Hi Ruopeng,

Do you know if freeview has a way to show the selected point on the 3D surface? Double-ckicking in the 3D window seems to choose the point I want on the 3D surface (projecting perpenducularly from the 2D screen to the underlying scalp surface point) and displays a red cross in the 3 2D views, but it show nothing in the 3D window.

Thanks, -Jeff

On 1/5/13 11:43 AM, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:

Hi Jeff I'm not sure you can, but Ruopeng would know. If not, we can add it to the FreeView feature request list.

cheers Bruce On Sat, 5 Jan 2013, Jeff Eriksen wrote:

...

Doug,

Freeview looks like the best way to get what I want. Still trying to figure out how to mark a point in the 3D viewing window, but at least when I mark them in the 2D windows I get all the coordinates I need.

Thanks, -Jeff

Message: 5 Date: Fri, 04 Jan 2013 13:36:59 -0500 From: Douglas N Greve greve@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FW: FW: how to obtain MRI coordinates of scalp surface points marked in tksurfer To: freesurfer@nmr.mgh.harvard.edu Message-ID: 50E7214B.6010407@nmr.mgh.harvard.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed

tksurfer may be putting all 0s in the RAS field because the head surface does not match the cortical surface (tksurfer is very inflexible in this way). One way around it is to find the vertex number, then find the RAS for that vertex by converting the surface to ascii. freeview might do a better job than tksurfer.

doug

On 01/03/2013 10:38 PM, Jeff Eriksen wrote: FreeSurfer experts, I am trying to mark points on a surface in tksurfer, then obtain their original voxel coordinates. These are some of the problems I have encountered, and some of the instructions and examples I do not yet understand. -Jeff

From: Bruce Fischl <fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu> Date: Thursday, January 3, 2013 6:27 PM To: Jeff Eriksen <eriksenj@ohsu.edu mailto:eriksenj@ohsu.edu> Subject: Re: [Freesurfer] FW: how to obtain MRI coordinates of scalp surface points marked in tksurfer

Can you cc the list so others can answer? Freeview can rotate....

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.

Hi Jeff,

You want to use the connectome mapping toolkit:

http://cmtk.org/

Cheers,

-Morgan

On Jun 18, 2013, at 9:50 AM, Jeff Eriksen eriksenj@ohsu.edu wrote:

I just attended the pre-OHBM FSL/FS course, and spoke to David Salat there about possibilities to create more detailed sub-parcellationsfrom the two major structural atlases. Could someone please let me know if David was right that such tools exist, and/or point me to them?

My goal is essentially to create relatively equal-area parcellations with say 100, 200, 500, 1000, 2000, 5000, etc. ROIs per hemisphere, retaining some type of labeling to indicate where each ROI came from.

Thanks, -Jeff

PS I am at the HBM meeting through mid-day Thursday if someone here is able to talk to me in person (maybe even David!). My cell is 971-533-3942 if someone in Seattle wants to call or text.

---

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.

There was a bug with mris_make_face_parcellation that merged some of the rois together when you tried to run the command twice to subdivide the parcellations further. So if you want to use it for this purpose make sure you use the newest version as it has been fixed now.

Best, Maritza

On Tue, 18 Jun 2013, Bruce Fischl wrote:

Hi Jeff

there are two utilities we provide for this (and yes, David is always correct!):

1. mris_make_face_parcellation - create approximately unifom-sized parcels

using icosahedral subdivisions. These can be uniform in the native space using the ?h.sphere, or in register and uniform in the group space using ?h.sphere.reg.

2. mris_divide_parcellation - divides an existing annotation file (e.g.

lh.aparc.annot) either with a specific set of divisions specified by the user, or so that no individual parcel is greater than a specified surface area.

cheers Bruce

On Tue, 18 Jun 2013, Jeff Eriksen wrote:

...

I just attended the pre-OHBM FSL/FS course, and spoke to David Salat there about possibilities to create more detailed sub-parcellationsfrom the two major structural atlases. Could someone please let me know if David was right that such tools exist, and/or point me to them?

My goal is essentially to create relatively equal-area parcellations with say 100, 200, 500, 1000, 2000, 5000, etc. ROIs per hemisphere, retaining some type of labeling to indicate where each ROI came from.

Thanks, -Jeff

PS I am at the HBM meeting through mid-day Thursday if someone here is able to talk to me in person (maybe even David!). My cell is 971-533-3942 if someone in Seattle wants to call or text.

