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-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@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 <bbillot@mit.edu>; Iglesias Gonzalez, Juan E. <JIGLESIASGONZALEZ@mgh.harvard.edu>
Subject: Re: [Freesurfer] recon-all-clinical rh.BA_exvivio.annot error

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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!
 

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