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:
> >
> > 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
> >
> >
> >
> >
> >
> >
> > _______________________________________________
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>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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