18 May
2020
18 May
'20
2:41 a.m.
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 < fischl@nmr.mgh.harvard.edu mailto:fischl@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, stdp82@virgilio.it mailto:stdp82@virgilio.it wrote: > > External Email - Use Cautionjust a kind reminder many thanks >> > Il 15 maggio 2020 alle 1.05 stdp82@virgilio.it mailto:stdp82@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" < dgreve@mgh.harvard.edu mailto:dgreve@mgh.harvard.edu > ha scritto: >> > Just add more --replaceonly args>> > On 5/14/2020 10:38 AM, stdp82@virgilio.it mailto:stdp82@virgilio.it wrote:>> > External Email - Use Caution>> > Moreover, how can I merge, with mri_binarize, morethalamic regions? >> > e.g. 8204 8205 8206 8217 8218>> > 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 doesnot 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 - UseCaution >> > indeed. I would like to merge tworegions 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 nodifference >> > On 5/13/2020 10:47 AM,stdp82@virgilio.it mailto:stdp82@virgilio.it wrote: >> > External Email - UseCaution >> > is the command line ok?>> > by running>> > mri_binarize --iThalamicNuclei.v10.T1.mgz --replace-only 8130 8133 --o L-VP.mgz >> > mri_diff --pomri/ThalamicNuclei.v10.T1.mgz L-VP.mgz >> > I obtaindiffcount 0 >> > Il 12 maggio 2020 alle0.53 stdp82@virgilio.it mailto:stdp82@virgilio.it ha scritto: >> > by runningmri_diff --po mri/ThalamicNuclei.v10.T1.mgz L-VP.mgz I obtain diffcount 0 >> > Il 11 maggio2020 alle 19.18 "Douglas N. Greve" < dgreve@mgh.harvard.edu mailto:dgreve@mgh.harvard.edu > ha scritto: >> > Try running thisto 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 5/11/20203:02 AM, stdp82@virgilio.it mailto:stdp82@virgilio.it wrote: >> > ExternalEmail - Use Caution >> > Byvisualizing the output by freeview, I found that it was the same of ThalamicNuclei.v10.T1.mgz. >> > Thanks>> > Il11 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: >> > ExternalEmail - 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 >> > Il30 aprile 2020 alle 18.51 "Douglas N. Greve" < dgreve@mgh.harvard.edu mailto:dgreve@mgh.harvard.edu > ha scritto: >> > Youcan 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 >> > On4/29/2020 7:57 PM, stdp82@virgilio.it mailto:stdp82@virgilio.it wrote: >> > ExternalEmail - Use Caution >> > Hilist, >> > 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 >> > extractsthe time course from each thalamic subregions. >> > IfI 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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