Re: [Freesurfer] vol2subfield single time course from multiple regions

--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:

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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:

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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 wrote:

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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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