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thanks!

Il 18 maggio 2020 alle 16.23 Bruce Fischl < 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 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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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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-
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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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