That was an error, 82 should not be in there. doug

On 07/30/2014 03:07 PM, Bruce Fischl wrote:

Hi Mohamad Right-non-WM-hypointensities are hypointense voxels (in T1 images) in the right hemisphere in regions that are not normally white matter (like the middle of the putamen).

I'll leave your other questions for Doug

cheers Bruce

On Wed, 30 Jul 2014, Alshikho, Mohamad J. wrote:

...

Hi,

I have a question about the flag ” –wm” in mri_binarize:

The following segments IDs 8 2 41 82 251 252 253 254 255 are included in this flag (based on the summary of this command line when I run it). Kindly what is the segment ID (Right-non-WM-hypointensities) means? and why the (left-non-WM-hypointensities ) is not included in this flag? Also what is maximum number of segments IDs that I can include in this command line using the flag –match ?

Thanks,

Mohamad

---

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

The new version uses 2, 41, 77, 251-255, but you should look through $FREESURFER_HOME/FreeSurferColorLUT.txt to get the ROIs you want

On 07/30/2014 06:39 PM, Alshikho, Mohamad J. wrote:

Thank you Doug, Do you mean an error in the script that running this command line ?! kindly what is the number of IDs that I can add after the flag --match ?

Mohamad

-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve Sent: Wednesday, July 30, 2014 4:50 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_binzrize (flag --wm )

That was an error, 82 should not be in there. doug

On 07/30/2014 03:07 PM, Bruce Fischl wrote:

...

Hi Mohamad Right-non-WM-hypointensities are hypointense voxels (in T1 images) in the right hemisphere in regions that are not normally white matter (like the middle of the putamen).

I'll leave your other questions for Doug

cheers Bruce

On Wed, 30 Jul 2014, Alshikho, Mohamad J. wrote:

...

Hi,

I have a question about the flag " -wm" in mri_binarize:

The following segments IDs 8 2 41 82 251 252 253 254 255 are included in this flag (based on the summary of this command line when I run it). Kindly what is the segment ID (Right-non-WM-hypointensities) means? and why the (left-non-WM-hypointensities ) is not included in this flag? Also what is maximum number of segments IDs that I can include in this command line using the flag -match ?

Thanks,

Mohamad

---

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 greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

---

Freesurfer mailing list 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