Dears,
Mkanalysis-sess does not accept -per-run and It looks like mkcontrast-sess cannot initiate Matlab in the terminal.
I have installed octave and addpath and save path both
/home/fsl/Desktop/freesurfer/matlab
/home/fsl/Desktop/freesurfer/fsfast/toolbox
I will appreciate in advance if you possibly could help me to solve the problem.
Best Regards,
Elahe'
Windows 7 and vmware10
Linux version:
------- freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 --------
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME /home/fsl/Desktop/freesurfer
FSFAST_HOME /home/fsl/Desktop/freesurfer/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR /home/fsl/Desktop/freesurfer/subjects
MNI_DIR /home/fsl/Desktop/freesurfer/mni
FSL_DIR /usr/local/fsl
Current working directory:
*pwd*
*/home/fsl*
*which freesurfer*
*/home/fsl/Desktop/freesurfer/**bin/freesurfer*
*which mkanalysis-sess*
*/home/fsl/Desktop/freesurfer/fsfast/bin/mkanalysis-sess*
*which mkcontrast-sess*
*/home/fsl/Desktop/freesurfer/fsfast/bin/mkcontrast-sess*
Command lines:
*mkdir FIVA*
*cd FIVA*
*mkdir MT_Localizer*
*cd MT_Localizer*
*mkdir subj1sess1 *
*cd subj1sess1*
*unpacksdcmdir -src /home/fsl/Desktop/MTLocalizer/IMAGES -targ . -run 2 bold nii f.nii -run 3 bold nii f.nii -run 4 bold nii f.nii -run 5 bold nii f.nii -run 6 bold nii f.nii -run 7 bold nii f.nii -run 8 bold nii f.nii -run 9 bold nii f.nii -run 10 bold nii f.nii -run 11 bold nii f.nii*
Within subj1sess1, made a text file named subjectname, and wrote subj001 (the name of my anatomical subject).
*cd ..*
*preproc-sess -s subj1sess1 -fsd bold -surface self lhrh -mni305 -fwhm 5 -per-run*
*plot-twf-sess -s subj1sess1 -fsd bold -mc*
*tkregister-sess -s subj1sess1 -fsd bold -per-run -bbr-sum*
*tkregister-sess -s subj1sess1 -fsd bold -per-run*
For each run, a paradigm file (paradigm.par) is included.
*mkanalysis-sess -a MT.lh -surface self lh -fsd bold -fwhm 5 -event-related -paradigm paradigm.par -nconditions 2 -refeventdur 16 -TR 2 **-nskip 4 **-polyfit 2 -spmhrf 0 -mcextreg -per-run*
*'ERROR flag -per-run unrecognized'*
It does not accept -per-run so I omitted that.
*mkanalysis-sess -a MT.lh -surface self lh -fsd bold -fwhm 5 -event-related -paradigm paradigm.par -nconditions 2 -refeventdur 16 -TR 2 -nskip 4 -polyfit 2 -spmhrf 0 -mcextreg*
*mkanalysis-sess -a MT.rh -surface self rh -fsd bold -fwhm 5 -event-related -paradigm paradigm.par -nconditions 2 -refeventdur 16 -TR 2 -nskip 4 -polyfit 2 -spmhrf 0 -mcextreg *
*mkcontrast-sess -analysis MT.lh -contrast M_S -a 2 -c 1 *
Non-Null Conditions
INFO: Found 1 Delays
Condition Weights: -1.00000000000000000000 1.00000000000000000000
mkcontrast -anadir MT.lh -wcond -1.00000000000000000000 1.00000000000000000000 -sumconds -o MT.lh/12.mat -wdelay 1 -no-octave
$Id: mkcontrast,v 1.10 2010/07/16 16:20:10 greve Exp $
cmtxfile MT.lh/12.mat
nconds 2, wcond -1.00000000000000000000 1.00000000000000000000
ndelays 1, wdelay 1
ndelays 1, wpsa
sumconds 1
sumdelays 0
nircorr 0
TER 0.050000
rdelta
rtau
ERROR running mkcontrast
mkcontrast -anadir MT.lh -wcond -1.00000000000000000000 1.00000000000000000000 -sumconds -o MT.lh/12.mat -wdelay 1 -no-octave