Not sure what's going wrong. The warning about not finding avg152T1_brain.mat is irrelevant. What version of freesurfer and reg-feat2anat are you using? Can you check the reg to standard space? You can do this by looking at the feat report or with

reg-feat2anat --feat /home/eleung1/Vaina/N002/TrioTim-35006-20070211-180738-596000/feat/005_n002-global-fsl.feat --subject n002 --manxfm func2std

doug


Elaine Leung wrote:
Hello,

I'm trying to display some FEAT statistics on a surface I created
using Freesurfer using instructions from
http://www.fmrib.ox.ac.uk/fsl/freesurfer/index.html.  The automatic
registration function reg-feat2anat seems to have failed and I'm not
sure what I should do to re-orient the slices better.  I've attached a
picture, hopefully it will convey my problem.

Also, looking at the log files, I noticed the line

INFO: could not find
/home/eleung1/freesurfer/fsl/etc/standard/avg152T1_brain.mat file for
direction cosine info.
INFO: use Analyze 7.5 hdr->hist.orient value: 0, transverse unflipped (default).
INFO: if not valid, please provide the information in
/home/eleung1/freesurfer/fsl/etc/standard/avg152T1_brain.mat file

Where do I get the file avg152T1_brain.mat?

Thanks for your help,
Elaine 



Tue Feb 20 11:42:45 EST 2007
/home/eleung1/freesurfer/subjects
/home/eleung1/freesurfer/bin//reg-feat2anat
--feat /home/eleung1/Vaina/N002/TrioTim-35006-20070211-180738-596000/feat/005_n002-global-fsl.feat --subject n002
Linux brodmann.bu.edu 2.6.9-22.0.1.ELsmp #1 SMP Thu Oct 27 13:14:25 CDT 2005 i686 i686 i386 GNU/Linux
mri_convert /home/eleung1/freesurfer/subjects/n002/mri/brain.mgz /home/eleung1/Vaina/N002/TrioTim-35006-20070211-180738-596000/feat/005_n002-global-fsl.feat/reg/freesurfer/tmp/anat.nii.gz
mri_convert /home/eleung1/freesurfer/subjects/n002/mri/brain.mgz /home/eleung1/Vaina/N002/TrioTim-35006-20070211-180738-596000/feat/005_n002-global-fsl.feat/reg/freesurfer/tmp/anat.nii.gz 
reading from /home/eleung1/freesurfer/subjects/n002/mri/brain.mgz...
TR=2530.00, TE=3.39, TI=1100.00, flip angle=7.00
i_ras = (-1, -8.15313e-11, 3.35233e-10)
j_ras = (3.14573e-09, -4.86297e-10, -1)
k_ras = (9.86348e-10, 1, 1.31955e-09)
writing to /home/eleung1/Vaina/N002/TrioTim-35006-20070211-180738-596000/feat/005_n002-global-fsl.feat/reg/freesurfer/tmp/anat.nii.gz...
example_func ras_good_flag 1
-------------------------------------------------------
Initializing exf2anat with header
tkregister2 --targ /home/eleung1/freesurfer/subjects/n002/mri/brain.mgz --mov /home/eleung1/Vaina/N002/TrioTim-35006-20070211-180738-596000/feat/005_n002-global-fsl.feat/example_func.nii.gz --reg /home/eleung1/Vaina/N002/TrioTim-35006-20070211-180738-596000/feat/005_n002-global-fsl.feat/reg/freesurfer/anat2exf.register.dat.init --fslregout /home/eleung1/Vaina/N002/TrioTim-35006-20070211-180738-596000/feat/005_n002-global-fsl.feat/reg/freesurfer/exf2anat.init.fsl.mat --regheader --noedit
target  volume /home/eleung1/freesurfer/subjects/n002/mri/brain.mgz
movable volume /home/eleung1/Vaina/N002/TrioTim-35006-20070211-180738-596000/feat/005_n002-global-fsl.feat/example_func.nii.gz
reg file       /home/eleung1/Vaina/N002/TrioTim-35006-20070211-180738-596000/feat/005_n002-global-fsl.feat/reg/freesurfer/anat2exf.register.dat.init
LoadVol        0
$Id: tkregister2.c,v 1.49.2.4 2006/03/27 21:48:16 greve Exp $
Diagnostic Level -1
INFO: using NIfTI-1 sform 
INFO: loading target /home/eleung1/freesurfer/subjects/n002/mri/brain.mgz
Ttarg: --------------------
-1.000   0.000   0.000   128.000;
 0.000   0.000   1.000  -128.000;
 0.000  -1.000   0.000   128.000;
 0.000   0.000   0.000   1.000;
INFO: loading movable /home/eleung1/Vaina/N002/TrioTim-35006-20070211-180738-596000/feat/005_n002-global-fsl.feat/example_func.nii.gz
INFO: using NIfTI-1 sform 
Tmov: --------------------
-3.125   0.000   0.000   100.000;
 0.000   0.000   2.200  -60.500;
 0.000  -3.125   0.000   100.000;
 0.000   0.000   0.000   1.000;
mkheaderreg = 1, float2int = 0
---- Input registration matrix (computed) --------
 1.000   0.000  -0.000   7.451;
-0.000   0.000   1.000  -20.153;
-0.000  -1.000  -0.000  -59.694;
