Thanks. In the point 2) the tp1.gz and tp2.nii,gz are the ces.nii.gz that are computed using isxconcat-sess?
>----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
