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/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
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.txtcomputing 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 calcINFO: assuming MGZ format for volumes.Using TH3 vertex volume calcTotal 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 directoryerror: mris_anatomical_stats: could not read annotation file ./rh.BA_exvivo.annotcomputing 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 calcINFO: assuming MGZ format for volumes.Using TH3 vertex volume calcTotal face volume 183858Total vertex volume 183685 (mask=0)error: No such file or directoryerror: could not read annot file ./rh.BA_exvivo.thresh.annoterror: No such file or directoryerror: mris_anatomical_stats: could not read annotation file ./rh.BA_exvivo.thresh.annotAll done!
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