would have no way of knowing if they are changes in the brain or changes in
> the instrument used to measure the brain.
>
> a.y
> --
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Ma
External Email - Use Caution
Dear experts,
I am reviewing a study that proposes a longitudinal study in patients
across several years on the effect of medical treatment in terms of fcMRI
and DTI-connectivity measures.
However, in several but not all patients, the scanner was upgr
External Email - Use Caution
On Tue, May 29, 2018, 20:16 Avi Gharehgazlou wrote:
> External Email - Use Caution
>
> Hello experts,
>
> I am using QDEC to compared LGI values between groups (typically develping
> and ASD). I made a "diagnosis.levels" file, putting my 2 gro
External Email - Use Caution
Ûghrf7f77f7f7ef
On Thu, May 3, 2018, 19:32 Matthew Grecsek wrote:
> External Email - Use Caution
>
> I'm using the following flags on my recon -all: -mprage -time -multistrip
> -subcortseg
>
> and getting the following errors at this section
>
> Hi Markus, okay - I'll directly send you a tar of the vtk library. A
> reinstall of vtk might work, because those shared objects that we
> distribute are usually sym-linked
>
> Can you also send the fs buildstamp? You can get this by running the
> command ‘bugr’ after so
usually sym-linked
>
> Can you also send the fs buildstamp? You can get this by running the
> command ‘bugr’ after sourcing freesurfer
>
> Andrew
>
>
> On Sep 19, 2017, at 11:02 AM, Markus Gschwind
> wrote:
>
> Dear Andrew,
>
> after the System admin executed your
5.6
>
> then do you get the same error from freeview?
>
> -Andrew
>
> On Sep 15, 2017, at 12:10 PM, Markus Gschwind
> wrote:
>
> Dear Andrew,
>
> The command gives this result:
>
> [gschwind@login1 ~]$ /sbin/ldconfig -N -v $(sed 's/:/ /' <<<
&g
t;
> -Andrew
>
>> On Sep 15, 2017, at 12:10 PM, Markus Gschwind > <mailto:markus.gschw...@gmail.com>> wrote:
>>
>> Dear Andrew,
>>
>> The command gives this result:
>>
>> [gschwind@login1 ~]$ /sbin/ldconfig -N -v $(sed 's/:/ /&#
is not a symbolic link
> /sbin/ldconfig:
> /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkVolumeRenderingTCL.so.5.6
> is not a symbolic link
> /sbin/ldconfig:
> /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libMapReduceMPI.so.5.6
>
Dear experts,
I am installing freeusrfer on our cluster which is running Centos6.
[gschwind@login1 ~]$ uname -a
Linux login1.cluster 2.6.32-696.1.1.el6.x86_64 #1 SMP Tue Apr 11 17:13:24
UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
Freeview aborts without any other complaint.
[gschwind@login1 ~]$ fr
Hi experts,
I am installing freeusrfer on our cluster which is running Centos6.
[gschwind@login1 ~]$ uname -a
Linux login1.cluster 2.6.32-696.1.1.el6.x86_64 #1 SMP Tue Apr 11 17:13:24
UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
Freeview aborts without any other complaint.
[gschwind@login1 ~]$ free
HI,
Please see the solution for this known error below, as given in this list
form Zeke some months ago:
Good luck, Markus
2015-09-22 6:05 GMT+02:00 :
> Hello,
>
> This is a known when running freesurfer on Ubuntu systems. The solution is
> addressed in the FAQ section on the frresurfer download
Hi Isabel,
open a terminal and type:
cd /Applications/freesurfer
sudo mv license.txt .license
That's it.
Best,
M
2015-06-17 22:19 GMT+02:00 isabel martinez tejada <
isa_martinez...@hotmail.com>:
> I cannot put a "." in the file name because Mac doesn't allow it. It says
> that a file that st
MT+02:00 Markus Gschwind :
> Hi Martin!
>
> Thanks!
> Yes, indeed typing in the command
> export SUBJECTS_DIR= before starting qdec solved the first
> problem... there are others to follow...
>
> When now writing the table stats file:
>
> Data table loading complete
he case, try setting the subject dir on the command line before starting
> qdec:
> setenv SUBJECTS_DIR ~/Documents/ARNAUD/
> (or the full path). If you use a bash shell, use the equivalent export
> command for that.
>
> Best, Martin
>
>
> On 09/12/2014 03:30 PM, Marku
Dear all,
I am trying to make work Qdec on my system ubuntu 12.04.
freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0
After I have loaded my qdec.table.dat and renamed the analysis folder ,
when I then try to create the "stats tables", I get an error and it blocks
at 20% of the waiting bar.
