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It is not corrected for eTIV. You can compute eTIV as you suggest, ie,
running autorecon1 then running mri_segstats --xfm2etiv
subject/mri/transforms/talairach.xfm etiv.dat
On 5/9/2023 8:01 AM, Asmin Alam wrote:
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Dear FreeSurfer Experts,
I am running my subjects through autorecon-1 and then
the mri_segment_hypothalamic_subunits function to obtain the divisions of
the hypothalamus. However, I just wanted to confirm whether the results are
already corrected for
Hi Tamara,
yes, it is in the aseg stats . You can extract that information for all
subjects using asegstats2table
Best, Martin
Am 23.11.2017 um 20:43 schrieb Tamara Tavares:
Hello,
Just a quick question regarding the computed intracranial volume. I
have ran Freesurfer version 5.1 and I
yes, that is correct
On 11/23/17 2:43 PM, Tamara Tavares wrote:
Hello,
Just a quick question regarding the computed intracranial volume. I
have ran Freesurfer version 5.1 and I have been using the intracranial
volume from the aseg.stats file to correct for head size. I just want
to ensure
Hello,
Just a quick question regarding the computed intracranial volume. I have
ran Freesurfer version 5.1 and I have been using the intracranial volume
from the aseg.stats file to correct for head size. I just want to ensure
this is where I get the intracranial volume from.
Thank you in advance
Hello FreeSurfer experts
I was looking into the aseg.stat files following reconall runs and found that
intracranial volume measurements were really small for some subjects, while
other measures were comparable ( example below)
May you suggest the reason for that.
Cortex vol
Hi,
Is there a command that can be used just to extract just the intracranial
volume of all participants?
Many kind regards
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The
Hi Linn
the ICV is estimated as part of the recon-all process and ends up in one
of the stats files. Is that good enough?
Bruce
On Tue, 5 Feb 2013, Linn
Mittlestein wrote:
Hi,
Is there a command that can be used just to extract just the intracranial
volume of all participants?
Many
Dear Bruce,
Thank you for your kind reply. I was however wondering whether there is a
specific command used to extract this value from all stats files from
multiple subjects
Kind regards
On Tue, Feb 5, 2013 at 3:06 PM, Bruce Fischl fis...@nmr.mgh.harvard.eduwrote:
Hi Linn
the ICV is
Hi Linn
I think the answer is yes, but Doug or Nick can hopefully give you
details
Bruce
On Tue, 5 Feb 2013, Linn Mittlestein wrote:
Dear Bruce,
Thank you for your kind reply. I was however wondering whether there is a
specific command used to extract this value from all stats files from
Not only this value, but you can run asegstats2table and specify only
one segmentation. It will give you that segmentation as well as various
other whole brain measures. You run this on multiple subjects to give
you a table of values.
doug
On 2/5/13 7:51 PM, Bruce Fischl wrote:
Hi Linn
I
Hi,
I have calculated relative volume by dividing each volume by the
intracranial volume and multiply it with 100. When I add the relative
volume of total gray matter, cortical white matter, lateral ventricle,
3rd centricle, 4th ventricle and ventral DC, I get 82-86 %. Can this be
caused by
Hi Knut
can you check the accuracy of the talairach xform? And what version are
you using?
Bruce
On Tue, 25 Sep 2012, Knut J Bjuland wrote:
Hi,
I have calculated relative volume by dividing each volume by the
intracranial volume and multiply it with 100. When I add the relative
volume of
On 09/25/2012 03:09 PM, Bruce Fischl wrote:
check the accuracy of the talairach xform
Hi
I am using Freesurfer version 5.1 with all bug fixes. I have snapshots
off all talairach xforms made through qa_tools. I have seen on a few
subjects that the talirach transformation went okay. The pial
Hi everyone,
We have run FreeSurfer on roughly 60 subjects for a study, and are
noticing some strange discrepancies for intracranial volume in
aseg.stats for 8 of them. Here is a subset of what we see in one of the
bad aseg.stats files:
# Measure CorticalWhiteMatter, CorticalWhiteMatterVol,
Hi Nikhil,
this indicates a problem with the talairach.xfm computation. The ICV is
computed from the Talairach transform (which basically determines how
much stretching is needed to get this image to the talairach space where
the ICV is approx known). There is no mask.
See
Hi, all,Does anybody know what the intracranial volume and supratentorial volume include? Does it include only the parenquima volume (white matter / gray matter volumes) or it includes the ventricules and CSF? What about the WM hhypointensities? Are they included in the WM Volume measurement or in
it includes all of those
cheers
Bruce
On Tue, 16 Aug 2011, carolina.mr wrote:
Hi, all,
Does anybody know what the intracranial volume and supratentorial volume
include? Does it include only the parenquima volume (white matter / gray
matter volumes) or it
includes the ventricules and
Hi Bruce:
Following up on Carolina's question, if I understand correctly,
Is ICV = GM+WM+Ventricular Volume ?
and
Supratentorial Volume = GM+WM ?
thanks,
Alan
On Tue, Aug 16, 2011 at 10:03 AM, Bruce Fischl
fis...@nmr.mgh.harvard.eduwrote:
it includes all of those
cheers
Bruce
On Tue,
Hi Alan
the ICV we compute is from the det of the talairach xform using Randy
Buckner's method (see his paper on this topic). It includes everything
inside the skull implicitly.
I'll leave Supratentorial for someone else, as I don't remember.
cheers
Bruce
On Tue, 16 Aug
2011, Alan
btw, the intracranial volume is an estimate based on the talairach
transform (it is not computed by counting voxels in the cranium).
doug
Bruce Fischl wrote:
it includes all of those
cheers
Bruce
On Tue, 16 Aug 2011, carolina.mr wrote:
Hi, all,
Does anybody know what the
Supratentorial is GM+WM+Ventricles+WMHypointensities+Thalamus+VentralDC
Bruce Fischl wrote:
Hi Alan
the ICV we compute is from the det of the talairach xform using Randy
Buckner's method (see his paper on this topic). It includes everything
inside the skull implicitly.
I'll leave
Thanks Doug and Bruce!
On Tue, Aug 16, 2011 at 10:58 AM, Douglas N Greve gr...@nmr.mgh.harvard.edu
wrote:
Supratentorial is GM+WM+Ventricles+**WMHypointensities+Thalamus+**
VentralDC
Bruce Fischl wrote:
Hi Alan
the ICV we compute is from the det of the talairach xform using Randy
Hi experts,
I was wondering it is possible to account for total intracranial volume in qdec
statistical calculations, and if so, where do I find that under the 'general
stats data tables'
Thanks,
Philip York
UCDenver Radiology
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