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
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
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
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
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
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
freesurfer@nmr.mgh.harvard.edu