Hi,
I've used mris_divide_parcellation to generate split the automatic parcellation into subregions. When I view the resulting annotation in tksurfer, the label names do not correspond to the subdivision names, so I am unable to tell which division is which (ie, which is rostralanteriorcingulate_div4, as none of them have this name). Is there a way to display these new label names?
Thanks, Cate
Cate,
Have you loaded your own colortable? ie, the one that contains your own labels. In tksurfer, its File -> Label -> Load Color Table
Nick
On Sun, 2007-05-13 at 15:32 -0400, Catherine Hartley wrote:
Hi,
I've used mris_divide_parcellation to generate split the automatic parcellation into subregions. When I view the resulting annotation in tksurfer, the label names do not correspond to the subdivision names, so I am unable to tell which division is which (ie, which is rostralanteriorcingulate_div4, as none of them have this name). Is there a way to display these new label names?
Thanks, Cate _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The color table should be embedded in the annot. Are you sure you're loading the new annotation? Is it different than ?h.aparc.annot. They should at least have slightly different sizes (and diff with unix diff).
doug
On Sun, 13 May 2007, Nick Schmansky wrote:
Cate,
Have you loaded your own colortable? ie, the one that contains your own labels. In tksurfer, its File -> Label -> Load Color Table
Nick
On Sun, 2007-05-13 at 15:32 -0400, Catherine Hartley wrote:
Hi,
I've used mris_divide_parcellation to generate split the automatic parcellation into subregions. When I view the resulting annotation in tksurfer, the label names do not correspond to the subdivision names, so I am unable to tell which division is which (ie, which is rostralanteriorcingulate_div4, as none of them have this name). Is there a way to display these new label names?
Thanks, Cate _______________________________________________ Freesurfer mailing list 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
i did not load the color table separately in addition to the .annot. do i need to? i didn't create a customized color table. the parcellation (?h.aparc.splitcingulate.annot) i created using mris_divide_parcellation automatically generated the label names, but when it loads, the names for the colored labels are not accurate.
the sizes of the subregions are certainly different, but i don't know how they are ordered/numbered and it isn't obvious in looking at their volume measurements which is which.
thanks again, -cate
----- Original Message ----- From: Doug Greve greve@nmr.mgh.harvard.edu Date: Sunday, May 13, 2007 7:55 pm Subject: Re: [Freesurfer] labels for split parcellation To: Nick Schmansky nicks@nmr.mgh.harvard.edu Cc: Catherine Hartley cate@nyu.edu, Freesurfer Mailing List freesurfer@nmr.mgh.harvard.edu
The color table should be embedded in the annot. Are you sure you're loading the new annotation? Is it different than ?h.aparc.annot. They should at least have slightly different sizes (and diff with unix diff).
doug
On Sun, 13 May 2007, Nick Schmansky wrote:
Cate,
Have you loaded your own colortable? ie, the one that contains your
own
labels. In tksurfer, its File -> Label -> Load Color Table
Nick
On Sun, 2007-05-13 at 15:32 -0400, Catherine Hartley wrote:
Hi,
I've used mris_divide_parcellation to generate split the automatic parcellation into subregions. When I view the resulting annotation in tksurfer, the label names do not correspond to the subdivision names, so I am unable to tell which division is which (ie, which is rostralanteriorcingulate_div4, as none of them have this name). Is there a way to display these new label names?
Thanks, Cate _______________________________________________ Freesurfer mailing list 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
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
Hi Cate,
do you have two parcellations loaded at the same time? Be sure you only load the new parcellation (whatever you called it). It should have a colortable in it that accounts for the new units.
cheers, Bruce
On Sun, 13 May 2007, Catherine Alexandra Hartley wrote:
i did not load the color table separately in addition to the .annot. do i need to? i didn't create a customized color table. the parcellation (?h.aparc.splitcingulate.annot) i created using mris_divide_parcellation automatically generated the label names, but when it loads, the names for the colored labels are not accurate.
the sizes of the subregions are certainly different, but i don't know how they are ordered/numbered and it isn't obvious in looking at their volume measurements which is which.
thanks again, -cate
----- Original Message ----- From: Doug Greve greve@nmr.mgh.harvard.edu Date: Sunday, May 13, 2007 7:55 pm Subject: Re: [Freesurfer] labels for split parcellation To: Nick Schmansky nicks@nmr.mgh.harvard.edu Cc: Catherine Hartley cate@nyu.edu, Freesurfer Mailing List freesurfer@nmr.mgh.harvard.edu
The color table should be embedded in the annot. Are you sure you're loading the new annotation? Is it different than ?h.aparc.annot. They should at least have slightly different sizes (and diff with unix diff).
doug
On Sun, 13 May 2007, Nick Schmansky wrote:
Cate,
Have you loaded your own colortable? ie, the one that contains your
own
labels. In tksurfer, its File -> Label -> Load Color Table
Nick
On Sun, 2007-05-13 at 15:32 -0400, Catherine Hartley wrote:
Hi,
I've used mris_divide_parcellation to generate split the automatic parcellation into subregions. When I view the resulting annotation in tksurfer, the label names do not correspond to the subdivision names, so I am unable to tell which division is which (ie, which is rostralanteriorcingulate_div4, as none of them have this name). Is there a way to display these new label names?
Thanks, Cate _______________________________________________ Freesurfer mailing list 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
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Bruce,
Only one parcellation was loaded. It looks great. There's no problem with the colors, just the label names. They don't correspond to the names of the parcellation if i do an aparc2stats, for example.
