ve a lesion probability map directly by using the flag
> "--save-posteriors Lesions" so you don't need to try different thresholds.
>
> Thanks,
> Stefano
>
>
> Subject: [Freesurfer] Large number of false negative MS lesions in SAMSEG
> Date: Sun, 14 Aug 2022 20:54:50 +02
External Email - Use Caution
Hello,
I am testing SAMSEG on my group of MS patients. Unfortunately, even when
dropping threshold to 0.005 I have large number of false negative lesions
left behind by SAMSEG (80% in about 75 cases I tried), which are clearly
visible lesions. I
External Email - Use Caution
Hi all,
previous question from Florent triggered my interest in SAMSEG and I am
running now couple of cases to see what it gives. I would like to ask
- SAMSEG can also output a mesh. How is the mesh stored in file?
- how can it be visualized
ugh to do in
> matlab. Read in the aseg, use find to find the indices of all the voxels
> with a particular label, then replace the label with whatever intensity
> you want.
>
> cheers
> Bruce
> On Sat, 12 Aug 2017, Martin Kavec wrote:
>
> > Dear all,
> >
> &g
Dear all,
I ran my subjects through recon-all successfully. I am in a need to have
custom intensities for segmentation and parcellation in aparc+aseg. Say, 10
- ventricles, 20 - amygdala, 30 - putamen, ...
I would appreciate advice on how I could achieve that.
Thanks in advance,
Martin
, Martin Kavec martin.ka...@gmail.comwrote:
Hi Zeke,
Thanks a lot for explanation. I think I will install centOS into a
virtual machine for quick solution. I only need it to run CVS.
Thanks and best regards,
Martin
Sent from my iPad
On 2.12.2013, at 22:50, Z K zkauf
05:09 PM, Martin Kavec wrote:
Hi Lilla,
thanks for coming back. Unfortunately I was not able to compile
appropriate boost for my operating system Gentoo linux. Nevertheless I
do not understand why mris_resample misses the library if it should be
statically linked. Other binaries do not need
suggest is that you install the
same version, or one very close to it.
-Zeke
On 12/02/2013 02:50 PM, Martin Kavec wrote:
Hi Zeke,
Thanks for response. Well it was the first thing for me to try to compile
boost on gentoo, which went fine. However the libraries were not compatible
use for our latest release is 1.41.
Lilla
-
Martin Kavec Mon, 04 Nov 2013 14:10:53 -0800
Hi guys,
When running mri_cvs_register on linux (5.3.0), I get into problem with
mris_resample, which cannot find libboost_programs_options.so.5. I
Hi guys,
When running mri_cvs_register on linux (5.3.0), I get into problem with
mris_resample, which cannot find libboost_programs_options.so.5. I installed
the latest version of boost-1.52.0 for my system, but there are unresolved
symbols.
Which version is suitable for mris_resample?
can check out Anastasia Yendiki's excellent
TRACULA tool.
cheers
Bruce
On Thu, 5 Sep 2013, Martin Kavec wrote:
Hi all,
I have two questions:
1. Does tkmedit, or freeview work under VirtualBox
2. Is it possible to parcelate white matter in freesurfer?
Thanks,
Martin
Sent from my
Hi all,
I have two questions:
1. Does tkmedit, or freeview work under VirtualBox
2. Is it possible to parcelate white matter in freesurfer?
Thanks,
Martin
Sent from my iPad
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wmparc.mgz
if you have diffusion data you can check out Anastasia Yendiki's excellent
TRACULA tool.
cheers
Bruce
On Thu, 5 Sep 2013, Martin Kavec wrote:
Hi all,
I have two questions:
1. Does tkmedit, or freeview work under VirtualBox
2. Is it possible to parcelate white matter
Hi all,
Is there a command in Freesurfer, which would return to which label (e.g.
superior frontal white matter left) a coordinate x,y,z belongs to?
Thanks,
Martin
Sent from my iPad
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Hi,
I would like to know what method mri_normalize uses to normalize image
intensities of wm around 110. I do not mean to correct the bias field.
Thanks a lot.
