yes
On 9/19/17 3:22 AM, std...@virgilio.it wrote: > 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 > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
