Hi Martin, Yes, that's it, I wasn't changing the "Measure" in the "Design" tab !
Thank you very much for the advice and support ! Sincerely, Alex Le 13/11/2012 3:41 PM, Martin Reuter a écrit : > Hi Alex, > > just tested it with our dev version and it works for me. When you setup > the subjectsdir and have the file in $SUBJECT_DIR/qdec/.Qdecrc then > after starting qdec you should be able to select e.g. > long.thickness-rate under 'Measure' in the 'Design' tab. > > Best, 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.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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
