HI Everyone, I have a question about how to "write out" ROIs for these networks. I realize I can transform the mni template and Masks using mri_vol2vol to create a new "aseg_choi-17" file. But in order to do stats or use them as regions of interest in FSfast, they need to be included in the defaiult FreeSurferColorLUT.txt? So should I overwrite the first 17 seg ids? or can I use a custom (CHOI_7 netwroks Look upTable? Im using FS5.1, as I would imagine FS5.2 may already do these by default, but there are bugs in that version from what I understand. I want to recreate the subcortically defined regions to the cortical functional scan. Thanks, Mario
This does not seem to work well, as the 7_Networks seg file and template is in MNI152 space, is there a method to back transform the striatal segmentations to 1.) first MNI305 space. 2.) native subject space. I found mni152reg to transform the subject to 152 space, but I need the Choi 7 networks into mni205, then native... I will keep trying unless there is another way I am missing.
On Wed, May 8, 2013 at 9:45 AM, Mario Ortega mario.ortega@gmail.com wrote:
HI Everyone, I have a question about how to "write out" ROIs for these networks. I realize I can transform the mni template and Masks using mri_vol2vol to create a new "aseg_choi-17" file. But in order to do stats or use them as regions of interest in FSfast, they need to be included in the defaiult FreeSurferColorLUT.txt? So should I overwrite the first 17 seg ids? or can I use a custom (CHOI_7 netwroks Look upTable? Im using FS5.1, as I would imagine FS5.2 may already do these by default, but there are bugs in that version from what I understand. I want to recreate the subcortically defined regions to the cortical functional scan. Thanks, Mario
Hi Mario, can you tell me more about what you are trying to do? doug
On 05/08/2013 01:03 PM, Mario Ortega wrote:
This does not seem to work well, as the 7_Networks seg file and template is in MNI152 space, is there a method to back transform the striatal segmentations to 1.) first MNI305 space. 2.) native subject space. I found mni152reg to transform the subject to 152 space, but I need the Choi 7 networks into mni205, then native... I will keep trying unless there is another way I am missing.
On Wed, May 8, 2013 at 9:45 AM, Mario Ortega <mario.ortega@gmail.com mailto:mario.ortega@gmail.com> wrote:
HI Everyone, I have a question about how to "write out" ROIs for these networks. I realize I can transform the mni template and Masks using mri_vol2vol to create a new "aseg_choi-17" file. But in order to do stats or use them as regions of interest in FSfast, they need to be included in the defaiult FreeSurferColorLUT.txt? So should I overwrite the first 17 seg ids? or can I use a custom (CHOI_7 netwroks Look upTable? Im using FS5.1, as I would imagine FS5.2 may already do these by default, but there are bugs in that version from what I understand. I want to recreate the subcortically defined regions to the cortical functional scan. Thanks, Mario
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