I have run 1) isxconcat-sess -sf sessid_LONG_tp1 -analysis fc.rhseed.surf.rh -contrast R_SEED -o LONG_tp1 isxconcat-sess -sf sessid_LONG_tp2 -analysis fc.rhseed.surf.rh -contrast R_SEED -o LONG_tp2
2) fscalc /LONG_tp1/fc.rhseed.surf.rh/R_SEED/ces.nii.gz -sub/ LONG_tp2/fc.rhseed. surf.rh/R_SEED/ces.nii.gz -o /LONG/fc.rhseed.surf.rh/ces.nii.gz fscalc /LONG_tp1/fc.rhseed.surf.rh/R_SEED/ces.nii.gz -sub /LONG_tp2/fc.rhseed. surf.rh/R_SEED/ces.nii.gz -o /LONG/fc.rhseed.surf.rh/ces.nii.gz fscalc /LONG_tp1/fc.rhseed.surf.rh/R_SEED/cesvar.nii.gz -sub /LONG_tp2/fc. rhseed.surf.rh/R_SEED/cesvar.nii.gz -o /LONG/fc.rhseed.surf.rh/cesvar.nii.gz fscalc /LONG_tp1/fc.rhseed.surf.rh/R_SEED/cesvar.nii.gz -sub /LONG_tp2/fc. rhseed.surf.rh/R_SEED/cesvar.nii.gz -o /LONG/fc.rhseed.surf.rh/cesvar.nii.gz 3) GroupDescriptorFile 1 Class Main Input subject1pair Main Input subject2pair Main Input subject3pair Main Input subject4pair Main Input subject5pair Main Input subject6pair Main Input subject7pair Main Input subject8pair Main Input subject9pair Main Input subject10pair Main mean.txt which contains 1 0 4) cd /LONG/fc.rhseed.surf.rh mri_glmfit --glmdir long --y ces.nii.gz --wls cesvar.nii.gz --surface fsaverage rh --nii.gz --fsgd long.fsgd --C mean.mtx I have this error: Loading y from /LONG/fc.rhseed.surf.rh/ces.nii.gz ... done reading. INFO: gd2mtx_method is dods Saving design matrix to long/Xg.dat Computing normalized matrix Normalized matrix condition is 1 Matrix condition is 1 Found 149926 points in label. Pruning voxels by thr: 1.175494e-38 Found 149926 voxels in mask Saving mask to long/mask.nii.gz Reshaping mriglm->mask... search space = 74490.844410 ERROR: MRInormWeights: value less than or eq to 0. c=0, r=0, s=0, v=-0.00516849 >----Messaggio originale---- >Da: "Douglas N Greve" <gr...@nmr.mgh.harvard.edu> >Data: 18-set-2017 23.03 >A: <freesurfer@nmr.mgh.harvard.edu> >Ogg: Re: [Freesurfer] R: Re: R: Re: FS-FAST longitudinal analyis > >oh, I see now. In fsfast, you would > >1. run isxconcat-sess on each time point separately (stacks all subjects >into one file) > >2. Compute the difference between the time points, eg, > >fscalc tp1.nii.gz sub tp2.nii.gz -o diff.nii.gz > >3. Then continue from "Create Second FSGD File" on the wiki. > >Don't smooth since that has probably been done when you ran the fsfast >analysis > > > >On 09/18/2017 04:58 PM, std...@virgilio.it wrote: >> My apologies for the trivial question. Anyway, the web page reports information >> for cortical thickness analysis. I understand it. >> No information I found on fs-fast longitudinal analysis. >> Thus, when I run fs-fast longitudinal analysis, the steps 1-5 should be >> performed? Or they are only for morphometry? >> Many thanks >> >>> ----Messaggio originale---- >>> Da: "Douglas N Greve" <gr...@nmr.mgh.harvard.edu> >>> Data: 18-set-2017 20.03 >>> A: <freesurfer@nmr.mgh.harvard.edu> >>> Ogg: Re: [Freesurfer] R: Re: FS-FAST longitudinal analyis >>> >>> I don't understand what you don't understand. Isn't the web page clear >>> enough? Are those 5 steps on the web page? >>> >>> >>> On 09/18/2017 02:20 AM, std...@virgilio.it wrote: >>>> Thanks, but I not understand if the follow step that you suggested me >>>> should be used also for FS-FAST analysis. >>>> >>>> Specifically, I'm refferring to: >>>> >>>> 1Sample each individual's surface onto the average surface. >>>> 2Compute the difference between each of the pairs in the average >>>> surface space. >>>> 3Concatenate the differences into one file. >>>> 4Smooth on the surface (optional) >>>> 5Perform analysis with mri_glmfit on this file >>>> >>>> Importantly, should I create the two fsgd files as reported in the web >>>> page and below? Or only the second is due? >>>> >>>> One is: >>>> GroupDescriptorFile 1 >>>> Class Main >>>> Input subject1 Main >>>> Input subject1match Main >>>> Input subject2 Main >>>> Input subject2match Main >>>> Input subject3 Main >>>> Input subject3match Main >>>> Input subject3 Main >>>> Input subject3match Main >>>> >>>> the other is: >>>> GroupDescriptorFile 1 >>>> Class Main >>>> Variables Age >>>> Input subject1pair Main 30 >>>> Input subject2pair Main 40 >>>> Input subject3pair Main 50 >>>> Input subject4pair Main 60 >>>> >>>> Thanks >>>> >>>> Regards >>>> >>>> >>>> Stefano >>>> >>>> ----Messaggio originale---- >>>> Da: "Douglas Greve" <gr...@nmr.mgh.harvard.edu> >>>> Data: 18-set-2017 0.13 >>>> A: <freesurfer@nmr.mgh.harvard.edu> >>>> Ogg: Re: [Freesurfer] FS-FAST longitudinal analyis >>>> >>>> That looks correct. You can also checkout the instructions here: >>>> >>>> https://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis >>>> >>>> >>>> On 9/17/17 6:07 PM, std...@virgilio.it wrote: >>>>> Hi list, >>>>> >>>>> I'm not sure that the files reported below are correct to assess >>>>> the longitudinal difference between T1 and T2. >>>>> Please, could you check it? The result which I have obtained bu >>>>> running mri_glmfit is too strange. >>>>> Thanks >>>>> Best regards >>>>> Stefano >>>>> >>>>> 1) PAIRWISE.fsgd file >>>>> ------------------- >>>>> GroupDescriptorFile 1 >>>>> Class subj1 >>>>> Class subj2 >>>>> ... >>>>> Class subjN >>>>> Variables TP1-vs-TP2 >>>>> Input subj1_tp1 subj1 1 >>>>> Input subj1_tp2 subj1 -1 >>>>> Input subj2_tp1 subj2 1 >>>>> Input subj2_tp2 subj2 -1 >>>>> ... >>>>> Input subjN_tp1 subjN 1 >>>>> Input subjN_tp2 subjN -1 >>>>> ---------------------------- >>>>> >>>>> 2) mean.mtx >>>>> 1 1 ... 1 0 >>>>> ------------------------------ >>>>> 3) tp-effect.mtx >>>>> 0 0 ... 0 1 >>>>> ------------------------------ >>>>> 4) mri_glmfit --glmdir PAIRWISE --y ces.nii.gz --wls >>>>> cesvar.nii.gz --surface fsaverage rh --nii.gz --fsgd >>>>> PAIRWISE.fsgd doss --C mean.mtx --C tp-effect.mtx >>>>> >>>>> >>>>> _______________________________________________ >>>>> 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 >>> -- >>> Douglas N. Greve, Ph.D. >>> MGH-NMR Center >>> gr...@nmr.mgh.harvard.edu >>> Phone Number: 617-724-2358 >>> Fax: 617-726-7422 >>> >>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >>> >>> _______________________________________________ >>> 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 >> >> > >-- >Douglas N. Greve, Ph.D. >MGH-NMR Center >gr...@nmr.mgh.harvard.edu >Phone Number: 617-724-2358 >Fax: 617-726-7422 > >Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >www.nmr.mgh.harvard.edu/facility/filedrop/index.html >Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > >_______________________________________________ >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
