Dear FreeSurfer experts,
I am trying to use the following command to merge the volume file of a template with original T1 orientation*, with a file like rawavg to get the full brain volume, but the following attached image gets produced and I am pretty sure, as a freesurfer novice, I am using a wrong command line. I have tried mri_mask as well but do not think it is the command to go. I also checked if two volumes are in the same orientation using mri_orient.
mri_binarize --i rawavg.mgz --o scanner.template_angle.mgz --wm+vcsf
* (I have the native oriented version of this volume template as well, and I attached a photo of the template as well)
I would deeply appreciate if someone could help me correct my command line. Thank you all for the time and help
Idil
mri_binarize needs a mask or segmentation as input (eg, aparc+aseg.mgz). can you elaborate on what you are trying to do? what do you mean by a template?
On 08/11/2017 03:01 PM, Yagmur Ozdemir 19 wrote:
Dear FreeSurfer experts,
I am trying to use the following command to merge the volume file of a template with original T1 orientation*, with a file like rawavg to get the full brain volume, but the following attached image gets produced and I am pretty sure, as a freesurfer novice, I am using a wrong command line. I have tried mri_mask as well but do not think it is the command to go. I also checked if two volumes are in the same orientation using mri_orient.
mri_binarize --i rawavg.mgz --o scanner.template_angle.mgz --wm+vcsf
- (I have the native oriented version of this volume template as well,
and I attached a photo of the template as well)
I would deeply appreciate if someone could help me correct my command line. Thank you all for the time and help
Idil
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
I tried using it both as an input and output and the produced files both seemed wrong, so I was trying different combinations.
The template (a picture of it is attached in my initial email) is a mask for primary visual areas, and to export and use it in a different software I am trying to superimpose it on top of a complete skull stripped volume file like rawavg. I am trying to reconstruct that volume file in that other software hoping to visualize&use the mask on the software's native surface file.
Thank you for the help, Idil ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: Monday, August 14, 2017 9:36 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_binarize/mri_mask command help
mri_binarize needs a mask or segmentation as input (eg, aparc+aseg.mgz). can you elaborate on what you are trying to do? what do you mean by a template?
On 08/11/2017 03:01 PM, Yagmur Ozdemir 19 wrote:
Dear FreeSurfer experts,
I am trying to use the following command to merge the volume file of a template with original T1 orientation*, with a file like rawavg to get the full brain volume, but the following attached image gets produced and I am pretty sure, as a freesurfer novice, I am using a wrong command line. I have tried mri_mask as well but do not think it is the command to go. I also checked if two volumes are in the same orientation using mri_orient.
mri_binarize --i rawavg.mgz --o scanner.template_angle.mgz --wm+vcsf
- (I have the native oriented version of this volume template as well,
and I attached a photo of the template as well)
I would deeply appreciate if someone could help me correct my command line. Thank you all for the time and help
Idil
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: 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/
_______________________________________________ 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.
do the commands on this link get you where you need to be?
https://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat
On 08/14/2017 03:04 PM, Yagmur Ozdemir 19 wrote:
I tried using it both as an input and output and the produced files both seemed wrong, so I was trying different combinations.
The template (a picture of it is attached in my initial email) is a mask for primary visual areas, and to export and use it in a different software I am trying to superimpose it on top of a complete skull stripped volume file like rawavg. I am trying to reconstruct that volume file in that other software hoping to visualize&use the mask on the software's native surface file.
Thank you for the help, Idil ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: Monday, August 14, 2017 9:36 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_binarize/mri_mask command help
mri_binarize needs a mask or segmentation as input (eg, aparc+aseg.mgz). can you elaborate on what you are trying to do? what do you mean by a template?
On 08/11/2017 03:01 PM, Yagmur Ozdemir 19 wrote:
Dear FreeSurfer experts,
I am trying to use the following command to merge the volume file of a template with original T1 orientation*, with a file like rawavg to get the full brain volume, but the following attached image gets produced and I am pretty sure, as a freesurfer novice, I am using a wrong command line. I have tried mri_mask as well but do not think it is the command to go. I also checked if two volumes are in the same orientation using mri_orient.
mri_binarize --i rawavg.mgz --o scanner.template_angle.mgz --wm+vcsf
- (I have the native oriented version of this volume template as well,
and I attached a photo of the template as well)
I would deeply appreciate if someone could help me correct my command line. Thank you all for the time and help
Idil
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: 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/
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
freesurfer@nmr.mgh.harvard.edu
-
Douglas N Greve -
Yagmur Ozdemir 19