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

$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