There is a lot of inhomogenaity there. Is this a 7T scan? One thing you can try is to run samseg on it first to get a bias corrected scan, eg, samseg --i anat.mgz --o samseg (this should finish in less than 20 min, but you can also add --threads N where N is the number of cpus to make it go faster) Then feed samseg/mode01_bias_corrected.mgz into freesurfer.
On 10/5/2023 12:55 PM, Siegel-Ramsay, Jennifer wrote:
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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:
*MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach http://secure-web.cisco.com/1kkJIUzEvH0ScGRNqsTstzKtzyE2xMeizp0oaQP3-n-ioGWEiy3ukI0hGCv5DsesCQ455aVjqJQ6cOqBiFhsx2JOJ2GI5BEm_VjMUUtG2kWHrtWstADRZrXKkfPwjhgiiNzGW9rysF89gLwP3wsKkRuSvde1_H_yr0fZbJyYAC2k_JJ_3Dk6P75f8G1bFLLogoHSxAApbHFZNrUsn-zaV087G6_cdSDaARinngxjtwCdSe7mT4mJ1A9fIa9QazR5QQbxNDo5VPUIJ5Gm7FFdTV_Dxo-5WGgX45XoNJCfu6VCixzmTm5_xtd1e6mObDT1xrD6GmyN-dbzxbEVwwdtr8A/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FTalairach
Ok, I’ve tried going through this *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach_freeview https://secure-web.cisco.com/1QtKKJUk_dNKuv9HQvIxbFlVKsOnN9ROC0VGd25vitNurR2rD-k9Z1A80EMby1Ntog2tbylntanHvAfPlrcgHpiIsty_E6PDIETUGCh5kEjhNrOAREHzWaDOkUEV1SFHkIQJh6ZWo3B7ckKHCZHyq48zxNTeD1u9vBWulHJ_eVlnyhJTdC3xVuwky8MlEWKjfwsH1LdFbeO2ONZ4Qh96CVjFvdys8ffQNPwK_Y-9sY9IAofqPrbn3kbhArX5IcuE7m_jEbxOmNQ9wRudnqTaNzFkA_HmkEQ3ZNmB33BeiF7ElQC4-58ZYCNseFHd4dR0dC5dJdkewPmRM8QST6U58HA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FTalairach_freeview 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
The above should come out registered to this one which is the sub-ut0002/mri/brainmask.mgz:reg=sub-ut0002/mri/transforms/talairach.xfm
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 *MailScanner has detected a possible fraud attempt from ".." claiming to be* dellmedschool.utexas.edu <../../../../../lep66/AppData/Local/Microsoft/Windows/INetCache/Content.Outlook/H3ICGTO9/dellmedschool.utexas.edu>
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