Thanks which is the command line for computation of (cesvar1+cesvar2)/2?
>----Messaggio originale---- >Da: "Douglas Greve" <gr...@nmr.mgh.harvard.edu> >Data: 19-set-2017 17.25 >A: <freesurfer@nmr.mgh.harvard.edu> >Ogg: Re: [Freesurfer] R: Re: R: Re: R: Re: FS-FAST longitudinal analyis > >Don't do the subtraction on cesvar. Instead compute cesvar = >(cesvar1+cesvar2)/2 > > >On 9/19/17 4:17 AM, std...@virgilio.it wrote: >> 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 >> >> > >_______________________________________________ >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
