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" <[email protected]> > > To: "Martin Reuter" <[email protected]> > > Cc: "FS Mailing List" <[email protected]> > > 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 > >>>> [email protected] > >>>> 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 > > [email protected] > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > _______________________________________________ Freesurfer mailing list [email protected] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