Dat
Hi Barbara,
You haven't told us which OS you use.
For example in Mac OS it is necessary to start up MATLAB by typing matlab
into the X11 terminal, otherwise the system OS will not recognize the
commands given via matlab (e.g. system('mycommand') .)
Best,
Markus
2014-09-09 13:45 GMT+02:00 Barbara
Hi!
You probably mean
mris_expand
which creates a surf inside or outside of white, e.g.
mris_expand surf/lh.white -1 surf/lh.white_1mm_inside
# use positive values for outside ?h.white border
mris_expand -thickness surf/lh.white -1 surf/lh.white_in100%_thickness
# this samples in % of GM thick
Hi,
You can see here what to do:
https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall
no 4., 5 and 6 especailly.
Cheers,
M
2014-06-18 0:45 GMT+02:00 Sam Raby :
> I have downloaded the following file
>
> freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz
>
> and have extracted the
ames in 5.4 seconds = 63.223 FPS
> 374 frames in 6.3 seconds = 58.905 FPS
>
> Best,
> Vy
>
>
> On Tue, Jun 3, 2014 at 4:27 PM, Markus Gschwind > wrote:
>
>> Hi!
>>
>> Can the connection be slow?
>>
>> Can you type in your local terminal and
Hi!
Can the connection be slow?
Can you type in your local terminal and also in the ssh remote terminal the
following:
glxgears
and let it run a while and past here the output.
Cheers!
Markus
2014-06-03 23:16 GMT+02:00 Vy Dinh :
> Hi,
>
> I discovered that installing Freesurfer onto my loca
ainmask.gcuts.T-0.5.mgz
>
> Carefully inspect the output, overlaid as a heatmap on the T1 and/or
> previous brainmask.mgz. You might have to clone back in some brain voxels.
>
> -Louis
>
>
> On Fri, 11 Apr 2014, Markus Gschwind wrote:
>
> Dear Louis (and Bruce),
>>
;> It will only skullstrip the T1 and generate a new brainmask.mgz. So
>> you'll need to run autorecon2 and 3 afterwards.
>> -Louis
>>
>>
>> On Mon, 7 Apr 2014, Markus Gschwind wrote:
>>
>> Dear Louis!
>>> Thank you for the link.
>>>
Thank you Zeke, that seems to work all fine!
Best, Markus
2014-04-08 21:17 GMT+02:00 Z K :
> Markus,
>
> Thanks for pointing that out. I have added those files to the ftp link.
>
> -Zeke
>
>
> On 04/04/2014 04:16 PM, Markus Gschwind wrote:
>
>> Thank you Zeke,
&
Great, thanks! I'll give it a try!
Best, Markus
2014-04-07 22:40 GMT+02:00 Louis Nicholas Vinke :
> Hi Markus,
> It will only skullstrip the T1 and generate a new brainmask.mgz. So you'll
> need to run autorecon2 and 3 afterwards.
> -Louis
>
>
> On Mon, 7
it. Does the intensity normalization remove the contrast?
>> If so, you can try making it less aggressive with the -gentle flag or
>> playing with individual parameters (like -b).
>>
>> I can't remember the graph cuts stuff. Hopefully Nick or Zeke or someone
>
rom the OSX snow leopard installation.
> They can be downloaded from here:
>
> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/fsdev/zkaufman/fsl
>
> Copy them into your "$FREESURFER_HOME/bin" directory.
>
> -Zeke
>
>
>
> On 04/04/2014 12:32 PM, Markus Gs
Dear Freesurfers,
As discovered here,
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg35160.html
it seams that some Mac OSX installations suffered from incomplete files.
I just veryfied that I had downloaded the complete image and wget says yes:
Logging in as anonymous ... Logged
Hi Ruthger!
Use mris_expand to create a surf inside or outside of white
e.g.
mris_expand surf/lh.white -1 surf/lh.white_1mm_inside
# use positive values for outside ?h.white border
mris_expand -thickness surf/lh.white -1 surf/lh.white_in100%_thickness
# this samples in % of GM thickness, use po
reve [
> gr...@nmr.mgh.harvard.edu]
> > Sent: Wednesday, April 02, 2014 12:41 AM
> > To: freesurfer@nmr.mgh.harvard.edu
> > Subject: Re: [Freesurfer] preprocessing question
> >
> > thanks, it must be something in our distribution script affecting mac
> >
>
Thanks Doug,
I notice that on my Mac
build freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0
...I don't have fslmaths.fsl neither. There are only
$ which $FREESURFER_HOME/bin/fsl*
> /Applications/freesurfer/bin/fsl_label2voxel
> /Applications/freesurfer/bin/fsl_rigid_register
> /Applications/
Harels-MacBook-Pro:/Applications/freesurfer/BSMT_PROJECT] eiran%
> echo $FSLDIR
> /usr/local/fsl
>
> Thanks!
> Eiran
>
>
>
>
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu [
> freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Markus Gschwind [
> markus.gschw..
/usr/local/fsl.
> Is MATLAB necessary to run FSL?
> EIran
>
>
>
>
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu [
> freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Markus Gschwind [
> markus.gschw...@gmail.com]
> *Sent:* Tuesday, April 01, 2014 12:55 PM
>
nks, i did install fsl and when i type fslmaths it gives me the help
> for that command.
> Any other suggestions?
> Eiran
> --
>
>
>
>
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu [
> freesurfer-boun...@nmr.mgh.harvard.edu] on behalf
Hi!
Have you installed FSL? (http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/)
What happens if you type in your terminal
fslmaths
?
Best,
Markus
2014-04-01 9:59 GMT+02:00 Eiran Harel :
>Dear freesurfers,
> I have installed freesurfer and fsl on my Mac:
>
> * freesurfer-Darwin-snowleopard-i686
; $ mris_expand surf/lh.white -1 surf/lh.white_inner1mmWM
> expanding surface surf/lh.white by -1.0 mm and writing it to
> surf/lh.white_inner1mmWM
Thanks again!
2014-03-27 13:29 GMT+01:00 Bruce Fischl :
> Hi Markus
>
> use mris_expand.
>
> cheers
> Bruce
>
&g
you!
Markus
2014-03-26 15:36 GMT+01:00 Douglas Greve :
>
> On 3/26/14 8:24 AM, Markus Gschwind wrote:
>
> Dear Doug and Bruce,
>
> I have three more questions concerning 'pctsurfcon'.
>
> 1) The inner sampling distance is set to 1mm by default, but the outer
&g
y this
has been chosen like this. What was the rationale?
2) I think it is possible to run glmfit on the ?h.w-g.pct.mgh file in order
to get some group stats, right?
3) Is it also possibe to run the xhemi on the w-g.pct.mgh file?
Thank you so much!
Markus
2014-03-24 23:51 GMT+01:00 Markus Gschwind
gt; On 03/24/2014 06:18 PM, Bruce Fischl wrote:
> > it really depends on the size of the abnormality. I would guess 2 is
> > too big, and you want something more like 1, and sampling not averaging
> > On Mon, 24 Mar 2014, Markus Gschwind wrote:
> >
> >> Hi Bruce!
&
t; just inside of it
>
>
> cheers
> Bruce
>
>
> On Mon, 24 Mar 2014, Markus Gschwind wrote:
>
> Dear Bruce,
>> Thanks for the rapid answer!
>>
>> Do you mean that I take the voxel values of brainmask.mgz at the place
>> where
>> the ?h.white sur
e would be more informative
>
> cheers
> Bruce
>
> On Mon, 24 Mar 2014, Markus Gschwind wrote:
>
> Dear all,
>> I would like to capture regions where the gray matter/ white matter
>> junction is blurred in order to detect possible focal
>> cortical dysplasias.
&
Dear all,
I would like to capture regions where the gray matter/ white matter
junction is blurred in order to detect possible focal cortical dysplasias.
As I understood the WM/GM segmentation is done by the script mri_segment.
Would it be possible detect those regions where the gradient between
Hi,
Can you send us a screenshot of the original MRI before skull stripping?
Thanks!
Markus
On 20 mars 2014, at 14:46, Saurabh Thakur wrote:
> Hello Freesurfer expert ,
>
> I am sending you the image of brain.mgz screen-shot.
>
> Is the area highlighted is part of cortex or it is due to skul
Ah! Bright!
Thanks Doug!
2014-03-13 17:20 GMT+01:00 Douglas N Greve :
> Just create a symlink, ie,
>
> cd $SUBJECTS_DIR
> ln -s $FREESURFER_HOME/fsaverage_sym
>
>
>
>
> On 03/13/2014 09:57 AM, Markus Gschwind wrote:
> > Dear all,
> >
> > I hav
Dear all,
I have a question concerning the xhemi commands as explained here:
http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi
2. The command
surfreg --s $subject --t fsaverage_sym --lh
is absolutely searching for fsaverage_sym in the $SUBJECTS_DIR.
