Hi Sooyun,

To convert the Choi's parcellation to the MNI152 template from FSL, you should just use mri_vol2vol, rather than FIRST. The command is as follows: "mri_vol2vol --mov original_choi_MNI152_parcellation.nii.gz --targ $FSLDIR/data/standard/MNI152_T1_2mm_brain.nii.gz --regheader --o FSL_choi_MNI152_parcellation.nii.gz --no-save-reg --interp nearest"

Please note the use of the "--regheader" flag. The Choi volume is in exactly the SAME space as the $FSLDIR/data/standard/MNI152_T1_2mm_brain.nii.gz, it's just that the header information is different. Therefore the "regheader" flag takes care of that.

Cheers,
Thomas


On Mon, Jan 27, 2014 at 4:31 PM, 조수연 <syduam2452@kaist.ac.kr> wrote:

Hello,

I'm a FreeSurfer beginner and would like to ask a question about Choi's stratium parcellations. I was doing a research to incoorporate the parcellations by Choi on my subjects' images to delve further to understand the distincitve characteristics of each parcels. I decided to use the Choi2012_7Networks_MNI152_FreeSurferConformed1mm_LooseMask.nii.gz. Since my images were on the standardized model from FSL, I transformed Choi's image to the MNI standard using FIRST of FSL. Since both images were now on the same MNI space, I viewed both of them on FSL to make sure that the Loose mask covered my image completely, but found that the tail bit of my image was a couple of pixels too longer than Choi's Loosened mask. Do you think there is a way that I can further "loosen" up Choi's image to fit my image? Or can you recommend me a different solution to this problem?

I'll wait for your reply. Thanks!

 

Sincerely, Sooyun Cho.


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