External Email - Use Caution thanks!
> Il 18 maggio 2020 alle 16.23 Bruce Fischl < fis...@nmr.mgh.harvard.edu > mailto:fis...@nmr.mgh.harvard.edu > ha scritto: > > > --replaceonly <label 1 to remove> <label 1 to replace with> \ > --replaceonly <label 2 to remove> <label 2 to replace with> \ > . > . > . > > On Mon, 18 May 2020, std...@virgilio.it mailto:std...@virgilio.it wrote: > > > > > External Email - Use Caution > > > > As reported in previous mails I have do it but with some problems. > > > > Moreover, how can I do with multiple arguments (more than 2)? > > > > > > > > Il 17 maggio 2020 alle 21.30 Bruce Fischl < > > fis...@nmr.mgh.harvard.edu mailto:fis...@nmr.mgh.harvard.edu > ha > > scritto: > > > > > > Hi Stefano > > > > --replaceonly takes two arguments - the label you want to replace > > and > > the > > one you want to replace it with > > > > cheers > > Bruce > > > > > > On Sun, 17 May 2020, std...@virgilio.it mailto:std...@virgilio.it > > wrote: > > > > > > > > External Email - Use Caution > > > > just a kind reminder > > > > many thanks > > > > > > > > Il 15 maggio 2020 alle 1.05 std...@virgilio.it > mailto:std...@virgilio.it ha scritto: > > > > > > > > mri_binarize --i > > $SUBJECTS_DIR/mri/ThalamicNuclei.v10.T1.mgz > > --replaceonly 8204 --replaceonly 8205 --replaceonly 8206 > > --replaceonly 8217 --replaceonly 8218 --o > > $SUBJECTS_DIR/R-Intralaminar.mgz > > > > ERROR: Option 8205 unknown > > > > > > mri_binarize --i $SUBJECTS_DIR/mri/ThalamicNuclei.v10.T1.mgz > > --replaceonly 8204 --replaceonly 8205 --replaceonly 8217 > > --replaceonly > > 8218 --o $SUBJECTS_DIR/R-Intralaminar.mgz > > > > ERROR: Option 8217 unknown > > Il 14 maggio 2020 alle 17.39 "Douglas N. Greve" > > < dgr...@mgh.harvard.edu mailto:dgr...@mgh.harvard.edu > ha scritto: > > > > > > > > Just add more --replaceonly args > > > > > > > > On 5/14/2020 10:38 AM, std...@virgilio.it > mailto:std...@virgilio.it wrote: > > > > > > > > External Email - Use Caution > > > > > > > > Moreover, how can I merge, with mri_binarize, more > > thalamic regions? > > > > > > > > e.g. 8204 8205 8206 8217 8218 > > > > > > > > Il 13 maggio 2020 alle 23.03 "Douglas N. > > Greve" < dgr...@mgh.harvard.edu mailto:dgr...@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, > > std...@virgilio.it mailto:std...@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" > > < dgr...@mgh.harvard.edu mailto:dgr...@mgh.harvard.edu > ha > > scritto: > > > > > > > > That means there is no > > difference > > > > > > > > On 5/13/2020 10:47 AM, > > std...@virgilio.it mailto:std...@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 > > std...@virgilio.it mailto:std...@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" > > < dgr...@mgh.harvard.edu mailto:dgr...@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, > > std...@virgilio.it mailto:std...@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 > > < > > fis...@nmr.mgh.harvard.edu mailto:fis...@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, > > std...@virgilio.it mailto:std...@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" > > < > > dgr...@mgh.harvard.edu mailto:dgr...@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, > > std...@virgilio.it mailto:std...@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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