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 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,
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
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.
---
> 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
;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
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
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
;
> 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
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
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
; 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 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
___
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
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
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
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
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,
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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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,
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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: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
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
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
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
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
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
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 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,
>
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,
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
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
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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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
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'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
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
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
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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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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\/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
>
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:
>&
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
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
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
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
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 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,
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
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 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
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,
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
___
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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
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
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
__
> 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,
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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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 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
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,
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 Fatima,
Your findings are not surprising. There is plenty of literature
describing problems with the VBM technique. You may read
e.g., Kennedy et al (2009), Neurobiology of Aging, vol. 10,
1657-1676 and references cited herein.
Ed
On 8 Jul 2011, at 15:02, freesurfer-requ...@nmr.mgh.harvard.ed
Hi Doug,
This works fine, thank you.
Ed
On 26 May 2011, at 16:58, Douglas N Greve wrote:
> Hi Ed,
>
> unpacksdcmdir was programmed only with Siemens in mind. Try using
> dcmunpack. I've never tried it on Philips, so let me know how it
> works.
>
> doug
>
>
&g
Hi,
I'm trying to use unpacksdcmdir and noticed that it only works
with Siemens DICOM files. I don't understand this restriction,
because the two tags on which is scanned (run/series number,
tag 0x20,0x11 and protocol name, tag 0x18,0x1030) are
present also in e.g. Philips DICOM files (I even assu
Hi,
A while ago we were asked if still support was needed
for FreeSurfer on a PPC Mac. I was one of the "happy"
few who needed this.
But I now can inform you that as far as I'm concerned
you can discontinue this support.
Thank you for all your support sofar.
Ed
_
4*256*256*256*72/(1024*1024)
> ans =
> 4608
>>>
>
> On Wed, 11 May 2011, Ed Gronenschild
> wrote:
>
>> I did.
>> However, without any other concurrent process
>> running I get exactly the same problem. I guess
>> that this is due to the 2GB
2011, Ed Gronenschild wrote:
>
>> 16 GB
>>
>> On 11 May 2011, at 15:24, Bruce Fischl wrote:
>>
>>> Hi Ed,
>>>
>>> how much RAM do you have in your machine?
>>> Bruce
>>>
>>>
>>> On Wed, 11 May 2011, Ed
>&g
16 GB
On 11 May 2011, at 15:24, Bruce Fischl wrote:
> Hi Ed,
>
> how much RAM do you have in your machine?
> Bruce
>
>
> On Wed, 11 May 2011, Ed
> Gronenschild wrote:
>
>> Hi,
>>
>> We are on a Intel Mac and are facing a memory problem with
>>
Hi,
We are on a Intel Mac and are facing a memory problem with mri_glmfit.
We want to apply it to a 4D volume consisting of 72 3D volumes
of 256 * 256 * 256 voxels each, with 1 byte per voxel. During
processing we get the error message that it could not allocate
262144 bytes for the 9313th slice.
Dear FreeSurfer developers,
With tksurfer you have to watch out to select the correct
hemisphere when loading an overlay or annotation.
My suggestion to the developers is to implement an
easy check since it is known to which hemisphere the
displayed surface belongs.
As far as I know, the only file
Dear Tanja,
Concerning your question 3 do the following:
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
On 0
wrote:
> Hi Ed, that subject is out-of-synch (maybe it got aborted). You'll
> need
> to re-run some portion of recon-all depending upon where in the stream
> it aborted.
>
> doug
>
> Ed Gronenschild wrote:
>> Hi,
>>
>> A serious error was encounte
Hi,
A serious error was encountered in running recon-all with option
-qcache.
The error occurred during execution of mri_surf2surf and the
message was:
number of vertices in ../subjectID/surf/lh.thickness does not match
surface (141969,131763).
It means the number of vertices in lh.sphere.re
on
the pial surface.
Thank you for your suggestions.
Ed
On 19 Jan 2011, at 17:31, Bruce Fischl wrote:
it's 'curv' format (read_curv.m I think)
On Wed, 19 Jan 2011, Ed
Gronenschild wrote:
What is the format of ?.thickness files?
On 19 Jan 2011, at 15:43, Bruce Fischl wrote:
re
a time, but apparently it's faded
> from all
> of our memories. You could do it in matlab by loading the
> parcellation and
> just setting every vertex with the parcellation value to the same
> scalar.
>
> cheers
> Bruce
>
>
> On Tue, 18 Jan 2011, Ed Gro
Hi,
I've done some statistics on thickness and volume
of the default cortical regions (segIDs 1000 - 1035
and 2000 - 2035) for a number of subjects.
How can I show for instance the p values
(expressed as -log(p)) as an overlay on the pial
surface of fsaverage?
Ed
Hi,
I've done some statistics on thickness and volume
of the default cortical regions (segIDs 1000 - 1035
and 2000 - 2035) for a number of subjects.
How can I show for instance the p values
(expressed as -log(p)) as an overlay on the pial
surface of fsaverage?
Ed
Hi,
The Mac OSX 10.6 version offers the possibility to
run in 64 bits mode (by pressing simultaneously
the 6 and 4 keys during startup).
I was wondering if Freesurfer can be used in 64 bits
mode? In other words: does it use the 64 bits or
does it run only in compatibility mode and in fact
in 32 bi
Hi,
Is there a tool to derive the cortical surface areas of
the cortical structures listed in aseg.stats?
Ed
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The information in th
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.
>>
>>
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
>
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:
>>
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
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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The inf
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.
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
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
, "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,
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
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'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,
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,
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
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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
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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
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
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
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,
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
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