diff --git a/hippunfold/config/snakebids.yml b/hippunfold/config/snakebids.yml
index 295b46d3..a350a176 100644
--- a/hippunfold/config/snakebids.yml
+++ b/hippunfold/config/snakebids.yml
@@ -147,8 +147,17 @@ parse_args:
     default: False
     action: 'store_true'
 
+  --use_gpu:
+    help: 'Enable gpu for inference by setting resource gpus=1 in run_inference rule (default: %(default)s)'
+    default: False
+    action: 'store_true'
+
+  --nnunet_disable_tta:
+    help: 'Disable test-time augmentation for nnU-net inference, speeds up inference by 8x, at expense of accuracy (default: %(default)s)'
+    default: False
+    action: 'store_true'
 
-    
+   
 #--- workflow specific configuration -- 
 
 singularity:
diff --git a/hippunfold/workflow/rules/nnunet.smk b/hippunfold/workflow/rules/nnunet.smk
index dee8ee59..01d37a96 100644
--- a/hippunfold/workflow/rules/nnunet.smk
+++ b/hippunfold/workflow/rules/nnunet.smk
@@ -59,21 +59,22 @@ rule run_inference:
         out_folder = 'templbl',
         task = parse_task_from_tar,
         chkpnt = parse_chkpnt_from_tar,
+        disable_tta = '' if config['nnunet_disable_tta'] else '--disable_tta'
     output: 
         nnunet_seg = bids(root='work',datatype='seg_{modality}',**config['subj_wildcards'],suffix='dseg.nii.gz',desc='nnunet',space='corobl',hemi='{hemi,Lflip|R}')
     shadow: 'minimal' 
-    threads: 16 
+    threads: 16
     resources:
-        gpus = 1,
+        gpus = 1 if config['use_gpu'] else 0,
         mem_mb = 32000,
-        time = 30,
+        time = 30 if config['use_gpu'] else 60,
     group: 'subj'
     shell: 'mkdir -p {params.model_dir} {params.in_folder} {params.out_folder} && ' #create temp folders
            'cp -v {input.in_img} {params.temp_img} && ' #cp input image to temp folder
            'tar -xvf {input.model_tar} -C {params.model_dir} && ' #extract model
            'export RESULTS_FOLDER={params.model_dir} && ' #set nnunet env var to point to model
            'export nnUNet_n_proc_DA={threads} && ' #set threads
-           'nnUNet_predict -i {params.in_folder} -o {params.out_folder} -t {params.task} -chk {params.chkpnt} && ' # run inference
+           'nnUNet_predict -i {params.in_folder} -o {params.out_folder} -t {params.task} -chk {params.chkpnt} {params.disable_tta} && ' # run inference
            'cp -v {params.temp_lbl} {output.nnunet_seg}' #copy from temp output folder to final output
 
 
diff --git a/requirements.txt b/requirements.txt
deleted file mode 100644
index fe4abfbb..00000000
--- a/requirements.txt
+++ /dev/null
@@ -1,44 +0,0 @@
-amply==0.1.4
-appdirs==1.4.4
-attrs==20.3.0
-bids-validator==1.5.8
-certifi==2020.12.5
-chardet==3.0.4
-click==7.1.2
-ConfigArgParse==1.2.3
-datrie==0.8.2
-docopt==0.6.2
-docutils==0.16
-gitdb==4.0.5
-GitPython==3.1.11
-idna==2.10
-ipython-genutils==0.2.0
-jsonschema==3.2.0
-jupyter-core==4.7.0
-nbformat==5.0.8
-nibabel==3.2.1
-num2words==0.5.10
-numpy==1.19.4
-packaging==20.8
-pandas==1.1.5
-patsy==0.5.1
-psutil==5.7.3
-PuLP==2.3.1
-pybids==0.12.3
-pyparsing==2.4.7
-pyrsistent==0.17.3
-python-dateutil==2.8.1
-pytz==2020.4
-PyYAML==5.3.1
-ratelimiter==1.2.0.post0
-requests==2.25.0
-scipy==1.5.4
-six==1.15.0
-smmap==3.0.4
-snakebids==0.2.0
-snakemake==5.30.1
-SQLAlchemy==1.3.20
-toposort==1.5
-traitlets==5.0.5
-urllib3==1.26.2
-wrapt==1.12.1
diff --git a/setup.py b/setup.py
index 6bf9b982..f865abdc 100644
--- a/setup.py
+++ b/setup.py
@@ -36,7 +36,7 @@
     install_requires=[
         "snakebids>=0.2.0",
         "snakemake>=5.28.0",
-        "nnunet>=1.6.6",
+        "nnunet @ git+https://github.com/ylugithub/nnUNet.git@v1.6.6",
         "appdirs",
         "pandas",
         "nibabel",