Apologies to all. This command seems to be running just fine if I remove the --fwhm flag all together. I was just confused by the error message. I suspect that since I did not include qcache option in the initial recon-all command, this might have messed things up, maybe.

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Lauri Tuominen <Lauri.Tuominen@theroyal.ca>
Sent: November-03-22 2:39 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Longitudinal stream bug ?

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Hi FreeSurfer Developers,
I am trying to run a longitudinal analysis on Ubuntu 20.04.1 LTS, freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551, and Python 3.8.5.

I use the following command:

long_mris_slopes --qdec ../tables/long.all.table.dat \
      --meas thickness \
      --hemi lh \
      --sd $SUBJECTS_DIR \
      --do-spc --do-label \
      --generic-time \
      --fwhm 15 \
      --qcache fsaverage \
      --stack-spc ../group/lh.generictime.thickness-spc.stack.mgh \
      --isec-labels lh.generictime.fsaverage.cortex.label

Error message I get is this:

mris_calc -o ./tmp-template_P08_lh_thickness_mfuld5s6/betam.mgh ./tmp-template_P08_lh_thickness_mfuld5s6/betam.mgh add ./tmp-template_P08_lh_thickness_mfuld5s6/beta0.mgh

Saving result to './tmp-template_P08_lh_thickness_mfuld5s6/betam.mgh' (type = MGH )                       [ ok ]

Traceback (most recent call last):
File "/mnt/scratch/software/freesurfer//python/scripts/long_mris_slopes", line 1005, in <module>
    if fwhm > 0:
TypeError: '>' not supported between instances of 'str' and 'int'

I tried to search for this error but did not see anything. Would anyone have any thoughts on how to fix this?
Thanks in advance
Lauri Tuominen