Hi Alex,
the .Qdecrc (with captial Q) needs to be in the qdec directory within the $SUBJECTS_DIR. Can you check if that is the case?
Thanks, Martin
On Tue, 2012-11-13 at 13:51 -0500, Alex Hanganu wrote:
Hello Martin,
thanks again for your help. We created the .Qdecrc file in the qdec directory. It still gives the same error. Also we made some changes to the .Qdecrc file, for example we changed the ...long.thickness.. to ...long-thickness..., but the error remaines the same.
We performed additionally the same analysis on linux, starting with long_mris_slopes, and we updated there also all the files and scripts, but when we open qdec, the error is the same.
Qdec just doesn't see the .Qdecrc file.
two systems - mac and linux, same error.
Are there some other Qdec files that need to be updated ? besides qdec.bin and qdeclibs.tgz (for mac)
Best regards,
Alex.
Le 10/11/2012 9:17 AM, Martin Reuter a écrit :
Hi Alex.
Take a look at the wiki page: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/LongitudinalTutorial
you need to create a .Qdecrc file in the qdec directory to tell qdec about the filenames with the .long in it:
Also QDEC will not know about our new files (e.g. lh.long.thickness-spc...). We can tell it to look for them by creating a qdec/.Qdecrc file in the qdec directory that contains the following lines:
MEASURE1 = long.thickness-avg MEASURE2 = long.thickness-rate MEASURE3 = long.thickness-pc1 MEASURE4 = long.thickness-spcYou can then run qdec and do all kinds of analysis on any of those files and other variables from the qdec table:
qdec --table ./qdec/cross.qdec.table.datBest, Martin----- Original Message ----- From: "Alex Hanganu" al.hanganu@yahoo.ca To: "Martin Reuter" mreuter@nmr.mgh.harvard.edu Cc: "FS Mailing List" Freesurfer@nmr.mgh.harvard.edu Sent: Friday, November 09, 2012 9:47 PM Subject: Re: [Freesurfer] Qdec - longitudinal. File missing
Hello Martin, thanks for your answer,
I used the --qcache. The cmd was:
long_mris_slopes --qdec qdecfile --meas thickness --hemi lh --do-avg --do-rate --do-pc1 --do-spc --do-stack --do-label --time months --fwhm 10 --qcache fsaverage --sd SUBJECTS_DIR
All the bases subjects have the specific files after this cmd: lh.long.thickness-avg[pc1/rate/spc].fwhm0[5, 10, 15, 20, 25].fsaverage.mgh
but the file that qdec asks for - is missing in all the bases subjects. Qdec asks for: lh.thickness ... but long_mris_slopes created: lh.long.thickness...
it seems to be a qdec error ? maybe.
btw, i changed the qdec.bin and qdeclibs.tgz with the last versions, from the release notes link. Also i used the last version of long_mris_slopes, from 2012/05/30. We work on mac leopard, but the recon-all -all / -base and -long was performed on linux (cluster).
Sincerely, Alex.
Le 09/11/2012 9:14 PM, Martin Reuter a écrit :
Hi Alex,
check the bases of other subjects. Are there any fwhm????fsaverage files?
Did you run with the --qcache flag? Then these should have been created. Maybe you passed a specific fwhm value different from 10?
Best, Martin
On Fri, 2012-11-09 at 17:13 -0500, Alex Hanganu wrote:
Dear FreeSurfer Experts,
we performed the long_mris_slopes cmd and finished without error. According to the "Longitudinal Processing Tutorial", we created after that the cross sectional form of the qdec table, and then the qdec/.Qdecrc file.
When running the qdec analyses, we receive an error:
Couldn't open ...subjects-base/surf/lh.thickness.fwhm.10.fsaverage.mgz or mgh file.
The file is missing, it wasn't created.
What did we miss ?
Thanks,
Sincerely, Alex.
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