Re: [Freesurfer] preprocessing question

2014-04-03 Thread Eiran Harel
...@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

Re: [Freesurfer] preprocessing question

2014-04-03 Thread Markus Gschwind
...@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

Re: [Freesurfer] preprocessing question

2014-04-03 Thread Eiran Harel
/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

Re: [Freesurfer] preprocessing question

2014-04-02 Thread Eiran Harel
@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

Re: [Freesurfer] preprocessing question

2014-04-02 Thread Douglas N Greve
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

[Freesurfer] preprocessing question

2014-04-01 Thread Eiran Harel
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

Re: [Freesurfer] preprocessing question

2014-04-01 Thread Markus Gschwind
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

2014-04-01 Thread Markus Gschwind
:* 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

Re: [Freesurfer] preprocessing question

2014-04-01 Thread Eiran Harel
-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

Re: [Freesurfer] preprocessing question

2014-04-01 Thread Markus Gschwind
*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

Re: [Freesurfer] preprocessing question

2014-04-01 Thread Bruce Fischl
-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

Re: [Freesurfer] preprocessing question

2014-04-01 Thread Eiran Harel
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

Re: [Freesurfer] preprocessing question

2014-04-01 Thread Eiran Harel
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

Re: [Freesurfer] preprocessing question

2014-04-01 Thread Douglas N Greve
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

Re: [Freesurfer] preprocessing question

2014-04-01 Thread Eiran Harel
...@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

Re: [Freesurfer] preprocessing question

2014-04-01 Thread Douglas N Greve
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

Re: [Freesurfer] preprocessing question

2014-04-01 Thread Markus Gschwind
: 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

Re: [Freesurfer] preprocessing question

2014-04-01 Thread Douglas N Greve
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

Re: [Freesurfer] preprocessing question

2006-08-30 Thread Doug Greve
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

Re: [Freesurfer] preprocessing question

2006-08-29 Thread Frederick Klauschen
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

Re: [Freesurfer] preprocessing question

2006-08-29 Thread Bruce Fischl
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

[Freesurfer] preprocessing question

2006-08-25 Thread Goldman, Aaron (NIH/NIMH) [C]
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