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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.
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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To add to what Thomas said, I would use mri_label2vol whenever transferring segmentations or labels. In this case, probably it won't make much difference.
doug
On 01/27/2014 05:49 AM, Thomas Yeo wrote:
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 mailto: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. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto: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.
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조수연