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

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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  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:

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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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