External Email - Use Caution 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) awk: cannot open is (No such file or directory) 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 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: https://secure-web.cisco.com/17CZKr8Ge1u_y0y-bPaJu-_9XB23QgjYEQBi5jj2tgcD2CUz72ZAgdsFqNqpfC5m_9XuDQh91BGQDeFbsQu2onKxrnlRocUye-y9owoDwEeY9WC_brLleukm3VGtgzslSLyMBceEsuL_lxQIhMeVI2YB1t0F5eYPSeB0yOl5gHambT7cYV4rIZFT9bgxsdYpYwYsikOV-sRWXB6YAddk00aD49N-p5jvREzp2i9ScsgSmzjCuOBugM61ZsbotCidj1CGb8oIEu3yT_mkGRcD0W_xl_9BHlDp7wjR-hiZwJhFt153X84J_7w4i1oDNgAF3bxwVCV4SWbjs_ZjBs_gdsg/https%3A%2F%2Fgithub.com%2Ffreesurfer%2Ffreesurfer%2Fblob%2Fv7.4.0%2Fscripts%2ForientLAS%23L65) 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 ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.
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