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This is a bit of a guess, but I think the issue is that the script requires python2, but your python interpreter (the 'python' command on your system) points to python3.

You can check whether this is the case by running:

python --version

If that prints 'Python 3.x.y', the solution is to use a python2 interpreter to call mris_slopes_long. You will have to give it the full path to the script though. E.g., if your python2 interpreter is 'python2' and you have FreeSurfer setup correctly in your shell, then you could do:

python2 $FREESURFER_HOME/bin/long_mris_slopes <args>

To run your command (where <args> is all the arguments you posted).

Tim

-- Dr. Tim Schäfer Postdoc Computational Neuroimaging Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany

On 10/22/2021 3:05 AM Veena Nair krsna927@gmail.com wrote:

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Hello, I am trying to do some preliminary analysis of a longitudinal dataset, following the tutorial.

I am running FS on Ubuntu 20.04 and freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c

I have finished processing the dataset; to prepare the data for the statistical analysis, I am running this command.

long_mris_slopes --qdec long.qdec.table.dat --meas thickness --hemi lh --do-avg --do-rate --do-pcl --do-spc --do-stack --do-label --time years --qcache fsaverage --sd $SUBJECTS_DIR

But I get the following error- File "/opt/softwarepackages/freesurfer/bin/long_mris_slopes", line 448 print '\nERROR: Specify --qdec (and other required arguments)\n' ^ SyntaxError: invalid syntax I tried (as sudo) fixing the typo in the script, but that didn't help!! I tried switching from python version 3 to 2 [a previous post on this issue had recommended the solution], but that didn't help.

I would appreciate any inputs on how to fix this issue.

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