Hello there!
I was wondering if I could get some help on an issue I am noticing in the segmentation of the left thalamus and left Pallidum on my scans. I've included pictures of tkmedit so you can see what I mean. The tkmedit uses this code: tkmedit SZ2014 brainmask.mgz lh.white -aux norm.mgz -aux-surface rh.white -segmentation aparc+aseg.mgz
All of my scans have been through the entire recon-all process and , out of my sample of about 172 patients and controls, just about 29 of them show this odd segmentation on, almost always, the left hemisphere. The left thalamus seems to be over estimating the size and the pallidum is underestimating its size. I was wondering why this would be and if the community thought it would be okay to go back and manually edit the segementation to fit the subcorticals structures better?
Also, since I have never done such editing, is it advisable or even possible to do so?
Hi Jeffrey
you can't tell the boundaries overlaying on the brainmask.mgz as it will erode thalamus and pallidum. Look at the norm.mgz to check whether the borders are accurate Bruce On Tue, 15 Nov 2016, Jeffrey Crawford wrote:
Hello there!
I was wondering if I could get some help on an issue I am noticing in the segmentation of the left thalamus and left Pallidum on my scans. I’ve included pictures of tkmedit so you can see what I mean. The tkmedit uses this code: tkmedit SZ2014 brainmask.mgz lh.white -aux norm.mgz -aux-surface rh.white -segmentation aparc+aseg.mgz
All of my scans have been through the entire recon-all process and , out of my sample of about 172 patients and controls, just about 29 of them show this odd segmentation on, almost always, the left hemisphere. The left thalamus seems to be over estimating the size and the pallidum is underestimating its size. I was wondering why this would be and if the community thought it would be okay to go back and manually edit the segementation to fit the subcorticals structures better?
Also, since I have never done such editing, is it advisable or even possible to do so?
Thank you for replying so promptly. I changed it to the norm.mgz, but it didn't alter how the segementation aligned with the brain. The norm.mgz shows the pallidum in more detail, but also that it is not contained with the segementation.
So, I suppose my original question is still the same.
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Tuesday, November 15, 2016 12:06 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Left Thalamus and Pallidum segmentation problem
Hi Jeffrey
you can't tell the boundaries overlaying on the brainmask.mgz as it will erode thalamus and pallidum. Look at the norm.mgz to check whether the borders are accurate Bruce On Tue, 15 Nov 2016, Jeffrey Crawford wrote:
Hello there!
I was wondering if I could get some help on an issue I am noticing in the segmentation of the left thalamus and left Pallidum on my scans. I’ve included pictures of tkmedit so you can see what I mean. The tkmedit uses this code: tkmedit SZ2014 brainmask.mgz lh.white -aux norm.mgz -aux-surface rh.white -segmentation aparc+aseg.mgz
All of my scans have been through the entire recon-all process and , out of my sample of about 172 patients and controls, just about 29 of them show this odd segmentation on, almost always, the left hemisphere. The left thalamus seems to be over estimating the size and the pallidum is underestimating its size. I was wondering why this would be and if the community thought it would be okay to go back and manually edit the segementation to fit the subcorticals structures better?
Also, since I have never done such editing, is it advisable or even possible to do so?
Hi Jeffrey
if you upload the entire subject dir (gzip and tar) we will take a look cheers Bruce On Tue, 15 Nov 2016, Jeffrey Crawford wrote:
Thank you for replying so promptly. I changed it to the norm.mgz, but it didn't alter how the segementation aligned with the brain. The norm.mgz shows the pallidum in more detail, but also that it is not contained with the segementation.
So, I suppose my original question is still the same.
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Tuesday, November 15, 2016 12:06 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Left Thalamus and Pallidum segmentation problem
Hi Jeffrey
you can't tell the boundaries overlaying on the brainmask.mgz as it will erode thalamus and pallidum. Look at the norm.mgz to check whether the borders are accurate Bruce On Tue, 15 Nov 2016, Jeffrey Crawford wrote:
Hello there!
I was wondering if I could get some help on an issue I am noticing in the segmentation of the left thalamus and left Pallidum on my scans. I’ve included pictures of tkmedit so you can see what I mean. The tkmedit uses this code: tkmedit SZ2014 brainmask.mgz lh.white -aux norm.mgz -aux-surface rh.white -segmentation aparc+aseg.mgz
All of my scans have been through the entire recon-all process and , out of my sample of about 172 patients and controls, just about 29 of them show this odd segmentation on, almost always, the left hemisphere. The left thalamus seems to be over estimating the size and the pallidum is underestimating its size. I was wondering why this would be and if the community thought it would be okay to go back and manually edit the segementation to fit the subcorticals structures better?
Also, since I have never done such editing, is it advisable or even possible to do so?
Here is the tar zip of the subject folder. This is the first time I have ever done this type of compression, so please let me know if anything seems awry.
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Tuesday, November 15, 2016 3:05 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Left Thalamus and Pallidum segmentation problem
Hi Jeffrey
if you upload the entire subject dir (gzip and tar) we will take a look cheers Bruce On Tue, 15 Nov 2016, Jeffrey Crawford wrote:
Thank you for replying so promptly. I changed it to the norm.mgz, but it didn't alter how the segementation aligned with the brain. The norm.mgz shows the pallidum in more detail, but also that it is not contained with the segementation.
So, I suppose my original question is still the same.
