rvard.edu>
Sent: Wednesday, July 6, 2016 10:21:41 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Intensity stats question
On 07/06/2016 01:05 PM, Sabrina Yu wrote:
>
> Hello,
>
>
> I have a couple of questions about the wmparc.stats file generated.
>
Hello,
I have a couple of questions about the wmparc.stats file generated. What volume
is the data based on? Has the intensity of the volume been corrected? I just
need the average voxel intensity over the ROIs, but am unsure if this intensity
is based on an intensity normalized brain volume.
tion
>
> cheers
> Bruce
> On Wed, 29 Jun 2016, Sabrina Yu wrote:
>
>> Hello,
>> I have a question about taking out the intensity normalization commands in
>> recon-all. I want to eliminate all normalization steps so that the WM will
>> not be
Hello,
I have a question about taking out the intensity normalization commands in
recon-all. I want to eliminate all normalization steps so that the WM will not
be set at an average of 110. Using the ReconAllDevTable
(https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllDevTable
ntirely sure about that, but if my manual edits don't work I'll let
Bruce know and we can discuss other workarounds.
-Ani
On 06/02/2016 12:55 PM, Sabrina Yu wrote:
Hi Ani,
Thanks so much for your explanation, it makes sense that the brain is too
deformed for one continuous surface. If we are not
he data a bit to see if we can improve surfaces. If
>> that doesn't work then we can discuss other options for how to get the
>> information you need.
>>
>> Thanks!
>>
>> -Ani
>>
>>> On 05/23/2016 05:47 PM, Sabrina Yu wrote:
>&g
Hello,
I have created my own subcortical ROI in freesurfer (saved as .label file), and
am trying to generate an intensity stats file for this ROI. Reading the mailing
list, I think that the best way to do this is to:
1) mri_label2vol to convert my ROI to a volume file
2) mri_label_volume to
r] Brainmask edit error
because it violates too many of our assumptions about the topology and
geometry of the brain.
cheers
Bruce
On Mon, 23 May 2016, Sabrina Yu
wrote:
>
> Hi Bruce,
>
> Thank you for your reply. I've uploaded the .mgz and surfaces using FTP to
> FreeSu
ct one
of us will take a look, but it may not be possible to get good surfaces
with that extensive a stroke
cheers
Bruce
On Wed, 18 May 2016, Sabrina Yu wrote:
>
> Hello,
>
>
> I'm having problems with regenerating the surfaces for stroke cases after
> editing the brainmask.
You can re-run it and
> specify the temporary folder with --tmp, and those files will be in
> there. I don't know what they will be called but hopefully it will be
> obvious.
>
> doug
>
> On 2/4/16 2:14 PM, Sabrina Yu wrote:
>> Hi sorry, haven't heard back yet from Frees
anks!
From: Sabrina Yu
Sent: Thursday, January 28, 2016 10:51 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] Fw: Gray matter intensity
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2750073/#R57
Figure 1 (c). The mean maps of signal inten
edu>
Sent: Thursday, January 28, 2016 10:47 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Fw: Gray matter intensity
which figure(s) in particular?
On 01/28/2016 01:41 PM, Sabrina Yu wrote:
> Hi,
>
> Sorry for bringing this thread up again. Referring back to the f
n 12/21/2015 12:57 PM, Sabrina Yu wrote:
> Hello,
>
> Thank you for the very helpful replies! I have another quick question. Which
> commands would I use to generate images like the ones in Figure 1 (C)
> generated in the Salat paper
> (http://www.ncbi.nlm.nih.gov/pmc/articles/P
n 12/15/2015 01:00 PM, Sabrina Yu wrote:
>
> Hi,
>
>
> Just following up on my previous email (see below) as I have not yet
> heard back. I also have another question regarding the lh.wm.mgh and
> rh.wm.mgh generated by pctsurfcon. How do I view these as surface
> overl
rvard.edu>
Sent: Monday, December 21, 2015 10:08 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Fw: Gray matter intensity
freeview or tksurfer. Load the relevant map as an overlay
On 12/21/2015 12:57 PM, Sabrina Yu wrote:
> Hello,
>
> Thank you for the very helpful re
.
From: Sabrina Yu
Sent: Thursday, December 10, 2015 2:47 PM
To: Freesurfer support list
Subject: Gray matter intensity
Hello,
I have been following the instructions in this email thread:
https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2014-April/037240.html.<ht
le. We know that it's possible to calculate these
from the WM/GM ratio from pctsurfcon, but it'd be great if there was a more
direct way to get this data.
Thank you,
Sabrina Yu
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Freesurfer@nmr.mgh.harvard.edu
Hi again,
Just following up with my last email. Also, is it more accurate to compare the
gray-white contrast on both hemispheres in the same ROI than to compare white
matter intensity only?
Thanks,
Sabrina
On Fri, Dec 4, 2015 at 10:53 AM -0800, "Sabrina Yu"
<sabrina...
On Thu, Dec 3, 2015 at 5:52 PM -0800, "Douglas Greve"
<gr...@nmr.mgh.harvard.edu<mailto:gr...@nmr.mgh.harvard.edu>> wrote:
I guess I'm not sure what you are trying to do. Can you elaborate?
On 12/3/15 6:24 PM, Sabrina Yu wrote:
> Hi Doug,
>
> Thanks for the quick rep
ROI?
On 12/04/2015 12:56 PM, Sabrina Yu wrote:
> Absolutely, sorry for the confusion. I am looking at decreased
> ipsilesional myelination signal intensity in patients with unilateral
> strokes. The goal is to run the T1 scans through FreeSurfer, then
> determine the ratio of
vard.edu>> wrote:
there should be a {lh,rh}.w-g.pct.stats files in
$SUBJECTS_DIR/subject/stats. That will have the mean gray-white contrast
for each ROI in the aparc. Does that work for you?
On 12/04/2015 01:29 PM, Sabrina Yu wrote:
> I think averaged over an ROI is what is best. Any way t
Hi there,
Would it be possible to use pctsurfcon to calculate the ratio of white matter
signal intensity between left and right hemispheres?
Thank you
Sabrina
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Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
he homolgous
vertex on the contralateral hemisphere
http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi
On 12/03/2015 05:25 PM, Sabrina Yu wrote:
>
> Hi there,
>
>
> Would it be possible to use pctsurfcon to calculate the ratio of white
> matter signal intensity between left and ri
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