Never mind, I believe I fixed the issue. Just missed a step. Thanks!
--Rebecca Sheley
On Wed, Oct 25, 2017 at 12:14 PM, Rebecca Sheley <rlshe...@buffalo.edu>
wrote:
> Hello Freesurfer Team,
>
> I'm having trouble running preproc-sess, but only with the
> mkbrainmask-sess step. I tried just running this step and got this output.
> Do you have any insights on why this might be happening?
>
> My tmp folder is empty.
> The cwd directory is the folder where my data are located.
> Freesurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
> OS: Ubuntu
>
> Here is the command I ran:
>
> mkbrainmask-sess -s FS_0184 -d `pwd`
>
> Here is the output:
>
> /home/rebecca/SC/FS_0184
> Wed Oct 25 11:59:31 EDT 2017
> mkbrainmask -i template.nii.gz -o masks/brain.nii.gz -thresh 0.1 -ndil 1
> -nerode 0
> FSLMATHS fslmaths.fsl
> Scratch Dir is /tmp/mkbrainmask_29130
> /home/rebecca/SC/FS_0184/bold
> mri_convert template.nii.gz /tmp/mkbrainmask_29130/in.nii
> mri_convert template.nii.gz /tmp/mkbrainmask_29130/in.nii
> $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
> reading from template.nii.gz...
> TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00
> i_ras = (1, 0, 0)
> j_ras = (0, 1, 0)
> k_ras = (0, 0, 1)
> writing to /tmp/mkbrainmask_29130/in.nii...
> # ---------- Using FSL's BET to Extract Brain------------------ #
> /home/rebecca/SC/FS_0184/bold
> bet.fsl /tmp/mkbrainmask_29130/in.nii /tmp/mkbrainmask_29130/brain -m -f
> 0.1
> Segmentation fault (core dumped)
> mri_binarize --i /tmp/mkbrainmask_29130/brain_mask.nii --min .01 --o
> /tmp/mkbrainmask_29130/brain_mask.nii
> niiRead(): error opening file /tmp/mkbrainmask_29130/brain_mask.nii
>
> $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $
> cwd /home/rebecca/SC/FS_0184/bold
> cmdline mri_binarize --i /tmp/mkbrainmask_29130/brain_mask.nii --min .01
> --o /tmp/mkbrainmask_29130/brain_mask.nii
> sysname Linux
> hostname wernickesarea
> machine x86_64
> user rebecca
>
> input /tmp/mkbrainmask_29130/brain_mask.nii
> frame 0
> nErode3d 0
> nErode2d 0
> output /tmp/mkbrainmask_29130/brain_mask.nii
> Binarizing based on threshold
> min 0.01
> max +infinity
> binval 1
> binvalnot 0
>
> Thanks!
> --Rebecca Sheley
>
>
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