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Hello,
We are trying to run freesurfer through fMRIprep and for the first time ever, I have a series of anatomical scans that are failing during registration. Normally we run this on the normalized T1 scan outputs and have no problem, but these are the original images non-normalized images. My random guess is that there might be too much inhomogeneity in the T1 signal to run freesurfer? I am very new and have rarely used freesurfer.
Here is the fMRIprep error (full log attached)
#@# Talairach Failure Detection Mon Oct 2 15:32:02 CDT 2023 /work/06950/j/ls6/project_nndcbipolar/derivatives/fmriprep-v23.1.3/sourcedata/freesurfer/sub-ut0006/mri
talairach_afd -T 0.005 -xfm transforms/talairach.xfm
ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0000, pval=0.0000 < threshold=0.0050)
Manual Talairach alignment may be necessary, or include the -notal-check flag to skip this test, making sure the -notal-check flag follows -all or -autorecon1 in the command string. See: http://secure-web.cisco.com/1kkJIUzEvH0ScGRNqsTstzKtzyE2xMeizp0oaQP3-n-ioGWE...
Ok, I've tried going through this https://secure-web.cisco.com/1QtKKJUk_dNKuv9HQvIxbFlVKsOnN9ROC0VGd25vitNurR2... to figure out what is going wrong with the T1 images during the freesurfer registration with fMRIprep.
Freesurfer isn't liking our T1 images. This image is the freesurfer output (output under derivatives/frmiprep/sourcedata/sub-ut0002/mri/T1.mgz
[cid:image005.png@01D9F782.EC5FF0E0]
The above should come out registered to this one which is the sub-ut0002/mri/brainmask.mgz:reg=sub-ut0002/mri/transforms/talairach.xfm
[cid:image006.png@01D9F782.EC5FF0E0]
I can't go in and manually alter the T1 to be in alignment in tkregisterfv because I don't have any of the needed files output in the surf folder.
Getting...
ERROR: cannot find /home/jovyan/freesurfer-subjects-dir/sub_ut0002/surf/lh.white
I am attaching the full crash log from fMRIprep and also the script output. I wonder if you could help me understand what might be going wrong?
Thanks,
Jennifer
Jennifer Siegel-Ramsay, PhD Postdoctoral Fellow Department of Psychiatry and Behavioral Sciences Dell Medical School | The University of Texas at Austin dellmedschool.utexas.edu<../../../../../lep66/AppData/Local/Microsoft/Windows/INetCache/Content.Outlook/H3ICGTO9/dellmedschool.utexas.edu>
