Try running mri_segstats --seg ThalamicNuclei.v10.T1.mgz --ctab-default --sum sum.dat --id 8130 And send the contents of sum.dat
On 5/13/2020 7:37 PM, stdp82@virgilio.it wrote:
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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 mailto: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 mailto:dgreve@mgh.harvard.edu ha scritto:
That means there is no difference
On 5/13/2020 10:47 AM, stdp82@virgilio.it mailto: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 obtain diffcount 0
Il 12 maggio 2020 alle 0.53 stdp82@virgilio.it mailto:stdp82@virgilio.it ha scritto:
by running mri_diff --po mri/ThalamicNuclei.v10.T1.mgz L-VP.mgz I obtain diffcount 0
> Il 11 maggio 2020 alle 19.18 "Douglas N. Greve" > dgreve@mgh.harvard.edu mailto: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 > mailto:stdp82@virgilio.it wrote: >> >> External Email - Use Caution >> >> 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 >>> mailto:fischl@nmr.mgh.harvard.edu> ha scritto: >>> >>> >>> Hi Stefano >>> >>> can you elaborate? Why do you suspect there is an error? >>> >>> cheers >>> Bruce >>> On Mon, 11 May >>> 2020, stdp82@virgilio.it mailto:stdp82@virgilio.it wrote: >>> >>>> External Email - Use Caution >>>> >>>> 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 --o >>>> Left-Ventroposterior.mgz >>>> >>>> Il 30 aprile 2020 alle 18.51 "Douglas N. Greve" >>>> < dgreve@mgh.harvard.edu mailto:dgreve@mgh.harvard.edu> ha >>>> scritto: >>>> You can use mri_binarize --i ThalamicNuclei.v10.T1.mgz >>>> --replace-only segid segidreplace ... --o newseg.mgz >>>> to create a new segmentation with merged segments, then using >>>> vol2subfield with the newseg seg as --sf >>>> On 4/29/2020 7:57 PM, stdp82@virgilio.it >>>> mailto:stdp82@virgilio.it wrote: >>>> External Email - Use Caution >>>> Hi list, >>>> vol2subfield --i fmcpr.nii.gz --reg register.dof6.lta --sf >>>> ThalamicNuclei.v10.T1.mgz --stats stats.dat --avgwf >>>> avgwf.dat --avgwfvol avgwfvol.mgz --o f2subf.nii.gz >>>> extracts 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 >>>> >>>> >>>> >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer@nmr.mgh.harvard.edu >>>> mailto:Freesurfer@nmr.mgh.harvard.edu >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> >>>> >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer@nmr.mgh.harvard.edu >>>> mailto:Freesurfer@nmr.mgh.harvard.edu >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> >>>> >>>> >>>> >>>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> mailto: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. >
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