Thank you Paul that is very helpful, but I could use a little more specific help.

A little more context: I ran a group vertexwise analysis with all my subjects mapped to the fsaverage and traced my group cluster in QDEC and saved the label. Now I would like to somehow get it into afni in the same space and use it for some functional analyses.

I mapped the label to each individual subjects space, but the next step I am running into issues.

I don't seem to see any medial wall in the aparc annotation. Plus I am not familiar with the color table, I was just wondering what that would look like.

Any help from anyone would be much appreciated!

Tara

----- Original Message ----- From: "Paul Beach" pabeach1@gmail.com To: "Freesurfer support list" freesurfer@nmr.mgh.harvard.edu, miskovi2@uwm.edu Sent: Thursday, June 5, 2014 12:26:00 PM Subject: Re: [Freesurfer] Freesurfer Surface based ROI to AFNI?

Hi Tara,

I do this regularly, though I don't define my Freesurfer ROIs/labels in QDEC.

The following will do the process into individual subject space

First : mri_label2label --srclabel path_to_label/label.label --trgsubject {$subj} --regmethod surface --hemi hemisphere

Do this for as many labels as you have...

Then : Create a color table file (.ctab file) for each hemisphere that contains your ROIs. Take a look at the FreesurferColorLUT.txt file for help with that. The first entry should be the Freesurfer defined medial wall, which you can get from each subject's aparc.annot via mri_annotation2label.

Then create an annotation file using your .ctab file and your ROIs - one for each hemisphere

mris_label2annot --s {$subj} --ldir-default --h hemisphere --ctab hemisphere.ctab_file_name.txt --annot name_for_your_annotation_file \

--l hemi.FS_medial_wall.label \

--l hemi.ROI1.label \ --l hemi.ROI2.label \

--l hemi.ROI3.label \

...

Then create a segmentation file from the annotation file

mri_aparc2aseg --s {$subj} --annot annotion_you_created_without_hemi_designation --o segmentation_file_name+aseg.mgz

Then make a gmroi_vol file from which you can extract your ROIs

mri_label2vol --seg segmentation_file_name+aseg.mgz --regheader segmentation_file_name+aseg.mgz --o you_gmroi_volume.nii.gz --temp orig/001.mgz

Copy the gmroi_vol to your subject's afni directory

Use 3dcalc to extract individual ROIs from the gmroi_volume. The number you put in depends on your .ctab file order. The first ROI would be 1001. Like the ColorLUT, the first digit being '1' is typically for L. hemi, while '2' would be for the R. hemi.

3dcalc -a your_gmroi_volume.nii.gz -expr 'equals(a,####)' -prefix ROI_name.nii.gz

You can then do your AFNI-based analyses with your ROIs.

Hopefully that's all clear. Let me know if I can help in another way.

Cheers, Paul

On Thu, Jun 5, 2014 at 12:13 PM, Tara Ann Miskovich < miskovi2@uwm.edu > wrote:

Hi all,

I am wondering if any one has any experience with converting a freesurfer surface based ROI created in QDEC into a format I could use on functional data in afni.

Thank you,

Tara

_______________________________________________ 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.

Hello all,

I believe Ziad Saad and friends have written AFNI/SUMA to make this easy. If you run @SUMA_Make_Spec_FS on your freesurfer files, it will convert all the volume-space segmentation and parcellation files to be readable in AFNI. Takes only a couple of minutes.

Run @SUMA_Make_Spec_FS -help to see the command line syntax. Look for the relevant files in the SUMA folder. You can also edit the @SUMA program to add any file you have newly created that is not a standard freesurfer file.

Anthony

On 6/9/14, 11:15 AM, Tara Ann Miskovich wrote:

Thank you Paul that is very helpful, but I could use a little more specific help.

A little more context: I ran a group vertexwise analysis with all my subjects mapped to the fsaverage and traced my group cluster in QDEC and saved the label. Now I would like to somehow get it into afni in the same space and use it for some functional analyses.

I mapped the label to each individual subjects space, but the next step I am running into issues.

I don't seem to see any medial wall in the aparc annotation. Plus I am not familiar with the color table, I was just wondering what that would look like.

Any help from anyone would be much appreciated!

Tara

----- Original Message ----- From: "Paul Beach" pabeach1@gmail.com To: "Freesurfer support list" freesurfer@nmr.mgh.harvard.edu, miskovi2@uwm.edu Sent: Thursday, June 5, 2014 12:26:00 PM Subject: Re: [Freesurfer] Freesurfer Surface based ROI to AFNI?

Hi Tara,

I do this regularly, though I don't define my Freesurfer ROIs/labels in QDEC.

The following will do the process into individual subject space

First : mri_label2label --srclabel path_to_label/label.label --trgsubject {$subj} --regmethod surface --hemi hemisphere

Do this for as many labels as you have...

Then : Create a color table file (.ctab file) for each hemisphere that contains your ROIs. Take a look at the FreesurferColorLUT.txt file for help with that. The first entry should be the Freesurfer defined medial wall, which you can get from each subject's aparc.annot via mri_annotation2label.

Then create an annotation file using your .ctab file and your ROIs - one for each hemisphere

mris_label2annot --s {$subj} --ldir-default --h hemisphere --ctab hemisphere.ctab_file_name.txt --annot name_for_your_annotation_file \

--l hemi.FS_medial_wall.label \

--l hemi.ROI1.label \ --l hemi.ROI2.label \

--l hemi.ROI3.label \

...

