Hi Bruce,

Thanks for the quick response. I got lost with the mri_binarize step, could you please explain to me how to find the value for the '--match' for different structures related to the aparc+aseg.mgz file?

Many thanks, Tomer

Hi Tomer

if you binarize the aparc+aseg.mgz with mri_binarize that should be pretty close. Do you need it in the functional geometry? If so, you can use mri_vol2vol to convert it (with a register.dat created by bbregister)

cheers Bruce

On Sat, 7 Apr 2012, Tomer Livne wrote:

...

Hi, I'll appreciate some help with the following issue. I need to define an ROI in a whole brain volume to be used as a mask in PyMVPA. That means having a whole brain .nii file with '1' within the ROI and '0' in every other voxel. Is there a way to define a functional ROI in a whole brain volume, in a similar way to what I get when running funcroi with an annotation from aparc for a specific hemi? Or alternatively, is there a way to convert the aparc based ROI for a single hemi surface into a whole brain volume?     Best, Tomer

Hi Bruce,

I seem to be missing something, sorry. How would I define this range? Also, how can I combine this mask with the functional results (obtained by running 'selxavg3-sess -s sj -analysis X.lh ...)? What I'll need eventually is a mask constrained both by anatomical and functional considerations (preferably with automatic anatomical segmentation as achieved by funcroi).

Thanks again, Tomer

Hi Tomer

don't use match - that would be for specific values. Instead specify a range via:

mri_binarize --min 1 --max 256 --i aparc+aseg.mgz --o aparc+aseg.mask.mgz

cheers Bruce

On Sat, 7 Apr 2012, tomer@nmr.mgh.harvard.edu wrote:

...

Hi Bruce,

Thanks for the quick response. I got lost with the mri_binarize step, could you please explain to me how to find the value for the '--match' for different structures related to the aparc+aseg.mgz file?

Many thanks, Tomer

...

Hi Tomer

if you binarize the aparc+aseg.mgz with mri_binarize that should be pretty close. Do you need it in the functional geometry? If so, you can use mri_vol2vol to convert it (with a register.dat created by bbregister)

cheers Bruce

On Sat, 7 Apr 2012, Tomer Livne wrote:

...

Hi, I'll appreciate some help with the following issue. I need to define an ROI in a whole brain volume to be used as a mask in PyMVPA. That means having a whole brain .nii file with '1' within the ROI and '0' in every other voxel. Is there a way to define a functional ROI in a whole brain volume, in a similar way to what I get when running funcroi with an annotation from aparc for a specific hemi? Or alternatively, is there a way to convert the aparc based ROI for a single hemi surface into a whole brain volume?     Best, Tomer

---

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

Hi Doug,

Thanks for the FreeSurferColorLUT.txt link, that solved the anatomical issue. I am trying to further limit this anatomical mask to voxels that were significant in the analysis of the functional data (performed on a surface, e.g. lh).

Thanks, Tomer

If you want a simple brain mask, you can use brainmask.mgz. If you want to create a mask for a particular anatomical ROI, then you can use mri_binarize with --match. You can get a list of indicies from $FREESURFER_HOME/FreeSurferColorLUT.txt. I'm not sure what you are asking in terms of your selxavg3 question.

doug

On 4/7/12 1:04 PM, tomer@nmr.mgh.harvard.edu wrote:

...

Hi Bruce,

I seem to be missing something, sorry. How would I define this range? Also, how can I combine this mask with the functional results (obtained by running 'selxavg3-sess -s sj -analysis X.lh ...)? What I'll need eventually is a mask constrained both by anatomical and functional considerations (preferably with automatic anatomical segmentation as achieved by funcroi).

Thanks again, Tomer

...

Hi Tomer

don't use match - that would be for specific values. Instead specify a range via:

mri_binarize --min 1 --max 256 --i aparc+aseg.mgz --o aparc+aseg.mask.mgz

cheers Bruce

On Sat, 7 Apr 2012, tomer@nmr.mgh.harvard.edu wrote:

...

