cheers

yu junjie

------------------ Original ------------------

From: "Bruce Fischl"<fischl@nmr.mgh.harvard.edu>;

Date: Wed, Apr 24, 2019 09:52 PM

To: "Freesurfer support list"<freesurfer@nmr.mgh.harvard.edu>;

Subject: Re: [Freesurfer] recon-all error

hmmm, how long did you let it run? I've never seen this before. Can you
upload your subject to our ftp site?

cheers
Bruce
On Wed, 24 Apr 2019, 1013364183 wrote:

>
> External Email - Use Caution
>
> Dear freesurfer
> We run the recon-all command of freesurfer, but when it runs to the randomSeed 0 step below, it
> will not run anymore, that is, the running terminal has been stuck in the following statement for
> more than 10 days.We want to ask why this happens? How should we solve this problem?
> The running statement is as follows:
> only generating white matter surface
> using aseg volume ../mri/aseg.presurf to prevent surfaces crossing the midline
> not using aparc to prevent surfaces crossing the midline
> INFO: assuming MGZ format for volumes.
> using brain.finalsurfs as T1 volume...
> $Id: mris_make_surfaces.c,v 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $
> $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $
> reading volume
> /fileserver/projects/Nian/EDSR_20181118_1/result/freesurfer/neck-stripping187547/mri/filled.mgz...
> reading volume/fileserver/projects/Nian/EDSR_20181118_1/result/freesurfer/neck-stripping187547/mri/brain.finalsur
> fs.mgz...
> reading volume/fileserver/projects/Nian/EDSR_20181118_1/result/freesurfer/neck-stripping187547/mri/../mri/aseg.pr
> esurf.mgz...
> reading volume
> /fileserver/projects/Nian/EDSR_20181118_1/result/freesurfer/neck-stripping187547/mri/wm.mgz...
> 1792 bright wm thresholded.
> 583658 bright non-wm voxels segmented.
> reading original surface position from
> /fileserver/projects/Nian/EDSR_20181118_1/result/freesurfer/neck-stripping187547/surf/lh.orig...
> computing class statistics...
> border white: 318655 voxels (1.90%)
> border gray 363634 voxels (2.17%)
> WM (109.0): 109.3 +- 4.5 [70.0 --> 110.0]
> GM (109.0) : 101.3 +- 17.8 [30.0 --> 110.0]
> setting MIN_GRAY_AT_WHITE_BORDER to 92.2 (was 70)
> setting MAX_BORDER_WHITE to 114.5 (was 105)
> setting MIN_BORDER_WHITE to 110.0 (was 85)
> setting MAX_CSF to 35.0 (was 40)
> setting MAX_GRAY to 105.5 (was 95)
> setting MAX_GRAY_AT_CSF_BORDER to 60.0 (was 75)
> setting MIN_GRAY_AT_CSF_BORDER to 56.6 (was 40)
> repositioning cortical surface to gray/white boundary
> smoothing T1 volume with sigma = 2.000
> vertex spacing 0.26 +- 0.11 (0.00-->2.25) (max @ vno 28887 --> 31618)
> face area
>
>
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