Re: [Freesurfer] Mean intensity with mri_segstats : different results with .annot or .label

You can use fscalc to multiply the pet and area maps,eg fscalc pet.lh.nii.gz mul lh.white.avg.area.mgh -o weighted.nii.gz On 11/14/2016 11:53 AM, Matthieu Vanhoutte wrote: > Ok I will try both. > > Best, > Matthieu > > 2016-11-14 17:50 GMT+01:00 Douglas N Greve

Re: [Freesurfer] Mean intensity with mri_segstats : different results with .annot or .label

If you did not smooth them explicitly, then there will be only a little vertex-like smoothing. As to which weighting is better, I'm not sure. If the ROI is big, it probably won't make much difference. Can you try both and see? On 11/14/2016 11:39 AM, Matthieu Vanhoutte wrote: > Dear Douglas,

Re: [Freesurfer] Mean intensity with mri_segstats : different results with .annot or .label

Good question. I'm not sure as there could be reasons to do either. I guess if you are not smoothing your data, then weighting by area would be the most appropriate doug On 11/11/2016 05:41 PM, Matthieu Vanhoutte wrote: > > Is it better to compute mean to weight by number of vertices or >

Re: [Freesurfer] Mean intensity with mri_segstats : different results with .annot or .label

Is it better to compute mean to weight by number of vertices or surface area ? Best, Matthieu Le 11 nov. 2016 11:33 PM, "Douglas N Greve" a écrit : > Vertices do not have equal areas and are not equally spaced > > > On 11/11/2016 05:11 PM, Matthieu Vanhoutte wrote: >

Re: [Freesurfer] Mean intensity with mri_segstats : different results with .annot or .label

Vertices do not have equal areas and are not equally spaced On 11/11/2016 05:11 PM, Matthieu Vanhoutte wrote: > > Thank you Douglas for giving me a way to compute area from segmented > surface data. > > Are vertices equally spaced along cortex or do triangles all have same > area ? > > Best, >

Re: [Freesurfer] Mean intensity with mri_segstats : different results with .annot or .label

Thank you Douglas for giving me a way to compute area from segmented surface data. Are vertices equally spaced along cortex or do triangles all have same area ? Best, Matthieu Le 11 nov. 2016 10:55 PM, "Douglas N Greve" a écrit : If you want to do it on fsaverage,

Re: [Freesurfer] Mean intensity with mri_segstats : different results with .annot or .label

If you want to do it on fsaverage, then mris_segstats --i $SUBJECTS/fsaverage/surf/lh.white.avg.area.mgh --seg lh.sign_clust.bin.mgh --excludeid 0 --sum lh.bin.area.sum --accumulate On 11/11/2016 04:48 PM, Matthieu Vanhoutte wrote: > > Dear Douglas, > > Yes I would like to in order to

Re: [Freesurfer] Mean intensity with mri_segstats : different results with .annot or .label

Dear Douglas, Yes I would like to in order to compute mean of some means. Maybe not if it is equivalent to number of vertices (are vertices distributed equaly distant on the cortical surface ?) In case I need surface area, do I have to convert overlay to annotation file to be used with

Re: [Freesurfer] Mean intensity with mri_segstats : different results with .annot or .label

NVox is the number of vertices. The Volume_mm3 is not meaningful. Do you want area? On 11/11/2016 04:53 AM, Matthieu Vanhoutte wrote: > Dear Douglas, > > I come back to you concerning stats made from binary .mgh surface data > file: > > mri_segstats --i lh.fsaverage.sm10.mgh --seg

Re: [Freesurfer] Mean intensity with mri_segstats : different results with .annot or .label

Dear Douglas, I come back to you concerning stats made from binary .mgh surface data file: mri_segstats --i lh.fsaverage.sm10.mgh --seg lh.sign_clust.bin.mgh --excludeid 0 --sum lh.bin.sum --avgwf lh.wav.bin.txt In the output file « lh.bin.sum » all is considered as volume input/output as

Re: [Freesurfer] Mean intensity with mri_segstats : different results with .annot or .label

Thank you Douglas ! Le 10 nov. 2016 7:21 PM, "Douglas N Greve" a écrit : > You need to weight by the number of vertices > > n = [27805 2321 552]; > m = [8.8194 10.3661 10.3365]; > sum(n.*m)/sum(n) > > ans = > > 8.9637 > > > On 11/10/2016 06:44 AM, Matthieu

Re: [Freesurfer] Mean intensity with mri_segstats : different results with .annot or .label

You need to weight by the number of vertices n = [27805 2321 552]; m = [8.8194 10.3661 10.3365]; sum(n.*m)/sum(n) ans = 8.9637 On 11/10/2016 06:44 AM, Matthieu Vanhoutte wrote: > Dear Freesurfer's experts, > > Could anyone please explain me the difference I got with command line > in

Re: [Freesurfer] Mean intensity with mri_segstats : different results with .annot or .label

Dear Freesurfer's experts, Could anyone please explain me the difference I got with command line in below mail ? Best regards, Matthieu 2016-08-12 12:07 GMT+02:00 Matthieu Vanhoutte : > Dear experts, > > I am in trouble with two ways of computing mean intensity

Re: [Freesurfer] Mean intensity with mri_segstats : different results with .annot or .label

Hello FS's experts, Would anyone have an advice for my problem ? Best regards, Matthieu 2016-08-12 12:07 GMT+02:00 Matthieu Vanhoutte : > Dear experts, > > I am in trouble with two ways of computing mean intensity with > mri_segstats. > > First I have used on

[Freesurfer] Mean intensity with mri_segstats : different results with .annot or .label

Dear experts, I am in trouble with two ways of computing mean intensity with mri_segstats. First I have used on .annot files with three different labels inside (SegId 1 to 3) : *mri_segstats --annot fsaverage lh cache.th23.pos.sig.ocn.annot --i lh.PET.fsaverage.sm10.mgh --sum lh.pet.sum* which