Hi Doug,

Thanks very much!!

Best, Daniel

On Jul 16, 2013, at 9:14 PM, "Douglas Greve" <greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu> wrote:

use

$FREESURFER_HOME/average/mni152.register.dat

doug

On 7/16/13 8:36 PM, Yang, Daniel wrote: Dear FreeSurfer Experts,

I am interested in a specific ROI in the DK atlas, and I know that I can use tkregister2 to obtain a register.dat, and then mri_annotation2label + mri_label2vol to convert the annotation of the ROI to an .nii.gz.

However, it seems that the end product is in the TAL space? If yes, how can I convert it to the MNI 152 space?

Many thanks!!

Best, Daniel -- Yung-Jui "Daniel" Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454

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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.

does htis answer your question? It is from running mri_label2vol with --help doug

--temp tempvolid

Template volume. The output volume will have the same size and geometry as the template. Template must have geometry information (ie, direction cosines and voxel sizes). Required.

On 07/17/2013 12:11 PM, Yang, Daniel wrote:

Hi Doug,

Can I ask a basic question about mri_label2vol? in mri_label2vol, what should be the input for "--temp"? I understand it's supposed to be the template image. If it's the native space, should it be rawavg.mgz or orig.mgz for that individual?

Great thanks!

Best, Daniel

-- Yung-Jui "Daniel" Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454

On 7/16/13 9:13 PM, "Douglas Greve" <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:

use

$FREESURFER_HOME/average/mni152.register.dat

doug

On 7/16/13 8:36 PM, Yang, Daniel wrote:

...

Dear FreeSurfer Experts,

I am interested in a specific ROI in the DK atlas, and I know
that I can use tkregister2 to obtain a register.dat, and then
mri_annotation2label + mri_label2vol to convert the annotation of
the ROI to an .nii.gz.

However, it seems that the end product is in the TAL space? If
yes, how can I convert it to the MNI 152 space?

Many thanks!!

Best,
Daniel
-- 
Yung-Jui "Daniel" Yang, PhD
Postdoctoral Researcher
Yale Child Study Center
New Haven, CT
(203) 737-5454


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

rawavg is in whatever the native acquisition geometry and bits/voxel is. Orig is always 8 bits/voxel and 256^3, 1mm isotropic

On Thu, 18 Jul 2013, Yang, Daniel wrote:

Hi Doug,

Thanks for your reply. So the template file is merely used for its size and geometry to fit the output, right?

By the way, could you tell me the difference between rawavg.mgz and orig.mgz? Suppose I have just 1 scan, they are the same, and if I have two or more scans, rawavg is the average and orig is always the first scan?

Sorry for some simple questions.

Thanks, Daniel

On Jul 17, 2013, at 12:18 PM, "Douglas N Greve" greve@nmr.mgh.harvard.edu wrote:

...

does htis answer your question? It is from running mri_label2vol with --help doug

--temp tempvolid

Template volume. The output volume will have the same size and geometry as the template. Template must have geometry information (ie, direction cosines and voxel sizes). Required.

On 07/17/2013 12:11 PM, Yang, Daniel wrote:

...

Hi Doug,

Can I ask a basic question about mri_label2vol? in mri_label2vol, what should be the input for "--temp"? I understand it's supposed to be the template image. If it's the native space, should it be rawavg.mgz or orig.mgz for that individual?

Great thanks!

Best, Daniel

-- Yung-Jui "Daniel" Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454

On 7/16/13 9:13 PM, "Douglas Greve" <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:

use

$FREESURFER_HOME/average/mni152.register.dat

doug

On 7/16/13 8:36 PM, Yang, Daniel wrote:

...

Dear FreeSurfer Experts,

I am interested in a specific ROI in the DK atlas, and I know that I can use tkregister2 to obtain a register.dat, and then mri_annotation2label + mri_label2vol to convert the annotation of the ROI to an .nii.gz.

However, it seems that the end product is in the TAL space? If yes, how can I convert it to the MNI 152 space?

Many thanks!!

Best, Daniel -- Yung-Jui "Daniel" Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.eduhttps://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: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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

Hi Doug,

I think I figured out what the difference between rawavg and orig is. So rawavg is the output of motion correction based on all the orig/00?.mgz, while orig is rawavg conformed to 1mm in coronal slices, correct?

Thanks, Daniel

On Jul 18, 2013, at 8:53 AM, "Yang, Daniel" yung-jui.yang@yale.edu wrote:

Hi Doug,

Thanks for your reply. So the template file is merely used for its size and geometry to fit the output, right?

By the way, could you tell me the difference between rawavg.mgz and orig.mgz? Suppose I have just 1 scan, they are the same, and if I have two or more scans, rawavg is the average and orig is always the first scan?

Sorry for some simple questions.

Thanks, Daniel

On Jul 17, 2013, at 12:18 PM, "Douglas N Greve" greve@nmr.mgh.harvard.edu wrote:

...

does htis answer your question? It is from running mri_label2vol with --help doug

--temp tempvolid

Template volume. The output volume will have the same size and geometry as the template. Template must have geometry information (ie, direction cosines and voxel sizes). Required.

On 07/17/2013 12:11 PM, Yang, Daniel wrote:

...

Hi Doug,

Can I ask a basic question about mri_label2vol? in mri_label2vol, what should be the input for "--temp"? I understand it's supposed to be the template image. If it's the native space, should it be rawavg.mgz or orig.mgz for that individual?

Great thanks!

Best, Daniel

-- Yung-Jui "Daniel" Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454

On 7/16/13 9:13 PM, "Douglas Greve" <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:

use

$FREESURFER_HOME/average/mni152.register.dat

doug

On 7/16/13 8:36 PM, Yang, Daniel wrote:

...

Dear FreeSurfer Experts,

I am interested in a specific ROI in the DK atlas, and I know that I can use tkregister2 to obtain a register.dat, and then mri_annotation2label + mri_label2vol to convert the annotation of the ROI to an .nii.gz.

However, it seems that the end product is in the TAL space? If yes, how can I convert it to the MNI 152 space?

Many thanks!!

Best, Daniel -- Yung-Jui "Daniel" Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.eduhttps://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: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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