Thanks, Cate
----- Original Message ----- From: Bruce Fischl fischl@nmr.mgh.harvard.edu Date: Sunday, May 13, 2007 8:34 pm Subject: Re: [Freesurfer] labels for split parcellation To: Catherine Alexandra Hartley cate@nyu.edu Cc: Doug Greve greve@nmr.mgh.harvard.edu, Freesurfer Mailing List freesurfer@nmr.mgh.harvard.edu, Nick Schmansky nicks@nmr.mgh.harvard.edu
Hi Cate,
do you have two parcellations loaded at the same time? Be sure you only load the new parcellation (whatever you called it). It should have a colortable in it that accounts for the new units.
cheers, Bruce
On Sun, 13 May 2007, Catherine Alexandra Hartley wrote:
i did not load the color table separately in addition to the .annot.
do i need to? i didn't create a customized color table. the parcellation (?h.aparc.splitcingulate.annot) i created using mris_divide_parcellation automatically generated the label names, but when it loads, the names for the colored labels are not accurate.
the sizes of the subregions are certainly different, but i don't
know how they are ordered/numbered and it isn't obvious in looking at their volume measurements which is which.
thanks again, -cate
----- Original Message ----- From: Doug Greve greve@nmr.mgh.harvard.edu Date: Sunday, May 13, 2007 7:55 pm Subject: Re: [Freesurfer] labels for split parcellation To: Nick Schmansky nicks@nmr.mgh.harvard.edu Cc: Catherine Hartley cate@nyu.edu, Freesurfer Mailing List freesurfer@nmr.mgh.harvard.edu
The color table should be embedded in the annot. Are you sure you're loading the new annotation? Is it different than ?h.aparc.annot. They should at least have slightly different sizes (and diff with unix diff).
doug
On Sun, 13 May 2007, Nick Schmansky wrote:
Cate,
Have you loaded your own colortable? ie, the one that contains your
own
labels. In tksurfer, its File -> Label -> Load Color Table
Nick
On Sun, 2007-05-13 at 15:32 -0400, Catherine Hartley wrote:
Hi,
I've used mris_divide_parcellation to generate split the automatic parcellation into subregions. When I view the resulting annotation in tksurfer, the label names do not correspond to the subdivision names, so I am unable to tell which division is which (ie, which
is
rostralanteriorcingulate_div4, as none of them have this name).
Is
there a way to display these new label names?
Thanks, Cate _______________________________________________ Freesurfer mailing list 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
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
ok, we'll have to check. I thought this was working. Nick: can you take a look? On Sun, 13 May 2007, Catherine Alexandra Hartley wrote:
Hi Bruce,
Only one parcellation was loaded. It looks great. There's no problem with the colors, just the label names. They don't correspond to the names of the parcellation if i do an aparc2stats, for example.
Thanks, Cate
----- Original Message ----- From: Bruce Fischl fischl@nmr.mgh.harvard.edu Date: Sunday, May 13, 2007 8:34 pm Subject: Re: [Freesurfer] labels for split parcellation To: Catherine Alexandra Hartley cate@nyu.edu Cc: Doug Greve greve@nmr.mgh.harvard.edu, Freesurfer Mailing List freesurfer@nmr.mgh.harvard.edu, Nick Schmansky nicks@nmr.mgh.harvard.edu
Hi Cate,
do you have two parcellations loaded at the same time? Be sure you only load the new parcellation (whatever you called it). It should have a colortable in it that accounts for the new units.
cheers, Bruce
On Sun, 13 May 2007, Catherine Alexandra Hartley wrote:
i did not load the color table separately in addition to the .annot.
do i need to? i didn't create a customized color table. the parcellation (?h.aparc.splitcingulate.annot) i created using mris_divide_parcellation automatically generated the label names, but when it loads, the names for the colored labels are not accurate.
the sizes of the subregions are certainly different, but i don't
know how they are ordered/numbered and it isn't obvious in looking at their volume measurements which is which.
thanks again, -cate
----- Original Message ----- From: Doug Greve greve@nmr.mgh.harvard.edu Date: Sunday, May 13, 2007 7:55 pm Subject: Re: [Freesurfer] labels for split parcellation To: Nick Schmansky nicks@nmr.mgh.harvard.edu Cc: Catherine Hartley cate@nyu.edu, Freesurfer Mailing List freesurfer@nmr.mgh.harvard.edu
The color table should be embedded in the annot. Are you sure you're loading the new annotation? Is it different than ?h.aparc.annot. They should at least have slightly different sizes (and diff with unix diff).
doug
On Sun, 13 May 2007, Nick Schmansky wrote:
Cate,
Have you loaded your own colortable? ie, the one that contains your
own
labels. In tksurfer, its File -> Label -> Load Color Table
Nick
On Sun, 2007-05-13 at 15:32 -0400, Catherine Hartley wrote:
Hi,
I've used mris_divide_parcellation to generate split the automatic parcellation into subregions. When I view the resulting annotation in tksurfer, the label names do not correspond to the subdivision names, so I am unable to tell which division is which (ie, which
is
rostralanteriorcingulate_div4, as none of them have this name).
Is
there a way to display these new label names?
Thanks, Cate _______________________________________________ Freesurfer mailing list 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
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Catherine Alexandra Hartley -
Catherine Hartley
-
Doug Greve -
Nick Schmansky