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Thank you for your reply. I checked and matlab was in my path.

Nevertheless, I finally found a solution myself that I am happy to share for future reference.

1. I ran the command "which matlab" to get the path to matlab 2. I ran the command "export MATLAB='path-to-matlab'" 3. I ran the command "set MATLAB"

Afterward, mkcontrast-sess was running without any issues for me. ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@MGH.HARVARD.EDU Sent: 19 September 2020 00:29 To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mkcontrast-sess error

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

cmtxfile task-ARC_events.mni305/low-baseline-response.mat

nconds 15, wcond 0 0 0 0 0 1.00000000000000000000 0 0 0 0 0 0 0 0 0

ndelays 1, wdelay 1

ndelays 1, wpsa

sumconds 1

sumdelays 0

nircorr 0

TER 1.75

rdelta

rtau

cmtxfile task-ARC_events.mni305/low-baseline-response.mat

monly 0

NCond 15

WCond 0 0 0 0 0 1.00000000000000000000 0 0 0 0 0 0 0 0 0

NDelay 1

WDelay 1

TER 1.75

sumconds 1

sumdelays 0

nircorr 0

TPreStim 0

RmPreStim 0

rdelta 0 0

rtau 0 0

ndelays 1

CNorm 1

setwdelay 0

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?

1) freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 2) 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

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