FYI, fsaverage is already in MNI305 space

On 08/01/2018 11:14 AM, Peled, Noam wrote:

Thanks Lilla!

Just to be sure, when using the --mni flag, should I remove the  --template flag?

Also, is there any way I can calculate the registration directly to MNI305 and not MNI152?

Thanks again,

Noam

---

*From:* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Lilla Zollei lzollei@nmr.mgh.harvard.edu *Sent:* Wednesday, August 1, 2018 8:35:49 AM *To:* Freesurfer support list *Subject:* Re: [Freesurfer] mri_cvs_register using fsaverage

Hi Noam,

Can you can use the --mni flag?

"Use the CVS atlas in MNI152 space as a target for registration (as opposed to the default CVS template)"

Lilla

On Wed, 1 Aug 2018, Peled, Noam wrote:

...

I need to transfer one of our patient's electrodes locations (depth

electrodes, they aren't located on the cortical surface) to MNI305 space.

...

For that, I'm trying to use mri_cvs_register to register the patient

to fsaverage. I'm using to the following command:

...

mri_cvs_register --mov subjid --template fsaverage --outdir

output_name --nocleanup

...

And I'm getting the following error: fsaverage : at least one mean and/or Gaussian curvature file is

missing (.H, .K)

...

Indeed, fsaverage doesn't have the rh/lh.inflated.K/H files. Any ideas?

Thanks, Noam

---

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

Yes, you can remove the template flag.

And no, not at the moment.

Thanks Lilla!

Just to be sure, when using the --mni flag, should I remove the  --template flag?

Also, is there any way I can calculate the registration directly to MNI305 and not MNI152?

Thanks again,

Noam

---

From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Lilla Zollei lzollei@nmr.mgh.harvard.edu Sent: Wednesday, August 1, 2018 8:35:49 AM To: Freesurfer support list Subject: Re: [Freesurfer] mri_cvs_register using fsaverage

Hi Noam,

Can you can use the --mni flag?

"Use the CVS atlas in MNI152 space as a target for registration (as opposed to the default CVS template)"

Lilla

On Wed, 1 Aug 2018, Peled, Noam wrote:

...

I need to transfer one of our patient's electrodes locations (depth electrodes, they aren't located on the cortical surface) to MNI305 space. For that, I'm trying to use mri_cvs_register to register the patient to fsaverage. I'm using to the following command:

mri_cvs_register --mov subjid --template fsaverage --outdir output_name --nocleanup

And I'm getting the following error: fsaverage : at least one mean and/or Gaussian curvature file is missing (.H, .K)

Indeed, fsaverage doesn't have the rh/lh.inflated.K/H files. Any ideas?

Thanks, Noam

It doesn't seem to work

Here are the commands I was using:

mri_cvs_register --mov $SUBJECT --mni --outdir $SUBJECTS_DIR/$SUBJECT/mri_cvs_register_to_mni --nocleanup applyMorph --template $SUBJECTS_DIR/cvs_avg35_inMNI152/mri/orig.mgz --transform $SUBJECTS_DIR/$SUBJECT/mri_cvs_register_to_mni/combined_tocvs_avg35_inMNI152_elreg_afteraseg-norm.tm3d point_list $SUBJECTS_DIR/$SUBJECT/electrodes/electrodes_to_morph.txt $SUBJECTS_DIR/$SUBJECT/electrodes/electrodes_morph_to_MNI152.txt a

The file electrodes_to_morph.txt contains the electrodes in the $SUBJECT's orig space (T1 voxels) As a sanity check, I checked the electrodes' values in brainmask.mgz. When checking the electrodes in electrodes_to_morph.txt against $SUBJECT/mri/brainmask.mgz, only a few were outside the brain. But when checking the electrodes after the morphing in electrodes_morph_to_MNI152.txt against cvs_avg35_inMNI152/mri/brainmask.mgz, at least half of them were outside the brain.

Any ideas? Thanks, Noam

________________________________ From: Peled, Noam Sent: Saturday, August 18, 2018 3:08:22 PM To: Freesurfer support list Subject: Re: [Freesurfer] mri_cvs_register using fsaverage

Thanks Lilla!

A follow-up question: How can I use the applyMorph function to morph the points to the MNI152 space?

I'm trying to use the combined_tocvs_avg35_inMNI152_elreg_afteraseg-norm.tm3d file I've got from the mri_cvs_register call.

Which template should I use? I can't use fsaverage because it's in the MNI305 space. Should I use cvs_avg35_inMNI152 instead?

And to morph it to MNI305, should I use the inverse matrix of

M = [[0.9975, - 0.0073, 0.0176, -0.0429], [0.0146, 1.0009, -0.0024, 1.5496], [-0.0130, -0.0093, 0.9971, 1.1840], [0, 0, 0, 1.0000]]

As mentioned in the last section in http://freesurfer.net/fswiki/CoordinateSystems?

Thanks!

Noam

________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Lilla Zollei lzollei@nmr.mgh.harvard.edu Sent: Wednesday, August 1, 2018 2:33:19 PM To: Freesurfer support list Subject: Re: [Freesurfer] mri_cvs_register using fsaverage

Yes, you can remove the template flag.

And no, not at the moment.

Thanks Lilla!

Just to be sure, when using the --mni flag, should I remove the --template flag?

Also, is there any way I can calculate the registration directly to MNI305 and not MNI152?

