samseg does not have a CC seg. You can get the CC with something like
mri_cc -aseg samseg/seg.mgz -o samseg/seg+cc.mgz -lta samseg/cc_up.lta
you can ignore the lta output
On 1/28/2025 7:00 PM, Taghizadeh Mortezaei, Nima wrote:
Dear FreeSurfer Support Team,
I am using FreeSurfer version 7.4.1
Dear FreeSurfer Support Team,
I am using FreeSurfer version 7.4.1 and recently ran SAMSEG on a subject’s MRI
data. However, I noticed that the corpus callosum does not appear as a distinct
label in the segmented structures. After reviewing the output files and label
definitions, I was unable to
cd $SUBJECTS_DIR/$subject
Sample the aseg onto the surface (looking for the max between -2 and + 2 mm).
This will sample all the segmentations, but we are only interested in CC
mri_vol2surf --regheader $subject--mov aseg.mgz --projdist-max -2 .5 2 --o
lh.aseg.mgz --hemi lh
Create a binary map of
External Email - Use Caution
Thank you very much.
I am very interested in this if it is possible.
Is it possible to acquire any other area information of the corpus callosum?
Thank you again,
Fernanda
Em qua, 25 de set de 2019 às 21:10, Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvar
We don't output or have tools to compute it. I can tell you how you can get a
number for it, but it would not be with a validated method. Let me know.
On 9/24/2019 5:37 AM, Fernanda Hansen P. de Moraes wrote:
External Email - Use Caution
Dear Freesurfer experts,
how can I extract the c
External Email - Use Caution
Dear Freesurfer experts,
how can I extract the corpus callosum cross sectional area for each
hemisphere?
Thank you very much in advance,
Fernanda Hansen P. de Moraes
fernandahmor...@gmail.com
Física Médica | Rede D'Or São Luiz
Doutoranda em Ciências
Is the corpus callosum segmentation based on the Hofer and Frahm functional
parcellation, a mathematical formula, or, as listed on the website, 5 equal
subdivision roughly along the long axis? What is the preferred citation for
this?
Thanks.
___
Freesurf
liano
From: alessia_giuli...@hotmail.it
To: freesurfer@nmr.mgh.harvard.edu
Date: Fri, 6 Jun 2014 06:46:29 +
Subject: Re: [Freesurfer] Corpus Callosum segmentation reliability
Dear Bruce,
the two subject dirs are here
https://www.dropbox.com/sh/k1z5o0e6sq90qq0/AABx38QxKvxDhUe2lV9imaa9a.
The ori
Dear Bruce,
did you see the images that I have sent you?
Thanks,
Alessia Giuliano
From: alessia_giuli...@hotmail.it
To: freesurfer@nmr.mgh.harvard.edu
Date: Fri, 6 Jun 2014 06:46:29 +
Subject: Re: [Freesurfer] Corpus Callosum segmentation reliability
Dear Bruce,
the two subject dirs are
: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Corpus Callosum segmentation reliability
hmmm, that is puzzling. Can you upload the two subject dirs with the
rotated direction cosines and I'll take a look?
thanks
Bruce
On Thu, 5 Jun 2014, Alessia
Giuliano wrote:
> Dear Bruce,
lessia Giuliano
Date: Thu, 5 Jun 2014 08:30:10 -0400
From: fis...@nmr.mgh.harvard.edu
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Corpus Callosum segmentation reliability
Hi Alessia
when you say "the image was rotated" do you mean you actually transformed
the image,
to improve the CC segmentation in order to consider
the volumes of its subregions to be reliable?
Thank you,
Alessia Giuliano
Date: Thu, 5 Jun 2014 08:30:10 -0400
From: fis...@nmr.mgh.harvard.edu
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Corpus Callosum segmentation reliability
H
Hi Alessia
when you say "the image was rotated" do you mean you actually transformed
the image, or you simply changed the image header to reflect a new
orientation? I wouldn't think the latter would have a big effect, but the
former will involve an additional image interpolation (blurring) a
th
respect to CC eigen axes, but independently from the initial orientation of
the scan.
Thank you,
Alessia Giuliano
Date: Mon, 26 May 2014 12:02:26 -0400
From: fis...@nmr.mgh.harvard.edu
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Corpus Callosum segmentation
Hi Alessia
i
respect to CC eigen axes, but independently from the initial
orientation of the scan.
Thank you,
Alessia Giuliano
Date: Mon, 26 May 2014 12:02:26 -0400
From: fis...@nmr.mgh.harvard.edu
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Corpus Callosum segmentation
Hi Alessia
it's t
Hi Alessia
it's tought to tell from a single slice as the subject's head orientation
might be a bit slanted. The subregions in the CC are defined purely by the
distance along the CC's eigenaxis.
cheers
Bruce
On Mon, 26 May
2014, Alessia Giuliano wrote:
Dear FreeSurfer team,
I'm intreste
Hi all,
I need to perform segmentation of the whole Corpus Callosum but I don't really
know how the determine which thickness should I use to extract all of it (or at
least most of it).
