Sorry about that, mailing list cc’d. Reply vs reply all… Stuff attached, but also uploaded. (message bounced)
The colorscale.tiff is an example of the strange color scale abnormality, and the colorscaleabnormality.png shows the settings to get a similar one.
The PPTX shows the results – better.
The vertex-for-examination.png shows a vertex location that I have questions about – in the BrainSuite image this vertex is apparently normal, and in FreeSurfer results it’s low.
With regards to the original question: – still some abnormalities, but the head-coil difference appeared to have played a large role in the lack of signal in the group comparison.
Thanks, JP --- James C. Patterson II, MD, PhD Professor of Psychiatry LSU Health - Shreveport ---
From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Tuesday, September 11, 2012 6:22 AM To: Patterson, James Subject: Re: [Freesurfer] Differences between BrainSuite and FreeSurfer
Good. Send a tif with your threshold and max (and cc the list)
On Sep 11, 2012, at 6:58 AM, "Patterson, James" <JPatte@lsuhsc.edumailto:JPatte@lsuhsc.edu> wrote: It was the head coil! There are still some differences, but I need to control variables better before I come to you with that.
One last thing: Can you tell me why the color scales are strange looking when I choose Blue-red? This isn’t the complex setting….am I missing a library file or something? Running Mac OSX latest version
--- James C. Patterson II, MD, PhD Professor of Psychiatry LSU Health - Shreveport ---
From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Monday, September 10, 2012 8:22 PM To: Patterson, James Subject: Re: [Freesurfer] Differences between BrainSuite and FreeSurfer
Hi James Just click on it in tksurfer and it will show the vertex number Bruce
On Sep 10, 2012, at 2:11 PM, "Patterson, James" <JPatte@lsuhsc.edumailto:JPatte@lsuhsc.edu> wrote:
<image001.jpg>
<image002.png>Bruce, I’m not sure how to get a vertex location out, but left hemisphere, and in the area circled.
---
James C. Patterson II, MD, PhD
Professor of Psychiatry
LSU Health - Shreveport
---
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Monday, September 10, 2012 8:32 AM To: Patterson, James Subject: Re: [Freesurfer] Differences between BrainSuite and FreeSurfer
Hi James
can you give me a vertex location and hemisphere where you expect to see an effect in FS, but don't?
thanks
Bruce
On Sat, 8 Sep 2012, Patterson, James wrote:
Hello,
I'm trying to figure out why I am getting differences in apparent cortical thickness between BrainSuite11a and Freesurfer.
I have a patient scan - high res SPGR BRAVO off a GE 1.5T scanner.
In BrainSuite, their are marked decreases in cortical thickness that is consistent with the patients TBI.
In FreeSurfer, the changes are quite bit more subtle, and when I compare this one image to a group of normal images (the feature that is very attractive about freesurfer), I do not get anything close to what I would expect.
Is there a way to post images? Or perhaps links to images on another site?
I am not sure where to begin to search for answers as to why I am getting these differences.
I would be happy to answer more questions - I likely have not provided enough information.
James Patterson
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edumailto: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.
<colorscale.tiff>
Hi James
the recon looks pretty accurate to me. One thing you might try is acquiring a 1mm isotropic T2-space FLAIR in addition to the structural (if there is the equivalent sequence on GE). It allows us to distinguish between dura and gray matter, which can look identical on a T1.
cheers Bruce
On Tue, 11 Sep 2012, Patterson, James wrote:
Sorry about that, mailing list cc?d. Reply vs reply all?
Stuff attached, but also uploaded. (message bounced)
The colorscale.tiff is an example of the strange color scale abnormality, and the colorscaleabnormality.png shows the settings to get a similar one.
The PPTX shows the results ? better.
The vertex-for-examination.png shows a vertex location that I have questions about ? in the BrainSuite image this vertex is apparently normal, and in FreeSurfer results it?s low.
With regards to the original question: ?still some abnormalities, but the head-coil difference appeared to have played a large role in the lack of signal in the group comparison.
Thanks,
JP
James C. Patterson II, MD, PhD
Professor of Psychiatry
LSU Health - Shreveport
From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Tuesday, September 11, 2012 6:22 AM To: Patterson, James Subject: Re: [Freesurfer] Differences between BrainSuite and FreeSurfer
Good. Send a tif with your threshold and max (and cc the list)
On Sep 11, 2012, at 6:58 AM, "Patterson, James" JPatte@lsuhsc.edu wrote:
It was the head coil! There are still some differences, but I need to control variables better before I come to you with that. One last thing: Can you tell me why the color scales are strange looking when I choose Blue-red? This isn?t the complex setting?.am I missing a library file or something? Running Mac OSX latest version --- James C. Patterson II, MD, PhD Professor of Psychiatry LSU Health - Shreveport ---From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Monday, September 10, 2012 8:22 PM To: Patterson, James Subject: Re: [Freesurfer] Differences between BrainSuite and FreeSurfer
Hi James
Just click on it in tksurfer and it will show the vertex number
Bruce
On Sep 10, 2012, at 2:11 PM, "Patterson, James" JPatte@lsuhsc.edu wrote:
<image001.jpg> <image002.png>Bruce, I?m not sure how to get a vertex location out, but left hemisphere, and in the area circled. --- James C. Patterson II, MD, PhD Professor of Psychiatry LSU Health - Shreveport --- -----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Monday, September 10, 2012 8:32 AM To: Patterson, James Subject: Re: [Freesurfer] Differences between BrainSuite and FreeSurfer Hi James can you give me a vertex location and hemisphere where you expect to see an effect in FS, but don't? thanks Bruce On Sat, 8 Sep 2012, Patterson, James wrote: > Hello, > > I'm trying to figure out why I am getting differences in apparent cortical thickness between BrainSuite11a and Freesurfer. > > I have a patient scan - high res SPGR BRAVO off a GE 1.5T scanner. > > In BrainSuite, their are marked decreases in cortical thickness that is consistent with the patients TBI. > > In FreeSurfer, the changes are quite bit more subtle, and when I compare this one image to a group of normal images (the feature that is very attractive about freesurfer), I do not get anything close to what I would expect. > > Is there a way to post images? Or perhaps links to images on another site? > > I am not sure where to begin to search for answers as to why I am getting these differences. > > I would be happy to answer more questions - I likely have not provided enough information. > > James Patterson > _______________________________________________ > 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. <colorscale.tiff>
OK, thanks. I am making this a new thread...what about that color scale problem? I'm not sure what to do - I can only use the one color scale for some reason.
--- James C. Patterson II, MD, PhD Professor of Psychiatry LSU Health - Shreveport ---
The colorscale.tiff is an example of the strange color scale abnormality, and the colorscaleabnormality.png shows the settings to get a similar one.
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Patterson, James