Thanks again,

Noam

---

From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Lilla Zollei lzollei@nmr.mgh.harvard.edu Sent: Wednesday, August 1, 2018 8:35:49 AM To: Freesurfer support list Subject: Re: [Freesurfer] mri_cvs_register using fsaverage

Hi Noam,

Can you can use the --mni flag?

"Use the CVS atlas in MNI152 space as a target for registration (as opposed to the default CVS template)"

Lilla

On Wed, 1 Aug 2018, Peled, Noam wrote:

...

I need to transfer one of our patient's electrodes locations (depth electrodes, they aren't located on the cortical surface) to MNI305 space. For that, I'm trying to use mri_cvs_register to register the patient to fsaverage. I'm using to the following command:

mri_cvs_register --mov subjid --template fsaverage --outdir output_name --nocleanup

And I'm getting the following error: fsaverage : at least one mean and/or Gaussian curvature file is missing (.H, .K)

Indeed, fsaverage doesn't have the rh/lh.inflated.K/H files. Any ideas?

Thanks, Noam

Thanks Lilla!

I'm working with the dev version on my laptop, but indeed I've downloaded it before the patch. I've updated the version and now everything is working!

Thanks so much,

Noam

________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Lilla Zollei lzollei@nmr.mgh.harvard.edu Sent: Sunday, August 19, 2018 3:16:31 AM To: Freesurfer support list Subject: Re: [Freesurfer] mri_cvs_register using fsaverage

Hi Noam,

What version of FS are you using? I have incorporated a change into dev in January. Have you seen this note?

https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2018-January/055460.ht...

Lilla

On Sat, 18 Aug 2018, Peled, Noam wrote:

It doesn't seem to work

Here are the commands I was using:

mri_cvs_register --mov $SUBJECT --mni --outdir $SUBJECTS_DIR/$SUBJECT/mri_cvs_register_to_mni --nocleanup applyMorph --template $SUBJECTS_DIR/cvs_avg35_inMNI152/mri/orig.mgz --transform $SUBJECTS_DIR/$SUBJECT/mri_cvs_register_to_mni/combined_tocvs_avg35_inMNI152_elreg_afteraseg-norm.tm3d point_list $SUBJECTS_DIR/$SUBJECT/electrodes/electrodes_to_morph.txt $SUBJECTS_DIR/$SUBJECT/electrodes/electrodes_morph_to_MNI152.txt a

The file electrodes_to_morph.txt contains the electrodes in the $SUBJECT's orig space (T1 voxels) As a sanity check, I checked the electrodes' values in brainmask.mgz. When checking the electrodes in electrodes_to_morph.txt against $SUBJECT/mri/brainmask.mgz, only a few were outside the brain. But when checking the electrodes after the morphing in electrodes_morph_to_MNI152.txt against cvs_avg35_inMNI152/mri/brainmask.mgz, at least half of them were outside the brain.

Any ideas? Thanks, Noam

---

From: Peled, Noam Sent: Saturday, August 18, 2018 3:08:22 PM To: Freesurfer support list Subject: Re: [Freesurfer] mri_cvs_register using fsaverage

Thanks Lilla!

A follow-up question: How can I use the applyMorph function to morph the points to the MNI152 space?

I'm trying to use the combined_tocvs_avg35_inMNI152_elreg_afteraseg-norm.tm3d file I've got from the mri_cvs_register call.

Which template should I use? I can't use fsaverage because it's in the MNI305 space. Should I use cvs_avg35_inMNI152 instead?

And to morph it to MNI305, should I use the inverse matrix of

M = [[0.9975, - 0.0073, 0.0176, -0.0429], [0.0146, 1.0009, -0.0024, 1.5496], [-0.0130, -0.0093, 0.9971, 1.1840], [0, 0, 0, 1.0000]] As mentioned in the last section in http://freesurfer.net/fswiki/CoordinateSystems?

Thanks!

Noam

---

From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Lilla Zollei lzollei@nmr.mgh.harvard.edu Sent: Wednesday, August 1, 2018 2:33:19 PM To: Freesurfer support list Subject: Re: [Freesurfer] mri_cvs_register using fsaverage

Yes, you can remove the template flag.

And no, not at the moment.

...

Thanks Lilla!

Just to be sure, when using the --mni flag, should I remove the --template flag?

Also, is there any way I can calculate the registration directly to MNI305 and not MNI152?

Thanks again,

Noam

---

_

...

From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Lilla Zollei lzollei@nmr.mgh.harvard.edu Sent: Wednesday, August 1, 2018 8:35:49 AM To: Freesurfer support list Subject: Re: [Freesurfer] mri_cvs_register using fsaverage

Hi Noam,

Can you can use the --mni flag?

"Use the CVS atlas in MNI152 space as a target for registration (as opposed to the default CVS template)"

Lilla

On Wed, 1 Aug 2018, Peled, Noam wrote:

...

I need to transfer one of our patient's electrodes locations (depth electrodes, they aren't located on the cortical surface) to MNI305 space. For that, I'm trying to use mri_cvs_register to register the patient to fsaverage. I'm using to the following command:

mri_cvs_register --mov subjid --template fsaverage --outdir output_name --nocleanup

And I'm getting the following error: fsaverage : at least one mean and/or Gaussian curvature file is missing (.H, .K)

Indeed, fsaverage doesn't have the rh/lh.inflated.K/H files. Any ideas?

Thanks, Noam