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.hang...@yahoo.ca> > To: "Martin Reuter" <mreu...@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. >>>> >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer@nmr.mgh.harvard.edu >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> >>>> >>> >>> >>> 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. >> >> >> >> > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