Martin
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Freesurfer@nmr.mgh.harvard.edu
...@nmr.mgh.harvard.edu wrote:
Hi Martin,
Could you give more details? Which version of mri-cvs-register are you using?
Was there a log file that you could share also?
Thanks, Lilla
--Original Message--
From: Martin Kavec
To: Freesurfer mailing list
To: Lilla Zollei
Subject: mri_cvs_register can
Hi all,
I am trying to run mri_cvs_register but for some reasons it always
terminates with:
ERROR: Can not find or read
$SUBJECTS_DIR/MY_SUBJECTS/cvs/combined_tocvs_avg35__elreg_aseg.m3z
My command is as follows:
mri_cvs_register --mov MY_SUBJECT
Indeed the file is not there, but another one
, Nov 4, 2011 at 12:40 PM, lzol...@nmr.mgh.harvard.edu wrote:
Hi Martin,
Could you give more details? Which version of mri-cvs-register are you using?
Was there a log file that you could share also?
Thanks, Lilla
--Original Message--
From: Martin Kavec
To: Freesurfer mailing list
Hi David,
FreeSurfer's binaries for MAC are still 32-bit and apparently cvs
tries to allocate more that is possible. The lines of the error code
below suggest that. I had the same problem and had to opt for x86_64
linux binaries, where the cvs runs fine. It needs ~ 6 GB of memory and
takes ~ 2
Hi all,
I am trying to run mri_cvs_register on MAC distribution o Freesurfer
5.0, but it is failing on surf2vol. Looking into the
$FREESURFER_HOME/bin, surf2vol is completely missing. Could you please
provide this file?
Thanks,
Martin
___
Freesurfer
Hi all,
I wonder if there are any plans to support CUDA on Mac platform. I see there
are libraries available for the platform.
Thanks a lot for feedback,
Martin
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Freesurfer@nmr.mgh.harvard.edu
Hi,
I am trying to run mri_cvs_register between a subject and another set of 10
healthy subjects (all analyzed with FS-5.0.0), but in all cases it fails on:
trying to execute elastic registration - cmd line =
surf2vol -fixed_mri .
error executing surf2vol at
Hi Patricia,
when you convert your labels to volume, they will not be actually the cortical
masks, but rather a line of voxels on the junction of GM and WM, which should
be fine for seeding and targeting the tractography.
Best,
Martin
On Friday 18 June 2010 02:24:52 ox...@yahoo.com wrote:
Hi Patrica,
recently I asked the question about surface tracking on the FSL mailing list
and got an answer that you can track FROM the surface, but not TO surface, in
other words you can not use FS label as a waypoint. The way to go is as Dough
suggest in his followup.
Best,
Martin
On
Hi Dough,
On Monday 17 May 2010 22:29:28 Douglas N Greve wrote:
So is the problem that cortex is 2000 every where including your label
Yes this is the case, but I have already found a way around to get to where I
wanted. mri_label2voi --help has the example which helped me.
Thanks anyway,
Hi,
I have a problem using mri_aparc2aseg with a custom annotations containing
labels created manually in tksurfer and exported.
Basically, I would like to end up with a volume file similar as aparc+aseg.mgz
but containing only a strip of a cortex corresponding to a label defined using
Hi guys,
I am exactly in the same shoes (T1s and T2 FLAIRs), so could you please also
keep me in the club?
Many thanks,
Martin
On Thursday 13 May 2010 02:22:06 Laluz, Victor wrote:
Thank you for the prompt answer, as always Bruce!!
I would be very interested in the techniques for
Hi,
using tksurfer, I have created labels corresponding to significantly thinner
cortex between two groups of my subjects. After that I converted the labels to
volumes (mri_label2vol), which I would like to use for further analysis.
However, the volumes cover only the interface between gray
Hi Jan,
the place to look at is
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach
Best,
Martin
On Tuesday 30 March 2010 12:30:35 Janani Dhinakaran wrote:
Hello everyone,
I wanted to know what I can do to fix this error- it occurs when I'm
running recon-all -all -s Subject
Hi,
in our population of MCI patients, unfortunately parts of the cerebellum were
not completely scanned. I ran the data throught the whole FS-4.5.0 pipeline
and I see that the eTIV normalized volumes of the segmented structues have
very large variance compared to the eTIV normalized group of
Thanks a lot for the opinion, Bruce!
