Re: [Freesurfer] Anatomy File Orientation Question

[Douglas Greve]

You do not need to specify that. In fact, you should not because it may 
mess up the orientation. You do not need to add any special arguments to 
mri_convert. You can also specify .nii instead of .nii.gz




On 9/27/16 3:14 PM, Sepeta, Leigh wrote:

Hi all,

Sorry to re-post:

I am trying to bring my FreeSurfer brainmask into SPM and then to 
coregister it (along with some ROIs from FreeSurfer) to the same 
subject's mprage already processed (coregistered to functional data) 
in SPM. To do this, I used:


mri_convert brainmask.mgz brainmask.nii.gz (then used gunzip)

and then looked at the brainmask and mprage in SPM and they both seem 
to be oriented correctly (left is left, right is right for each 
one--using anatomical landmarks as the guide). However, in reading up 
on this topic, many people advise using commands like these (often 
with RAS) when converting mgz to nii:


 mri_convert --in_type mgz --out_type nii --out_orientation RAS 
brainmask.mgz brainmask.nii.gz


OR

 mri_convert --out_orientation RAS -rt nearest --reslice_like 
  


OR

mri_convert -rl rawavg.mgz -rt nearest brainmask.mgz brainmask.nii.gz


Are any of the options (-rl, RAS, etc) in the last 3 commands listed 
necessary when going between mgz/nii for freesurfer to spm analyses if 
you know that the mgz and nii files are in the same orientation?


Thank you,
Leigh



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[Freesurfer] Anatomy File Orientation Question

[Sepeta, Leigh]

Hi all,

Sorry to re-post:

I am trying to bring my FreeSurfer brainmask into SPM and then to coregister it 
(along with some ROIs from FreeSurfer) to the same subject's mprage already 
processed (coregistered to functional data) in SPM. To do this, I used:

mri_convert brainmask.mgz brainmask.nii.gz (then used gunzip)

and then looked at the brainmask and mprage in SPM and they both seem to be 
oriented correctly (left is left, right is right for each one--using anatomical 
landmarks as the guide). However, in reading up on this topic, many people 
advise using commands like these (often with RAS) when converting mgz to nii:

 mri_convert --in_type mgz --out_type nii --out_orientation RAS  brainmask.mgz 
brainmask.nii.gz

OR

 mri_convert --out_orientation RAS  -rt nearest --reslice_like   

OR

mri_convert -rl rawavg.mgz -rt nearest brainmask.mgz brainmask.nii.gz


Are any of the options (-rl, RAS, etc) in the last 3 commands listed necessary 
when going between mgz/nii for freesurfer to spm analyses if you know that the 
mgz and nii files are in the same orientation?

Thank you,
Leigh




,,
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the sole use of the intended recipient(s) and may contain confidential and 
privileged information. Any unauthorized review, use, disclosure or 
distribution is prohibited. If you are not the intended recipient, please 
contact the sender by reply e-mail and destroy all copies of the original 
message.
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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.

[Freesurfer] Anatomy File Orientation Question

[Sepeta, Leigh]

Hi all,

I am trying to bring my FreeSurfer brainmask into SPM and then to coregister it 
(along with some ROIs from FreeSurfer) to the same subject's mprage already 
processed (coregistered to functional data) in SPM. To do this, I used:

mri_convert brainmask.mgz brainmask.nii.gz (then used gunzip)

and then looked at the brainmask and mprage in SPM and they both seem to be 
oriented correctly (left is left, right is right for each one--using anatomical 
landmarks as the guide). However, in reading up on this topic, many people 
advise using commands like these (often with RAS) when converting mgz to nii:

 mri_convert --in_type mgz --out_type nii --out_orientation RAS  brainmask.mgz 
brainmask.nii.gz

OR

 mri_convert --out_orientation RAS  -rt nearest --reslice_like   

OR

mri_convert -rl rawavg.mgz -rt nearest brainmask.mgz brainmask.nii.gz


Are any of the options (-rl, RAS, etc) in the last 3 commands listed necessary 
when going between mgz/nii for freesurfer to spm analyses if you know that the 
mgz and nii files are in the same orientation?

Thank you,
Leigh




,,
Confidentiality Notice: This e-mail message, including any attachments, is for 
the sole use of the intended recipient(s) and may contain confidential and 
privileged information. Any unauthorized review, use, disclosure or 
distribution is prohibited. If you are not the intended recipient, please 
contact the sender by reply e-mail and destroy all copies of the original 
message.
___
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.