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 fischl@nmr.mgh.harvard.edu Date: 2013/3/20 Subject: Re: [Freesurfer] subcortseg error - ?h.white surfaces not available Cc: Nick Schmansky nicks@nmr.mgh.harvard.edu

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 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

The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.