From practical point of view, removing the cerebellum from each subjuct should
be rather easy since I have its segmentation. Howabout the template? Is there
any segmentation of the cerebellum for the template, or I would have to do it
manually? I suppose I
Hi Nick,
could you please also provide us with a INTEL MAC qdec.bin binary?
Many thanks in advance,
Martin
On Wednesday 17 March 2010 21:18:19 Nick Schmansky wrote:
you have a couple options:
1) assuming you are using 64b linux, you can download a new version of
qdec which supports
Hi,
in my group analysis I found a significant difference in correlation of
physiological parameter X and cortical thickness Y1 in an ROI. For each
subject and each cortical parcel I also have a average of parameter Y2 and its
correlation to X (calculated using GLM in SPSS).
Y1 ~ X
Y2 ~ X
My
Hi Jeff,
I see this relatively often. Eventhough the talairach registration is fine, the
ICV is underestimated. In this case I take old ICV, which helps.
mri_segstats --subject $MYSUBJECT --old-etiv-only
This is in 99% of these cases a cure. This is not just a blind attempt. In
these cases I
Hi Shriks,
as far as I can see -cortparc, -cortparc2, -parcstats, and -parcstats2 flags
(and possibly beyond) of the autorecon3 stage do the parcallation. But I am
not sure whether there have been any significant changes between your version
and the current version of the FS, which could
feed it a list of vertex indices to build
circular ROIs about.
It should be available in the 5.0 release of FreeSurfer, but if you'd
like to use it already, send me an email and I can send you a beta version.
Cheers
-=R
Martin Kavec wrote:
:)
thanks. In volume images dilation is usually
Hi Bruce,
if I dilate an arbitrarily shaped label in tksurfer, how much is it actually
dilated?
Thanks,
Martin
On Sat, Nov 7, 2009 at 8:18 PM, Bruce Fischl fis...@nmr.mgh.harvard.eduwrote:
Hi Yigal,
yes, you can select the vertex, make a label out of it, then dilate it
however many times
, 2009 at 8:36 PM, Bruce Fischl fis...@nmr.mgh.harvard.eduwrote:
once every time you click dilate label
On Sat, 7 Nov 2009, Martin Kavec wrote:
Hi Bruce,
if I dilate an arbitrarily shaped label in tksurfer, how much is it
actually
dilated?
Thanks,
Martin
On Sat, Nov 7, 2009 at 8:18 PM
I wonder how log does it ususally take to complete cluster-wise correction for
multiple comparisons using mri_glm-sim. I have a group analysis of 19
subjects with 1 continuous and 1 discrete factor (two levels) and the
mri_glm-sim is running now for about 4 days. Is there any way to track the
Hi,
I would like to study cortical thickness in a cohort of patient with respect
to MMSE and CDR. I prepared a fsgd file where I have both MMSE and CDR
listed:
GroupDescriptorFile 1
Title Mytitle
Class Male
Class Female
Variable Age
Variable MMSE
Variable CDR
Class Ctrl
Class MCI
Input
an effect, I just want to see whether the
atrophy areas correlated with CDR and MMSE differ.
Thanks,
Martin
This will improve both DOF and
efficiency.
doug
Martin Kavec wrote:
Hi,
I would like to study cortical thickness in a cohort of patient with
respect to MMSE and CDR. I prepared
Fatima,
try
rm -rf $FREESURFER_HOME
The command which Pedro gave you assumed that your freesurfer installation
directory was /usr/local/, which may not be the case. If you had freesurfer
correctly installed before, you must have had the $FREESURFER_HOME variable
set correctly. Thus the command
be extremely grateful.
Thank you and kind regards,
Fatima
*From:* freesurfer-boun...@nmr.mgh.harvard.edu [mailto:
freesurfer-boun...@nmr.mgh.harvard.edu] *On Behalf Of *Martin Kavec
*Sent:* 13 August 2009 11:53
*To:* Ahmed, F, Me
*Cc:* Freesurfer Mailing List; Pedro Paulo de Magalhães
Guys,
I am using Philips DICOMs from INTERA and ACHIEVA generation systems without
any problems. So far I have done about 600 analyses. INTERAs are on 11.4
software version and ACHIEVAs went from release 2 up to the current 2.6.1
(and soon release 3)
However the images do not go directly from
Hi Don,
I am in a similar situation. I am on a IBM BladeCenter cluster (though with
one blade only) with 2 Quad core Intels, and I experience intermittent
crashes of mri_volmask as well. Similarly as you, when I run the mri_volmask
on the crashed subject on a desktop, this passes perfectly
Hi Iwo,
you do not say which command exactly you ran. brainmask is created in
the first step of the processing pipeline, so to obtain it you should have
successfully completed the following:
recon-all -autorecon1 -s YOUR_SUBJECT
Best,
Martin
On Thursday 28 May 2009 11:24:27 Iwo Bohr wrote:
Hi Falk,
On Thursday 28 May 2009 11:56:51 Falk Lüsebrink wrote:
Hello,
Im having trouble to generate a correct aseg.mgz for one volume of mine.
The nu_noneck.mgz is also incorrect and therefore I think the -careg stage
of autorecon2 might fail. Is there a way to do some kind quality
Hi,
I am running FS-4.3.0 and after recon-all -all, I am finding in aseg.stats of
quite a few of my subjects that brain mask volume (1735600 mm^3) is greater
than ICV (1701891 mm^3).
The talairach failure detection passed fine: talairach.xfm OK (p=0.7556,
pval=0.6675 = threshold 0.005 ).
The
Hi Nick,
On Tuesday 12 May 2009 15:39:47 Nick Schmansky wrote:
Martin,
That etiv number seems high. Does the -tal-check stage pass? did you
rerun the -segstats stage? that calculates etiv.
The data were first pushed through the whole FS pipeline in 2006. As I look at
the recon-all.log,
:
Hi Martin,
-make all is what we would suggest. Is there any reason the timestamps
would be wrong on your files to make make all rebuild everything?
cheers,
Bruce
On Sun, 10
May 2009, Martin Kavec wrote:
Hi,
I have a bunch of analyzes (about 30), for which recon-all -all
terminates
Hi Bruce,
On Tuesday 12 May 2009 13:28:36 Bruce Fischl wrote:
Hi Martin,
there are probably some files it wants to see early in the stream that
didn't exist in 2006. I think the only cure is to string together the
individual commands you want to run (you can find them in the recon-all
Bruce,
but I am running 4.3.0
Thanks,
Martin
On Tuesday 12 May 2009 14:55:05 Bruce Fischl wrote:
Hi Martin,
I'll leave this for Nick, but we fixed the atlas eTIV calculations in the
new version. Not sure which step you need to rerun though.
Bruce
Hi,
I have a bunch of analyzes (about 30), for which recon-all -all terminates
prematurely at mris_volmask (and core is created). On one case I ran the
mris_volmask and the rest of analysis by executing commands manually, which
went fine, but it's laborious. Is there quicker way to complete
on your files to make make all rebuild everything?
cheers,
Bruce
On Sun, 10
May 2009, Martin Kavec wrote:
Hi,
I have a bunch of analyzes (about 30), for which recon-all -all
terminates prematurely at mris_volmask (and core is created). On one case
I ran the mris_volmask and the rest
Greve wrote:
but you are using aparc+aseg to generate the mask, so if aparc+aseg is
perfect, the mask should be as well. Do the mask and aparc+aseg match?
On Mon, 6 Apr 2009, Martin Kavec wrote:
Doug,
ribbon (aparc+aseg) looks perfect, and corresponds to the surfaces
?h.white.
Thanks
wrote:
This looks like a problem we had with an older version. What version of
freesurfer are you running?
Martin Kavec wrote:
Hi,
I am trying to mask a non-brain tissue left by watershed based on the
cortical surfaces. I found that all what I need to be left is in
aparc+aseg.mgz, so I
orig.mgz -seg ribbon.mgz
aparc+aseg is suppossed to inherit the cortex from ribbon.mgz
doug
On Mon, 6 Apr 2009, Martin Kavec wrote:
Hi Dough,
this data were analyzed using 4.0.4. So indeed it not the latest, which I
am running normally. From which version has this been fixed, so I can
wm from gray
matter. David Salat has thought about this much more than I have, and may
have more to add.
cheers,
Bruce
Thanks a lot,
Martin
On Mon, 12 Jan 2009, Martin Kavec wrote:
Hi,
I have been running quite a few clinical subjects (close to 300) through
FS pipeline
Hi,
For my group analysis I am thinking of reusing a specific set of cortical ROIs
from already published data. I suppose that a target template (fsaverage) and
ROIs itself should be sufficient to have. If I use the same fsaverage for my
cohort, I should be able to get the data out of the ROIs
Hi,
I have been running quite a few clinical subjects (close to 300) through FS
pipeline and comparing cortical thickness from parcellated cortex for each
individual subject to its agematched controls. The subject clinical symptoms
are not specific, ranging from amnesia, reduced ability to
Hi Rysia,
I would look at wm.mgz loaded as auxiliary volume and switch to main volume
frequently to see, whether you have anything in wm.mgz, which needs to be
fixed. There is a tutorial on fixing wm.mgz on the followning web-page:
Hi,
I am trying to run a group analysis on cortical thickness between patients and
controls. In the qdec.dat I set a MMSE for all the controls 0.0. Now,
whenever I try to covariate thickness against age and MMSE, the qdec
complains that there is no spectrum in MMSE values. I tried to set MMSE
Thanks for the replay, Nick!
On Monday 27 October 2008 16:48:26 Nick Schmansky wrote:
Martin,
To answer question 1, the fsaverage surface is used as a target surface
to which the data (ie thickness) of each subject in the group is sampled
and then smoothed, so the accuracy of the recon of
Hello all,
I have started with a group analysis using qdec and have some questions:
1. loading fsaverage into tkmedit along with rh.white and lh.white surprised
me that the pial surfaces do not run under the skull, as I see it on a single
subject but copy the white matter. It is also correct,
Mark,
once I had a similar problem on an autopsied brain, where it was very
difficult to obtain an MPRAGE-like contrast. So instead, I acquired
T2-weighted and inverted it. This gave me contrast very similar to MPRAGE,
though my analysis failed anyway, due to too strong bias field. So you
Mark,
without prior knowledge of what you do, I can just recommend you the recon-all
option -notal-check. You can find out more about it by
running recon-all -help | less.
So your command would look like:
recon-all -autorecon1 -notal-check -s $YOURRAT
Best,
Martin
On Monday 13 October 2008
Christian,
I suspect that in example3-frontal and example2-frontal you have motion
artifacts causing increased intensity in the cortex. On the other,
example1-horizontal and example1-sagittal seem to have pretty low SNR,
specially in GM, but very good GM-WM contrast. I wonder, if they were not
Hi Prapti,
yesterday I had a similar question and went to search the wiki page to educate
myself more, after Bruce responce. The following webpage defines the steps
taken during the options you asks:
http://surfer.nmr.mgh.harvard.edu/fswiki/OtherUsefulFlags
There you can see that your
Greetings to all,
I have several pathological subjects, which need substantial editing involving
removing of dura reminders, filling WM due to the lesions, and adding control
points due to the WM atrophy. I ran recon-all -all first to have initial
reconstruction, which helps me to focus on
Thanks a lot for clarification, Bruce.
Best,
Martin
On Thursday 28 August 2008 22:00:29 Bruce Fischl wrote:
Hi Martin,
I think recon-all -autorecon2-cp -autorecon3 should be fine (it's a
superset of the -wm stuff).
Bruce
On Thu, 28 Aug 2008, Martin Kavec wrote:
Greetings to all,
I
Hi,
On my macbook pro (MAC OS X 10.5) I have recently updated my X to 2.3.0 and
now I can not launch tkmedit:
$ tkmedit $SUBJ brainmask.mgz rh.white -aux-surface lh.white
Converting main surface: 100% done.
Converting main surface: 100% done.
Converting original surface: 100%
is known to work on mac
os 10.5 using the default X setup.
Nick
On Wed, 2008-07-23 at 22:43 +0200, Martin Kavec wrote:
Hi,
On my macbook pro (MAC OS X 10.5) I have recently updated my X to 2.3.0
and now I can not launch tkmedit:
$ tkmedit $SUBJ brainmask.mgz rh.white -aux-surface
Hi,
I would like to rerun recon-all (from the latest freesurfer) on a few cases
from OASIS brains study, to get control values for my patient group. Since my
computational options are rather limitted, I would like to avoid running
redundant steps, which would anyway give me the same results,
On Monday 09 June 2008 21:57:36 Bruce Fischl wrote:
I guess it's possible but the -make switch is designed to prevent this. Are
the surfaces topologically incorrect? What is the euler number for them?
Bruce, this depends on at which point the topology fixing was interrupted. For
this thread I
Hi Maria,
On Monday 09 June 2008 15:00:10 Marie Schaer wrote:
Martin,
Which version of freesurfer did you use to generate the surfaces?
with the latest one, 4.0.4
Because the number of topological defects in your surface (64) is very
high. You may have to relaunch the surfaces (orig and
On Monday 09 June 2008 21:14:35 Michael Harms wrote:
No, I don't have any examples (although we haven't been looking either).
However, Martin's email regarding problems he is encountering on the LGI
computation seems premised on having surfaces with topological problems
even under v4 -- hence
Hi,
I get the following warning followed by error in LGI calculation:
... remeasuring lGI value for vertex iV = 6301. It may take a few minutes.
WARNING -- Problem for vertex iV = 6301, lGI value is aberrantly high
(lGI=48.6447)...
...lGI
Hi folks,
I am scratching my head, how did you guys set the color scheme of the lgi
overlay on:
http://surfer.nmr.mgh.harvard.edu/fswiki/LGI
the image with text Example of lGI overlay on the brain using a colocoded
scale
What I do is I load pial surface and overlay ?h.pial_lgi, but can not
Thanks to all of you for ideas. You may also find interesting to look at:
http://www.wikibooks.org
page on VBM, which has large section of Criticism. The most striking for me is
the inaccuracy of the spatial normalization, which may account for as much as
10.8 mm.
On Thursday 15 May 2008
Gentlemen,
I am giving a lecture about aging brain. I only discuss freesurfer, since
that's the method we use for the brain volume and cortical thickness
assessment. There are other methods, such as VBM and SIENA potentially
providing similar information. I would appreciate if you could point
stats file (can't add it to the one that is
already there).
doug
Martin Kavec wrote:
Hi,
is it possible to obtain LGI values of cortices, similarly as curvature
indices in ?h.aparc.stats? Could this value possibly be included in
the ?h.aparc.stats files?
Thanks in advance,
Martin
/ curv file
Have a nice day,
Marie
On 9 mai 08, at 10:29, Martin Kavec wrote:
Thanks for responce, Dough.
I've looked at recon-all as you suggested, and came up with the
following
commandline:
mris_anatomical_stats -mgz -f
lh.lgi.stats -b -a ../label/lh.aparc.annot -c ../label
Hi,
is it possible to obtain LGI values of cortices, similarly as curvature
indices in ?h.aparc.stats? Could this value possibly be included in
the ?h.aparc.stats files?
Thanks in advance,
Martin
--
**
Senior Clinical Research Associate
MRI Unit of the
Hi Nick,
I am just giving a try to the new mris_compute_lgi matlab script kindly
provided by Marie, and so far so good. I would appreciate the new binary for:
Mac OS X 10.5.2, linux_x86, and linux_x86_64.
Thanks a lot.
Martin
On Thursday 24 April 2008 18:40:12 Nick Schmansky wrote:
Martin
Hi,
I have an emergency here with recon-all -all on a VIP, which segfaults on
mri_ca_label -align -nobigventricles ...I tried to run it from the command
line and left out the -nobigventricles argument, since actually the subject
has enlarged ventricles, but it didn't help.
