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
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 rlsheley@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
freesurfer@nmr.mgh.harvard.edu
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Rebecca Sheley