---

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

Hi Jeff, do you just want to map the annotations from fsaverage to your individual subject? If so, you can use mri_surf2surf, something like

mri_surf2surf --srcsubject fsaverage --trgsubject yoursubject --hemi lh \ --sval-annot $SUBJECTS_DIR/fsaverage/label/lh.aparc.annot \ --tval $SUBJECTS_DIR/yoursubject/label/lh.subj1.aparc.annot

doug

On 07/12/2013 06:45 PM, Jeff Eriksen wrote:

I have the Yeo resting-state fMRI atlases which I downloaded from

http://www.freesurfer.net/fswiki/CorticalParcellation_Yeo2011

They consist of 3 versions, fsaverage being of interest here. The fsaverage folder provided includes the typical FS folders corresponding a recon-all for the average brain for this atlas. I wish to use this high resolution atlas to parcellate my individual subjects. I am unclear how to go about this. I have perused wiki pages on

Annotation files FS labels Automatic surface labeling process Surface registration process

but still do not find a clear path to my goal. Specifically I would like to end up with a matching set of surface and annot files, as high of resolution as possible, for each of my subjects. Using some specific numbers, the Yeo atlas has around 300,000 vertices when combining the lh.pial and rh.pial surfaces. The matching annot files I believe are l&rh.Yeo2011_17Networks_N1000.annot, which together should also have 300,000 vertices. I suppose what I need to do is align each of my subjects to this atlas and project the atlas onto each subject to get a new surface and annot file for that subject, which will have some unique number of vertices for each subject.

Please point me to the right set of documentation that will tell me how to do this. Thanks,

-Jeff

---

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

Bruce,

This is what the wiki page says about

mri_label2label - converts a label in one subject's space to a label in another subject's space using either TalairachSpace https://surfer.nmr.mgh.harvard.edu/fswiki/TalairachSpace or SphericalSpace https://surfer.nmr.mgh.harvard.edu/fswiki/SphericalSpace as an intermediate registration space

I am not facile enough with all the ins and outs to be able to figure out how to use this to concatenate the lh and rh annot file from a single subject, so would appreciate a specific example.

I do note that another function is listed under the "see also", mri_merge_labels, but it just seems to be for simple label files, not annot file. If there was one called mri_merge_annot and it worked like this:

mri_merge_annot -i lh.annot -i rh.annot -o bh.annot

Then I could easily understand it.

-Jeff

On 7/13/13 11:31 AM, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:

Hi Jeff mri_label2label should do what you want Cheers Bruce

On Jul 12, 2013, at 6:45 PM, Jeff Eriksen eriksenj@ohsu.edu wrote:

...

I have the Yeo resting-state fMRI atlases which I downloaded from

http://www.freesurfer.net/fswiki/CorticalParcellation_Yeo2011

They consist of 3 versions, fsaverage being of interest here. The fsaverage folder provided includes the typical FS folders corresponding a recon-all for the average brain for this atlas. I wish to use this high resolution atlas to parcellate my individual subjects. I am unclear how to go about this. I have perused wiki pages on

Annotation files FS labels Automatic surface labeling process Surface registration process

but still do not find a clear path to my goal. Specifically I would like to end up with a matching set of surface and annot files, as high of resolution as possible, for each of my subjects. Using some specific numbers, the Yeo atlas has around 300,000 vertices when combining the lh.pial and rh.pial surfaces. The matching annot files I believe are l&rh.Yeo2011_17Networks_N1000.annot, which together should also have 300,000 vertices. I suppose what I need to do is align each of my subjects to this atlas and project the atlas onto each subject to get a new surface and annot file for that subject, which will have some unique number of vertices for each subject.

Please point me to the right set of documentation that will tell me how to do this. Thanks,

-Jeff

---

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.

Hi Jeff,

If you run recon-all on your individual subjects, it would have automatically generate the registration files (?h.sphere.reg) to fsaverage. Doug's reply about mri_surf2surf should work. You just need to apply mri_surf2surf separately for the left and right annots.

Cheers, Thomas

On Sun, Jul 14, 2013 at 10:27 PM, Jeff Eriksen eriksenj@ohsu.edu wrote:

Bruse,

I apologize, I thought you were answering another question that I had submitted, which I had foremost in my mind. I will look at mri_label2label in more detail now in the proper context.

Thanks, -Jeff

On 7/13/13 11:31 AM, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:

...

Hi Jeff mri_label2label should do what you want Cheers Bruce

On Jul 12, 2013, at 6:45 PM, Jeff Eriksen eriksenj@ohsu.edu wrote:

...

I have the Yeo resting-state fMRI atlases which I downloaded from

http://www.freesurfer.net/fswiki/CorticalParcellation_Yeo2011

They consist of 3 versions, fsaverage being of interest here. The fsaverage folder provided includes the typical FS folders corresponding a recon-all for the average brain for this atlas. I wish to use this high resolution atlas to parcellate my individual subjects. I am unclear how to go about this. I have perused wiki pages on

Annotation files FS labels Automatic surface labeling process Surface registration process

but still do not find a clear path to my goal. Specifically I would like to end up with a matching set of surface and annot files, as high of resolution as possible, for each of my subjects. Using some specific numbers, the Yeo atlas has around 300,000 vertices when combining the lh.pial and rh.pial surfaces. The matching annot files I believe are l&rh.Yeo2011_17Networks_N1000.annot, which together should also have 300,000 vertices. I suppose what I need to do is align each of my subjects to this atlas and project the atlas onto each subject to get a new surface and annot file for that subject, which will have some unique number of vertices for each subject.

Please point me to the right set of documentation that will tell me how to do this. Thanks,

-Jeff

---

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.

---

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