The BA/MT/V1/V2 maps are label files in the subjects/fsaverage/label directory distributed with freesurfer. See also:

http://surfer.nmr.mgh.harvard.edu/fswiki/BrodmannAreaMaps

The entorhinal maps are not included with freesurfer.

Nick

On Tue, 2009-05-19 at 13:15 -0400, Bruce Fischl wrote:

We also have a number of these probability maps constructed on the surface, and I think they are now part of the distribution (is that true Nick?). We have maps for BA17, 18, 1, 2, 3a, 3b, 4a, 4p, 6, 44, 45, area MT and entorhinal cortex (the last of which we built ourselves from ex vivo MRI). Note that the surface maps are much more accurate than the volume maps, so you are better off using them as opposed to taking say the map in Tal coords and mapping it to your subject.

cheers, Bruce

On Tue, 19 May 2009, Douglas N Greve wrote:

...

We have a program called mri_vol2surf which does the projection, and tksurfer which does the visualization. But you need to make sure that the surface and volume are in registration. This is done with tkregister2. Usually, the volume you are sampling to the surface and the surface itself are from the same subject.

You might want to check out our tutorial on this:

https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultiModal

doug

m.e.kirlangic@fz-juelich.de wrote:

...

Dear Freesurfer Community,

I am quite new in freesurfer, getting just acquainted with the tools. What I am currently trying to do is, projecting 3-D voxel data (i.e. postmortem probability maps of Prof. Katrin Amunts and Prof. Karl Zilles in Research Center Juelich -Germany) onto the cortical surface. For the time being, I assume that both types of data are registered to a reference space (e.g., Collin27-brain).

Which functions I would/could need for the calculations and visualization? Which data format(s) is/are required in order to be able to make use of the available freesurfer functions? Any guidance and all tips are very welcome :-) And sorry for any inconvenience using the terminology!

Thanks, Eylem Kirlangic

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Forschungszentrum Juelich GmbH 52425 Juelich

Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzende des Aufsichtsrats: MinDir'in Baerbel Brumme-Bothe Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender), Dr. Ulrich Krafft (stellv. Vorsitzender), Prof. Dr. Harald Bolt, Prof. Dr. Sebastian M. Schmidt

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Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Hi Eylem,

I'm not sure what you mean. Do you mean you have some new areas that you want to project onto the surface of an existing subject? For that you will need the subject surfaces, which we are happy to give you.

cheers, Bruce On Wed, 27 May 2009, Eylem Kirlangic wrote:

If I am to introduce further areas for projection (or construction on the surface), what procedure should I follow?

Thanks, Eylem

Nick Schmansky wrote:

...

The BA/MT/V1/V2 maps are label files in the subjects/fsaverage/label directory distributed with freesurfer. See also:

http://surfer.nmr.mgh.harvard.edu/fswiki/BrodmannAreaMaps

The entorhinal maps are not included with freesurfer.

Nick

On Tue, 2009-05-19 at 13:15 -0400, Bruce Fischl wrote:

...

We also have a number of these probability maps constructed on the surface, and I think they are now part of the distribution (is that true Nick?). We have maps for BA17, 18, 1, 2, 3a, 3b, 4a, 4p, 6, 44, 45, area MT and entorhinal cortex (the last of which we built ourselves from ex vivo MRI). Note that the surface maps are much more accurate than the volume maps, so you are better off using them as opposed to taking say the map in Tal coords and mapping it to your subject.

cheers, Bruce

On Tue, 19 May 2009, Douglas N Greve wrote:

...

We have a program called mri_vol2surf which does the projection, and tksurfer which does the visualization. But you need to make sure that the surface and volume are in registration. This is done with tkregister2. Usually, the volume you are sampling to the surface and the surface itself are from the same subject.

You might want to check out our tutorial on this:

https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultiModal

doug

m.e.kirlangic@fz-juelich.de wrote:

...

Dear Freesurfer Community,

I am quite new in freesurfer, getting just acquainted with the tools. What I am currently trying to do is, projecting 3-D voxel data (i.e. postmortem probability maps of Prof. Katrin Amunts and Prof. Karl Zilles in Research Center Juelich -Germany) onto the cortical surface. For the time being, I assume that both types of data are registered to a reference space (e.g., Collin27-brain).

Which functions I would/could need for the calculations and visualization? Which data format(s) is/are required in order to be able to make use of the available freesurfer functions? Any guidance and all tips are very welcome :-) And sorry for any inconvenience using the terminology!

