see http://dx.plos.org/10.1371/journal.pone.0038234
On 22 Oct 2013, at 18:18, freesurfer-requ...@nmr.mgh.harvard.edu wrote:
Message: 2
Date: Tue, 22 Oct 2013 16:15:44 +
From: "West, John D."
Subject: [Freesurfer] Subject processing difference between computers
To: "freesurfer "
Message-I
Hi,
From what I can read in the wiki about wm editing, I understand
that edited wm voxels have values of either 255 (added) or
1 (removed) and no other values. These are stored in the file
wm.mgz. Is that correct?
Before processing a lot of data I want to be sure that running
recon-all with the o
;
> cheers
> Bruce
> On Tue, 4 Feb 2014, Ed Gronenschild
> wrote:
>
>> Hi,
>>
>> From what I can read in the wiki about wm editing, I understand
>> that edited wm voxels have values of either 255 (added) or
>> 1 (removed) and no other values. The
x27;d edit the base. If that is
not sufficient, you can edit the cross or the long. Edits from the
cross should be transferred to the long, except if the long already
contain manual edits.
Best, Martin
On Feb 4, 2014, at 9:06 AM, Ed Gronenschild
wrote:
Hi Bruce,
When I have a look in
Hi,
Using recon-all (freesurfer v5.1.0, MacOSX10.6) I noticed a rotation
of the T1 data early in the pipeline, i.e., converting rawavg.mgz to
orig.mgz., see excerpt of output of mri_info below
rawavg.mgz:
xform info: x_r = 0.0081, y_r = -0.0913, z_r = 0.9958, c_r = 0.0813
;conform" process
>
> cheers
> Bruce
> On Thu, 6
> Feb 2014, Ed Gronenschild wrote:
>
>> Hi,
>>
>> Using recon-all (freesurfer v5.1.0, MacOSX10.6) I noticed a rotation
>> of the T1 data early in the pipeline, i.e., converting rawavg.mgz t
---
> Conte Center for the Neuroscience of Mental Disorders
> Washington University School of Medicine
> Department of Psychiatry, Box 8134
> 660 South Euclid Ave. Tel: 314-747-6173
> St. Louis, MO 63110Email: mha...@wustl.edu
>
>
>
>
> O
Dear Kim,
This may be of interest to you:
http://dx.plos.org/10.1371/journal.pone.0038234
Cheers,
Ed
On 24 Mar, 2014, at 17:00, freesurfer-requ...@nmr.mgh.harvard.edu wrote:
Message: 3
Date: Mon, 24 Mar 2014 12:28:29 +0900
From: jh kim
Subject: Re: [Freesurfer] Difference in volumes btw 5.
Hi,
When using tkmedit or freeview, a surface is converted
into a contour superimposed onto T1. I would like
to do the same using the command:
mri_surf2vol --surf pial --hemi lh --template subjID/mri/T1.mgz \
--identity --o lh.pial.mgz --mkmask
I notice that the "contour" in lh.pial.mgz is not c
Hi Bruce,
I'm confused about this.
The manual-intervention workflow directives listed in recon-all (6 beta)
tell that the series of commands should be:
-autorecon2
-autorecon2-cp
-autorecon3
-autorecon2 processes stages 6-23
and
-autorecon2-cp process stages 12-23
So it seems to be a waste of t
Hi developers,
My environment:
MacPro OSX10.7 installed on a partition of 20 GByte;
FreeSurfer v6 beta
During processing recon-all on 4 subjects in parallel
using 4 terminal windows, the 20 GByte partition got
full. This happened twice and I managed to trace down
the offending stage in the pipeli
Hi freesurfites,
The mri folder of the fsaverage subject contains
the segmenation files, such as aparc+aseg.mgz, etc.
and in the surf folder there the corresponding surface
files (?h.pial. ?h.white, etc).
Question: which T1 data was used for these
segmentations?
Cheers,
Ed
___
; Bruce
> On Mon, 25 Mar 2013, Ed
> Gronenschild wrote:
>
>> Hi freesurfites,
>>
>> The mri folder of the fsaverage subject contains
>> the segmenation files, such as aparc+aseg.mgz, etc.
>> and in the surf folder there the corresponding surface
>> fi
Hi,
The paper entitled
“The Effects of FreeSurfer Version, Workstation Type,
and Macintosh Operating System Version on Anatomical
Volume and Cortical Thickness Measurements”,
PLoSONE, Vol 7(6), e38234 (2012)
may be of interest to all of you. It can be found at:
http://dx.plos.org/10.1371/journ
also the
users and developers of FSL about possible similar effects.
Ed Gronenschild,
Petra Habets,
Heidi Jacobs,
Ron Mengelers,
Nico Rozendaal,
Jim van Os,
Machteld Marcelis
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Dear Marise and Laura,
As Bruce et al frequently warned users about, you should never mix
different versions.
The effects have been quantified recently by our group, see
http://dx.plos.org/10.1371/journal.pone.0038234
I can add to this that the differences between v5.1.0 and v5.0.0 are
som
Hi,
I would like to register FLAIR to T1.
Specifications FLAIR:
axial acquisition, 24 slices,
pixel size = 0.45 * 0.45 mm^2
slice thickness = 5.50 mm (no gap).
The slices run from the top of the brain
to just below the eyes. This is contrary
to the T1 scan which covers the full head
down to the n
Hi Bruce,
It is slightly better but still displacements
in all directions and rotations too exist.
Ed
On 10 Jul 2012, at 16:13, Bruce Fischl wrote:
> try -init-spm
>
> cheers
> Bruce
> On Tue, 10 Jul 2012, Ed Gronenschild wrote:
>
>> Hi,
>>
>>
Hi Bruce,
Unfortunately, this has no effect.
Ed
On 10 Jul 2012, at 16:40, Bruce Fischl wrote:
> Hi Ed
>
> you are using -t2, right? You can also try -init-header
>
> cheers
> Bruce
> On Tue, 10 Jul 2012,
> Ed Gronenschild wrote:
>
>> Hi Bruce,
>
cation. Is
> this from
> the same session? I've always had it work on flair images using one
> of the
> types of initialization.
>
> cheers
> Bruce
>
>
> On Tue, 10 Jul 2012, Ed Gronenschild wrote:
>
>> Hi Bruce,
>>
>> Unfortunately, this
Hi,
I'm performing a clusterwise correction for multiple comparisons
with the command
mri_glmfit-sim --glmdir my_glmdir --sim mc-z 5000 1.3 basename \
--sim-sign abs
For version v4.5.0 this took about 40 hours to complete.
However, for v5.1.0 it is now running for more than
6 days and from the c
ntil Doug is back from vacation. Is
this from
the same session? I've always had it work on flair images using
one of the
types of initialization.
cheers
Bruce
On Tue, 10 Jul 2012, Ed Gronenschild wrote:
Hi Bruce,
Unfortunately, this has no effect.
Ed
On 10 Jul 2012, at 16:40, Bruce
Doug is back from vacation. Is
this from
the same session? I've always had it work on flair images using
one of the
types of initialization.
cheers
Bruce
On Tue, 10 Jul 2012, Ed Gronenschild wrote:
Hi Bruce,
Unfortunately, this has no effect.
Ed
On 10 Jul 2012, at 16:40, Bruce Fisc
Hi,
I want to apply a cluster correction with mri_glmfit-sim with
the --cache option:
mri_glmfit-sim --glmdir my_glmdir --cache 1.3 abs
It fails with the error message that it can't find the file:
FSDir/average/mult-comp-cor/fsaverage/lh/cortex/fwhm34/abs/th1.3/mc-
z.csd
(FSDir is the directo
ver go above it, or maybe should never go above
it. I
can create tables at higher smoothing levels, but 34mm is a lot of
smoothing. How much did you apply to the data?
doug
On 09/27/2012 05:48 AM, Ed Gronenschild wrote:
Hi,
I want to apply a cluster correction with mri_glmfit-sim with
the --cache
:15, Ed Gronenschild wrote:
On 28 Sep 2012, at 18:00, freesurfer-requ...@nmr.mgh.harvard.edu
wrote:
Message: 27
Date: Fri, 28 Sep 2012 10:03:47 -0400
From: Douglas N Greve
Subject: Re: [Freesurfer] Fmri_glmfit-sim with pre-cached fails
To: freesurfer@nmr.mgh.harvard.edu
Message-ID
Hi,
For your information: for version 5.1.0 we have
found no differences in the results between
MacOSX 10.6 and 10.7 (53 subjects).
Cheers,
Ed
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Hi Bruce and colleagues,
I hope you did survive Sandy without too much damage.
Cheers,
Ed
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The information in this e-mail is intend
Hi,
Can you give me a reference to the method used for the
clusterwise correction for multiple comparisons (CSD)?
Is it Hagler et al, NeuroImage 2006, vol 33, 1093-1103?
Cheers,
Ed
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lumn 1 is nearly identical to column 17.
> doug
>
>
> On 01/24/2013 06:36 AM, Ed Gronenschild wrote:
>> Hi,
>>
>> Running mri_glmfit ( v5.0.0, Mac OSX10.6) I got he following
>> error message:
>>
>> ERROR: matrix is ill-conditioned or badly scaled, cond
Hi Bruce,
What do you mean: no support anymore or no new development?
Cheers,
Ed
On 30 Jan 2013, at 13:41, Jacobs H (NP) wrote:
> Message: 7
> Date: Mon, 21 Jan 2013 19:19:25 -0500 (EST)
> From: Bruce Fischl
> Subject: Re: [Freesurfer] beta
> To: Colin Reveley
> Cc: Joshua Lee , freesurfer@nm
ns are
very
similar.
doug
On 01/30/2013 05:10 AM, Ed Gronenschild wrote:
Hi Doug,
It is indeed correct that columns 1 and 17 are highly correlated.
However,
for another version of the fsgd file, where the corresponding
class and
covariate values where identical but with other covariat
some way.
doug
Message: 7
Date: Tue, 26 Feb 2013 10:08:07 +0100
From: Ed Gronenschild
Subject: Re: [Freesurfer] Problem with glmfit: matrix is
ill-conditioned
To: "freesurfer@nmr.mgh.harvard.edu"
Message-ID:
<2031202f-e366-48cb-82a9-3142378ad...@maastrichtuniversit
Hi Nick,
Congratulations and thank you and the whole team (the Freesurfites)
very much for your efforts.
Cheers,
Ed
On 03 Mar, 2013, at 18:00, freesurfer-requ...@nmr.mgh.harvard.edu wrote:
>
> Freesurfers,
>
> At long last, a new version of Freesurfer is available for download!
>
> For a list o
Hi,
How do you compute the cortical thickness for each structure
as listed in the ?h.aparc.stats file? Is it equal to the thickness
for each vertex averaged over all vertices within each structure?
Ed
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Hi,
How do you compute the cortical thickness for each structure
as listed in the ?h.aparc.stats file? Is it equal to the thickness
at each vertex averaged over all vertices within the structure?
Ed
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Hi,
I noticed a difference in the file nu.mgz between FreeSurfer
version v5.0.0 and v5.1.0 (running on Mac OSX10.6). It looks
as if nu.mgz in v5.1.0 is an intensity scaled-down version of
nu.mgz in v5.0.0.
The release notes tell that a bug is fixed in mri_nu_correct.mni,
I don't know if that may c
Jon,
The reason is that already in one step earlier in the pipeline,
the nu-correct stage, a difference arises. See thread on
"Differences in nu.mgz between v5.0.0 and v5.1.0"
Cheers,
Ed
Hi,
We have noticed differences in Talairach registration (and
therefore ICV estimates) in some of our
Hi,
I'm looking for a tool to fill holes of only 1 voxel in size
in a binary mask.
I posted this also to the FSL mailing list but none of the
suggested solutions could do this or were robust enough.
Ed
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> output
> voxel to be set to 1
>
> cheers
> Bruce
>
>
> On Fri, 30 Sep 2011,
> Ed
> Gronenschild wrote:
>
>> Hi,
>>
>> I'm looking for a tool to fill holes of only 1 voxel in size
>> in a binary mask.
>> I posted this also
Hi Bruce,
I've grabbed the dev version
freesurfer-Darwin-leopard-i686-dev.tar.gz (date 2 Oct 2011, 13:10)
at
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev/
and tried
mri_morphology fill_holes 26
but got the message that the operation "fill_holes"
is not supported.
Ed
__
0400, Bruce Fischl wrote:
>> the dev build probably didn't complete. Nick?
>> On Mon, 3 Oct 2011, Ed
>> Gronenschild wrote:
>>
>>> Hi Bruce,
>>>
>>> I've grabbed the dev version
>>>
>>> freesurfer-Darwin-leopard-i686-dev.t
Dear Joana,
Two things:
1.
You should be very careful to use fslswapdim since it may result
in an unintended left-right flipping. It's better to use
fslreorient2std.
2.
The tool dt-recon computes the coregistration of the lowb volume to
the anatomical volume, see register.dat.
You can then u
Hi,
There are various methods to estimate the diffusion tensor, like
linear-least squares, non-linear least-squares, German-McClure
M-estimator.
I would like to know which method is used by FreeSurfer in
the dt_recon command?
Cheers,
Ed
___
Freesur
Hi,
After editing a text file holding the b vecs to be supplied
as input to dt_recon this tool did not interpret the text
file correctly. It turned out that dt_recon did not recognise
the end-of line character in this file: this was decimal
code 13 (called "CR"). It seems that dt_recon only
accept
Hi Rudolph,
I used TextEdit. On a Mac with OS version earlier than OS10.6
this problem didn't occur. With TextEdit it is not possible to save
as UNIX format.
Thanks for the trick to use sed.
Ed
On 9 Nov 2011, at 15:27, Rudolph Pienaar wrote:
> On 11/9/11 07:59 , Ed Gronenschi
Dear Antonella,
In theory, FA can be sqrt(3/2) = 1.2247449. This occurs if
eigenvalues 2 and 3 are zero. You will find these high
FA values (>1) mainly outside the brain.
Ed
On 3 Feb 2012, at 11:31, freesurfer-requ...@nmr.mgh.harvard.edu wrote:
Dear all,
I use dt_recon to process my DTI dat
Hi,
I would like to use mri_robust_register to co-register
b-volumes to the reference b0-volume in a DTI dataset.
The documentation informs that it is not quite suitable
in case of large intensity differences which apply to
my case. How to proceed? Is a dev version available
for this purpose?
Che
Hi,
I got an error during the first step in recon-all (Mac OS 10.6.8,
FreeSurfer v5.1.0). The eror message in the log file is:
WARNING: file ./MR.1.3.12.2.1107.5.2.18.41016.201008031106017688438785.dcm
does not contain a Siemens ASCII header
has this file been anonymized?
ERROR: cannot unpa
Hi Jamaan,
Yes, I got the same error.
Ed
On 27 Mar 2012, at 13:36, Jamaan Alghamdi wrote:
> Hi Ed,
>
> Have you tried using mri_convert command directly without running recon-all.
>
> Best wishes,
> Jamaan
>
> Hi,
>
> I got an error during the first step in recon-all (Mac OS 10.6.8,
> FreeS
Hi,
I followed the instructions to visualize the hippocampal subfield segmentation
by entering the command (in the subject's mri directory)
freeview nu.mgz \
> -p-labels posterior_left_* posterior_Left-Hippocampus.mgz \
> -p-labels posterior_right_* posterior_Right-Hippocampus.mgz \
> -p-pr
vard.edu>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Is it a siemens dicom? If so, what happened to the ascii header?
Did you
do something to the file? What are the contents of the image? Eg, a
T1?
doug
On 03/27/2012 05:35 AM, Ed Gronenschild wrote:
Hi,
I got an error durin
t; messages from freeview.
Ed
On 3 Apr 2012, at 21:29, Koen Van Leemput wrote:
> Hi Ed,
>
> What version of the FreeSurfer build are you using?
>
> Also, could you please let me know what the result is of "ls
> posterior_left_CA2*"?
>
> Thanks,
>
> Koen
quot;
>
> and let me know what the result is?
>
> Thanks, and sorry this seems so difficult to sort out.
>
> Koen
>
>
> On Wed, Apr 4, 2012 at 6:14 AM, Ed Gronenschild
> wrote:
>> Hi Koen,
>>
>> As already mentioned, I'm using v5.1.0, Mac
check with the engineers what exactly happened. Do you
> remember which file you downloaded?
>
> Thanks,
>
> Koen
>
>
>
> On Wed, Apr 4, 2012 at 6:59 AM, Ed Gronenschild
> wrote:
>> Hi Koen,
>>
>> No worries.
>> The result of grep is:
>&
\/DG/g" FreeSurferColorLUT.txt
>
> Thanks,
>
> Koen
>
>
>
>
> On Wed, Apr 4, 2012 at 9:32 AM, Ed Gronenschild
> wrote:
>> I have downloaded the file
>> freesurfer-Darwin-leopard-i686-stable-pub-v51.0..dmg,
>> date 26/05/2011.
>>
>> Ed
>
Hi
I'm not sure but does the Talairach stage precede the
nu-correct stage in version v5.1.0? If so, is there an option
to switch these two stages?
Cheers,
Ed
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Hi,
As of version 5.1 the Talairach stage precedes the nu-correction stage.
Is there an option or possibility to switch this order?
Cheers,
Ed
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sults that people were seeing
> prior to v5.1. it will still run the current nu_correct stage to
> create
> nu.mgz (the nu used in talairach gets discarded).
>
> Nick
>
>
>
> On Mon, 2012-04-16 at 09:10 +0200, Ed Gronenschild wrote:
>> Hi,
>>
>> As
prior to the
> talairach stage, as will be the case with v5.2. so you can just run:
>
> recon-all -s subjid -all -clean-tal
>
> n.
>
>
> On Tue, 2012-04-17 at 08:58 +0200, Ed Gronenschild wrote:
>> Hi Nick,
>>
>> The option -talairach-nu is not recognized i
Hi,
I'm using the version of recon-all that Nick provided
at April 17 to be able to run nu_correct prior to the
Talairach stage. (I'm on a Mac, OSX 10.6, version
v5.1.0). The command given was
recon-all -autorecon-all -hippo-subfileds -no-wsgcaatlas \
-clean-tal -s subject.
recon-all stopped and
9 May 2012, at 18:53, Nick Schmansky wrote:
> can you send the recon-all.log file? does it say why the
> lh.orig_corrected file wasnt created?
>
> On Wed, 2012-05-09 at 09:56 +0200, Ed Gronenschild wrote:
>> Hi,
>>
>> I'm using the version of recon-all that Nick p
Hi,
I want to use parameters different from default for mri_nu_correct.mni.
This command uses nu_correct for which I would like to set the following
options:
-distance 25
-stop 0.0001
-fwhm 0.1
These settings are more approriate when using 3T T1 data.
How can I invoke these in recon-all? Can I
Hi
I tried to use option --fwhm 0.1 with mri_nu_correct.mni and
noticed that this is incorrectly interpreted as option --distance 0.1.
This script reads
if($#FWHM) set cmd = ($cmd -distance $FWHM);
whereas this should be
if($#FWHM) set cmd = ($cmd -fwhm $FWHM);
Is it possib
Hi,
Whenever I want to convert DICOM files to .mgz file I have to
remove spaces in the directory name or file names otherwise
recon-all -i ... -s ... will not work.
Bracketing the names within quotes will not help.
Is there some workaround?
ed
___
Fr
try
recon-all -all -i dicom\ file.dcm -s .
Sita.
On Wed, 6 May 2009, Ed Gronenschild wrote:
Hi,
Whenever I want to convert DICOM files to .mgz file I have to
remove spaces in the directory name or file names otherwise
recon-all -i ... -s ... will not work.
Bracketing the name
Hi,
During processing with the command recon-all autorecon-all -s mysubject
I got an error with the following message:
mri_watershed error:
GLOBAL region of the brain empty !
What to do? Can I use a different option for the watershed algoritme?
Ed
Hi,
To which voxel space (native, Talairach or any other
standard space) do the measured cortical thickness
and areas/volumes in the statistical output files refer?
Ed
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Hi,
I would like to extract the WM and GM segmentations
used for the final cortical thickness calculations as
nifti files. How can I do that?
Ed
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t segmentation.mgz segmentation.nii
>
> should do it
>
> doug
>
> Ed Gronenschild wrote:
>> Hi,
>>
>> I would like to extract the WM and GM segmentations
>> used for the final cortical thickness calculations as
>> nifti files. How can I do that?
>>
>>
Doug,
I want all GM.
Ed
On 26 Aug, 2009, at 18:53 , freesurfer-requ...@nmr.mgh.harvard.edu
wrote:
For WM, you can use aparc+aseg.mgz and use indices 2 and 41. Do you
want
a particular GM or all GM?
Ed Gronenschild wrote:
Doug,
The file "segmentation.mgz" doesn't exis
Hi,
I got the following error during processing my subject nr 104 with
recon-all:
ERROR: - FindPacePath: could not find path.
The error log tells that it occurred during execution of the command
mris_topo_fixer -mgz -warnings 104 rh
What to do?
Ed
__
you specify otherwise.
>
> cheers,
> Bruce
> On
> Tue, 1 Sep 2009, Ed Gronenschild wrote:
>
>> Hi,
>>
>> I got the following error during processing my subject nr 104 with
>> recon-all:
>>
>> ERROR: - FindPacePath: could not find path.
>>
um or skull connected to cortex) then things
> will fail. Make sure nothing is dramatically wrong with it or the
> aseg.mgz
> first.
>
> Bruce
>
>
> On
> Tue, 1 Sep 2009, Ed Gronenschild wrote:
>
>> Hi Bruce,
>>
>> The log file tells that mris
Hi Nick,
I'm using Freesurfer on different Macs, of which one with Tiger OS and
ppc.
So, I kindly ask you to continue support for Tiger OS and ppc for at
least
this year.
Ed
On 13 Jan 2010, at 23:14, freesurfer-requ...@nmr.mgh.harvard.edu wrote:
>
> for the Mac OS users out there:
>
> who s
Hi,
Question for the developers.
Is it possible to adjust the dt-recon tool such that
the output files are in zipped NIFTI format (.nii.gz)
in view of the enormous amount of data that is
generated. It can accept .nii.gz files as input.
Thank you in advance,
Ed
___
Bruce,
Is it .niz or nii.gz?
Ed
On 9 Feb 2010, at 15:04, Bruce Fischl wrote:
> Hi Ed,
>
> we should add this as the default, but for now you can just go into
> the
> dt_recon script and do a global replace of:
>
> .nii --> .niz
>
> cheers,
> Bruce
>
>
Hi,
Reviewing the results of recon-all I noticed that
the segmentation of wm and gm was OK but that
the computed pial surface chopped away an
unacceptable amount of gm voxels, too many to
manually edit. Is there a way to cure this problem
by choosing some options?
I used version 4.5.0 on a Mac Int
Hi,
On an Intel Mac the Edit Voxels Tool does not work,
contrary to a PPC Mac.
This applies both to version v4.3.1 and v4.5.0.
Ed
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Hi,
I post this message once again because I didn't get
any reply.
On an Intel Mac the "Edit Voxels Tool" in tkmedit does
not work, contrary to a PPC Mac.
This applies both to version v4.3.1 and v4.5.0.
Ed
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Hi,
The FreeSurfer package is bundled with a subset of FSL.
However, I think most of us also installed the full FSL package.
The global variable FSL_DIR points to the directory of FSL.
My question is if it is possible to read from recon-all log files
which FSL package is used?
Ed
__
Hi,
I've mailed this once before and tried to solve a persistent problem.
Reviewing the results of recon-all I noticed that the derived pial
surface chopped away an unacceptable amount of gm voxels.
First of all I tried to manually edit some wm voxels, however with
no success.
Then I tried another
Hi,
I tried to find out this from previous contributions
but got lost.
There's some confusion on which file(s) to use
for segmented volumes.
FreeSurfer generates the following image and
text files:
- aseg.mgz
- aseg.stats
- aparc+aseg.mgz
- wmparc.mgz
- wmparc.stats
To my best knowledge aseg.stat
llison Stevens wrote:
> You're right - aseg.stats refers to the aseg.mgz and you should use
> that.
> You would only use the wm parcellations from the wmparc.mgz
>
> --
>
> On Fri, 18 Jun 2010, Ed Gronenschild wrote:
>
>> Hi,
>>
>> I tried to find ou
ations as it
> uses the more accurate surface-based volumetric calculation.
>
> doug
>
> Ed Gronenschild wrote:
>> But what about the labels starting with "lh-ctx-"
>> and "rh_ctx-", like for instance lh-ctx-fusiform (index=1007).
>> In the wm
Hi,
In the wmparc.stats file a large number of ctx structures
and the corresponding volumes, like ctx-lh-parahippocampal.
For some of these structures the volumes are also listed
in the ?h.aparc.stats files.
Which volumes are correct?
Ed
___
Freesurfer
Hi,
One of the volumes listed in the aseg.stats is
called "CSF". Its volume is too small to indicate
the total CSF volume of the brain. What is its
meaning?
If I would like to get the total CSF volume how
should I proceed?
Ed
___
Freesurfer mailing li
Hi,
What exactly is the definition of
- Brain Mask Volume
- Brain Segmentation Volume
as listed in the aseg.stats file?
Moreover, and correct me if I'm wrong,
the Intracranial volume is the scaled
intracranial volume of the MNI template.
Is the latter intracranial volume just a
number or is it
Hi,
I'm trying to use mri_segstats and get the following error:
ERROR: could not open stats/aseg1.stats for writing
The full command I gave was:
mri_segstats --seg mri/aseg.mgz --sum stats/aseg1.stats --pv mri/
norm.mgz --empty --excludeid 0 --excl-ctxgmwm --supratent --
subcortgray --in mri/
Hi,
In the v5.0.0 aseg.stats file I can find the following volumes:
- left/right cortical gray matter
- subcortical gray matter
- total cortical gray matter
- total gray matter volume
and
- left/right cortical white matter
- total cortical white matter
How can
Hi,
I post this once again because I didn't get any response.
In the v5.0.0 aseg.stats file I can find the following volumes:
- left/right cortical gray matter
- subcortical gray matter
- total cortical gray matter
- total gray matter volume
and
- left/right cortica
, "mris_wm_volume" is the best option to determine the
white matter volume.
See this wiki page for usage:
http://surfer.nmr.mgh.harvard.edu/fswiki/MorphometryStats
Best wishes,
Christian
---
Christian Scheel
Department of Psychiatry
University of Cologne
Am 26.10.2010 15:22,
e matter volume.
See this wiki page for usage:
http://surfer.nmr.mgh.harvard.edu/fswiki/MorphometryStats
Best wishes,
Christian
---
Christian Scheel
Department of Psychiatry
University of Cologne
Am 26.10.2010 15:22, schrieb Ed Gronenschild:
Hi,
I post this once again because I didn
were the
most accurate.
Allison
--
On Wed, 27 Oct 2010, Ed Gronenschild wrote:
Dear Bruce/Allison,
Could you please try to give response to my question
which wm and gm volumes I shoud use, see my
today's submission below.
Ed
On 27 Oct 2010, at 14:41, freesurfer-requ...@nmr.mgh.harvard
Dear Isabelle,
In the System Preferences -> Keyboard & Mouse you should
select the buttons as follows:
left one: primary button,
right one: secondary button
top on: Button 3
You will now have a 3-button mouse that works fine with FreeeSurfer.
Ed
Hello,
Just getting started with Freesurfer.
Hi,
Is it possible to give the exact definition of the output of dt_recon,
in particular:
- adc
- ra
- radialdiff
- ivc
Ed
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Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The inf
943.557923 c = 192176.447567
>rh surface-based volumes (mm3): wTot = 243959.351030, pTot =
> 438113.303648 c = 194153.952618
>
> These might be repeated through out the file if you're re-run. Make
> sure
> they are the last set.
>
> The wTot and pTot should give you the same v
d from the pial-white includes
> the
> subcortical structures. Once those are subtracted, you should get
> the #s
> in the aseg.stats file.
>
> doug
>
> Ed Gronenschild wrote:
>> Hi Doug,
>>
>> I checked the numbers again and found the difference:
>>
ace, and since the
> lh/rh.white surfaces also "enclose" the subcortical gray and
> ventricles,
> those would be included in the total. The whole purpose of
> mris_wm_volume is to remove those structures from the WM volume
> calculation).
>
> cheers,
> -MH
>
atter
> structures.
> This will not include cerebellar white matter.
>
> doug
>
> Ed Gronenschild wrote:
>> Hi Doug,
>>
>> This thread about GM and WM volumes was initiated by my question
>> on how to get the total cerebral GM and WM volumes.
>>
>>
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