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 <a.mtbook@gmail.com>
      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 <fischl@nmr.mgh.harvard.edu>
      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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