There have been some updates to recon-all-clinical for 7.4.1 - see the instruction here https://surfer.nmr.mgh.harvard.edu/fswiki/recon-all-clinical
The updated version also uses colortable_BA_thresh.txt, which you need to download from https://github.com/freesurfer/freesurfer/blob/dev/distribution/average/colortable_BA_thresh.txt Yujing From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> On Behalf Of Melissa Marie Rundle Sent: Wednesday, December 11, 2024 11:24 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Cc: Benjamin Billot <bbil...@mit.edu>; Iglesias Gonzalez, Juan E. <jiglesiasgonza...@mgh.harvard.edu> Subject: Re: [Freesurfer] recon-all-clinical rh.BA_exvivio.annot error External Email - Use Caution Hello, We are getting the error below for every subject when we run recon-all-clinical. It's only for the rh, not the lh. We are using Freesufer 7.4.1 with the synthseg python script. Let me know if there is a fix/update/patch for this. Thanks, Melissa ERROR: cannot find or read /usr/local/freesurfer/dev/average/colortable_BA.txt ERROR: cannot find or read /usr/local/freesurfer/dev/average/colortable_BA.txt computing statistics for each annotation in ./rh.BA_exvivo.annot. reading volume /data/recon-all-clinical/3CAMC005746_125300857_20240220/mri/wm.mgz... reading input surface /data/recon-all-clinical/3CAMC005746_125300857_20240220/surf/rh.white... reading input pial surface /data/recon-all-clinical/3CAMC005746_125300857_20240220/surf/rh.pial... reading input white surface /data/recon-all-clinical/3CAMC005746_125300857_20240220/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 183858 Total vertex volume 183685 (mask=0) error: No such file or directory error: could not read annot file ./rh.BA_exvivo.annot error: No such file or directory error: mris_anatomical_stats: could not read annotation file ./rh.BA_exvivo.annot computing statistics for each annotation in ./rh.BA_exvivo.thresh.annot. reading volume /data/recon-all-clinical/3CAMC005746_125300857_20240220/mri/wm.mgz... reading input surface /data/recon-all-clinical/3CAMC005746_125300857_20240220/surf/rh.white... reading input pial surface /data/recon-all-clinical/3CAMC005746_125300857_20240220/surf/rh.pial... reading input white surface /data/recon-all-clinical/3CAMC005746_125300857_20240220/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 183858 Total vertex volume 183685 (mask=0) error: No such file or directory error: could not read annot file ./rh.BA_exvivo.thresh.annot error: No such file or directory error: mris_anatomical_stats: could not read annotation file ./rh.BA_exvivo.thresh.annot All done! ________________________________ This electronic message is intended only for the use of the individual(s) and entity named as recipients in the message. If you are not an intended recipient of this message, please notify the sender immediately and delete the material from any computer. Do not deliver, distribute or copy this message, and do not disclose its contents or take any action in reliance on the information it contains. Thank you.
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