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