Does anyone know what would be typical thickness of CC (the distance along
coronal axis) or if is there a wa
Hi Roxana - How tracula works is decribed in detail here:
http://www.frontiersin.org/Journal/DownloadFile.ashx?pdf=1&FileId=8155&articleId=10815&Version=1&ContentTypeId=21&FileName=fninf-05-00023.pdf
To add a new tract to the tracula atlas that is not currently part of it,
the tract would first
Dear FreeSurfers,
I would like to get the tracts in Corpus Callosum body, not just the forceps
major and forceps minor given by tracula. Is there a way to get that with
Tracula?
Thank you.
Roxana.
---
Rox
mostly, although the partial volume estimation will change it a bit.
On Wed,
18 Jul 2012, Alfredo Damasceno wrote:
Dear all,
The total corpus calllosum volume is not in the aseg.stats file, but instead
I find CC post, mid post, central, mid ant, and anterior. Is it the same of
the sum of the
yes, it is the sum
doug
On 07/18/2012 03:09 PM, Alfredo Damasceno wrote:
> Dear all,
>
> The total corpus calllosum volume is not in the aseg.stats file, but
> instead I find CC post, mid post, central, mid ant, and anterior. Is
> it the same of the sum of these parts?
>
> Thanks
> Alfredo
>
>
>
Dear all,
The total corpus calllosum volume is not in the aseg.stats file, but instead I
find CC post, mid post, central, mid ant, and anterior. Is it the same of the
sum of these parts?
Thanks
Alfredo ___
some of it was in one of Diana Rosas' paper:
H.D. Rosasa, S.Y. Leea, A.C. Bendera, A.K. Zaletaa, M. Vangelc, P. Yu, et
al, Altered white matter microstructure in the corpus callosum in
Huntington's disease: Implications for cortical "disconnection",
Neuroimage, 49(4):2995-3004, 2010.
but basic
Hi:
Any reference about how freesurfer divides the corpus callosum in
CC_Posterior, CC_Mid_Posterior, CC_Central, CC_Mid_Anterior,
CC_Anterior ?...
Sincerely,
Gonzalo Rojas Costa
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://ma
Hi Alan
we divide it into equal length sections along it's primary eigen-axis,
and identify it as the region of maximal left/right wm adjacency.
cheers
Bruce
On Fri, 18
Nov 2011, Alan Francis wrote:
Hi Bruce et al,
Thanks for the stimulating discussion on the Hippocampal subfields. I hav
Hi Bruce et al,
Thanks for the stimulating discussion on the Hippocampal subfields. I have
a question. How exactly does FS segment and parcellate the Corpus Callosum
volume ?
thanks again,
Alan
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
Hi Carolina,
I think we gave some details about the method here:
H.D. Rosas, S.Y. Leea, A.C. Bendera, A.K. Zaletaa, M. Vangelc, P. Yu, et
al, Altered white matter microstructure in the corpus callosum in
Huntington's disease: Implications for cortical "disconnection",
Neuroimage, 49(4):2995-30
Hi,How is the segmentation of the corpus callosum is done? What are the proportions used? Are they equal in longitudinal lenth or it follows some a special segmentation?Do you know how to access the map (color map / visualization) of this segments?Thank you, Carolina
___
yes, although that's configurable on the mri_cc cmdline
On Wed, 16 Mar 2011,
Gonzalo Rojas Costa wrote:
> Hi:
>
> The CC volume in aseg.mgz is computed using two slices to the left
> and two sagital slices to the right the midline ?...
>
> Sincerely,
>
>
>
Hi:
The CC volume in aseg.mgz is computed using two slices to the left
and two sagital slices to the right the midline ?...
Sincerely,
--
Gonzalo Rojas Costa
Laboratory for Advanced Medical Image Processing
Department of Radiology
Las Condes Clinic
Lo Fontecilla 441, Las Condes, Santiag
Hi,
We are planning to do shape analysis of the corpus callosum. In order
to do that we need the coordinates (x,y,z) of the voxels comprising
the cc in the subcortical segmentation.
We are using FS v. 3.0.2. The corpus callosum info in the aseg.stats
shows all zeros for all subjects, does that m
try using the aseg.auto_noCCseg.mgz as input
On Thu, 27 May 2010, Gonzalo Rojas
wrote:
Hi Bruce:
I test the command "mri_cc -aseg aseg.mgz -o test.mgz -t 5 patient", but I
get the message "mri_cc: volume
/usr/local/freesurfer/subjects/patient/mri/aseg.mgz already has CC in it"...
How c
Hi Bruce:
I test the command "mri_cc -aseg aseg.mgz -o test.mgz -t 5 patient",
but I get the message "mri_cc: volume
/usr/local/freesurfer/subjects/patient/mri/aseg.mgz already has CC in it"...
How can get the volumetry of corpus callosum in 5 sagital sliced for
example ?...
