fscalc, which is a general math program for volumes
On 09/19/2017 12:34 PM, std...@virgilio.it wrote: > 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 > > -- 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
