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Hi Yujing,

I followed the instructions in the release notes.

MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://surfer.nmr.mgh.harvard.edu/fswiki/recon-all-clinical

 Please replace $FREESURFER_HOME/bin/recon-all-clinical.sh with the latest version HERE. Development versions newer than June 15th 2023 do not have this problem.]

The original errors went away but new errors came because the colortable_BA_thresh file was missing. It took a bit of detective work to figure out what was causing the error. Maybe you could change the release notes to tell us what the correct fix is?

Michael



On Tue, Jun 27, 2023 at 3:06 PM Huang, Yujing <YHUANG43@mgh.harvard.edu> wrote:

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recon-all-clinical.sh in 7.4.0 and 7.4.1 should not be referring to colortable_BA_thresh.txt. The changes should be only available in dev version of Freesurfer to fix issues mentioned in this posting MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg75079.html

 

You can use mri_segstats (MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://surfer.nmr.mgh.harvard.edu/fswiki/mri_segstats) to generate the missing stats/aseg.stats.

 

Yujing

 

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Michael Mc Laughlin
Sent: Tuesday, June 27, 2023 8:23 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Missing file colortable_BA_thresh.txt for recon-all-clinical

 

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I finally was able to run recon-all-clinical.sh without errors!

 

There is a file in the development fork on Github called colortable_BA_thresh.txt in the average directory that is not present in the 7.4.1 release. When I downloaded this and put it into the 7.4.1 release, the replacement recon-all-clinical.sh ran without any errors.

 

I also solved the mystery of the missing lateral ventricles. The file mri/brainmsk.mgz in the clinical version is a synthetic file that doesn't contain any ventricles. The equivalent to brainmsk.mgz in the clinical version is synthSR.mgz. This has the missing ventricles and indeed all the other brain components like the cerebellum etc.

 

Alas, despite running error free, there is still no stats/aseg.stats file. I hope that this is on the TODO list for the developers. In the meantime I will write a matlab function to extract the aseg stats from mri/aseg.mgz, which seems to have all the necessary data. If anyone wants a copy of this please email me.

 

Michael McLaughlin,

 

 

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