External Email - Use Caution
mri_segstats --seg $SUBJECTS_DIR/mri/ThalamicNuclei.v10.T1.mgz --ctab-default --sum sum.dat --id 8130
Using defalt ctab /Applications/freesurfer/FreeSurferColorLUT.txt
$Id: mri_segstats.c,v 1.122 2017/01/23 18:23:14 greve Exp $
cwd
cmdline mri_segstats --seg $SUBJECTS_DIR/mri/ThalamicNuclei.v10.T1.mgz --ctab-default --sum sum.dat --id 8130
sysnameDarwin
hostname iMac.local
machinex86_64
user ...
whitesurfnamewhite
UseRobust0
Loading $SUBJECTS_DIR/mri/ThalamicNuclei.v10.T1.mgz
Voxel Volume is 0.125 mm^3
Generating list of segmentation ids
Found 1 segmentations
Computing statistics for each segmentation
Reporting on 0 segmentations
Using PrintSegStat
mri_segstats done
Il 14 maggio 2020 alle 17.39 "Douglas N. Greve" dgreve@mgh.harvard.edu ha scritto:
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 mailto:stdp82@virgilio.it wrote: > >External Email - Use Caution 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> mailto: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: > > > >External Email - Use Caution 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: > > > > > >External Email - Use Caution 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. 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