Issue with Session-Specific Outputs in sMRIPrep

Software Support
1

Hi everyone,

I’m running sMRIPrep on a BIDS dataset that contains multiple sessions for a single subject. However, the output does not seem to include session-specific files, and instead, I only get general files under the anat folder without individual session folders containing preprocessed images.

I was expecting to get session-specific preprocessed files (e.g., sub-0286_ses-20161116_space-MNI152Lin_desc-preproc_T1w.nii.gz) but only got a general anat file and some transformation files for each session. Am I missing something in the configuration? Any suggestions on how to properly organize the outputs per session?

Thanks in advance for your help!

Here’s the output structure::

sub-0286/
└── anat/
└──── sub-0286_space-MNI152Lin_desc-preproc_T1w.nii.gz
└────other preprocessing output files
└── ses-20161116/
└── anat/
└────sub-0286_ses-20161116_from-orig_to-T1w_mode-image_xfm.txt
└── ses-20070515/
└── anat/
└────sub-0286_ses-20070515_from-orig_to-T1w_mode-image_xfm.txt

2

Hi @Mohammed_Ikbal, and welcome to neurostars!

Did you use BIDS filter files to only process individual sessions at a time? Otherwise sMRIPrpe creates an average.

Best,
Steven

3

Hi @Steven ,

Thanks for your reply. Actually, I didn’t use a BIDS filter file when processing my dataset. Could you give me a hint about the BIDS filter file structure?

Best,
Mohammed

4

https://fmriprep.org/en/stable/faq.html#how-do-i-select-only-certain-files-to-be-input-to-fmriprep

5

@Steven

Just to ensure I am on the right track, I am currently developing a deep-learning-based diagnostic system, and need to process each session individually. To achieve this, I understand that I need to run the command with specific BIDS filters for each session, right?

Also, I observed that the preprocessing time for a single session is approximately 35 minutes. This duration seems quite lengthy, especially considering that I am using linear registration without FreeSurfer segmentation. Could you provide any insights or recommendations on how to optimize this runtime?

Thank you in advance for your assistance!

6

Hi @Mohammed_Ikbal,

Yes, you’d need to run separate instances with separate BIDS filters passed for each instance.

That run time is normal.

Best,
Steven