Re: [Freesurfer] Error with long_mris_slopes: Surface files do not exist

[Martin Reuter]

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-lecaval...@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-boun...@nmr.mgh.harvard.edu 
> <mailto:freesurfer-boun...@nmr.mgh.harvard.edu> 
> <freesurfer-boun...@nmr.mgh.harvard.edu 
> <mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> de la part de Martin Reuter 
> <mreu...@nmr.mgh.harvard.edu <mailto:mreu...@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
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Re: [Freesurfer] Error with long_mris_slopes: Surface files do not exist

[Martin Reuter]

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



> On Aug 15, 2016, at 11:06 PM, Corriveau-Lecavalier Nick 
>  wrote:
> 
> 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
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.