Do I really have to copy the whole fsaverage
ey are calibrated, but you
> have to try and see.
>
> cheers
> Bruce
>
> On Wed, 12 Mar 2014, Markus Gschwind wrote:
>
> Dear all,
>> I am planning to create a "local cortical thickness normal template" in
>> order to test single patients against it.
&
Dear all,
I am planning to create a "local cortical thickness normal template" in
order to test single patients against it.
For that purpose I was planning to use 50-100 MPRAGE scans of healthy
subjects (balanced for age range and sex).
My question is, if I should worry about the scanner where t
Hi!
Can you specify what happens when you try to read the files?
On 4 mars 2014, at 06:44, Saurabh Thakur wrote:
> Hello Freesurfer,
>
> I am trying to runs MRIread.m file in matlab.
>
> But it is not reading the brain.mgz or any other format.
>
> Can u help in this regards.
>
> Thanks
ut freeview crashes when I try to look at it...
Actually I have no clue what the output_type should be...
Thanks so much!
Markus
2014-02-03 Bruce Fischl :
> Hi Markus
>
> the --s option should be a subject name, not a path to a volume
>
> cheers
> Bruce
>
> On Mon, 3 Fe
Hi again,
It is certainly a beginners question, and probably the code examples given
below are not right...
Is there anyone that could advice me how to do this?
Thanks so much!
Markus
2014-02-01 Markus Gschwind :
> Dear all,
>
> I want to create a surface of a partially altered
Dear all,
I want to create a surface of a partially altered brain T1 (temporal lobe
cut away by hand).
I figured out that this would be done with mri_vol2surf.
This command asks for a register.dat file.
I think that I can get it using this command:
SUBJECT_DIR=/Users/FREESURFER
bbregister --s
Dear Experts,
I have installed Freesurfer 5.3 under ubuntu 12.04.
It is running fine except for Freeview which is causing heavy graphic
trouble (thousands of colored squares in the black fields where the brains
should be displayed.
Tksurfer is working fine.
Glxgears is showing the rotating blue
popups
> up displaying turning gears, or perhaps an error message is displayed?
>
> -Zeke
>
> On 01/28/2014 03:40 AM, Markus Gschwind wrote:
> > Dear all,
> >
> > For the error
> >
> > freeview.bin: error while loading shared libraries: libjpeg.so.6
*libGL error: Try again with LIBGL_DEBUG=verbose for more details.*
Any ideas?
Thank you in advance!
Markus
2014/1/27 Markus Gschwind
> Dear experts!
>
> I installed freesurfer on a machine running Ubuntu 12.04.
>
> I have got some error messages when testing:
>
> ~$ freevie
Dear experts!
I installed freesurfer on a machine running Ubuntu 12.04.
I have got some error messages when testing:
~$ freeview -v $SUBJECTS_DIR/bert/mri/norm.mgz -v
$SUBJECTS_DIR/bert/mri/aseg.mgz:colormap=lut:opacity=0.2 -f
$SUBJECTS_DIR/bert/surf/lh.white:edgecolor=yellow -f
$SUBJECTS_DIR/be
ch file or directory
CTABfindAnnotation: ct was NULL
No such file or directory
CTABfindAnnotation: ct was NULL
No such file or directory
What does this error mean, at all?
Thank you and please excuse my insisting!
Markus
2013/12/14 Markus Gschwind
> Thank you Bruce,
>
> I read that mris_sam
you have in /Documents/myROIfile.mgz
>
> cheers
> Bruce
>
>
> On Sat, 14 Dec 2013, Markus Gschwind wrote:
>
> Dear Bruce,
>> Thank you for your answer. I have not yet gotten it correctly.
>>
>> 1) Where does that file come from? Should I create it? how?
>&
notations into colors to display and human
> reasable names.
>
> cheers
> Bruce
>
> On Fri, 13 Dec 2013, Markus Gschwind wrote:
>
> I can precise the question, actually there are three:
>>
>> 1) ist the command correct?
>>
>> mris_sample_parc
I can precise the question, actually there are three:
1) ist the command correct?
mris_sample_parc -v -sdir subject001 rh ~/Documents/myROIfile.mgz
> rh.myROIfile.annot
>
2) I do not understand the meaning of this claimed file
cma_parcellation_colors.txt
Actually this does not exist. In the Wik
Dear all,
I am trying to create a annotation file from a ROI_file with multiple ROIs
with values form 1:10 using mris_sample_parc
I had verified that myROIfile and subject001/surf/rh.white and also
mri/T1.mgz loadable together in freeview (=same space).
when running the command
mris_sample_parc
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