Hi Doug,

I have a followup question on this topic. I understand the two command you mentioned in this thread to warp a segmentation to the MNI152 space.

In the subjects dir, I see there is an average subject "cvs_avg35_inMNI152" which is already in MNI space (and the volume size is 256^3). I want to just reslice the aparc+aseg.mgz to size of the MNI template (91*109*91)

Since this subject is already in MNI152 space, I can just do the following right?

mri_label2vol --subject cvs_avg35_inMNI152 --aparc+aseg --temp spm-T1.nii --o aparc+aseg2.nii --regheader aparc+aseg.mgz

(where spm-T1.nii is the T1 template from spm)

Or would you recommend a different approach ?

Thanks

Mehul

ps: Earlier I used mri_convert as follows:

mri_convert aparc+aseg.mgz -rt nearest -rl spm-T1.nii aparc+aseg1.mgz

But then I recalled your advice (from earlier) to use mri_label2vol convert the segmentation labels and followed it!

On Mon, Nov 25, 2013 at 3:46 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu> wrote:

Note: you can run each command with --help to get info

something like
mni152reg --s subject
to create the registration file (it will go into
$SUBJECTS_DIR/$subject/mri/transforms/reg.mni152.2mm.dat

then something like

mri_label2vol --seg $SUBJECTS_DIR/$subject/mri/aseg.mgz --reg
$SUBJECTS_DIR/$subject/mri/transforms/reg.mni152.2mm.dat
--o aseg.$subject.mni152.nii

doug

On 11/25/2013 11:09 AM, ebelleau@uwm.edu wrote:
> Hi Douglas,
>
> Thanks for the reply. I am very new to Freesurfer and am more used to scripting with AFNI.
>
> Would you mind giving me a bit of sample code to get used to what this may look like? Can I script this in a .tcsh file?
>
> Also, once I convert the aseg to MNI space, can I simply average or add the individual masks (which could be done in afni) or is there a better way to do this in Freesurfer?
>
> Also, is this a linear or non-linear warp?
>
> Thanks,
>
> Emily
>
> ----- Original Message -----
> From: "Douglas N Greve" <greve@nmr.mgh.harvard.edu>
> To: freesurfer@nmr.mgh.harvard.edu
> Sent: Thursday, November 21, 2013 12:57:07 PM
> Subject: Re: [Freesurfer] Warping to MNI space
>
>
> Do you mean the aseg.mgz for an individual? If so, you can run mni152reg
> to register that subject to mni152space. Next you can run mri_label2vol
> to map the aseg to the 152 space.
> doug
>
>
> On 11/17/2013 07:26 PM, ebelleau@uwm.edu wrote:
>> Hello,
>>
>> I plan on using the aseg.nii to create a grey matter mask. I want to warp these grey matter masks to MNI space. I have been trying to use @auto_tlrc in AFNI to do this warping but am having some trouble.
>>
>> The reason I need this in MNI space is because I plan to make a group grey matter mask that I use to restrict my funtional fmri data analysis, which is in MNI space (MNI_avg_152T1).
>>
>> How might I go about doing the warping and I wanted to double check the order of doing things? Should I create the grey matter masks first then warp to MNI? Or do I warp the aseg files to MNI and then create the grey matter masks?
>>
>> Thanks so much!
>>
>> Emily
>> _______________________________________________
>> 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
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