You just found a very strange bug. I've fixed it in the version here:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/fsl_rigid_register
If you want to know about the bug, read on!
If you run fsl_rigid_register with -help, it will give you some help
information. As it turns out, it looks for the string "help" anywhere on
the cmd line. So, when it saw "phelpslab", it assumed you wanted help!
I've changed it (and a few others:). to make sure that it looks for
-help and not just help. So don't make a directory called p-helps-lab
doug
Catherine Hartley wrote:
Hi,
I'm trying to run mri_motion_correct.fsl to generate the rawavg.mgz file,
and it's failing somewhere before the process completes. I can't seem to
figure out from reading the log file just what is going wrong. Any insight
would be much appreciated!
Thanks
------
mri_motion_correct.fsl log file
$Id: mri_motion_correct.fsl,v 1.4 2006/01/01 21:56:44 greve Exp $
/Applications/freesurfer/bin//mri_motion_correct.fsl
/Volumes/phelpslab/Cate/extinction/AS083182
Darwin saks.psych.nyu.edu 8.9.1 Darwin Kernel Version 8.9.1: Thu Feb 22
20:55:00 PST 2007; root:xnu-792.18.15~1/RELEASE_I386 i386 i386
Mon Jun 11 18:33:21 EDT 2007
/Applications/freesurfer/bin//mri_convert
/Applications/freesurfer/fsl/bin/flirt
-----------------------------------------
Converting mri/orig/002.mgz
Mon Jun 11 18:33:23 EDT 2007
/Volumes/phelpslab/Cate/extinction/AS083182
mri_convert mri/orig/002.mgz
/Volumes/phelpslab/Cate/extinction/AS083182/tmp-mri_motion_correct.fsl-12111
/cor-1.img -odt float
mri_convert mri/orig/002.mgz
/Volumes/phelpslab/Cate/extinction/AS083182/tmp-mri_motion_correct.fsl-12111
/cor-1.img -odt float
reading from mri/orig/002.mgz...
TR=2500.00, TE=4.38, TI=900.00, flip angle=8.00
i_ras = (-0, -1, 0)
j_ras = (-0, -0, -1)
k_ras = (-1, 0, 0)
changing data type from 4 to 3 (noscale = 0)...
writing to
/Volumes/phelpslab/Cate/extinction/AS083182/tmp-mri_motion_correct.fsl-12111
/cor-1.img...
Analyze Output Matrix
-0.000 -0.000 -1.000 80.325;
-1.000 -0.000 0.000 129.500;
0.000 -1.000 0.000 128.777;
0.000 0.000 0.000 1.000;
--------------------
INFO: set hdr.hist.orient to -1
-----------------------------------------
Converting mri/orig/003.mgz
Mon Jun 11 18:33:26 EDT 2007
/Volumes/phelpslab/Cate/extinction/AS083182
mri_convert mri/orig/003.mgz
/Volumes/phelpslab/Cate/extinction/AS083182/tmp-mri_motion_correct.fsl-12111
/cor-2.img -odt float
mri_convert mri/orig/003.mgz
/Volumes/phelpslab/Cate/extinction/AS083182/tmp-mri_motion_correct.fsl-12111
/cor-2.img -odt float
reading from mri/orig/003.mgz...
TR=2500.00, TE=4.38, TI=900.00, flip angle=8.00
i_ras = (-0, -1, 0)
j_ras = (-0, -0, -1)
k_ras = (-1, 0, 0)
changing data type from 4 to 3 (noscale = 0)...
writing to
/Volumes/phelpslab/Cate/extinction/AS083182/tmp-mri_motion_correct.fsl-12111
/cor-2.img...
Analyze Output Matrix
-0.000 -0.000 -1.000 89.000;
-1.000 -0.000 0.000 126.608;
0.000 -1.000 0.000 129.500;
0.000 0.000 0.000 1.000;
--------------------
INFO: set hdr.hist.orient to -1
-----------------------------------------
Motion Correcting
/Volumes/phelpslab/Cate/extinction/AS083182/tmp-mri_motion_correct.fsl-12111
/cor-2.img
Mon Jun 11 18:33:28 EDT 2007
/Volumes/phelpslab/Cate/extinction/AS083182
fsl_rigid_register -maxangle 90 -r
/Volumes/phelpslab/Cate/extinction/AS083182/tmp-mri_motion_correct.fsl-12111
/cor-1.img -i
/Volumes/phelpslab/Cate/extinction/AS083182/tmp-mri_motion_correct.fsl-12111
/cor-2.img -o
/Volumes/phelpslab/Cate/extinction/AS083182/tmp-mri_motion_correct.fsl-12111
/resampled.img -tmpdir
/Volumes/phelpslab/Cate/extinction/AS083182/tmp-mri_motion_correct.fsl-12111
-cleanup
USAGE: fsl_rigid_register
Required Arguments:
-r refvol : reference/target volume
-i inputvol : input/moveable volume
-o outputvol : input resampled to reference
Optional Arguments
-fslmat fsmatfile : spec explicitly
-regmat regmatfile : get reg matrix as register.dat file
-xfmmat xfmmatfile : get reg matrix as MNI xfm file
-ltamat ltamatfile : get reg matrix as MGH lta file
-noinitgeom : do not initialize matrix based on geometry
-initxfm xfmfile : use this as an initial matrix
-applyxfm xfmfile : do not reg, just apply xfm to input
-maxangle maxangle : only search over +/- maxangle degrees
-interp method : <trilinear>, nearestneighbour, sinc
-dof dof : use dof instead of 6
-bins bins : number of bins to use (default 256)
-cost cost : objective function (default corratio)
valid costs are mutualinfo corratio normcorr normmi leastsq
-tmp tmpdir (default is ). Implies -nocleanup
-tmpdir tmpdir : same as -tmp
-nocleanup : do not delete temporary files
-cleanup : delete temporary files (default)
-version : print version and exit
-help : print help and exit
This is a front-end for the FSL (www.fmrib.ox.ac.uk/fsl/index.html)
flirt program. Computes the registration matrix that transforms
inputvol to refvol and resamples inputvol to outputvol using that
matrix. The matrix is stored in outputvol.fslmat. The registration is
constrained to be rigid (ie, 6 dof). The input and ref volumes are
automatically converted to analyze, and the output volume is
automatically converted from analyze to the output format. Note: if
using COR as output, the COR directory must exist prior to running
this script. The FLIRT/FSL registration matrix will be stored in
outvol.fslmat (unless -fslmat).
By default, an init FSL registration matrix is computed from the
geometry information in the header ref and input headers. This is a
good idea because the anlyze format does not keep the direction cosine
info around.
-fslmat fslmatfile
Store the FSL registration matrix in fslmatfile instead of outvol.fslmat
-regmat regmatfile
Convert the FSL matrix to register.dat format and save in regmatfile. You
will have to edit the subject name.
-ltamat ltamatfile
Convert the FSL matrix to an MGH lta file.
-noinitgeom
Do not compute init registration matrix from geometry.
-initxfm fslmatfile
Use matrix in fslmatfile as the initial registation matrix. If no
initialization is specified, the identity is assumed. Forces
-noinitgeom.
-maxangle maxangle
Search only +/- maxangle degrees around the initial starting
point. Default is 90.
-applyxfm
When the -applyxfm flag is is used, the input is resampled to the
output using the FSL mat file supplied as the argument to the
-applyxfm. The ref volume is still needed in order to get the proper
geometry for the output file. Forces -noinitgeom.
-dof dof
Non-rigid registration can be performed by changing the dof from 6.
BUGS:
If using COR as output, the COR directory must exist prior to running
this script.
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
--
Douglas N. Greve, Ph.D.
MGH-NMR Center
[EMAIL PROTECTED]
Phone Number: 617-724-2358
Fax: 617-726-7422
In order to help us help you, please follow the steps in:
surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
