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Hi,
I hope you are doing well, I subscribed to your mailing list to ask my question!
I was wondering if you knew the reason as to why my extraction code in
FreeSurfer listed regions such as "Whole_hippocampal_body" amongst other brain
regions twice
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I do not get the cingulate, for example...
On Wed, Dec 21, 2022 at 4:35 PM Rosalia Dacosta Aguayo
wrote:
> Hi Douglas,
>
> I am only getting the main volumes like putamen right and left, amygdala,
> right and left...just gross anatomy.
>
> Rosie
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Hi Douglas,
I am only getting the main volumes like putamen right and left, amygdala,
right and left...just gross anatomy.
Rosie
On Wed, Dec 21, 2022 at 4:32 PM Douglas N. Greve
wrote:
> what are you not getting?
>
> On 12/21/2022 10:11 AM,
what are you not getting?
On 12/21/2022 10:11 AM, Rosalia Dacosta Aguayo wrote:
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Maybe is -qcache ?
*
*
On Wed, Dec 21, 2022 at 4:10 PM Rosalia Dacosta Aguayo
wrote:
Dear Freesurfer group,
Could you tell me which is the flag I need to use
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Maybe is -qcache ?
On Wed, Dec 21, 2022 at 4:10 PM Rosalia Dacosta Aguayo
wrote:
> Dear Freesurfer group,
>
> Could you tell me which is the flag I need to use to get all the brain
> parcellation when I run recon-all? It seems I am getting the
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Dear Freesurfer group,
Could you tell me which is the flag I need to use to get all the brain
parcellation when I run recon-all? It seems I am getting the tables with
few volumes and I guess there is something wrong.
Best wishes and Merry Christmas,
Sorry for the delay. Answers below
On 12/21/2015 03:58 PM, Woo, Jonghye wrote:
> Dear Doug,
>
> I have following questions: I posted the question but no one answered it.
>
> 1. What is the best way to convert annotation to the segmentation mask
> (volume)?
mri_label2vol. Specify the annotation
Hi Angeliki
not sure if anyone answered, and also I'm not sure that I understand. If
the cerebellum is "brown" in the aseg.mgz that is good - it should be. Is
there a problem with the skull stripping that you are trying to fix?
cheers
Bruce
On Thu,
12 Nov 2015, Tsapanou, Angeliki wrote:
-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl
Sent: Wednesday, November 18, 2015 2:42 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] FreeSurfer question
Hi Angeliki
not sure if anyone answered, and also I'm not sure that I understand
it worked!
Thanks,
Angeliki
-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl
Sent: Wednesday, November 18, 2015 2:42 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] FreeSurfer question
Hi Angeliki
Hello,
I am dealing with a problem on FreeSurfer a couple of days now.
I want to fix the scull strip and I run the following commands:
cd /users/Angeliki/studyname
export SUBJECTS_DIR=studyname/subjid/session/T1/
recon-all -skullstrip -wsthresh 20 -clean-bm -no-wsgcaatlas -subjid FreeSurfer
Then,
Hi,
I was wondering if you happened to know why the origin of the rawavg.mgz
image is slightly different than the origin of my original structural image
that I reconed to obtain processed FreeSurfer data. Am I doing something
wrong or is this expected? Is there an image that FreeSurfer creates
Hi Shazia
did you only have one input image or did you have two to motion correct
and average? If only one, I thought they were exactly the same. Why do you
think they are different?
Bruce
On Fri, 20 Jun 2014, Shazia Dharssi wrote:
Hi,
I was wondering if you happened to know why the origin
Hi Catherine
can you clarify? Are you getting them properly segmented in the aseg? Is
this a disease population? There are a bunch of things going on in the
images you sent, although it's hard to be sure from a single slice. It
looks like your bandwidth is low enough that you are getting a lot
Hi,
I am currently editing some scans (ie adding control points etc),
however I keep finding that after the editing often the brains look
worse than they did before; especially the medial temporal lobe
area. I have taken care not to put too many control points in/made
sure not to place
Hi Catherine
what version are you running? We have a fix in 5.2 that helps this
problem. It's not quite out yet, but you could download a beta if you want
cheers
Bruce
On Wed, 9 Jan 2013, Catherine Bois wrote:
Hi,
I am currently editing some scans (ie adding control points etc),
however I
Hi Catherine,
If it's the mtl pial surface around the hippocampus then the pial surface
is not expected to be accurate in that region. See FAQ question at link
below.
Hi Doug,
Sorry for all the confusion, I misunderstood what we were looking for.
Right now what we want is the volume measurement in each of the
subcortical regions for each subject, which you suggested with the
asegstats2table command.
Thanks so much for your help!
Alex
Hi Alex, what do you
Hi Doug,
Yes, sorry about that! I realized after I'd sent the email to you that I
should've sent the email to the freesurfer list as well.
We were hoping to look at volume in subcortical regions of the brain --
basal ganglia, hippocampus, amygdala, etc. Do know if there are commands
to do the
Hi Alex, do you want to do it on an ROI basis? If so, you can use
asegstats2table to create a table of your subjects at the two time
points, then import this table into SPSS. Or you can run the table
through mri_glmfit to do the paired-t analysis.
doug
On 07/24/2012 01:56 PM, Alexandra Tanner
Hi Doug,
We don't want to do ROIs because we're trying to get a thickness map of
the entire subcortical region of the brain.
Prior to trying this, we ran a within subjects paired analysis that gave
us thickness maps of cortical surface. We ran these commands to look at
the thickness maps in each
Hi Alex, what do you mean by a thickness map of the subcortical region?
The subcortical structure are usually characterized by simple volume
measurements (eg, hippocampus has a volume of XXX mm3). There are tools
out there to do voxel based morphometry. Is this what you mean?
doug
On
Hi Tony, you can use bbregister to create the registration file. You
might also look at the multi-modal tutorial on our wiki as this goes
over the steps that you will need to get and apply the registration.
For the 2nd question, you can use mris_anatomical_stats.
Hello,
I have some basic questions regarding some Freesurfer reconstructions
that I've made on a set of infant brains (12-15month olds). Overall,
the reconstructions have been successful. The exception being that
the gray matter of the anterior temporal lobes are being
underestimated,
Hi Katie,
I don't have a lot of experience in that age range but... are you talking
about the wm.mgz or the ?h.white in terms of accuracy? You should use the
latter, as the wm.mgz is just an initial estimate that gets refined. If
it's unmyelinated white matter control points are probably not
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