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Hi Michael,
Your fix to download colortable_BA_thresh file is correct.
I didn’t realize recon-all-clinical page has been updated to point users to
latest (dev) version of the script. My fix is not intended to be put on top of
7.4.0/7.4.1.
You are correct. That page needs to be updated with instructions to download
missing colortable_BA_thresh file.
Best,
Yujing
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> On Behalf Of Michael Mc Laughlin
Sent: Tuesday, June 27, 2023 10:43 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Cc: Gopinath, Karthik <kgopin...@mgh.harvard.edu>
Subject: Re: [Freesurfer] Missing file colortable_BA_thresh.txt for
recon-all-clinical
External Email - Use Caution
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://secure-web.cisco.com/1T-iSAZfwnVtLDiuheYIIFjLZzS7FAReyxFCPERCiUUOiKrI_oOUnuxqjYqFix52qGjEbd78vG1e8iSQW6_d6NsoJbrZZodUwTaJXvhIZCU0PviMbMoRn0bzM8bGk76YYjZun6bx9FxU8oNJFMdM27KLBWPYy0IwK2zEC0TVUySaJrFVBNtYCqfBZR_G-rOIvAAQBiQFCWunBQEqbSyhVQT6QrNdm4LHn09BderQDtcsRb2WnARrRINcGDv__ez2vbf49kProetX7BvjbZilGrQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2Frecon-all-clinical<https://secure-web.cisco.com/1CdxIQH0irUTxU0_ASr2OXmiW1p1iEZNtk_XgyrahH6JLBn0o43pAf5fzJCTWqTPjvkGvVdCuyKCaMOhShEgGXwS-Yn2XWhxiooFTIeeXgUU4tLBx0DzlVvgDJ5zGJlfREDn0aUhPYnRObXatz4un16k7Skzwhd5qYNbc3dHKgyH4MK--B98Wk9ON2hokvLGxhqrwHbopswU9IcC6amjWIY5eeHt8Vj8zbBvPN-mMqVhnDD8zb9YNxVBKj8AFbDtxZGD_BO0-nIKfkk69Ix1QFgVvuw8j7qAcI0mI5LA6ygZ1CXHc6-vMTF7b7dH05nnZ3wWySDBxkp-adZWLphO4UA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2Frecon-all-clinical>
Please replace $FREESURFER_HOME/bin/recon-all-clinical.sh with the latest
version
HERE<https://secure-web.cisco.com/1P3JN6CBNHomG3q-lM4hcusxhcgVFkFalyz0XoR77Qh8DW1umcKXa_j8dcSWuWLszSR2mo-izKg3fyQ4cFLm8GJFN9-onxczbUk2SxGT-FXdQ0jJ3xzSVjL7mS3Rkkb2IRw94FLNUKXvdWccFpHkk1FAxIt0HVCmxYOMLbyU0nU2AR_w0ZZEJJ8E9V7Mu4NlGJXRY0k6fvDe1FwOISKNG9mbJlv2lFVYyQXJMKZy-2PUEjBWk2-uwQPwGP5ThP3QULTqwp8BwYhZbjFpTuj3QKT6grS-F3XA4lEdg6-XZkFspE_hN2OQdD4W5Lma2rYzfKDKj7NDc-2iBWw5ozKlziQ/https%3A%2F%2Fgithub.com%2Ffreesurfer%2Ffreesurfer%2Fblob%2Fdev%2Frecon_all_clinical%2Frecon-all-clinical.sh>.
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
<yhuan...@mgh.harvard.edu<mailto:yhuan...@mgh.harvard.edu>> wrote:
External Email - Use Caution
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
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You can use mri_segstats (MailScanner has detected a possible fraud attempt
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to generate the missing stats/aseg.stats.
Yujing
From:
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@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<mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] Missing file colortable_BA_thresh.txt for
recon-all-clinical
External Email - Use Caution
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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