Thanks which is the command line for computation of (cesvar1+cesvar2)/2?
----Messaggio originale---- Da: "Douglas Greve" greve@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, stdp82@virgilio.it wrote:
I have run
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
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
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
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" greve@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
- run isxconcat-sess on each time point separately (stacks all subjects
into one file)
- Compute the difference between the time points, eg,
fscalc tp1.nii.gz sub tp2.nii.gz -o diff.nii.gz
- 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, stdp82@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" greve@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, stdp82@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" <greve@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, stdp82@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
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