It looks like matlab is not in your path.
On 9/18/2020 5:55 AM, Bianca Sieveritz wrote:
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Dear FreeSurfer Developers,
I have preprocessed my functional data using the FsFast function preproc-sess and am now attempting to set up contrasts for first level analyses. I have been able to run mkanalysis-sess, but am receiving an error when I try to run mkcontrast-sess.
I am receiving the following output, when attempting to run mkcontrast-sess:
Command: mkcontrast-sess -analysis task-ARC_events.mni305 -contrast low-baseline-response -a 6
Output:
INFO: Found 15 Non-Null Conditions
INFO: Found 1 Delays
Condition Weights: 0 0 0 0 0 1.00000000000000000000 0 0 0 0 0 0 0 0 0
mkcontrast2 -config task-ARC_events.mni305/low-baseline-response.config -anadir task-ARC_events.mni305 -wcond 0 0 0 0 0 1.00000000000000000000 0 0 0 0 0 0 0 0 0 -sumconds -o task-ARC_events.mni305/low-baseline-response.mat -prestim 0 -wdelay 1 -no-octave
mkcontrast2 7.1.1
cmtxfiletask-ARC_events.mni305/low-baseline-response.mat
nconds15,wcond0 0 0 0 0 1.00000000000000000000 0 0 0 0 0 0 0 0 0
ndelays 1, wdelay 1
ndelays 1, wpsa
sumconds1
sumdelays 0
nircorr 0
TER 1.75
rdelta
rtau
cmtxfiletask-ARC_events.mni305/low-baseline-response.mat
monly0
NCond 15
WCond 0 0 0 0 0 1.00000000000000000000 0 0 0 0 0 0 0 0 0
NDelay1
WDelay1
TER 1.75
sumconds 1
sumdelays0
nircorr0
TPreStim0
RmPreStim0
rdelta 0 0
rtau 0 0
ndelays1
CNorm1
setwdelay0
setwcond 0
Matlab file is /tmp/mkcontrast2.21185.m
------- matlab output --------------------
MATLAB: Undefined variable.
ERROR running mkcontrast
mkcontrast2 -config task-ARC_events.mni305/low-baseline-response.config -anadir task-ARC_events.mni305 -wcond 0 0 0 0 0 1.00000000000000000000 0 0 0 0 0 0 0 0 0 -sumconds -o task-ARC_events.mni305/low-baseline-response.mat -prestim 0 -wdelay 1 -no-octave
I have searched the web but was unable to find a solution. Do you have any ideas, what may be causing the error?
- freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551
- Platform: I am running the script on our university's cluster. The
cluster is Linux based but I am unable to provide details regarding the specific Linux version.
Thank you for your help!
Best regards, Bianca Sieveritz
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer