look in ?h.aparc.stats files
On 4/27/2021 2:17 PM, Nils B. wrote:
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Dear Freesurfer developers,
I'm hoping you can help me once again.
Right now I'm working on how to extract certain measurements out of my
data set. I have two groups and MRI data from one t
External Email - Use Caution
Dear Freesurfer developers,
I'm hoping you can help me once again.
Right now I'm working on how to extract certain measurements out of my data
set. I have two groups and MRI data from one time point in elderly people.
The data quality is pretty bad but
Hi David
1. I think the main function of the 3T flag is to align to an Talairach
average of 3T data, so probably you should continue to use it.
2. There really is no hard threshold. For the control points you want to
use voxels that are entirely wm , no partial voluming and no pathology.
3.
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Hello FreeSurfer Experts!
I currently supply inhomogeneity-corrected (via N4 biascorrection) 3T T1w
scans through recon-all pipeline. The correction has solved many
segmentation errors which reduced the time spent on manual editing. I have
several ques
It should be relatively close, but they will not be identical since the
volume calculation is not linear
On 11/09/2016 03:40 PM, Daya P wrote:
> Hi all,
>
> I grey matter volume supposed to be equal to surface area x average
> thickness in each ROI when looking at mris_anatomical_stats for
> i
OK, then, I think that sorts out all my questions on this issue at this
time.
Thanks for the discussion and suggestions.
--pt
On Wed, Nov 9, 2016 at 3:34 PM, Douglas N Greve
wrote:
> That looks like a good list, but we don't keep track of all these
> things. To add to it, we have wmparc.mgz w
Hi all,
I grey matter volume supposed to be equal to surface area x average
thickness in each ROI when looking at mris_anatomical_stats for individual
subjects?
Thank you,
Daiana
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That looks like a good list, but we don't keep track of all these
things. To add to it, we have wmparc.mgz which is segmented WM
(3000-3035, 4000-4035).
On 11/09/2016 03:00 PM, P Taylor wrote:
> The FreeSurferColorLUT.txt file has over 1,200 regions listed in it,
> but I assume that not all of
The FreeSurferColorLUT.txt file has over 1,200 regions listed in it, but I
assume that not all of those could be output in those default recon-all
aparc+aseg* files. For example, I don't think I have ever seen a region:
"3001wm-lh-bankssts 230 155 215 0"
output.
So, I ass
Sorry, I'm not sure what your question is here?
On 11/8/16 5:25 PM, P Taylor wrote:
OK, thanks for that list of complementary ROIs.
I've always wondered what is the maximal set of regions that can be
returned by the standard recon-all with no other options for
aparc+aseg and aparc+aseg2009?
OK, thanks for that list of complementary ROIs.
I've always wondered what is the maximal set of regions that can be
returned by the standard recon-all with no other options for aparc+aseg and
aparc+aseg2009? Looking at the FreeSurferColorLUT.txt, I guess there is a
batch from lines 1-231 (spannin
Actually, what it does is to binarize all the labels that it thinks are
not GM, and then invert the mask to give GM. for what it is worth, there
are the non-GM numbers
MatchValues[nMatch++] = 2;
MatchValues[nMatch++] = 41;
MatchValues[nMatch++] = 77;
MatchValues[nMatch++]
OK. But going back to my question that kicked this thread off, actually
what I was looking for was just such a rule.
I could make a fairly solid list of GM from using this new "mri_binarize
--gm " on several recon-all outputs. Would it be possible to have the
rule (presumably a list of numbe
Yes. It just uses a rule on the numbers that it expects to be GM. At
some point, I'll add both tissue type and laterality info to the ROIs,
but not for version 6
On 11/8/16 12:03 PM, P Taylor wrote:
And a final question, which might be a silly one--
This GM map applies to both the aparc.a200
And a final question, which might be a silly one--
This GM map applies to both the aparc.a2009s+aseg.mgz and aparc+aseg.mgz
files, right?
Running "mri_binarize --gm ..." on each of those files separately gave the
same mask-- I believe this should be a general property?
Thanks,
pt
On Tue, Nov 8,
yes
On 11/8/16 11:51 AM, P Taylor wrote:
Ah, cool, that looks like it does the trick-- thanks much.
Will that version of mri_binarize be in the next release of FS?
Thanks,
pt
On Tue, Nov 8, 2016 at 11:35 AM, Douglas Greve
mailto:gr...@nmr.mgh.harvard.edu>> wrote:
Try this one
ht
Ah, cool, that looks like it does the trick-- thanks much.
Will that version of mri_binarize be in the next release of FS?
Thanks,
pt
On Tue, Nov 8, 2016 at 11:35 AM, Douglas Greve
wrote:
> Try this one https://gate.nmr.mgh.harvard.edu/safelinks/greve/mri_binarize
>
> On 11/8/16 11:26 AM, P
Try this one https://gate.nmr.mgh.harvard.edu/safelinks/greve/mri_binarize
On 11/8/16 11:26 AM, P Taylor wrote:
Thanks, I'd like to try that. However, my mri_binarize doesn't show
that option, and when I try running it, that option isn't recognized:
$ mri_binarize --gm --o map_gm.nii --i apa
Thanks, I'd like to try that. However, my mri_binarize doesn't show that
option, and when I try running it, that option isn't recognized:
$ mri_binarize --gm --o map_gm.nii --i aparc+aseg.mgz
ERROR: Option --gm unknown
Looking at the mri_binarize help, I see '--wm' exists, and that does,
indeed,
We don't currently have that information (ie, tissue type) stored with
the ROI. One thing you can do is to run mri_binarize with the --gm
option on aparc+aseg.mgz This uses some rules to determine what is GM
and creates a mask of GM. You can then feed this into mri_segstats with
--mask, and i
Thanks, that's useful for getting the ROI volumes and a list of all that's
been found for a particular data set.
I would still like to have a way to identify a listed region as gray matter
or not so that I can parse the file for only GM regions that have been
returned, particularly as different nu
I don't know that we have a complete list in one place of just the
aparc+aseg ROIs, but you can get one by running
mri_segstats --seg aparc+aseg.mgz --ctab-default --sum sum.dat
then look in the sum.dat file
On 11/03/2016 04:32 PM, P Taylor wrote:
> Is there an available list of GM regions wit
Is there an available list of GM regions within the list of regions in the
FreeSurferColorLUT.txt?
(In particular, I am interested in a list of GM regions output in a default
run of recon-all, which seems to have a maximum regionnumber of 2035. But
a full list is great, too-- I'm not sure which m
I am attempting to align the GM mask (lh.ribbon.mgz) to the T1 in native
space. I see this thread that states this command is the correct way:
mri_label2vol --seg lh.ribbon.mgz --temp rawavg.mgz --o
ribbon-in-rawavg.mgz --regheader ribbon.mgz
from:
http://www.mail-archive.com/freesurfer%40nmr.mgh
Hi Gonzalo, each of those commands has a --help flag which causes it to
print out documentation. Have you looked at that yet?
doug
On 02/28/2013 01:20 PM, Gonzalo Rojas Costa wrote:
> Hi:
>
>I need to compute the GM and WM volume for each lobe... I know that
> for GM, I must use:
>
> mri_annot
Hi:
I need to compute the GM and WM volume for each lobe... I know that
for GM, I must use:
mri_annotation2label --subject bert --hemi rh --lobesStrict lobesfile
mris_anatomical_stats -mgz -cortex ../label/lh.cortex.label -f
../stats/lh.lobesfile.stats -b -a ../label/lh.lobesfile.annot bert lh
Thanks Bruce and Douglas!
Andreia
Citando Douglas N Greve :
> mri_compute_volume_fractions will compute the fractions for each of
> the tissue types, no need to alter the segmentations.
> doug
>
>
>
> Bruce Fischl wrote:
>> Hi Andreia
>>
>> you could certainly change our segmentation labels
mri_compute_volume_fractions will compute the fractions for each of the tissue
types, no need to alter the segmentations.
doug
Bruce Fischl wrote:
> Hi Andreia
>
> you could certainly change our segmentation labels to just these 3 classes
> easily enough in matlab. Then we have tools for compu
Hi Andreia
you could certainly change our segmentation labels to just these 3 classes
easily enough in matlab. Then we have tools for computing partial volume
fractions (I think mri_compute_volume_fractions)
cheers
Bruce
On Wed, 28 Sep 2011, _andre...@sapo.pt wrote:
> Hello list,
>
> Followi
Hello list,
Following this email that I found in the archives:
"(...)
For the segmentation, FS still works voxelwise, but it's objective is
to identify each structure as a whole, whereas SPM and FSL/FAST
attempt to classify each voxel as being GM, WM or CSF. A short
description of the meth
Hi Kelly,
See also these threads where I advocate using mean cortical thickness as
an appropriate covariate for a thickness analysis:
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg11987.html
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg13459.html
Mean cortical th
Hi Kelly,
it's a bit of an open question what the relationshop between thickness
and icv is. It's probably not linear, maybe icv^(1/3)?
cheers
Bruce
On Fri, 28 May 2010, Kelly Silva wrote:
> Hello,
>
> I'm doing regression analyses with cortical thickness at
> the level of voxel. Should I co
Hello,
I'm doing regression analyses with cortical thickness at
the level of voxel. Should I correct the total GM volume by introducing
this parameter as a confounding variable? Shoud I include the
intracranial volume as an additional nuisance variable? If positive, I
assume that these variables
Hello Freesurfer experts,
Sorry for the repost, but I'm still hoping someone can answer our
questions found below.
We have generated a list of volumes, using asegstats2table (based on
aseg.stats files). We want to compute total grey matter (including
subcortical GM) and white matter volumes for ri
Hi Johanna,
This is probably a topological defect. Please follow
the steps in this wiki to correct the surfaces.
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TopologicalDefect
Sita.
On Thu, 11 Feb 2010, johanna feiler wrote:
Dear freesurfer experts,
After running the autorecon2
Dear Bruce,
Thank you very much for your patient instruction! In fact, I
used *"file--load
overlay*", then with below error information. Maybe I can try mris_calc.
Thanks again!
Best regards!
Joe
2010/2/2 Bruce Fischl
> it looks like you are trying to load the volume
it looks like you are trying to load the volume measures as a surface, not
as an overlay. Use file->load overlay. Note that you can also use mris_calc
to generate the volume
measures.
cheers
Bruce
On Tue, 2 Feb 2010, keepmoon wrote:
> Dear Bruce,
>
>This is the all information in tci:
Dear Bruce,
This is the all information in tci:
%
$ tksurfer xalbertM lh inflated
surfer: current subjects dir: /home/Joe/study
surfer: not in "scripts" dir ==> using cwd for session root
surfer: session root data dir ($session) set to:
surfer: /home/Joe/study
surfer: Readin
can you send us the complete output in the tcl window (the one with the %
prompt)
On Tue, 2 Feb 2010, keepmoon wrote:
> Dear Bruce and All,
>
> In my *View--Configure*there are three button which are activated
> (*Light, caption and phase Encoded Dat Display*), without "*functional
> ov
Dear Bruce and All,
In my *View--Configure*there are three button which are activated
(*Light, caption and phase Encoded Dat Display*), without "*functional
overlay*" option.
And in these activated buttons: light(light 0,...,light 3, with the
value, 0.4, 0.0, 0.6, 0.2. and bright
have you tried changing the threshold in configure->functional overlay?
What kind of values do you see?
On Tue, 2 Feb 2010, keepmoon wrote:
> Dear all experters,
>
>First I am appreciated for the help of Bruce.
> I tried to following his instruction, but I still have some problem and I
>
Dear all experters,
First I am appreciated for the help of Bruce.
I tried to following his instruction, but I still have some problem and I
can't show any result on the flated surface. I don't know whether my method
to calculate the volume is wrong or I display it wrongly. Expecting som
Hi Joe,
I think we output a volume measure for the gray matter as well - we simply
multiple the thickness by the surface area.
cheers
Bruce
On Mon, 1 Feb 2010, keepmoon wrote:
> Dear developer,
>
> I want to compare the grey matter volume by VBM to cortical thickness
> by freesurfer. But i
Dear developer,
I want to compare the grey matter volume by VBM to cortical thickness
by freesurfer. But in this process, I meet a problem: how to change the
points number of grey matter into the same with the vertex of thickness by
freesurfer?
Any help will be appreciated!
Best
can you send us the recon-all.log?
On Mon, 7 Dec 2009, Ritobrato Datta
wrote:
> Hello All,
>
> I ran recon-all for a subject and when I did the following to check the gray
> matter and white matter segmentation I found that it couldnt do it.
>
> tkmedit subjid brainmask.mgz lh.white -aux T1.mgz
Could be a problem with intensity normalization. Are the white matter
voxels mostly 110 in the T1.mgz? Also, look at the nu.mgz. I've seen
some problems where the nu_correct fails. Usually, this happens when
there are a few extremely bright voxels.
doug
Ritobrato Datta wrote:
> Hello All,
>
>
Hi Julie,
not sure what to say re FAST. They are different algorithms with the same
goal, and so will generate somewhat different results.
In general we find that the surface-based measures of cortex are more
accurate than the voxel ones.
cheers,
Bruce
On Fri, 4 Dec 2009,
Julie McEntee wr
Hi,
So far, I have results from autorecon1 & -subcortseg. The aseg.stats that
are obtained following these procedures contain measures of L &
R-Cerebral-White-Matter and Cerebral Cortex. If I created masks (bitmaps)
using these labels in FreeSurfer, would they be equivalent to whole-brain WM
and
mris_anatomical_stats -l
On Tue, 31 Mar 2009, Kelly Silva
wrote:
Hello,
Can I calculate GM in ROIs that I have done? How can I do that?
Thanks and regards, Kelly
Veja quais são os assuntos do momento no Yahoo! +Buscados
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Hello,
Can I calculate GM in ROIs that I have done? How can I do that?
Thanks and regards, Kelly
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hello
I want to use GM volume stats, i don't know whether it is or not, where?
