Hi Bruce-

It is still running, but the recon-all.log as it stands is attached.

Thanks for your help.

Regards,

Wil

From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu]
Sent: Sunday, October 16, 2011 6:27 PM
To: Irwin, William
Cc: freesurfer@nmr.mgh.harvard.edu; Irwin, William
Subject: Re: [Freesurfer] Hanging or running at 'SubCort Seg'?

Hi Wil

Can you send us the full recon-all.log?

Cheers

Bruce

On Oct 16, 2011, at 3:53 PM, "Irwin, William" <WIrwin@memory.ucsf.edu> wrote:

Hi-

I’m a bit stumped by a cased. The input volume looks very good. The first error was the Talairach transform would not complete, so I used the ‘-notal-check’ flag. As I have been focused on other things, I just let the job run, but after 2 weeks, it is stuck (I assume) as indicated. It is running on a fast processor with plenty of memory, so system constraints are not the issue

#@# SubCort Seg Sun Oct  9 16:41:44 PDT 2011

mri_ca_label -align -nobigventricles norm.mgz transforms/talairach.m3z /usr/local/freesurfer/average/RB_all_2008-03-26.gca as

eg.auto_noCCseg.mgz

mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz –lta /media/ClusterData2/data/localdata2/FreeSurfer/wirwin/wirwin_subject

s/FT047-5/mri/transforms/cc_up.lta FT047-5

Any suggestions as to what might be the problem?

Thanks much,

Wil

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