After running for
Hi Bruce,
On Friday 22 February 2008 16:36:34 Bruce Fischl wrote:
Hi Thomas,
the aseg includes hypointensities, but there's only so much you can do
with only a T1-weighted image. We do have some beta versions that use a
Could i possibly have the betas for testing?
Thanks,
Martin
Hi,
I have upgraded my Mac OS X to 10.5 and after that nu_correct says:
Can't locate MNI/Startup.pm $FREESURFERHOME/mni/bin/nu_correct line 37
Anybody has an idea, what could be wrong? Obviously, the file is there.
Thanks,
Martin
___
Freesurfer
software updates.
Nick
On Fri, 2008-02-01 at 15:29 +0100, Martin Kavec wrote:
Hi,
I have upgraded my Mac OS X to 10.5 and after that nu_correct says:
Can't locate MNI/Startup.pm $FREESURFERHOME/mni/bin/nu_correct line 37
Anybody has an idea, what could be wrong? Obviously, the file
In my experience, the FreeSurfer's brain extraction works better than the
BET. Although, now with an option of iterative BET in the latest FSL, the
outcomes are much better than before. In cases where brain extraction
failed in my analysis, I found that it was the bias field correction which
Very interesting debate you keep here, gentlemen.
I went on and divided FI by the area in one reference and one pathological
subjects (and age matched references). Now it seems that the NewFI is quite
correlated with cortical thickness. It even decreases from the frontal,
through parietal to
Hi,
I can not find my way to map the results of the FSL fMRI group analysis
(FLAME1+2) from different subjects on their average surface. Here is in more
details what I have done:
1. fMRI analysis of each subject in FSL
2. group analysis (FLAME1+2) in FSL
3. cortical reconstruction of each
' am not 100% sure it is in common space, but I would guess it is.
Thanks,
Martin
Martin Kavec wrote:
Hi,
I can not find my way to map the results of the FSL fMRI group analysis
(FLAME1+2) from different subjects on their average surface. Here is in
more details what I have done:
1
Bruce,
it's auditory cortex I am interested in. If there is a tutorial or explanation
somewhere, could you please point me to it. Is this already available in FS?
Thanks
Martin
On Tuesday 13 November 2007 14:38:52 you wrote:
what areas specifically? We have analyzed their data and have a
Hi,
sorry to bring an off topic, but I could not find a solution myself.
I was asked to prepare a short fly-by animation of a ?h.pial for a TV who
interviewed my boss last week. Would you have any recommendation on how to do
that? The ?h.pial is a mesh, which is ideal, because the surface of
Hi folks,
I have been puzzled for a while with the results from couple of my subjects.
They all have clearly visible cerebral atrophy (says neuroradiologist). I ran
them through FS-4.0.1 and aseg.stat gives me, as expected, severe loss of
gray matter (and others as well) as follows:
GM ICV
overall
thickness.
Thanks,
Martin
cheers,
Bruce
On Tue, 16 Oct 2007, Martin Kavec
wrote:
Hi folks,
I have been puzzled for a while with the results from couple of my
subjects. They all have clearly visible cerebral atrophy (says
neuroradiologist). I ran them through FS-4.0.1
Hi,
how can I map the aparc+aseg.mgz back to $SUBJECT_ID/mri/orig/001.mgz, but
without suffering from interpolation?
Thanks,
Martin
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,
Bruce
On Wed, 11 Jul 2007, Martin Kavec wrote:
Hi.
I have few questions regarding the recently published OASIS data analyzed
using Freesurfer:
1. How did you produce $SUBJECT_ID/mri/wmparc.mgz. I am running recon-all
-all on my subjects, but I don't get this file.
2. How did you
. It has been taken down until we
resolve it.
doug
Martin Kavec wrote:
Hi.
I have few questions regarding the recently published OASIS data analyzed
using Freesurfer:
1. How did you produce $SUBJECT_ID/mri/wmparc.mgz. I am running recon-all
-all on my subjects, but I don't get
Hi,
I was wondaring, what is the situation with OASIS data? Could you please share
with us, in which form you will make the results of your great effort
available?
Thanks in advance for the great job (and reply of course).
Martin
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