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Hi,

Thanks again for all your work on Freesurfer. I am just following up on this earlier message. Do you guys know of any way to effectively run trac-preproc even when warning text is output by the call to mri_info? I put a more complete description of the problem in my first email.

Thanks,

Amy

From: Mirro, Amy
Sent: Friday, March 28, 2025 1:50 PM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: trac-preproc: orientLAS and mri_info issue with unsigned shorts

Hi,

Thanks so much for all your work on Freesurfer. I am currently running tracula v7.4 and I am coming across the following error. I believe this error is occurring during the orientLAS call in trac-preproc (the output is copied from my log file):

orientLAS /storage1/fs1/fields_m/Active/Scanner_Update_DTI_Testing/PROTO1_3_k23/dmri/dwi_orig.1.nii.gz /storage1/fs1/fields_m/Active/Scanner_Update_DTI_Testing/PROTO1_3_k23/dmri/dwi_orig_las.1.nii.gz

INFO: input image orientation is LPS

INFO: input image determinant is 8

awk: cannot open is (No such file or directory)

mri_convert -oni INFO: -onj This -onk is -oid inf 0 0 -ojd -inf 0 0 -okd inf 0 0 -oc -rt nearest /storage1/fs1/fields_m/Active/Scanner_Update_DTI_Testing/PROTO1_3_k23/dmri/dwi_orig.1.nii.gz /storage1/fs1/fields_m/Active/Scanner_Update_DTI_Testing/PROTO1_3_k23/dmri/dwi_orig_las.1.nii.gz

I think the error in orientLAS might be due to the mri_info calls inside orientLAS (starting around here: MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://github.com/freesurfer/freesurfer/blob/v7.4.0/scripts/orientLAS#L65)

When I attempt to run mri_info on my niftis, I get the following warning : "INFO: this is an unsiged short. I'll try to read it, but it might not work if there are values over 32k -1 -0 0" I think that when mri_info returns this warning inside the orientLAS code, it causes orientLAS to fail, since the xyzR, xyzA, and xyzS variables are not set as expected.

Do you have any suggestions on how I could solve this? Is there perhaps a way to suppress the warning in mri_info? Or is there a straightforward way to convert unsigned short data?

Thanks,

Amy

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