Hi Sarah

can you look at the aparc.a2009s.annot in tksurfer and see if it looks right?

Bruce On Tue, 24 Apr 2012, Baum, Sarah H wrote:

Hi,

Currently it's not doing that. I'm using the aparc.a2009s_rank file that I've aligned to the anatomy with @SUMA_AlignToExperiment.

On 4/24/12 2:45 PM, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:

...

Hi Sarah

what parcellation do you mean? Our standard anatomically-based parcellatinos will color the same parcels the same color.

cheers Bruce On Tue, 24 Apr 2012, Baum, Sarah H wrote:

...

Hi-

I'm looking to compare two parcellations (one is a stroke patient with her brain as is, the other is the same subject with the lesion "fixed" run as a separate subject). It would be helpful if the parcellations would color the same area the same color, but currently every single ROI is colored differently than the corresponding parcellation in the other subject's brain. I looked up the color table in the .annot file, and the RGB coordinates listed for each region are exactly the same for each surface volume. Is there any easy way to make the colors the same?

If it helps? I use AFNI/SUMA for visualizing data.

Thanks in advance, Sarah

Sarah H. Baum Ph.D. Candidate, Neuroscience Sarah.H.Baum@uth.tmc.edu w: 713.500.5089 c: 571.225.7007

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Hi Sarah

if it is correct, you'll probably need to bug Ziad and the SUMA guys about why the colors are wrong. If you are resampling the parcellation make sure it is done with nearest neighbor and not e.g. trilinear or sinc

cheers Bruce On Tue, 24 Apr 2012, Baum, Sarah H wrote:

It might take me a little longer because our data is organized a little differently, but I will definitely check it out in tksurfer and get back to you on this.

On 4/24/12 3:12 PM, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:

...

Hi Sarah

can you look at the aparc.a2009s.annot in tksurfer and see if it looks right?

Bruce On Tue, 24 Apr 2012, Baum, Sarah H wrote:

...

Hi,

Currently it's not doing that. I'm using the aparc.a2009s_rank file that I've aligned to the anatomy with @SUMA_AlignToExperiment.

On 4/24/12 2:45 PM, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:

...

Hi Sarah

what parcellation do you mean? Our standard anatomically-based parcellatinos will color the same parcels the same color.

cheers Bruce On Tue, 24 Apr 2012, Baum, Sarah H wrote:

...

Hi-

I'm looking to compare two parcellations (one is a stroke patient with her brain as is, the other is the same subject with the lesion "fixed" run as a separate subject). It would be helpful if the parcellations would color the same area the same color, but currently every single ROI is colored differently than the corresponding parcellation in the other subject's brain. I looked up the color table in the .annot file, and the RGB coordinates listed for each region are exactly the same for each surface volume. Is there any easy way to make the colors the same?

If it helps? I use AFNI/SUMA for visualizing data.

Thanks in advance, Sarah

Sarah H. Baum Ph.D. Candidate, Neuroscience Sarah.H.Baum@uth.tmc.edu w: 713.500.5089 c: 571.225.7007

---

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.

sure. I advise bugging Ziad!

Bruce On Wed, 25 Apr 2012, Baum, Sarah H wrote:

Yes, everything is good in tksurfer, but something after @SUMA_Make_Spec_FS is causing an issue. Thanks for the help!

On 4/24/12 3:23 PM, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:

...

Hi Sarah

if it is correct, you'll probably need to bug Ziad and the SUMA guys about why the colors are wrong. If you are resampling the parcellation make sure it is done with nearest neighbor and not e.g. trilinear or sinc

cheers Bruce On Tue, 24 Apr 2012, Baum, Sarah H wrote:

...

It might take me a little longer because our data is organized a little differently, but I will definitely check it out in tksurfer and get back to you on this.

On 4/24/12 3:12 PM, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:

...

Hi Sarah

can you look at the aparc.a2009s.annot in tksurfer and see if it looks right?

Bruce On Tue, 24 Apr 2012, Baum, Sarah H wrote:

...

Hi,

Currently it's not doing that. I'm using the aparc.a2009s_rank file that I've aligned to the anatomy with @SUMA_AlignToExperiment.

On 4/24/12 2:45 PM, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:

...

Hi Sarah

what parcellation do you mean? Our standard anatomically-based parcellatinos will color the same parcels the same color.

cheers Bruce On Tue, 24 Apr 2012, Baum, Sarah H wrote:

> Hi- > > I'm looking to compare two parcellations (one is a stroke patient > with > her brain as is, the other is the same subject with the lesion > "fixed" > run as a separate subject). It would be helpful if the parcellations > would color the same area the same color, but currently every single > ROI > is colored differently than the corresponding parcellation in the > other > subject's brain. I looked up the color table in the .annot file, and > the > RGB coordinates listed for each region are exactly the same for each > surface volume. Is there any easy way to make the colors the same? > > If it helps? I use AFNI/SUMA for visualizing data. > > Thanks in advance, > Sarah > > > Sarah H. Baum > Ph.D. Candidate, Neuroscience > Sarah.H.Baum@uth.tmc.edu > w: 713.500.5089 > c: 571.225.7007 > > _______________________________________________ > 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.