Thanks, Eylem Kirlangic

---

---

Forschungszentrum Jülich GmbH 52425 Jülich

Sitz der Gesellschaft: Jülich Eingetragen im Handelsregister des Amtsgerichts Düren Nr. HR B 3498 Vorsitzende des Aufsichtsrats: MinDir'in Bärbel Brumme-Bothe Geschäftsführung: Prof. Dr. Achim Bachem (Vorsitzender), Dr. Ulrich Krafft (stellv. Vorsitzender), Prof. Dr. Harald Bolt, Prof. Dr. Sebastian M. Schmidt

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Hi Eylem,

the maps need to be remapped to bert since the surface recon was regenerated. Use mri_label2label for this with fsaverage as the source and bert as the target.

For mapping new areas you definitely don't want to average them in the colin space, then map from there as you will sacrifice a ton of accuracy. You are much better off painting the new labels onto the individual surface reconstructions (which we can give you), then averaging in the surface-based coordinate sytem. You can then use mri_label2label to map to any new subjects you want.

cheers, Bruce

On Thu, 28 May 2009, Eylem Kirlangic wrote:

Hello Bruce,

I want to be able to project further areas onto individual brains, of which the surfaces should be constructed. For the beginning I am trying to do that for the colin27T1 (a standard brain) and the sample data set Bert. I am currently calculating the surface for colin27T1. For Bert, I had already run recon-all automatically.

I can see the already integrated BA maps on the average surface using the command: tksurfer fsaverage lh inflated and, selecting the corresponding labels (like it is stated in the Tutorial for Broadman Area Maps). However, if I do the same thing for the data set Bert, then I just get scatterred colour lines or points on the generated surface(s) of Bert, which looks weird. (What could be the reason?)

I think I can summarize my objectives as follows:

1. using the existing labels for new subjects of which the surfaces shall be

constructed, 2) introducing further areas which are mapped here in our institute (probably meaning generating new labels corresponding to these areas???) for application on an average surface (or a standard surface) as an initial step, and 3) (later) being able to use these maps on new individual surfaces.

Since I am new to the topic, all support, and any correction in the formulation of the task is very welcome!

Thanks, Eylem

Bruce Fischl wrote:

...

Hi Eylem,

I'm not sure what you mean. Do you mean you have some new areas that you want to project onto the surface of an existing subject? For that you will need the subject surfaces, which we are happy to give you.

cheers, Bruce On Wed, 27 May 2009, Eylem Kirlangic wrote:

...

If I am to introduce further areas for projection (or construction on the surface), what procedure should I follow?

Thanks, Eylem

Nick Schmansky wrote:

...

The BA/MT/V1/V2 maps are label files in the subjects/fsaverage/label directory distributed with freesurfer. See also:

http://surfer.nmr.mgh.harvard.edu/fswiki/BrodmannAreaMaps

The entorhinal maps are not included with freesurfer.

Nick

On Tue, 2009-05-19 at 13:15 -0400, Bruce Fischl wrote:

...

We also have a number of these probability maps constructed on the surface, and I think they are now part of the distribution (is that true Nick?). We have maps for BA17, 18, 1, 2, 3a, 3b, 4a, 4p, 6, 44, 45, area MT and entorhinal cortex (the last of which we built ourselves from ex vivo MRI). Note that the surface maps are much more accurate than the volume maps, so you are better off using them as opposed to taking say the map in Tal coords and mapping it to your subject.

cheers, Bruce

On Tue, 19 May 2009, Douglas N Greve wrote:

...

We have a program called mri_vol2surf which does the projection, and tksurfer which does the visualization. But you need to make sure that the surface and volume are in registration. This is done with tkregister2. Usually, the volume you are sampling to the surface and the surface itself are from the same subject.

You might want to check out our tutorial on this:

https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultiModal

doug

m.e.kirlangic@fz-juelich.de wrote:

> Dear Freesurfer Community, > > I am quite new in freesurfer, getting just acquainted with the tools. > What I am currently trying to do is, projecting 3-D voxel data (i.e. > postmortem probability maps of Prof. Katrin Amunts and Prof. Karl > Zilles in Research Center Juelich -Germany) onto the cortical surface. > For the time being, I assume that both types of data are registered to > a reference space (e.g., Collin27-brain). > > Which functions I would/could need for the calculations and > visualization? Which data format(s) is/are required in order to be > able to make use of the available freesurfer functions? Any guidance > and all tips are very welcome :-) And sorry for any inconvenience > using the terminology! > > Thanks, Eylem Kirlangic > > > >

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Forschungszentrum Jülich GmbH 52425 Jülich

Sitz der Gesellschaft: Jülich Eingetragen im Handelsregister des Amtsgerichts Düren Nr. HR B 3498 Vorsitzende des Aufsichtsrats: MinDir'in Bärbel Brumme-Bothe Geschäftsführung: Prof. Dr. Achim Bachem (Vorsitzender), Dr. Ulrich Krafft (stellv. Vorsitzender), Prof. Dr. Harald Bolt, Prof. Dr. Sebastian M. Schmidt

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