Hi list!
I was wondering what could cause this type of subcortical effect during FS preprocessing? I am referring to the white blank space where half the thalamus, part of the putamen, and all of the globus pallidus are not visable and Freesurfer just sort of "assumes" that they exist with its segmentation.
My theory is that the dimensions of the Nii file I am using are being stretched and it is causing this "assumption" of white space. My dimensions on this Nii files are X = 160 , Y = 240, and Z = 256. This would lead me to believe that the FSaverage brain that my nii is being warped to match has a greater x axis than my nii.
Is this correct? If so, is there any fsaverage options that has smaller dimensions? I assume this is an issue for analysis of subcortical measures, but should this effect cortical regions at all?
Hope you all are well and my message finds someone promptly, Jeffrey Crawford
Hi Jeffrey
I’m not sure I understand. By default we will resample to 256^3 and 1mm iso, but that shouldn’t stretch anything. And don’t loom at the aseg on top of the brainmask. Look at it on the norm and you should see pallidum, putamen and thalamus. Cheers Bruce
On Sep 29, 2017, at 9:35 AM, Jeff Crawford jcrawf29@jhmi.edu wrote:
Jeffrey
Perfect! I looked at the norm.mgz and each of the subcortical regions was perfectly represented and matched the segmentation. What did you mean by "don't loom at the aseg on top of the brain mask?" I thought it was appropriate, because I am doing pial corrections and the online tutorial said I needed to use the brainmask.mgz. What is the difference between norm.mgz and brainmask.mgz in this case?
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Saturday, September 30, 2017 9:33 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Can someone tell me why my subcorticals look like this?
Hi Jeffrey
I’m not sure I understand. By default we will resample to 256^3 and 1mm iso, but that shouldn’t stretch anything. And don’t loom at the aseg on top of the brainmask. Look at it on the norm and you should see pallidum, putamen and thalamus. Cheers Bruce
On Sep 29, 2017, at 9:35 AM, Jeff Crawford jcrawf29@jhmi.edu wrote:
Jeffrey
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the brainmask is essentially a binary mask. YOu should use the brain.mgz not the brainmask for cortical stuff. For subcortical segmentations you should overlay the norm as it is the input to the aseg. The brain volume will have these borders eroded as it is only used for cortical surfaces not for the aseg
cheers Bruce
On Mon, 2 Oct 2017, Jeff Crawford wrote:
Perfect! I looked at the norm.mgz and each of the subcortical regions was perfectly represented and matched the segmentation. What did you mean by "don't loom at the aseg on top of the brain mask?" I thought it was appropriate, because I am doing pial corrections and the online tutorial said I needed to use the brainmask.mgz. What is the difference between norm.mgz and brainmask.mgz in this case?
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Saturday, September 30, 2017 9:33 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Can someone tell me why my subcorticals look like this?
Hi Jeffrey
I’m not sure I understand. By default we will resample to 256^3 and 1mm iso, but that shouldn’t stretch anything. And don’t loom at the aseg on top of the brainmask. Look at it on the norm and you should see pallidum, putamen and thalamus. Cheers Bruce
On Sep 29, 2017, at 9:35 AM, Jeff Crawford jcrawf29@jhmi.edu wrote:
Jeffrey
Freesurfer mailing list 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.
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Bruce Fischl -
Jeff Crawford