Thank you, Louis.
So, to compute aseg stats, I need to run autorecon1, 2 and 3 all together, right?
Slightly confused because in v5.1.0 I could get aseg stats without error by running autorecon1 and subcortseg (probably, autorecon2 too). No longer the case in v5.3.0?
Any options for this purpose?
Best, Akio
(2013/05/23 23:22), Louis Nicholas Vinke wrote:
Hi Akio, The ribbon.mgz is created in autorecon3, just before the segstats step. So you will have to also run autorecon3. Since you have already run autorecon1 and 2 you will just need to run something like:
recon-all -autorecon3 -s <subjID>
Sorry for the confusion. -Louis
On Thu, 23 May 2013, Akio Yamamoto wrote:
Nick,
I ran recon-all with -autorecon1 and -autorecon2 flags.
Not exactly the same as the previous one, but I got another error in mri_segstats. The recon-all.log file is also attached in this email.
It seems likely that mri_segstats has been revised drastically in v5.2.0 or later?
Thanks in advance for your help.
Akio
========== $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ cwd cmdline 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 --surf-wm-vol --surf-ctx-vol --totalgray --euler --ctab /usr/local/freesurfer/5.3.0/dist/ASegStatsLUT.txt --subject test sysname Linux hostname dhcp006 machine x86_64 user yamamoto UseRobust 0 atlas_icv (eTIV) = 1629767 mm^3 (det: 1.195328 ) mghRead(/home/yamamoto/freesurfer/5.3.0/dist/subjects/test/mri/ribbon.mgz, -1): could not open file
(2013/05/21 23:28), Nick Schmansky wrote:
Akio,
You should just run -autorecon2 instead of -subcortseg in order to get the subcortical segmentation.
Nick
Hi Freesurfer experts,
After installing v5.3.0 (CentOS 6 64bit), the command "recon-all -s test -i sample-001.mgz -i sample-002.mgz -autorecon1" finished without error.
Then, when I ran "recon-all -s test -subcortseg", I got the following error:
========== $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ cwd cmdline 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/5.3.0/dist/ASegStatsLUT.txt --subject test sysname Linux hostname dhcp006 machine x86_64 user yamamoto UseRobust 0 atlas_icv (eTIV) = 1629767 mm^3 (det: 1.195328 ) MRISread(/home/yamamoto/freesurfer/5.3.0/dist/subjects/test/surf/lh.white): could not open file ==========
I encountered this error in v5.2.0, and am still having the same error in v5.3.0. Is this a known issue?
I attached the recon-all.log file. Any help is greatly appreciated.
Best, Akio _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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