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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,
--replaceonly \
--replaceonly \
.
.
.
On Mon, 18 May 2020, std...@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
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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 < fis...@nmr.mgh.harvard.edu
> mailto:fis...@nmr.mgh.harvard.edu > ha
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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
>
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:
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just a kind reminder
many thanks
Il 15 maggio 2020 alle
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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
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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
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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" ha
> scritto:
>
> It problably means that seg 8130 does not exist in the input mgz. Can you
Just add more --replaceonly args
On 5/14/2020 10:38 AM, std...@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"
ha scritto:
It
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:
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In the FreeSurferColorLUT.txt 8130 is the left VM.
The volume is correctly
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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
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:
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indeed. I would like to merge two regions and extract the fMRI time
serie. if no difference is there,
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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"
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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 std...@virgilio.it ha
That means there is no difference
On 5/13/2020 10:47 AM, std...@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
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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
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:
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By visualizing the
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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 < fis...@nmr.mgh.harvard.edu
> mailto:fis...@nmr.mgh.harvard.edu > ha scritto:
>
>
> Hi
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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" ha
>
Hi Stefano
can you elaborate? Why do you suspect there is an error?
cheers
Bruce
On Mon, 11 May
2020, std...@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
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:
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