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

2020-05-18 Thread stdp82 
External Email - Use Caution

thanks!

> Il 18 maggio 2020 alle 16.23 Bruce Fischl < fis...@nmr.mgh.harvard.edu 
> mailto:fis...@nmr.mgh.harvard.edu > ha scritto:
> 
> 
> --replaceonly   \
> --replaceonly   \
> .
> .
> .
> 
> On Mon, 18 May 2020, std...@virgilio.it mailto:std...@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 <
> > fis...@nmr.mgh.harvard.edu mailto:fis...@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, std...@virgilio.it mailto:std...@virgilio.it 
> > wrote:
> > 
> > > 
> > > External Email - Use Caution
> > 
> > just a kind reminder
> > 
> > many thanks
> > 
> > > 
> > > Il 15 maggio 2020 alle 1.05 std...@virgilio.it 
> mailto:std...@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"
> > < dgr...@mgh.harvard.edu mailto:dgr...@mgh.harvard.edu > ha scritto:
> > 
> > > 
> > > Just add more --replaceonly args
> > 
> > > 
> > > On 5/14/2020 10:38 AM, std...@virgilio.it 
> mailto:std...@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" < dgr...@mgh.harvard.edu mailto:dgr...@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,
> > std...@virgilio.it mailto:std...@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"
> > < dgr...@mgh.harvard.edu mailto:dgr...@mgh.harvard.edu > ha
> > scritto:
> > 
> > > 
> > > That means there is no
> > difference
> > 
> > > 
> > > On 5/13/2020 10:47 AM,
> > std...@virgilio.it mailto:std...@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
> > std...@virgilio.it mailto:std...@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"
> > < dgr...@mgh.harvard.edu mailto:dgr...@mgh.harvard.edu >
> > ha scritto:
> > 
> > > 
> > > Try running this
> >

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

2020-05-18 Thread Bruce Fischl 

--replaceonly   \
--replaceonly   \
.
.
.

On Mon, 18 May 2020, std...@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 <
  fis...@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, std...@virgilio.it wrote:

  External Email - Use Caution

just a kind reminder

many thanks

  Il 15 maggio 2020 alle 1.05 std...@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"
< dgr...@mgh.harvard.edu> ha scritto:

  Just add more --replaceonly args

  On 5/14/2020 10:38 AM, std...@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" < dgr...@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,
std...@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"
< dgr...@mgh.harvard.edu> ha
scritto:

  That means there is no
difference

  On 5/13/2020 10:47 AM,
std...@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
std...@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"
< dgr...@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,
std...@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
<
fis...@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,
std...@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"
<
dgr...@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,
std...@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



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

2020-05-18 Thread stdp82 
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 < fis...@nmr.mgh.harvard.edu 
> mailto:fis...@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, std...@virgilio.it mailto:std...@virgilio.it wrote:
> 
> 
> > > External Email - Use Caution
> > 
> > just a kind reminder
> > 
> > many thanks
> > 
> > 
> > > 
> > > Il 15 maggio 2020 alle 1.05 std...@virgilio.it 
> mailto:std...@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"
> > < dgr...@mgh.harvard.edu mailto:dgr...@mgh.harvard.edu > ha scritto:
> > 
> > > 
> > > Just add more --replaceonly args
> > 
> > > 
> > > On 5/14/2020 10:38 AM, std...@virgilio.it 
> mailto:std...@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" < dgr...@mgh.harvard.edu mailto:dgr...@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,
> > std...@virgilio.it mailto:std...@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"
> > < dgr...@mgh.harvard.edu mailto:dgr...@mgh.harvard.edu > ha
> > scritto:
> > 
> > > 
> > > That means there is no
> > difference
> > 
> > > 
> > > On 5/13/2020 10:47 AM,
> > std...@virgilio.it mailto:std...@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
> > std...@virgilio.it mailto:std...@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"
> > < dgr...@mgh.harvard.edu mailto:dgr...@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,
> > std...@virgilio.it mailto:std...@virgilio.it
> > wrote:
> > 
> > > 
> > > External
> > Email -
> >

