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 <gr...@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:
>
> 1) /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
>
> 3) 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
>
>
>
>
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422
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