The downloaded colortable_BA_thresh.txt needs to be place in $FREESURFER_HOME/average/.

From: Huang, Yujing Sent: Wednesday, December 11, 2024 12:05 PM 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: recon-all-clinical rh.BA_exvivio.annot error

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/color...

Yujing

From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto: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.edumailto:freesurfer@nmr.mgh.harvard.edu> Cc: Benjamin Billot <bbillot@mit.edumailto:bbillot@mit.edu>; Iglesias Gonzalez, Juan E. <JIGLESIASGONZALEZ@mgh.harvard.edumailto:JIGLESIASGONZALEZ@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!

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