...@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 something
...@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] preprocessing question
a couple of thiings to check: make sure it is exectuable and make sure
that you rehash
/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
@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
...I don't have
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 12:41 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] preprocessing question
thanks
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
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 eir...@tlvmc.gov.il:
Dear freesurfers,
I have installed freesurfer and fsl on my Mac:
*
:* 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,
Markus
2014-04-01 10:25
-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
*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 necessary to have matlab working for
FSL to work.
There are many more matlab utils
-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 Doug
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
eir...@tlvmc.gov.ilmailto:eir...@tlvmc.gov.il:
Hi Markus,
[Eran-Harels-MacBook-Pro:/Applications/freesurfer
To: 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-snowleopard-i686-stable-pub
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: Tuesday, April 01, 2014 7:16 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] preprocessing
...@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
ftp
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: Tuesday, April 01, 2014 7:36 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] preprocessing question
: 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 03:59 AM, Eiran Harel wrote:
Dear freesurfers,
I have installed freesurfer and fsl on my Mac
of
Douglas N Greve [gr...@nmr.mgh.harvard.edu
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/bin
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
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
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
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
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