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

2020-05-17 Thread stdp82 
External Email - Use Caution

just a kind reminder

many thanks


> Il 15 maggio 2020 alle 1.05 std...@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" 
>  ha scritto:
> > 
> > Just add more --replaceonly args
> > 
> > On 5/14/2020 10:38 AM, std...@virgilio.it mailto:std...@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" 
> > >  mailto:dgr...@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, std...@virgilio.it 
> > > > mailto:std...@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"  
> > > > > mailto:dgr...@mgh.harvard.edu ha scritto:
> > > > > > 
> > > > > > That means there is no difference
> > > > > > 
> > > > > > On 5/13/2020 10:47 AM, std...@virgilio.it 
> > > > > > mailto:std...@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 std...@virgilio.it mailto:std...@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" 
> > > > > > > >  mailto:dgr...@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, 
> > > > > > > > > std...@virgilio.it mailto:std...@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
> > > > > > > > > > 
> > > > > > > > > >

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

2020-05-17 Thread Bruce Fischl 

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, std...@virgilio.it wrote:



External Email - Use Caution

just a kind reminder

many thanks


  Il 15 maggio 2020 alle 1.05 std...@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"
   ha scritto:

  Just add more --replaceonly args

  On 5/14/2020 10:38 AM, std...@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"  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,
std...@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"
 ha
scritto:

That means there is no
difference

On 5/13/2020 10:47 AM,
std...@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
  std...@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"
  
  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,
  std...@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
<
fis...@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,
std...@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"
<
dgr...@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,
  std...@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



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

2020-05-14 Thread stdp82 
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"  ha 
> scritto:
> 
> Just add more --replaceonly args
> 
> On 5/14/2020 10:38 AM, std...@virgilio.it mailto:std...@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" 
> >  mailto:dgr...@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, std...@virgilio.it 
> > > mailto:std...@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"  mailto:dgr...@mgh.harvard.edu ha 
> > > > scritto:
> > > > > 
> > > > > That means there is no difference
> > > > > 
> > > > > On 5/13/2020 10:47 AM, std...@virgilio.it 
> > > > > mailto:std...@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 std...@virgilio.it mailto:std...@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"  
> > > > > > > mailto:dgr...@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, 
> > > > > > > > std...@virgilio.it mailto:std...@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 < fis...@nmr.mgh.harvard.edu 
> > > > > > > > > mailto:fis...@nmr.mgh.harvard.edu > ha scritto:
> > > > > > > > > > 
> > > > > > > > > > 
> > > > > > > > > > Hi Stefano
> > > > > > > > > > 
> > > > > > > > > > can you elaborate? 
> > > > > > > > > > Why do you suspect there is an error?
> > > > > > > > > > 
> > > >

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

2020-05-14 Thread stdp82 
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"  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, std...@virgilio.it mailto:std...@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. 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" 
> >  mailto:dgr...@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, std...@virgilio.it 
> > > mailto:std...@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"  mailto:dgr...@mgh.harvard.edu ha 
> > > > scritto:
> > > > > 
> > > > > That means there is no difference
> > > > > 
> > > > > On 5/13/2020 10:47 AM, std...@virgilio.it 
> > > > > mailto:std...@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 std...@virgilio.it mailto:std...@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"  
> > > > > > > mailto:dgr...@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, 
> > > > > > > > std...@virgilio.it mailto:std...@virgilio.it wrote:
> > > > > > > > 
> > > > > > > > > > > > > > > > > 
> > > > > > > > > External Email - 
> > > > > > > > > Use Caution
> > > > > > > > > 
> > > > > > > > >

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

2020-05-14 Thread stdp82 
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"  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, std...@virgilio.it mailto:std...@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" 
> >  mailto:dgr...@mgh.harvard.edu ha scritto:
> > > 
> > > That means there is no difference
> > > 
> > > On 5/13/2020 10:47 AM, std...@virgilio.it 
> > > mailto:std...@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 
> > > > std...@virgilio.it mailto:std...@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"  
> > > > > mailto:dgr...@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, std...@virgilio.it 
> > > > > > mailto:std...@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 < 
> > > > > > > fis...@nmr.mgh.harvard.edu mailto:fis...@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, std...@virgilio.it 
> > > > > > > > mailto:std...@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"
> > > > > > > > > <

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

2020-05-14 Thread Douglas N. Greve 

Just add more --replaceonly args

On 5/14/2020 10:38 AM, std...@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" 
 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, std...@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" 
  ha scritto:


That means there is no difference

On 5/13/2020 10:47 AM, std...@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 std...@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" 
  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, std...@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 < 
fis...@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, std...@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"
< dgr...@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, std...@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



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

2020-05-14 Thread Douglas N. Greve 

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, std...@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. 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" 
 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, std...@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" 
  ha scritto:


