Still having issues with the subcortseg flag in v5.2.0 ...
Trying to take a look at the source code, I did checkout from the cvs but
it failed due to the following error:
cvs [checkout aborted]: Could not map memory to RCS archive
/usr/fscvsroot/dev/distribution/average/cvs_avg35.tar.gz,v: Cannot allocate
memory
Any problems with the cvs server?
Your help will be very much appreciated.
Akio
-- Forwarded message -
From: Bruce Fischl
Date: 2013/3/20
Subject: Re: [Freesurfer] subcortseg error - ?h.white surfaces not available
Cc: Nick Schmansky
I think something must be inconsistent with that flag. Can you use the
workaround for now?
On Wed, 20 Mar 2013, Akio Yamamoto wrote:
Hi Bruce,
>
> After completing autorecon1 stage, I run:
>
> recon-all -s test -autorecon2 -autorecon3
>
> and confirmed that it finished without errors, so I suspect mri_segstats
> did not work correctly with the "-subcortseg"
> flag in the new version 5.2.0.
>
> Here is the full command line where the error occurred:
>
> mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz
> --empty --brainmask mri/brainmask.mgz
> --brain-vol-from-seg --excludeid 0 --excl-ctxgmwm --subcortgray --in
> mri/norm.mgz --in-intensity-name norm
> --in-intensity-units MR --etiv --ctab
> /usr/local/freesurfer/5.2.0/dist/ASegStatsLUT.txt --subject test
>
>
> Now my questions are:
> 1. Is there any change in mri_segstats from the previous version 5.1.0?
> Or, is the "-subcortseg" flag no longer supported
> in v5.2.0?
>
> 2. Any workaround for the use of "-sobcortseg" just after completing
> autorecon1 in v5.2.0?
>
>
> Thanks for your help.
> Akio
>
>
> 2013/3/19 A. Yamamoto
> Hi Bruce,
>
> Here are command lines I used:
>
> recon-all -s test -i ./sample-001.mgz -i ./sample-002.mgz -autorecon1
> recon-all -s test -subcortseg
>
>
> The error occurred in the final process, i.e. calculation of stats on the
> automatic segmentation.
>
> Thanks,
> Akio
>
>
> 2013/3/19 Bruce Fischl
> Hi Akio
>
> what was your full command line?
>
> cheers
> Bruce
>
> On Mon, 18 Mar 2013, A. Yamamoto wrote:
>
> Hi,
>
> After upgrading to FreeSurfer 5.2.0, the command with
> "-subcortseg" flag
> exited with the following error.
>
>
> MRISread(/usr/local/freesurfer/5.2.0/dist/subjects/test/surf/lh.white):
> could not open file
>
>
> I confirmed that the "-autorecon1" stage finished without
> error.
> In v5.1.0 it worked fine, so I'm wondering if there is any
> change in
> mri_segstats??
>
>
> FYI, I have attached the last part of recon-all.log file.
>
> Thanks for your help.
> Akio
>
>
>
>
>
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