Update fMRIPrep reference files

[XinhuiLi]

Related problem

The dimension of current C-PAC v1.8.1 fMRIPrep reference file T1w_brain_template: /code/CPAC/resources/templates/tpl-MNI152NLin2009cAsym_res-01_desc-brain_T1w.nii.gz (193x229x193) is different from that of fMRIPrep-LTS reference file (193x235x198).

Proposed feature

Update fMRIPrep reference file to match fMRIPrep-LTS version.

Acceptance criteria

The CPAC:fMRIPrep-options anat to standard dimension is the same as the fMRIPrep-LTS anat to standard dimension.

Alternatives

No response

Additional context

fMRIPrep anatomical registration code:

[sgiavasis]

We can just pop this into v1.8.2.

[tergeorge]

Hi Xinhui,

Could you provide some more clarification on the issue? The template in the fmriprep container tpl-MNI152NLin2009cAsym_res-01_desc-brain_T1w.nii.gz which is from template flow has the same dimension as the one used in C-PAC. Could you tell us where you found the fMRIPrep-LTS reference file with 193x235x198 as its dimension?

Teresa

[shnizzedy]

@XinhuiLi I'm not sure where the "(193x235x198)" comes from? As far as I can tell the tpl-MNI152NLin2009cAsym_res-01_desc-brain_T1w.nii.gz in the fmriprep container (nipreps/fmriprep:21.0.1) is the one from template flow (its in-container path is /home/fmriprep/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-01_desc-brain_T1w.nii.gz). I downloaded the templateflow image into fcpindi/c-pac:latest and compared it to the one at /code/CPAC/resources/templates/tpl-MNI152NLin2009cAsym_res-01_desc-brain_T1w.nii.gz and

root@b7228ebe7eeb:/code/CPAC/resources/templates# diff -qs tpl-MNI152NLin2009cAsym_res-01_desc-brain_T1w.nii.gz templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-01_desc-brain_T1w.nii.gz 
Files tpl-MNI152NLin2009cAsym_res-01_desc-brain_T1w.nii.gz and templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-01_desc-brain_T1w.nii.gz are identical

root@b7228ebe7eeb:/code/CPAC/resources/templates# md5sum tpl-MNI152NLin2009cAsym_res-01_desc-brain_T1w.nii.gz 
ed4c3780e65f38ed87ffd85da3acb46c  tpl-MNI152NLin2009cAsym_res-01_desc-brain_T1w.nii.gz
root@b7228ebe7eeb:/code/CPAC/resources/templates# md5sum templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-01_desc-brain_T1w.nii.gz 
ed4c3780e65f38ed87ffd85da3acb46c  templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-01_desc-brain_T1w.nii.gz

[XinhuiLi]

Hi @tergeorge and @shnizzedy, you can find the template image I referred to at

/data3/cnl/fmriprep/Lei_working/FINAL_preprocessed_2021/fmriprep_default/working/fmriprep_wf/single_subject_0025427a_wf/anat_preproc_wf/anat_derivatives_wf/_in_tuple_MNI152NLin2009cAsym.resnative/gen_ref/tpl-MNI152NLin2009cAsym_res-01_T1w_reference.nii.gz

The template dimension may be changed after anat preprocessing. I got some trouble comparing the anat to standard results because of the image dimension so I opened this issue.