/fsl_label2voxel
Eiran
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Markus Gschwind
[markus.gschw...@gmail.com]
Sent: Thursday, April 03, 2014 3:43 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] preprocessing question
Hi Eiran and
s!
> Eiran
>
> From: freesurfer-boun...@nmr.mgh.harvard.edu [
> freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [
> gr...@nmr.mgh.harvard.edu]
> Sent: Wednesday, April 02, 2014 5:21 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] prepro
[gr...@nmr.mgh.harvard.edu]
Sent: Wednesday, April 02, 2014 5:21 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] preprocessing question
a couple of thiings to check: make sure it is exectuable and make sure
that you rehash your path. Make sure that if you type fslmaths.fsl that
it runs somethin
> From: freesurfer-boun...@nmr.mgh.harvard.edu
>> <mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
>> [freesurfer-boun...@nmr.mgh.harvard.edu
>> <mailto:freesurfer-boun...@nmr.mgh.harvard.edu>] on behalf of
>> Douglas N Greve [gr...@nmr.mgh.harvard.ed
@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] preprocessing question
thanks, it must be something in our distribution script affecting mac
On 04/01/2014 05:13 PM, Markus Gschwind wrote:
> Thanks Doug,
>
> I notice that on my Mac
> build freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0
&g
<mailto:gr...@nmr.mgh.harvard.edu>]
> > Sent: Tuesday, April 01, 2014 7:16 PM
> > To: freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>
> > Subject: Re: [Freesurfer] preprocessing question
> >
> > does $FREESURFER_HOME/
u [
> freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [
> gr...@nmr.mgh.harvard.edu]
> > Sent: Tuesday, April 01, 2014 7:16 PM
> > To: freesurfer@nmr.mgh.harvard.edu
> > Subject: Re: [Freesurfer] preprocessing question
> >
> > does $FREESURFER
ouglas N Greve
>> [gr...@nmr.mgh.harvard.edu]
>> Sent: Tuesday, April 01, 2014 7:16 PM
>> To: freesurfer@nmr.mgh.harvard.edu
>> Subject: Re: [Freesurfer] preprocessing question
>>
>> does $FREESURFER_HOME/bin/fslmaths.fsl exist?
>>
>> On 04/01/2014
-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve
[gr...@nmr.mgh.harvard.edu]
Sent: Tuesday, April 01, 2014 7:36 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] preprocessing question
That is weird. You can get a copy from here
rd.edu
> Subject: Re: [Freesurfer] preprocessing question
>
> does $FREESURFER_HOME/bin/fslmaths.fsl exist?
>
> On 04/01/2014 03:59 AM, Eiran Harel wrote:
>> Dear freesurfers,
>> I have installed freesurfer and fsl on my Mac:
>> *
>> *
>> * freesurfer-Darw
: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] preprocessing question
does $FREESURFER_HOME/bin/fslmaths.fsl exist?
On 04/01/2014 03:59 AM, Eiran Harel wrote:
>
> Dear freesurfers,
> I have installed freesurfer and fsl on my Mac:
> *
> *
> * freesurfer-Darwin-snowl
does $FREESURFER_HOME/bin/fslmaths.fsl exist?
On 04/01/2014 03:59 AM, Eiran Harel wrote:
>
> Dear freesurfers,
> I have installed freesurfer and fsl on my Mac:
> *
> *
> * freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0 *
> *Setting up environment for FreeSurfer/FS-FAST (and
list
Subject: Re: [Freesurfer] preprocessing question
Well, Eiran,
That seems all fine.
Maybe Bruce or Doug can jump in and help?
Sorry!
Markus
2014-04-01 15:25 GMT+02:00 Eiran Harel
mailto:eir...@tlvmc.gov.il>>:
Hi Markus,
[Eran-Harels-MacBook-Pro:/Applications/freesurfer/BSMT_P
urfer-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 4:40 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] preprocessing question
Well, Eiran,
That seems all fine.
Maybe Bruce or
.@gmail.com]
> *Sent:* Tuesday, April 01, 2014 2:48 PM
>
> *To:* Freesurfer support list
> *Subject:* Re: [Freesurfer] preprocessing question
>
> Hi,
>
> Although there are matlab utils as part of FSL in $FSL_DIR/etc/matlab that
> can be used in FSL, I think it is not n
-boun...@nmr.mgh.harvard.edu] on behalf of Markus Gschwind
[markus.gschw...@gmail.com]
Sent: Tuesday, April 01, 2014 2:48 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] preprocessing question
Hi,
Although there are matlab utils as part of FSL in $FSL_DIR/etc/matlab that can
be used in
;
> *To:* Freesurfer support list
> *Subject:* Re: [Freesurfer] preprocessing question
>
> Hi,
> what does it say when you type
> which fsl
> which fslmath
> ?
>
> It mud be the same thing as
> FSL_DIR /usr/local/fsl
>
> It is possible that
PM
To: Freesurfer support list
Subject: Re: [Freesurfer] preprocessing question
Hi,
what does it say when you type
which fsl
which fslmath
?
It mud be the same thing as
FSL_DIR /usr/local/fsl
It is possible that the FSL_DIR specified in the freesurfersetup is not the
good one…
Best,
M
of Markus Gschwind [
> markus.gschw...@gmail.com]
> *Sent:* Tuesday, April 01, 2014 11:11 AM
> *To:* Freesurfer support list
> *Subject:* Re: [Freesurfer] preprocessing question
>
> Hi!
>
> Have you installed FSL? (http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/)
> What happens
[markus.gschw...@gmail.com]
Sent: Tuesday, April 01, 2014 11:11 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] preprocessing question
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
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
Dear freesurfers,
I have installed freesurfer and fsl on my Mac:
freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME /Applications/freesurfer
FSFAST_HOME /Applications/freesurfer/fsfast
FSF_OUTPUT_F
Do you mean the matrix? You can get a freesurfer matrix with this:
cd subject/mri
tkregister2 --mov orig/001.mgz --s subject --regheader --reg reg.dat
--noedit
this will produce reg.dat which will be a text file with a
registration matrix. Interpreting the matrix is another story. If you
wan
Hi Frederick,
mri_info will give you the various transformations back to native (i.e.
scanner) RAS coords.
cheers,
Bruce
On Tue, 29 Aug 2006, Frederick Klauschen wrote:
Could you tell me the transformation vector that is
used to convert a e.g.(181x217x181) array to a FS
(256^3) array.
I woul
Could you tell me the transformation vector that is
used to convert a e.g.(181x217x181) array to a FS
(256^3) array.
I would like to backtransform from FS to native space.
Thanks,
Fred
--- Doug Greve <[EMAIL PROTECTED]> wrote:
>
> Which way do you want to go? Convert FS volumes back
> into the
Which way do you want to go? Convert FS volumes back into the native
space or the other way around?
To convert native space vols into FS, run something like:
tkregister2 --s subjectname --mov mri/orig/001.mgz --regheader --reg reg.dat
This will bring up both the conformed and nonconf volumes
Hi, I have a few datasets I ran in freesurfer that were originally in
181x217x181 format. As usual, these were converted to 256^3 early in the
process. Basically, I'd like to run some comparison stats between the
freesurfer volumes and the same subjects run in a couple other programs
(that are stil
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