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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.
Have a nice day!
Lauri
________________________________ 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?