T1 white matter segmentation

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Alshikho, Mohamad J.

17 Oct 2014 17 Oct '14

11:44 a.m.

Hi FS Experts,

The T1 and T2 images in my data set are as the attached images. Kindly do you recommend that I do segmentation for the white matter using recon-all on my T1 or T2 images or to the output of a registration process between T1 and T2

I highly appreciate any recommendation Looking forward to learn from you and thank you Mohamad

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Bruce Fischl

17 Oct 17 Oct

11:52 a.m.

Hi Mohamad

recon-all requires a T1, so use it. If the T2 is good quality you can use it to avoid dura in a subsequent invocation of recon-all with the -T2pial flag

cheers Bruce

On Fri, 17 Oct 2014, Alshikho, Mohamad J. wrote:

...

Hi FS Experts,

The T1 and T2 images in my data set are as the attached images. Kindly do you recommend that I do segmentation for the white matter using recon-all on my T1 or T2 images or to the output of a registration process between T1 and T2 I highly appreciate any recommendation Looking forward to learn from you and thank you Mohamad

Alshikho, Mohamad J.

11:58 a.m.

Hi Bruce, The T2 is very good and better than T1 So I will use the T2 image in the following command line recon-all -subjid subjid -T2pial

Is this correct? Thanks

Mohamad

________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Friday, October 17, 2014 11:52 AM To: Freesurfer support list Subject: Re: [Freesurfer] T1 white matter segmentation

Hi Mohamad

recon-all requires a T1, so use it. If the T2 is good quality you can use it to avoid dura in a subsequent invocation of recon-all with the -T2pial flag

cheers Bruce

On Fri, 17 Oct 2014, Alshikho, Mohamad J. wrote:

...

Hi FS Experts,

The T1 and T2 images in my data set are as the attached images. Kindly do you recommend that I do segmentation for the white matter using recon-all on my T1 or T2 images or to the output of a registration process between T1 and T2

I highly appreciate any recommendation Looking forward to learn from you and thank you Mohamad

Bruce Fischl

12:05 p.m.

first you have to run recon-all with the T1 On Fri, 17 Oct 2014, Alshikho, Mohamad J. wrote:

...

Hi Bruce, The T2 is very good and better than T1 So I will use the T2 image in the following command line recon-all -subjid subjid -T2pial

Is this correct? Thanks

Mohamad

From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Friday, October 17, 2014 11:52 AM To: Freesurfer support list Subject: Re: [Freesurfer] T1 white matter segmentation

Hi Mohamad

recon-all requires a T1, so use it. If the T2 is good quality you can use it to avoid dura in a subsequent invocation of recon-all with the -T2pial flag

cheers Bruce

On Fri, 17 Oct 2014, Alshikho, Mohamad J. wrote:

...
Hi FS Experts,

The T1 and T2 images in my data set are as the attached images. Kindly do you recommend that I do segmentation for the white matter using recon-all on my T1 or T2 images or to the output of a registration process between T1 and T2

I highly appreciate any recommendation Looking forward to learn from you and thank you Mohamad

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

Alshikho, Mohamad J.

21 Oct 21 Oct

12:32 a.m.

In this case if I don't have T1 MPRAGE can I use any other available T1 like sag_T1 or Ax_T1 (the name of run/series after using unpacksdcmdir)? or it is imperative to use T1 MPRAGE for the segmentation.

Bests, ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Friday, October 17, 2014 12:05 PM To: Freesurfer support list Subject: Re: [Freesurfer] T1 white matter segmentation

first you have to run recon-all with the T1 On Fri, 17 Oct 2014, Alshikho, Mohamad J. wrote:

...

Hi Bruce, The T2 is very good and better than T1 So I will use the T2 image in the following command line recon-all -subjid subjid -T2pial

Is this correct? Thanks

Mohamad

From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Friday, October 17, 2014 11:52 AM To: Freesurfer support list Subject: Re: [Freesurfer] T1 white matter segmentation

Hi Mohamad

recon-all requires a T1, so use it. If the T2 is good quality you can use it to avoid dura in a subsequent invocation of recon-all with the -T2pial flag

cheers Bruce

On Fri, 17 Oct 2014, Alshikho, Mohamad J. wrote:

...
Hi FS Experts,

The T1 and T2 images in my data set are as the attached images. Kindly do you recommend that I do segmentation for the white matter using recon-all on my T1 or T2 images or to the output of a registration process between T1 and T2

I highly appreciate any recommendation Looking forward to learn from you and thank you Mohamad

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

Bruce Fischl

9:06 a.m.

Hi Mohamad

it doesn't need to be an mprage, but it does need to be reasonably high resolution (no voxel dimension greater than about 1.5mm) and T1-weighted

cheers Bruce On Tue, 21 Oct 2014, Alshikho, Mohamad J. wrote:

...

In this case if I don't have T1 MPRAGE can I use any other available T1 like sag_T1 or Ax_T1 (the name of run/series after using unpacksdcmdir)? or it is imperative to use T1 MPRAGE for the segmentation.

Bests, ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Friday, October 17, 2014 12:05 PM To: Freesurfer support list Subject: Re: [Freesurfer] T1 white matter segmentation

first you have to run recon-all with the T1 On Fri, 17 Oct 2014, Alshikho, Mohamad J. wrote:

...
Hi Bruce, The T2 is very good and better than T1 So I will use the T2 image in the following command line recon-all -subjid subjid -T2pial

Is this correct? Thanks

Mohamad

From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Friday, October 17, 2014 11:52 AM To: Freesurfer support list Subject: Re: [Freesurfer] T1 white matter segmentation

Hi Mohamad

recon-all requires a T1, so use it. If the T2 is good quality you can use it to avoid dura in a subsequent invocation of recon-all with the -T2pial flag

cheers Bruce

On Fri, 17 Oct 2014, Alshikho, Mohamad J. wrote:

...
Hi FS Experts,

The T1 and T2 images in my data set are as the attached images. Kindly do you recommend that I do segmentation for the white matter using recon-all on my T1 or T2 images or to the output of a registration process between T1 and T2

I highly appreciate any recommendation Looking forward to learn from you and thank you Mohamad

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

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

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Alshikho, Mohamad J.
Bruce Fischl