Running fmriprep with a single t1 and multiple sessions

1

Hi everyone,

I have a dataset with 11 sessions per subject and a single t1-weighted image per subject (we used a headcase to stabilize the head for all sessions). To make sure the data were BIDS-compliant, I included the same t1 for all sessions under anat/ for each subject.

I assume that this is an issue because fmriprep by default tries to average the t1s across sessions and realizes that they are identical. I get the following error:

 Sigma too small: 0 (identical images?)
[init] ========================= TP 9 to TP 1 ==============================
         Register TP 9 ( /scratch/fmriprep_wf/single_subject_860_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_corr>
          to      TP 1 ( /scratch/fmriprep_wf/single_subject_860_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_corr>

Standard error:
CostFunctions::centroid is NAN (empty image? n = 0 )
Return code: 1

Does anyone have suggestions for how to use a single T1-weighted image for multiple sessions?

Thanks! I appreciate your help.

2

Put the T1 in the first session only. I believe all subsequent sessions will register to it.

3

Thanks! I started running session by session and have no issue there, which seems to point to the t1 copies being an issue. I’ll give your solution a try too.

4

If your software is complaining that two T1w images are identical before a registration step, you can just apply some small, random, rigid-body transformation to it, and to make sure it goes ahead, perhaps add some normally distributed noise. [Please, don’t do this]

Where does the BIDS specification say this is necessary? I’d rather say you made sure it is not BIDS compliant - it would be actually a good thing to add to the validator a check that makes sure two images are not identical.

Yes, just have the T1w stored within the session it was acquired.

Please don’t call this a solution, just solve the issue by not creating it in the first place :slight_smile:

(and yet, if you find an instance where BIDS suggests anything remotely resembling what you did, please report it on the GitHub repo because that must be addressed ASAP)

5

Hi Oscar,

Yeah, this sounds like a really bad idea. Not planning to artificially add noise.

The idea that each session required a t1 was a misplaced assumption on my part regarding the BIDS format.

I wholeheartedly agree that running session-by-session is not a solution. I was just collecting more data about my hypothesized problem and I was under a tight time constraint.

The solution from heffjos worked – I simply included the single t1 in the anat/ folder for the acquisition session and left the anat/ folder for the other sessions empty.

Thanks for your reply.

6

Thanks! This worked.

7

Glad you figured it out!

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