Hi Antonella, if you are using something from FSL, you should be posting to the FSL list. As I said before, I don't know where the JHU atlas came from or what space it is in. It does not appear that this application is related to the FreeSurfer tools. I bet the FSL folks could answer your question much more quickly and accurately than I can. doug
On 07/27/2012 01:12 PM, Antonella Kis wrote: > Hi Doug, > > Thanks again for your prompt reply. > > I have from FSL a JHU-WhiteMatter-labels-1mm.nii.gz file and for the > segmentations labels I have the JHU-WhiteMatter-labels-1mm.txt as you > can see in the attached files. > > Are them OK to be used? > > When you say to align my low b image to JHU atlas you mean to use Flirt ? > > Many thank. > Antonella > ------------------------------------------------------------------------ > *From:* Douglas N Greve <gr...@nmr.mgh.harvard.edu> > *To:* freesurfer@nmr.mgh.harvard.edu > *Sent:* Friday, July 27, 2012 12:10 PM > *Subject:* Re: [Freesurfer] Question regarding Volumetric masks > > 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 <gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>> > > *To:* freesurfer@nmr.mgh.harvard.edu > <mailto: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 > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > -- > > Douglas N. Greve, Ph.D. > > MGH-NMR Center > > gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> > <mailto:gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> > > Phone Number: 617-724-2358 > > Fax: 617-726-7422 > > > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto: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. > > > > > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu <mailto:gr...@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 > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