That means there is no difference

On 5/13/2020 10:47 AM, std...@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 std...@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" 
  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, std...@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 < 
fis...@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, std...@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"
< dgr...@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, std...@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



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

2020-05-13 Thread stdp82 
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. 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"  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, std...@virgilio.it mailto:std...@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" 
> >  mailto:dgr...@mgh.harvard.edu ha scritto:
> > > 
> > > That means there is no difference
> > > 
> > > On 5/13/2020 10:47 AM, std...@virgilio.it 
> > > mailto:std...@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 
> > > > std...@virgilio.it mailto:std...@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"  
> > > > > mailto:dgr...@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, std...@virgilio.it 
> > > > > > mailto:std...@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 < 
> > > > > > > fis...@nmr.mgh.harvard.edu mailto:fis...@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, std...@virgilio.it 
> > > > > > > > mailto:std...@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
> > > > > > > > > 
> > > > > > > > > 
> > > > > > >

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

2020-05-13 Thread Douglas N. Greve 
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, std...@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" 
 ha scritto:


That means there is no difference

On 5/13/2020 10:47 AM, std...@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 std...@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" 
  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, std...@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 < 
fis...@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, std...@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"
< dgr...@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, std...@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



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The information in this e-mail is intended only for the person to 
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the e-mail
contains patient information, please contact the Partners 
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you in error
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Re: [Freesurfer] vol2subfield single time course from multiple regions

2020-05-13 Thread stdp82 
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"  ha 
> scritto:
> 
> That means there is no difference
> 
> On 5/13/2020 10:47 AM, std...@virgilio.it mailto:std...@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 std...@virgilio.it 
> > mailto:std...@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" 
> > >  mailto:dgr...@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, std...@virgilio.it 
> > > > mailto:std...@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 < fis...@nmr.mgh.harvard.edu 
> > > > > mailto:fis...@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, std...@virgilio.it 
> > > > > > mailto:std...@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"
> > > > > > > < dgr...@mgh.harvard.edu 
> > > > > > > mailto:dgr...@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, std...@virgilio.it 
> > > > > > mailto:std...@virgilio.it wrote:
> > > > > > > 
> > > > > > > > > > > > > 
> > > > > > > > > > > > >   
> > > > > >   External Email - Use Caution
> > > > > > > 
> > > > > > > > > > > > > 
> > > > > > > > > > > > >   
> > > > > >   Hi list,
> > > > > > > 
> > > > > > > > > > > > > 
> > > > > > > > > > > > >   
> > > > > >

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

2020-05-13 Thread stdp82 
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 std...@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" 
>  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, std...@virgilio.it mailto:std...@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 < fis...@nmr.mgh.harvard.edu mailto:fis...@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, std...@virgilio.it mailto:std...@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"
> > > > > < dgr...@mgh.harvard.edu 
> > > > > mailto:dgr...@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, 
> > > > std...@virgilio.it mailto:std...@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 
> >

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

2020-05-13 Thread Douglas N. Greve 

That means there is no difference

On 5/13/2020 10:47 AM, std...@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 std...@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" 
 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, std...@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 < 
fis...@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, std...@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"
< dgr...@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, std...@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



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

2020-05-11 Thread stdp82 
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"  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, std...@virgilio.it mailto:std...@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 < 
> > fis...@nmr.mgh.harvard.edu mailto:fis...@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, std...@virgilio.it mailto:std...@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"
> > > > < dgr...@mgh.harvard.edu mailto:dgr...@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, 
> > > std...@virgilio.it mailto:std...@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

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

2020-05-11 Thread Douglas N. Greve 

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, std...@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 < fis...@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, std...@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"
< dgr...@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, std...@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



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

2020-05-11 Thread stdp82 
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 < fis...@nmr.mgh.harvard.edu 
> mailto:fis...@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, std...@virgilio.it mailto:std...@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"
> > < dgr...@mgh.harvard.edu mailto:dgr...@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, std...@virgilio.it 
> mailto:std...@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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Re: [Freesurfer] vol2subfield single time course from multiple regions

2020-05-10 Thread stdp82 
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"  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, std...@virgilio.it mailto:std...@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
> 



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

2020-05-10 Thread Bruce Fischl 

Hi Stefano

can you elaborate? Why do you suspect there is an error?

cheers
Bruce
On Mon, 11 May 
2020, std...@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"
   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, std...@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



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

2020-04-30 Thread Douglas N. Greve 
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, std...@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



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