I had understood that FS does not calculate the total GM volume, how can I make
it?
and can I calculate it for an individual ROI on a specific area?
Regards
Gabriel
Aseg.stat
Sent from my Nokia phone @E71
-Original Message-
From: Gabriel Go.Es.
Sent: 30/03/2009 07:14:32
Subject: [Freesurfer] GM
hello
I want to use GM volume stats, i don't know whether it is or not, where?
I had understood that FS does not calculate the total GM volume
hello
I want to use GM volume stats, i don't know whether it is or not, where?
I had understood that FS does not calculate the total GM volume, how can I make
it?
and can I calculate it for an individual ROI on a specific area?
Regards
Gabriel
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I think you mean FreeSurfer?
You can find this in aseg.stats inside stats directory in each subject.
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Netfilter & SpeedComm Telecom
--- Novo Netfilter 3.0 www.netfilter.com.br
On Fri
Hello,
How can I calculate the GM using the FSL?
Thanks, Kelly
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Hi Mike,
Thanks for your reply . I'll give it a try.
Anthony
--- On Tue, 13/1/09, Michael Harms wrote:
From: Michael Harms
Subject: Re: [Freesurfer] GM calculation?
To: slam_...@yahoo.com
Cc: freesurfer@nmr.mgh.harvard.edu
Date: Tuesday, 13 January, 2009, 9:28 PM
Hi Anthony,
For cor
Hi Anthony,
For cortical gray matter volume, compute statistics using the
{lh,rh}.cortex.label file.
i.e.,
mris_anatomical_stats -l lh.cortex.label -f $subj/stats/lh.cortex.stats
$subj lh
That will be roughly similar to computing the volume difference between
the pial and white surfaces, except
Hi all,
I'm doing some analyses which involve GM volume . It might sound trivial but I
wonder how could GM calculation be done in freesurfer? Is there a way to
compute it based on GM between white and pial surfaces, and will the result of
that approach be different from using what is given by a
On Wed, 28 Feb 2007, Juranek, Jenifer wrote:
I'd like to compute %GM, %WM, %CSF wrt ICV (eTIV)...including cerebellum
gray/white.
Are the values returned by mris_wm_volume and mris_volume for cortical
surfaces only (excluding cerebellum)?
yes, just cortex, and cerebral wm.
So, in this c
I'd like to compute %GM, %WM, %CSF wrt ICV (eTIV)...including cerebellum
gray/white.
Are the values returned by mris_wm_volume and mris_volume for cortical surfaces
only (excluding cerebellum)?
So, in this case...
1) are the values in aseg.stats appropriate for both cerebral and cerebellar
fra
HI Antionio
can you send a tif showing what you mean? The control points will only
help if the wm is darker there (which it frequently is)
Brce
On Fri, 17 Nov 2006,
Gallo, Antonio (NIH/NINDS) [F] wrote:
Dear All,
I have a question regarding the pial surface in medial temporal lobes
since
Dear All,
I have a question regarding the pial surface in medial temporal lobes
since segmentation fails to catch up some GM.
Do you have any suggestions (do control point to add GM exist?) to fix
this underextimation of GM ?
Many Thanks,
Antonio
Antonio Gallo, MD
NIB-NINDS-NIH
10
p.s. thanks to Xiao Han for writing up a wiki page on this:
https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferWiki/SurfaceNormal
On
Wed, 18 Jan 2006, XJ Kang wrote:
Hi,
Anywhere in the "surf" directory I can find the normal direction of each node
on the GM/WM surface? Or anyway I can cal
I've also just modified mri_surf2surf to extract the surface normals at
each vertex. You can get the new version from:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_surf2surf
There's an example in the --help on how to run it.
doug
Bruce Fischl wrote:
sure. You can co
sure. You can convert the surface into ascii with mris_convert or load it
directly into matlab with read_surf. The normal is then the cross product
of two of the legs of each triangle. Sorry, I don't remember the ordering
but it should be obvious if you have it wrong. The indices of the vertices
Hi,
Anywhere in the "surf" directory I can find the normal direction of each
node on the GM/WM surface? Or anyway I can calculate the normal
direction from the surface files? How about the direction between the
correspoding two points on the GM/WM surface and pial surface? Thanks.
XJ Kang
__
?h.white and ?h.pial. The stuff between them is cortical gray matter.
cheers,
Bruce
On
Thu, 2 Jun 2005, Campbell, Zeke (NIH/NINDS) wrote:
Dear All:
I would like to know which surface I should load on T1 volume to visualize
cortical GM segmentation.
Thanks.
Zeke Campbell
Dear All:
I would like to know which surface I should load on T1 volume to visualize
cortical GM segmentation.
Thanks.
Zeke Campbell
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