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In the FreeSurferColorLUT.txt 8130 is the left VM.
The volume is correctly calculated in the VM of the subject.
I have tried with:mri_binarize --i ThalamicNuclei.v10.T1.mgz --replaceonly 8126 8127 --o L-VA.mgz
mri_diff --po ThalamicNuclei.v10.T1.mgz L-VA.mgz
diffcount 3389
Volumes differ in pixel data
maxdiff 1.00000000 at 104 61 88 0
It seems works fine. Agree?
The concern remains on L-VP.
Il 13 maggio 2020 alle 23.03 "Douglas N. Greve" <dgreve@mgh.harvard.edu> ha scritto:
It problably means that seg 8130 does not exist in the input mgz. Can you confirm that it does?
On 5/13/2020 12:51 PM, stdp82@virgilio.it wrote:
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indeed. I would like to merge two regions and extract the fMRI time serie. if no difference is there, somewhat is wrong. the L-VP file contains the same information of ThalamicNuclei.v10.T1.
thanks
Il 13 maggio 2020 alle 17.02 "Douglas N. Greve" <dgreve@mgh.harvard.edu> ha scritto:
That means there is no difference
On 5/13/2020 10:47 AM, stdp82@virgilio.it wrote:
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is the command line ok?
by running
mri_binarize --i ThalamicNuclei.v10.T1.mgz --replace-only 8130 8133 --o L-VP.mgz
mri_diff --po mri/ThalamicNuclei.v10.T1.mgz L-VP.mgz
I obtaindiffcount 0
Il 12 maggio 2020 alle 0.53 stdp82@virgilio.it ha scritto:
by runningmri_diff --po mri/ThalamicNuclei.v10.T1.mgz L-VP.mgzI obtaindiffcount 0
Il 11 maggio 2020 alle 19.18 "Douglas N. Greve" <dgreve@mgh.harvard.edu> ha scritto:
Try running this to see if there is a difference
mri_diff --po ThalamicNuclei.v10.T1.mgz Left-Ventroposterior.mgz
Sometimes it is not easy to see a difference that is just a few voxels
On 5/11/2020 3:02 AM, stdp82@virgilio.it wrote:
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By visualizing the output by freeview, I found that it was the same of ThalamicNuclei.v10.T1.mgz.
Thanks
Il 11 maggio 2020 alle 2.19 Bruce Fischl < fischl@nmr.mgh.harvard.edu> ha scritto:
Hi Stefano
can you elaborate? Why do you suspect there is an error?
cheersBruceOn Mon, 11 May2020, stdp82@virgilio.it wrote:
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Please, could you check the command line.I suspect that an error is there.Thanks.Stefano
mri_binarize --i ThalamicNuclei.v10.T1.mgz --replace-only 8130 8133 --oLeft-Ventroposterior.mgz
Il 30 aprile 2020 alle 18.51 "Douglas N. Greve"< dgreve@mgh.harvard.edu> ha scritto:You can use mri_binarize --i ThalamicNuclei.v10.T1.mgz--replace-only segid segidreplace ... --o newseg.mgzto create a new segmentation with merged segments, then usingvol2subfield with the newseg seg as --sfOn 4/29/2020 7:57 PM, stdp82@virgilio.it wrote:External Email - Use CautionHi list,vol2subfield --i fmcpr.nii.gz --reg register.dof6.lta --sfThalamicNuclei.v10.T1.mgz --stats stats.dat --avgwfavgwf.dat --avgwfvol avgwfvol.mgz --o f2subf.nii.gzextracts the time course from each thalamic subregions.If I would like to merge multiple regions (e.g. --id 8115--id 8116) and extract a single time course from them,which is the way?Thanks
Stefano
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