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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:

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indeed. I would like to merge two regions and extract the fMRI time serie. if no difference is there, somewhat is wrong. the L-VP file contains the same information of ThalamicNuclei.v10.T1.

thanks

Il 13 maggio 2020 alle 17.02 "Douglas N. Greve" <dgreve@mgh.harvard.edu> ha scritto:

That means there is no difference

On 5/13/2020 10:47 AM, stdp82@virgilio.it wrote:

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is the command line ok?

by running

mri_binarize --i ThalamicNuclei.v10.T1.mgz --replace-only 8130 8133 --o L-VP.mgz

mri_diff --po mri/ThalamicNuclei.v10.T1.mgz L-VP.mgz  

I obtain

diffcount 0

Il 12 maggio 2020 alle 0.53 stdp82@virgilio.it 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 wrote:

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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:

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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:

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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

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