        "ComposeMultiTransform 3 {output} -R {input.ref} {input.corobl2unfold} {input.t1w2corobl}"
+        "ComposeMultiTransform 3 {output} -R {input.ref} {input.corobl2unfold} {input.native2corobl}"
 
 
-rule compose_warps_unfold_to_cropt1:
-    """ Compose warps from unfold to cropT1w """
+rule compose_warps_unfold_to_crop_native:
+    """ Compose warps from unfold to crop native """
     input:
         unfold2corobl=bids(
             root=root,
@@ -521,16 +521,16 @@ rule compose_warps_unfold_to_cropt1:
             root=work,
             datatype="seg",
             suffix="cropref.nii.gz",
-            space="T1w",
+            space="{native_modality}",
             hemi="{hemi}",
             **config["subj_wildcards"]
         ),
-        t1w2corobl=bids(
+        native2corobl=bids(
             root=work,
             datatype="anat",
             **config["subj_wildcards"],
             suffix="xfm.txt",
-            from_="T1w",
+            from_="{native_modality}",
             to="corobl",
             desc="affine",
             type_="itk"
@@ -544,7 +544,7 @@ rule compose_warps_unfold_to_cropt1:
             **config["subj_wildcards"]
         ),
     output:
-        unfold2cropt1=bids(
+        unfold2cropnative=bids(
             root=root,
             datatype="seg",
             **config["subj_wildcards"],
@@ -552,7 +552,7 @@ rule compose_warps_unfold_to_cropt1:
             suffix="xfm.nii.gz",
             hemi="{hemi}",
             from_="unfold",
-            to="T1w",
+            to="{native_modality}",
             mode="image"
         ),
     container:
@@ -560,4 +560,4 @@ rule compose_warps_unfold_to_cropt1:
     group:
         "subj"
     shell:
-        "antsApplyTransforms -o [{output.unfold2cropt1},1] -r {input.ref} -t [{input.t1w2corobl},1] -t {input.unfold2corobl} -i {input.unfold_ref} -v"
+        "antsApplyTransforms -o [{output.unfold2cropnative},1] -r {input.ref} -t [{input.native2corobl},1] -t {input.unfold2corobl} -i {input.unfold_ref} -v"