[Freesurfer] Creating annotation file for lobar regions...
Hi all -- Is there a simple way to create an annotation for frontal/temporal/occipital/parietal lobes based off the ?h.aparc.annot files in a FS 'label' dir? Ideally speaking, I'd like to have a ?h.lobar.annot with corresponding lobar.annot.ctab. Apologies if this question has come up before... a quick google didn't reveal anything. Many thanks -=R -- Rudolph Pienaar, M.Eng, D.Eng / email: rudo...@nmr.mgh.harvard.edu MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging 149 (2301) 13th Street, Charlestown, MA 02129 USA ___ Freesurfer mailing list 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 does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Creating annotation file for lobar regions...
Try running mri_annotation2label with --lobes lh.lobes.annot doug On Thu, 20 May 2010, Rudolph Pienaar wrote: > Hi all -- > > Is there a simple way to create an annotation for > frontal/temporal/occipital/parietal lobes based off the ?h.aparc.annot > files in a FS 'label' dir? Ideally speaking, I'd like to have a > ?h.lobar.annot with corresponding lobar.annot.ctab. > > Apologies if this question has come up before... a quick google didn't > reveal anything. > > Many thanks > -=R > > -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ Freesurfer mailing list 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 does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Creating annotation file for lobar regions...
Great -- many thanks, Doug. What are the newly annotated regions named?
Basically, once I do a MatLAB
[list, label, annot] = read_annotation('lh.lobes.annot');
what are the annot.struct_names?
>
> Try running mri_annotation2label with --lobes lh.lobes.annot
>
> doug
>
>
> On Thu, 20 May 2010, Rudolph Pienaar wrote:
>
>> Hi all --
>>
>> Is there a simple way to create an annotation for
>> frontal/temporal/occipital/parietal lobes based off the ?h.aparc.annot
>> files in a FS 'label' dir? Ideally speaking, I'd like to have a
>> ?h.lobar.annot with corresponding lobar.annot.ctab.
>>
>> Apologies if this question has come up before... a quick google didn't
>> reveal anything.
>>
>> Many thanks
>> -=R
>>
>>
>
--
Rudolph Pienaar, M.Eng, D.Eng / email: rudo...@nmr.mgh.harvard.edu
MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging
149 (2301) 13th Street, Charlestown, MA 02129 USA
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Re: [Freesurfer] Creating annotation file for lobar regions...
The names are below. Also, I should point out that this is a bit
"experimental" in that I chose which ROIs went into each "lobe". I'm not
an anatomist, and it would be a good idea for someone to check my
definitions. Also, I have a "cingulate" lobe because I originally did
this as part of a replication of the FSL thalamus DTI-based segmentation.
doug
From: int MRISaparc2lobes(MRIS *surf) in annotation.c
MRISmergeAnnotations(surf, 10, parcnames, "frontal");
MRISmergeAnnotations(surf, 9, parcnames, "temporal");
MRISmergeAnnotations(surf, 4, parcnames, "parietal");
MRISmergeAnnotations(surf, 4, parcnames, "occipital");
MRISmergeAnnotations(surf, 4, parcnames, "cingulate");
Rudolph Pienaar wrote:
> Great -- many thanks, Doug. What are the newly annotated regions named?
>
> Basically, once I do a MatLAB
>
> [list, label, annot] = read_annotation('lh.lobes.annot');
>
> what are the annot.struct_names?
>
>>
>> Try running mri_annotation2label with --lobes lh.lobes.annot
>>
>> doug
>>
>>
>> On Thu, 20 May 2010, Rudolph Pienaar wrote:
>>
>>> Hi all --
>>>
>>> Is there a simple way to create an annotation for
>>> frontal/temporal/occipital/parietal lobes based off the ?h.aparc.annot
>>> files in a FS 'label' dir? Ideally speaking, I'd like to have a
>>> ?h.lobar.annot with corresponding lobar.annot.ctab.
>>>
>>> Apologies if this question has come up before... a quick google didn't
>>> reveal anything.
>>>
>>> Many thanks
>>> -=R
>>>
>>>
>>
>
>
--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
___
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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
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