Then create a segmentation file from the annotation file

mri_aparc2aseg --s {$subj} --annot annotion_you_created_without_hemi_designation --o segmentation_file_name+aseg.mgz

Then make a gmroi_vol file from which you can extract your ROIs

mri_label2vol --seg segmentation_file_name+aseg.mgz --regheader segmentation_file_name+aseg.mgz --o you_gmroi_volume.nii.gz --temp orig/001.mgz

Copy the gmroi_vol to your subject's afni directory

Use 3dcalc to extract individual ROIs from the gmroi_volume. The number you put in depends on your .ctab file order. The first ROI would be 1001. Like the ColorLUT, the first digit being '1' is typically for L. hemi, while '2' would be for the R. hemi.

3dcalc -a your_gmroi_volume.nii.gz -expr 'equals(a,####)' -prefix ROI_name.nii.gz

You can then do your AFNI-based analyses with your ROIs.

Hopefully that's all clear. Let me know if I can help in another way.

Cheers, Paul

On Thu, Jun 5, 2014 at 12:13 PM, Tara Ann Miskovich < miskovi2@uwm.edu > wrote:

Hi all,

I am wondering if any one has any experience with converting a freesurfer surface based ROI created in QDEC into a format I could use on functional data in afni.

Thank you,

Tara

---

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.

Tara,

You have to run the mri_annot2label command on the individual subject's aparc.annot files (R&L hemi). This will give you the medial wall labels you can then use to construct your own annotation. You have to include it in your ctab file, after "unknown." I think it may be the bankssts.label that you'll need. Sorry for the confusion about that.

Btw - the ctab (or color table) file is just a text file you can create and save (either as .ctab or even .txt).

I've attached a .ctab file for reference. Keep in mind that this will look different from yours as I'm using the Yeo parcellations and they come with their own medial wall label.

On Mon, Jun 9, 2014 at 11:15 AM, Tara Ann Miskovich miskovi2@uwm.edu wrote:

Thank you Paul that is very helpful, but I could use a little more specific help.

A little more context: I ran a group vertexwise analysis with all my subjects mapped to the fsaverage and traced my group cluster in QDEC and saved the label. Now I would like to somehow get it into afni in the same space and use it for some functional analyses.

I mapped the label to each individual subjects space, but the next step I am running into issues.

I don't seem to see any medial wall in the aparc annotation. Plus I am not familiar with the color table, I was just wondering what that would look like.

Any help from anyone would be much appreciated!

Tara

----- Original Message ----- From: "Paul Beach" pabeach1@gmail.com To: "Freesurfer support list" freesurfer@nmr.mgh.harvard.edu, miskovi2@uwm.edu Sent: Thursday, June 5, 2014 12:26:00 PM Subject: Re: [Freesurfer] Freesurfer Surface based ROI to AFNI?

Hi Tara,

I do this regularly, though I don't define my Freesurfer ROIs/labels in QDEC.

The following will do the process into individual subject space

First : mri_label2label --srclabel path_to_label/label.label --trgsubject {$subj} --regmethod surface --hemi hemisphere

Do this for as many labels as you have...

Then : Create a color table file (.ctab file) for each hemisphere that contains your ROIs. Take a look at the FreesurferColorLUT.txt file for help with that. The first entry should be the Freesurfer defined medial wall, which you can get from each subject's aparc.annot via mri_annotation2label.

Then create an annotation file using your .ctab file and your ROIs - one for each hemisphere

mris_label2annot --s {$subj} --ldir-default --h hemisphere --ctab hemisphere.ctab_file_name.txt --annot name_for_your_annotation_file \

--l hemi.FS_medial_wall.label \

--l hemi.ROI1.label \ --l hemi.ROI2.label \

--l hemi.ROI3.label \

...

Then create a segmentation file from the annotation file

mri_aparc2aseg --s {$subj} --annot annotion_you_created_without_hemi_designation --o segmentation_file_name+aseg.mgz

Then make a gmroi_vol file from which you can extract your ROIs

mri_label2vol --seg segmentation_file_name+aseg.mgz --regheader segmentation_file_name+aseg.mgz --o you_gmroi_volume.nii.gz --temp orig/001.mgz

Copy the gmroi_vol to your subject's afni directory

Use 3dcalc to extract individual ROIs from the gmroi_volume. The number you put in depends on your .ctab file order. The first ROI would be 1001. Like the ColorLUT, the first digit being '1' is typically for L. hemi, while '2' would be for the R. hemi.

3dcalc -a your_gmroi_volume.nii.gz -expr 'equals(a,####)' -prefix ROI_name.nii.gz

You can then do your AFNI-based analyses with your ROIs.

Hopefully that's all clear. Let me know if I can help in another way.

Cheers, Paul

On Thu, Jun 5, 2014 at 12:13 PM, Tara Ann Miskovich < miskovi2@uwm.edu > wrote:

Hi all,

I am wondering if any one has any experience with converting a freesurfer surface based ROI created in QDEC into a format I could use on functional data in afni.

Thank you,

Tara

---

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.

--

Paul Beach DO/PhD candidate - Year VI Michigan State University

• College of Osteopathic Medicine
• Neuroscience Program
• MSU Co gnitive and Ge riatric N eurology T eam ( CoGeNT )