Doug, that worked very well, thanks.
mri_aparc2aseg --s ${subject} --labelwm --hypo-as-wm --rip-unknown
--volmask --wmparc-dmax 2 --o ${subj_dir}/mri/wmdivided.nii --annot
aparc.split
mri_annotation2label --ctab new.rh.ctab --subject ${subject} --hemi rh
--annotation aparc.split --outdir ${subj_di
great, thanks! I'll give that a try and let you know how it goes.
On Mon, Jul 7, 2014 at 12:50 PM, Douglas N Greve
wrote:
>
> Right, this is going to be a problem. One of the things you can do is to
> use the --ctab option of mri_annotation2label to create a colortable,
> something like
>
> m
Right, this is going to be a problem. One of the things you can do is to
use the --ctab option of mri_annotation2label to create a colortable,
something like
mri_annotation2label --ctab new.lh.ctab --s subject --hemi lh
--annotation newannot --outdir junk
You can do this for both hemis, t
the new white matter divided labels. I was not able to extract the labels
using the matching grey matter names, but was able to do so using the label
number seen in the tools from tkmedit. Seeing as there are over 100 labels,
is there a more efficient way?
On Mon, Jul 7, 2014 at 12:08 PM, Douglas
The name of which label?
On 07/02/2014 02:00 PM, Corinna Bauer wrote:
> Whereby the label name is derived from which, the GM labels? i.e.
> lh.rostralmiddlefrontal_div3
>
>
> On Wed, Jul 2, 2014 at 11:45 AM, Bruce Fischl
> mailto:fis...@nmr.mgh.harvard.edu>> wrote:
>
> yes, or mri_binarize -
yes
On Wed, 2 Jul 2014, Corinna Bauer wrote:
Whereby the label name is derived from which, the GM labels? i.e.
lh.rostralmiddlefrontal_div3
On Wed, Jul 2, 2014 at 11:45 AM, Bruce Fischl
wrote:
yes, or mri_binarize --match
cheers
Bruce
On Wed, 2 Jul 2014, Corinna Bau
I figured it out. Thanks for your help!
On Wed, Jul 2, 2014 at 2:00 PM, Corinna Bauer wrote:
> Whereby the label name is derived from which, the GM labels? i.e.
> lh.rostralmiddlefrontal_div3
>
>
> On Wed, Jul 2, 2014 at 11:45 AM, Bruce Fischl
> wrote:
>
>> yes, or mri_binarize --match
>>
>>
>
Whereby the label name is derived from which, the GM labels? i.e.
lh.rostralmiddlefrontal_div3
On Wed, Jul 2, 2014 at 11:45 AM, Bruce Fischl
wrote:
> yes, or mri_binarize --match
>
>
> cheers
> Bruce
>
>
> On Wed, 2 Jul 2014, Corinna Bauer wrote:
>
> And then for breaking the individual labels
yes, or mri_binarize --match
cheers
Bruce
On Wed, 2 Jul 2014, Corinna Bauer wrote:
And then for breaking the individual labels up, would mri_extract_label be
the best option?
On Wed, Jul 2, 2014 at 11:01 AM, Bruce Fischl
wrote:
Hi Corinna
you need to give some output extension
And then for breaking the individual labels up, would mri_extract_label be
the best option?
On Wed, Jul 2, 2014 at 11:01 AM, Bruce Fischl
wrote:
> Hi Corinna
>
> you need to give some output extension so it knows what file type to write
> (e.g. .mgz, .nii, .nii.gz. mgh, ...)
>
> cheers
> Bruce
Hi Corinna
you need to give some output extension so it knows what file type to write
(e.g. .mgz, .nii, .nii.gz. mgh, ...)
cheers
Bruce
On Wed, 2 Jul 2014, Corinna Bauer wrote:
Hi Bruce,
I am trying to do just that using the following command line:
mri_aparc2aseg --s ${subject} --labelwm -
Hi Bruce,
I am trying to do just that using the following command line:
mri_aparc2aseg --s ${subject} --labelwm --hypo-as-wm --rip-unknown
--volmask --o ${subj_dir}/mri/wmdivided --annot aparc.split
After the slice labeling, I get the following:
Used brute-force search on 872 voxels
Fixing Parah
Hi Corinna
not really, as that is a surface-based utility. You could divide the
cortical labels and then recrate the wmparc from it, which might do what
you want.
cheers
Bruce
On Tue, 1 Jul 2014, Corinna
Bauer wrote:
> hello,
> I was wondering if it was possible to use mris_divide_parcellat
hello,
I was wondering if it was possible to use mris_divide_parcellation on white
matter labels.
Thanks,
Corinna
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