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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