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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
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 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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Stefano
can you elaborate? Why do you suspect there is an error?
cheers Bruce On Mon, 11 May 2020, 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> 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 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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 CautionPlease, 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 --sfThalamicNuclei.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
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:
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
External Email - Use Caution
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 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 CautionPlease, 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 --sfThalamicNuclei.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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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 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> 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 CautionPlease, 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 --sfThalamicNuclei.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. >
That means there is no difference
On 5/13/2020 10:47 AM, 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 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 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.
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 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. 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. > > >> >>
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:
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 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
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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: > >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. 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. > > > > >> > > >> > >> >> _______________________________________________Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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:
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 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. 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. >
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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. 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. > > > > > > > > > > > > > > > > > > > > >
> > > > >> > > >> > > _______________________________________________Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >>
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" 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. 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. > > > > >> > > >> > >> >> _______________________________________________Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Just add more --replaceonly args
On 5/14/2020 10:38 AM, stdp82@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" 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. 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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External Email - Use Caution
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 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, more thalamic 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 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. 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. > > > > > > > > > > > > > > > > > > > > >
> > > > >> > > >> > > _______________________________________________Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >>
External Email - Use Caution
just a kind reminder
many thanks
Il 15 maggio 2020 alle 1.05 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> 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, more thalamic 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 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. 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. > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > >
> > > > _______________________________________________Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > >> >>
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 wrote:
External Email - Use Caution
just a kind reminder
many thanks
Il 15 maggio 2020 alle 1.05 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.mgzERROR: 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 ha scritto:
Just add more --replaceonly args On 5/14/2020 10:38 AM, stdp82@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" <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: 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> ha scritto: That means there is no difference On 5/13/2020 10:47 AM, 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 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.mgz I obtain diffcount 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: 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> 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 wrote:
External Email - Use CautionPlease, 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> 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 wrote: External Email - Use Caution Hi list, vol2subfield --i fmcpr.nii.gz --reg register.dof6.lta --sfThalamicNuclei.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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list 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.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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. 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. _______________________________________________ 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
--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, stdp82@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 < 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 wrote:
External Email - Use Cautionjust a kind reminder
many thanks
Il 15 maggio 2020 alle 1.05 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> ha scritto:
Just add more --replaceonly args On 5/14/2020 10:38 AM, 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> 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 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> ha scritto:
That means there is nodifference
On 5/13/2020 10:47 AM,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 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> 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 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> 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 wrote:
External
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> 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 wrote:
External
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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list 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.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
thanks!
Il 18 maggio 2020 alle 16.23 Bruce Fischl < fischl@nmr.mgh.harvard.edu mailto:fischl@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, stdp82@virgilio.it mailto:stdp82@virgilio.it wrote: > > External Email - Use CautionAs 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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