Hi Bruce,

Thanks for the quick response. I got lost with the mri_binarize step, could you please explain to me how to find the value for the '--match' for different structures related to the aparc+aseg.mgz file?

Many thanks, Tomer

...

Hi Tomer

if you binarize the aparc+aseg.mgz with mri_binarize that should be pretty close. Do you need it in the functional geometry? If so, you can use mri_vol2vol to convert it (with a register.dat created by bbregister)

cheers Bruce

On Sat, 7 Apr 2012, Tomer Livne wrote:

...

Hi, I'll appreciate some help with the following issue. I need to define an ROI in a whole brain volume to be used as a mask in PyMVPA. That means having a whole brain .nii file with '1' within the ROI and '0' in every other voxel. Is there a way to define a functional ROI in a whole brain volume, in a similar way to what I get when running funcroi with an annotation from aparc for a specific hemi? Or alternatively, is there a way to convert the aparc based ROI for a single hemi surface into a whole brain volume?

Best, Tomer

---

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

---

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

Thanks Doug,

I'll try that.

Tomer

On Apr 12, 2012, at 2:04 PM, Douglas N Greve wrote:

First, convert the annotation to a segmentation, something like

mri_annotation2label --subject subjectname --hemi lh --seg lh.aparc.mgh

Then binarize the segmentation and mask with your functional:

mri_binarize --i lh.aparc.mgh --match segid --mask sig.mgh --mask-thresh 2 --o seg.masked.mgh

Then run mri_label2vol on seg.masked.mgh to get the masked segmentation in the volume

doug

On 04/07/2012 01:28 PM, tomer@nmr.mgh.harvard.edu wrote:

...

Hi Doug,

Thanks for the FreeSurferColorLUT.txt link, that solved the anatomical issue. I am trying to further limit this anatomical mask to voxels that were significant in the analysis of the functional data (performed on a surface, e.g. lh).

Thanks, Tomer

...

If you want a simple brain mask, you can use brainmask.mgz. If you want to create a mask for a particular anatomical ROI, then you can use mri_binarize with --match. You can get a list of indicies from $FREESURFER_HOME/FreeSurferColorLUT.txt. I'm not sure what you are asking in terms of your selxavg3 question.

doug

On 4/7/12 1:04 PM, tomer@nmr.mgh.harvard.edu wrote:

...

Hi Bruce,

I seem to be missing something, sorry. How would I define this range? Also, how can I combine this mask with the functional results (obtained by running 'selxavg3-sess -s sj -analysis X.lh ...)? What I'll need eventually is a mask constrained both by anatomical and functional considerations (preferably with automatic anatomical segmentation as achieved by funcroi).

Thanks again, Tomer

...

Hi Tomer

don't use match - that would be for specific values. Instead specify a range via:

mri_binarize --min 1 --max 256 --i aparc+aseg.mgz --o aparc+aseg.mask.mgz

cheers Bruce

On Sat, 7 Apr 2012, tomer@nmr.mgh.harvard.edu wrote:

...

Hi Bruce,

Thanks for the quick response. I got lost with the mri_binarize step, could you please explain to me how to find the value for the '--match' for different structures related to the aparc+aseg.mgz file?

Many thanks, Tomer

> Hi Tomer > > if you binarize the aparc+aseg.mgz with mri_binarize that should be > pretty > close. Do you need it in the functional geometry? If so, you can use > mri_vol2vol to convert it (with a register.dat created by bbregister) > > cheers > Bruce > > > On Sat, 7 Apr 2012, Tomer Livne wrote: > >> Hi, I'll appreciate some help with the following issue. >> I need to define an ROI in a whole brain volume to be used as a mask >> in >> PyMVPA. That means >> having a whole brain .nii file with '1' within the ROI and '0' in >> every >> other voxel. >> Is there a way to define a functional ROI in a whole brain volume, >> in >> a >> similar way to what I >> get when running funcroi with an annotation from aparc for a >> specific >> hemi? Or alternatively, >> is there a way to convert the aparc based ROI for a single hemi >> surface into a whole brain >> volume? >> >> >> Best, >> Tomer >> >> >> >> _______________________________________________ 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

---

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

-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@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