Hi Nick,

I don’t understand what you are trying to do. I don’t think ?h.surface is a valid file (it is not created or used by freesurfer). Surfaces are for example ?h.white or ?h.pial. Also you say that thickness files exist and that the long_mris_slopes analysis worked for thickness. You cannot run that command for a “surface”. Thickness is a measure defined on the surface, so when running it for thickness, this is a surface based analysis. Again, there is no ?h.surface file and it should not be there.

Best, Martin

On Aug 16, 2016, at 7:23 PM, Corriveau-Lecavalier Nick nick.corriveau-lecavalier@umontreal.ca wrote:

Hi Martin,

I ran the -long for one subject again, but the ''rh.surface'' and ''lh.surface'' are still missing, even though to process finished without error (the thickness files do exist and are in their right place). Also, it would be a surprisingly weird coincidence if something went wrong with all of my subjects during the -long process.

Do you have any idea why these files are still missing? I joined the recon-all.log for the -long processes as well.

Regards,

---

De : freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu> de la part de Martin Reuter <mreuter@nmr.mgh.harvard.edu mailto:mreuter@nmr.mgh.harvard.edu> Envoyé : 16 août 2016 05:45 À : Freesurfer support list Objet : Re: [Freesurfer] Error with long_mris_slopes: Surface files do not exist

Hi Nick,

it looks like the base finished without error. But if your *.long.basid/surf/ are missing the lh.thickness , then something went wrong when processing the -long runs. I would recommend to run a single subject step by step to see what goes wrong (could be IO problems or disk space etc).

Best, Martin ________________________________ De : Corriveau-Lecavalier Nick Envoyé : 15 août 2016 17:06 À : freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu Objet : Error with long_mris_slopes: Surface files do not exist

Hello FreeSurfer developers,

I am trying to run the long_mris_slopes command for surfaces. It worked well the thickness, but when I run it for surfaces, my terminal tells me that the surface file (lh.surface or rh.surface) is missing. It appears that all my subjects are missing those files. I've search the list and no similar error seems to have been reported.

This is the exact command I used: long_mris_slopes --qdec /Applications/freesurfer/subjects/longitudinal_training/long_training.dat --meas surface --hemi rh --do-avg --do-rate --do-pc1 --do-spc --do-stack --do-label --time weeks --qcache fsaverage --sd /Applications/freesurfer/subjects/

I am running a on a OS X El Captain software, and the FreeSurfer version I am using is the most recent one. I also joined the recon-all.long of one of my subject (of the base, since I'm running longitudinal data), in case it could help.

Regards,

Nick <recon-all.log><recon-all.log><recon-all.log>_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer