We are getting ready for “production”, that is, fire up fmriprep on a dataset of few thousand sessions. I just tested fmriprep-1.5.4 with a (self created) singularity container, and seems to work well.
But before we fire up the pipeline on all the dataset I wanted to clarify some points:
- We have Freesurfer run on all these subjects, using the longitudinal pipeline. I looked at other posts and looks like fmriprep cannot use those outputs. Is this still the case?
- If fmriprep cannot use (by default) FS longitudinal data, which option do you suggest we can use:
- Let fmriprep create it’s own “T1w average + freesurfer” output. If we go this way, I am not sure how can we move the BOLD data in native space for a certain session if needed; the T1w average created by fmriprep is in a new space and I am not sure if the transformations to/from individual T1w sessions are somewhere in the output.
- Point fmriprep to use one of the processed Freesurfer sessions (either baseline or long folders).
- Point fmriprep to the sst created by Freesurfer, which should be similar to what fmriprep creates itself (right?).
If you are wondering, these are data with annual sessions from Huntington’s disease. The anatomical changes are certainly there (i.e., 1-3% atrophy in the putamen) but the changes are not hugely visible.
This is the structure of our existing Freesurfer content for a subject:
├── sst ├── sub-T2592_ses-01 ├── sub-T2592_ses-01.long.sst ├── sub-T2592_ses-02 ├── sub-T2592_ses-02.long.sst ├── sub-T2592_ses-03 ├── sub-T2592_ses-03.long.sst ├── sub-T2592_ses-04 ├── sub-T2592_ses-04.long.sst ├── sub-T2592_ses-05 ├── sub-T2592_ses-05.long.sst ├── sub-T2592_ses-06 ├── sub-T2592_ses-06.long.sst ├── sub-T2592_ses-07 └── sub-T2592_ses-07.long.sst
Regarding this point, are you planning to enable the use of FS longitudinal outputs in the near future?
- I noticed you are preparing for a new release soon. We are analyzing data just to share the community (no analyses project planned), so we don’t mind waiting 1-2 months to process the data with a better version of fmriprep. Can you give some hints when you might release the next version and what features might it have that are worth holding the processing for a little bit.
Thank you for your help and for providing such a complex well developed pipeline to the community.