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Tuesday, November 15, 2016 12:06 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Left Thalamus and Pallidum segmentation problem
Hi Jeffrey
you can't tell the boundaries overlaying on the brainmask.mgz as it will erode thalamus and pallidum. Look at the norm.mgz to check whether the borders are accurate Bruce On Tue, 15 Nov 2016, Jeffrey Crawford wrote:
Hello there!
I was wondering if I could get some help on an issue I am noticing in the segmentation of the left thalamus and left Pallidum on my scans. I’ve included pictures of tkmedit so you can see what I mean. The tkmedit uses this code: tkmedit SZ2014 brainmask.mgz lh.white -aux norm.mgz -aux-surface rh.white -segmentation aparc+aseg.mgz
All of my scans have been through the entire recon-all process and , out of my sample of about 172 patients and controls, just about 29 of them show this odd segmentation on, almost always, the left hemisphere. The left thalamus seems to be over estimating the size and the pallidum is underestimating its size. I was wondering why this would be and if the community thought it would be okay to go back and manually edit the segementation to fit the subcorticals structures better?
Also, since I have never done such editing, is it advisable or even possible to do so?
Hi Jeffrey
the tarred and gzipped subject folder should be a lot bigger - way too big to email. YOu'll need to upload it to our ftp site
cheers Bruce On Tue, 15 Nov 2016, Jeffrey Crawford wrote:
Here is the tar zip of the subject folder. This is the first time I have ever done this type of compression, so please let me know if anything seems awry.
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Tuesday, November 15, 2016 3:05 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Left Thalamus and Pallidum segmentation problem
Hi Jeffrey
if you upload the entire subject dir (gzip and tar) we will take a look cheers Bruce On Tue, 15 Nov 2016, Jeffrey Crawford wrote:
Thank you for replying so promptly. I changed it to the norm.mgz, but it didn't alter how the segementation aligned with the brain. The norm.mgz shows the pallidum in more detail, but also that it is not contained with the segementation.
So, I suppose my original question is still the same.
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Tuesday, November 15, 2016 12:06 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Left Thalamus and Pallidum segmentation problem
Hi Jeffrey
you can't tell the boundaries overlaying on the brainmask.mgz as it will erode thalamus and pallidum. Look at the norm.mgz to check whether the borders are accurate Bruce On Tue, 15 Nov 2016, Jeffrey Crawford wrote:
Hello there!
I was wondering if I could get some help on an issue I am noticing in the segmentation of the left thalamus and left Pallidum on my scans. I’ve included pictures of tkmedit so you can see what I mean. The tkmedit uses this code: tkmedit SZ2014 brainmask.mgz lh.white -aux norm.mgz -aux-surface rh.white -segmentation aparc+aseg.mgz
All of my scans have been through the entire recon-all process and , out of my sample of about 172 patients and controls, just about 29 of them show this odd segmentation on, almost always, the left hemisphere. The left thalamus seems to be over estimating the size and the pallidum is underestimating its size. I was wondering why this would be and if the community thought it would be okay to go back and manually edit the segementation to fit the subcorticals structures better?
Also, since I have never done such editing, is it advisable or even possible to do so?
Alright, I followed the directions online and believe I have sent my file "JeffSegFileExample" to your "transfer/incoming" folder in the ftp server.
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Tuesday, November 15, 2016 5:12 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] [WARNING : A/V UNSCANNABLE]RE: Left Thalamus and Pallidum segmentation problem
Hi Jeffrey
the tarred and gzipped subject folder should be a lot bigger - way too big to email. YOu'll need to upload it to our ftp site
cheers Bruce On Tue, 15 Nov 2016, Jeffrey Crawford wrote:
Here is the tar zip of the subject folder. This is the first time I have ever done this type of compression, so please let me know if anything seems awry.
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Tuesday, November 15, 2016 3:05 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Left Thalamus and Pallidum segmentation problem
Hi Jeffrey
if you upload the entire subject dir (gzip and tar) we will take a look cheers Bruce On Tue, 15 Nov 2016, Jeffrey Crawford wrote:
Thank you for replying so promptly. I changed it to the norm.mgz, but it didn't alter how the segementation aligned with the brain. The norm.mgz shows the pallidum in more detail, but also that it is not contained with the segementation.
So, I suppose my original question is still the same.
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Tuesday, November 15, 2016 12:06 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Left Thalamus and Pallidum segmentation problem
Hi Jeffrey
you can't tell the boundaries overlaying on the brainmask.mgz as it will erode thalamus and pallidum. Look at the norm.mgz to check whether the borders are accurate Bruce On Tue, 15 Nov 2016, Jeffrey Crawford wrote:
Hello there!
I was wondering if I could get some help on an issue I am noticing in the segmentation of the left thalamus and left Pallidum on my scans. I’ve included pictures of tkmedit so you can see what I mean. The tkmedit uses this code: tkmedit SZ2014 brainmask.mgz lh.white -aux norm.mgz -aux-surface rh.white -segmentation aparc+aseg.mgz
All of my scans have been through the entire recon-all process and , out of my sample of about 172 patients and controls, just about 29 of them show this odd segmentation on, almost always, the left hemisphere. The left thalamus seems to be over estimating the size and the pallidum is underestimating its size. I was wondering why this would be and if the community thought it would be okay to go back and manually edit the segementation to fit the subcorticals structures better?
Also, since I have never done such editing, is it advisable or even possible to do so?
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Jeffrey Crawford