I don't know anything about the JHU atlas. If you have an anatomical in line with the JHU atlas, then align your low b image directly to that. You can then map the JHU atlas into the native diffusion space with mri_label2vol. doug
On 07/27/2012 12:08 PM, Antonella Kis wrote:
Hi Doug,
Sorry to bother with the same issue, I just remembered something. My DTI data for each individual subjects is registered on the MNI152 using Flirt so I wonder if I should first register the atlas to the MNI and then apply to my subjects. Can I do this? Then do I need to run the mri_convert?
Thanks again for your help. Antonella
*From:* Douglas N Greve greve@nmr.mgh.harvard.edu *To:* freesurfer@nmr.mgh.harvard.edu *Sent:* Friday, July 27, 2012 11:09 AM *Subject:* Re: [Freesurfer] Question regarding Volumetric masks
Steps 2 and 3 look ok. The first step will probably fail. You need a registration between the JHU atlas and the individual. The people who developed the JHU atlas can probably tell you how to do this. doug
On 07/27/2012 10:39 AM, Antonella Kis wrote:
Dear All,
I want to use cingulate bundle as ROIs more exactly mask for fiber tracking. Can someone explain please how I can use the JHU-WhiteMatter-labels-1mm.nii.gz and their labels JHU-WhiteMatter-labels-1mm.txt to get a mask of my cingulate bundle in my diffusion space for each individual subjects? Do I need to draw ROIs and how I can do this more accurate?
Is the following correct:
- /mri_convert -rl [path to subject]/DATA/s001/nodif.nii.gz -rt
nearest /JHU-WhiteMatter-labels-1mm.nii.gz /s001_aseg2dif.nii.gz/
/2) /fslmaths //[path to subject]/DATA//s001_aseg2dif.nii.gz -uthr 35 -thr 35 /[path to working directory]/ROIS/Cingulum_(cingulate_gyrus)_R.nii.gz
- fslmaths Cingulum_(cingulate_gyrus)_R.nii.gz –div 35
Cingulum_(cingulate_gyrus)_R.nii.gz
If I want to run for the cingulate bundle the tractography should I repeat this steps for:
36 Cingulum_(cingulate_gyrus)_L 37 Cingulum_(hippocampus)_R 38 Cingulum_(hippocampus)_L
Thank you for your help. Antonella
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