Sincerel
mri_cc takes a '-t ' parameter, which is 2 by default (meaning
the cc goes out 2 slices in either direction from the midline). Run it
with -t 5 and it should do what you want
On Fri, 19 Mar 2010, Gonzalo Rojas wrote:
Hi:
How can I get the volumetry of the corpus callosum in only some
sagit
Hi:
How can I get the volumetry of the corpus callosum in only some
sagital slices ?... For example, 5 slices to the left and 5 to the right
the medial line ?...
Sincerely,
Gonzalo Rojas Costa
Laboratory for Advanced Medical Image Processing
Department of Radiology
Clínica Las Condes
Lo
Hi Bruce:
And, How can I send you ?...
Sincerely
Gonzalo Rojas Costa
Department of Radiology
Las Condes Clinic
Lo Fontecilla 441, Las Condes, Santiago, Chile.
Tel: 56-2-2105170
Cel: 56-9-97771785
www.clc.cl
Bruce Fischl escribió:
> Hi Gonzalo,
>
> we'll need to see the data and the ana
Hi Gonzalo,
we'll need to see the data and the analysis results to have any advice.
Bruce
On
Mon, 9 Nov 2009, Gonzalo Rojas wrote:
> Hi:
>
> I tried to segment a T1 volume of a 3 years old patient... It fails
> to segment the cortex in some specific regions, and the corpus callosum
> appears s
Hi:
I tried to segment a T1 volume of a 3 years old patient... It fails
to segment the cortex in some specific regions, and the corpus callosum
appears such as white matter... Why ?... Could I correct it ?...
Sincerely
--
Gonzalo Rojas Costa
Department of Radiology
Las Condes Clinic
Lo
yes.
On Wed, 29 Apr 2009, Wayne Su wrote:
Thank you Bruce,
So, if I want to report the volume of the Corpus Callosum, I should add up
the volumes of CC_Posterior, CC_Mid_Posterior, CC_Central, CC_Mid_Anterior,
CC_Anterior only. The ctx-?h-corpuscalosum/wm-?h-corpuscallosum is just
useless and b
Thank you Bruce,
So, if I want to report the volume of the Corpus Callosum, I should add up
the volumes of CC_Posterior, CC_Mid_Posterior, CC_Central, CC_Mid_Anterior,
CC_Anterior only. The ctx-?h-corpuscalosum/wm-?h-corpuscallosum is just
useless and better to remove them from wmparc.mgz since th
you're probably right. We used to segement the cc on the surface, but
this wasn't nearly as accurate as in the volume, which replaced it.
cheers
Bruce
On Wed,
29 Apr 2009, Wayne Su wrote:
The Freesurfer 4.3 segments the cc into 5 parts. But the wmparc.mgz has both
5 parts along with ctx-?h-c
The Freesurfer 4.3 segments the cc into 5 parts. But the wmparc.mgz has both
5 parts along with ctx-?h-corpuscallosum/ wm-?h-corpuscallosum. I think they
should not co-exist. Maybe I¹m wrong.
Wayne
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.e
Hi Ali,
yes, we segment the cc and save it in the aseg.mgz divided into 5 parts
anterior/posterior.
cheers,
Bruce
On Tue, 24 Mar 2009, Al-Radaideh Ali wrote:
Dear FreeSurfer Experts,
I wonder if Freesurfer saves the mask of corpus callosum or not. If so, could
you please tell me where it
Dear FreeSurfer Experts,
I wonder if Freesurfer saves the mask of corpus callosum or not. If so, could
you please tell me where it is saved or how can I get a cc mask?
Many thanks
Ali
This message has been checked for viruses but the contents of an attachment
may still contain software viruses
I would use the voxel labels of the cc. We can give you a beta if you want.
On Tue, 24
Jul 2007, Morgan Hough wrote:
Hi Bruce,
Would you believe results based on the current labels or do I need to wait
for the new version?
Cheers,
-Morgan
Bruce Fischl wrote:
Hi Morgan,
we have explici
Hi Bruce,
Would you believe results based on the current labels or do I need to
wait for the new version?
Cheers,
-Morgan
Bruce Fischl wrote:
Hi Morgan,
we have explicit labeling of the cc that is more accurate that will be
included in the upcoming release.
Bruce
On Tue, 24 Jul 2007, M
Hi Morgan,
we have explicit labeling of the cc that is more accurate that will be
included in the upcoming release.
Bruce
On
Tue, 24 Jul 2007, Morgan Hough wrote:
I was wondering if I can use the surface area estimate of the aparc corpus
callosum label as a decent subject specific measure
I was wondering if I can use the surface area estimate of the aparc
corpus callosum label as a decent subject specific measurement of its
cross-sectional area. Thanks in advance.
Cheers,
-Morgan
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.
Hi Valentina,
If you are referring to the corpus callosum value from the *h.aparc.annot,
this region and the values associated with it are not accurate. Our
motivation in including the corpus callosum as a region of interest within
our gray matter parcellation atlas was simply as an anatomic p
Hi,
I have two questions:
1. I was wondering if the values of corpus callosum are useful
2. Why the values of the corpus callosum are included in the gray matter
data (.aparc.stat)? I need the volume/area of the corpus callosum and I
don't understand if the volume given by the stat file is the who
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