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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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

---

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 greve@nmr.mgh.harvard.edu mailto:greve@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 FileDrop: 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 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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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 greve@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 <greve@nmr.mgh.harvard.edu

mailto:greve@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 greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu

<mailto:greve@nmr.mgh.harvard.edu mailto:greve@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 greve@nmr.mgh.harvard.edu mailto: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

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer