A question regarding a "nii-read" error I get when running a script for FA values output - Freesurfer

11 Feb 2013


      Hi,
My name is Rotem, I'm a PhD. student and recently started to work with
freesurfer software (freesurfer-Linux-centos4-stable-pub-v5.1.0). QUESTION
For several weeks, I have been trying to operate a script for FA values,
with no success, and would really appreciate your help with shading some
light regarding the problem and it's solution.
I have a data set, after an anatomical segmentation (file is attached,
named "Anatomical segmentation for fs", this is the script I'm using for
brain anatomical segmentation). What I'm trying to run now is the DTI
script, in which I run commands that at least for my understanding spouse
to give me at the end a table with all the FA values for each brain region
(ROI). The script I'm using to do this is attached and called
"DTI_RUN_NEW_FOR_FS".
*After running phase 5*, in which a mask file should be created (indeed I
have checked and the file is created in the same folder it should be):
fmri4-P67A-D3-B3:/usr/local/freesurfer/subjects> mri_mask
/usr/local/freesurfer/subjects/FOLDER_NAME/DTI/fa_FOLDER_NAME.nii
/usr/local/freesurfer/subjects/FOLDER_NAME/mri/brainmask.mgz
/usr/local/freesurfer/subjects/FOLDER_NAME/DTI/fa_FOLDER_NAME.mask.nii
DoAbs = 0
Found 16777216 voxels in mask
Writing masked volume to
/usr/local/freesurfer/subjects/FOLDER_NAME/DTI/fa_FOLDER_NAME.mask.nii...done.
*I run phase 6, and then get the following error message:*
fmri4-P67A-D3-B3:/usr/local/freesurfer/subjects> mri_segstats --seg
/usr/local/freesurfer/subjects/FOLDER_NAME/mri/wmparc.mgz --ctab
$FREESURFER_HOME/FreeSurferColorLUT.txt --i
usr/local/freesurfer/subjects/FOLDER_NAME/DTI/fa_FOLDER_NAME.mask.nii --sum
/usr/local/freesurfer/subjects/FOLDER_NAME/stats/all_stats_fa_FOLDER_NAME
$Id: mri_segstats.c,v 1.75.2.2 2011/04/27 22:18:58 nicks Exp $
cwd
cmdline mri_segstats --seg
/usr/local/freesurfer/subjects/FOLDER_NAME/mri/wmparc.mgz --ctab
/usr/local/freesurfer/FreeSurferColorLUT.txt --i
usr/local/freesurfer/subjects/FOLDER_NAME/DTI/fa_FOLDER_NAME.nii --sum
/usr/local/freesurfer/subjects/FOLDER_NAME/stats/all_stats_fa_FOLDER_NAME
sysname  Linux
hostname fmri4-P67A-D3-B3
machine  i686
user     fmri4
Loading /usr/local/freesurfer/subjects/FOLDER_NAME/mri/wmparc.mgz
Loading
usr/local/freesurfer/subjects/FOLDER_NAME/DTI/fa_FOLDER_NAME.mask.nii
niiRead(): error opening file
usr/local/freesurfer/subjects/FOLDER_NAME/DTI/fa_FOLDER_NAME.mask.nii
ERROR: loading
usr/local/freesurfer/subjects/FOLDER_NAME/DTI/fa_FOLDER_NAME.mask.nii
I think the problem is between phase 5 and 6, and is related to file format
(.nii) but don't have a hint regarding what can I do to solve this:( Can
someone please write me the correct code line ?
I would really appreciate your kind help since I run out of ideas for
solutions.
Thanks in advance,
Rotem