 0.000   0.000   0.000   1.000;
---------------------------------------
---- Input registration matrix --------
 1.000   0.000  -0.000   7.451;
-0.000   0.000   1.000  -20.153;
-0.000  -1.000  -0.000  -59.694;
 0.000   0.000   0.000   1.000;
subject = subject-unknown
RegMat ---------------------------
 1.000   0.000  -0.000   7.451;
-0.000   0.000   1.000  -20.153;
-0.000  -1.000  -0.000  -59.694;
 0.000   0.000   0.000   1.000;
register: file /home/eleung1/Vaina/N002/TrioTim-35006-20070211-180738-596000/feat/005_n002-global-fsl.feat/reg/freesurfer/anat2exf.register.dat.init written
FSLOUTPUTTYPE NIFTI_GZ 
tkreg2FSL: mov det = -21.4844, ref det = -1
betfunc /home/eleung1/Vaina/N002/TrioTim-35006-20070211-180738-596000/feat/005_n002-global-fsl.feat/example_func /home/eleung1/Vaina/N002/TrioTim-35006-20070211-180738-596000/feat/005_n002-global-fsl.feat/reg/freesurfer/tmp/exfbet
Tue Feb 20 11:42:55 EST 2007
flirt -ref /home/eleung1/Vaina/N002/TrioTim-35006-20070211-180738-596000/feat/005_n002-global-fsl.feat/reg/freesurfer/tmp/anat.nii.gz -in /home/eleung1/Vaina/N002/TrioTim-35006-20070211-180738-596000/feat/005_n002-global-fsl.feat/reg/freesurfer/tmp/exfbet.nii.gz -init /home/eleung1/Vaina/N002/TrioTim-35006-20070211-180738-596000/feat/005_n002-global-fsl.feat/reg/freesurfer/exf2anat.init.fsl.mat -out /home/eleung1/Vaina/N002/TrioTim-35006-20070211-180738-596000/feat/005_n002-global-fsl.feat/reg/freesurfer/tmp/exf-in-anat -interp trilinear -omat /home/eleung1/Vaina/N002/TrioTim-35006-20070211-180738-596000/feat/005_n002-global-fsl.feat/reg/freesurfer/exf2anat.fsl.mat -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90
WARNING: Both reference and input images have an sform matrix set
  The output image will use the sform from the reference image
-------------------------------------------------------
tkregister2 --s n002 --mov /home/eleung1/Vaina/N002/TrioTim-35006-20070211-180738-596000/feat/005_n002-global-fsl.feat/example_func.nii.gz --reg /home/eleung1/Vaina/N002/TrioTim-35006-20070211-180738-596000/feat/005_n002-global-fsl.feat/reg/freesurfer/anat2exf.register.dat --fslreg /home/eleung1/Vaina/N002/TrioTim-35006-20070211-180738-596000/feat/005_n002-global-fsl.feat/reg/freesurfer/exf2anat.fsl.mat --noedit --mgz
---- FSL registration matrix --------
 0.975   0.028   0.220   17.472;
 0.087  -0.961  -0.264   254.547;
 0.203   0.276  -0.939   103.727;
 0.000   0.000   0.000   1.000;
---------------------------------------
INFO: no target volume specified, assuming FreeSurfer orig volume.
target  volume orig
movable volume /home/eleung1/Vaina/N002/TrioTim-35006-20070211-180738-596000/feat/005_n002-global-fsl.feat/example_func.nii.gz
reg file       /home/eleung1/Vaina/N002/TrioTim-35006-20070211-180738-596000/feat/005_n002-global-fsl.feat/reg/freesurfer/anat2exf.register.dat
LoadVol        0
$Id: tkregister2.c,v 1.49.2.4 2006/03/27 21:48:16 greve Exp $
Diagnostic Level -1
INFO: using NIfTI-1 sform 
INFO: loading target /home/eleung1/freesurfer/subjects/n002/mri/orig.mgz
Ttarg: --------------------
-1.000   0.000   0.000   128.000;
 0.000   0.000   1.000  -128.000;
 0.000  -1.000   0.000   128.000;
 0.000   0.000   0.000   1.000;
INFO: loading movable /home/eleung1/Vaina/N002/TrioTim-35006-20070211-180738-596000/feat/005_n002-global-fsl.feat/example_func.nii.gz
INFO: using NIfTI-1 sform 
Tmov: --------------------
-3.125   0.000   0.000   100.000;
 0.000   0.000   2.200  -60.500;
 0.000  -3.125   0.000   100.000;
 0.000   0.000   0.000   1.000;
mkheaderreg = 0, float2int = 0
FSLOUTPUTTYPE NIFTI_GZ 
fsl2TkReg: mov det = -21.4844, ref det = -1
---- Input registration matrix (computed) --------
 0.975  -0.203   0.087  -1.687;
-0.220  -0.939   0.264  -25.687;
 0.028  -0.276  -0.961  -31.406;
 0.000   0.000   0.000   1.000;
---------------------------------------
---- Input registration matrix --------
 0.975  -0.203   0.087  -1.687;
-0.220  -0.939   0.264  -25.687;
 0.028  -0.276  -0.961  -31.406;
 0.000   0.000   0.000   1.000;
subject = n002
RegMat ---------------------------
 0.975  -0.203   0.087  -1.687;
-0.220  -0.939   0.264  -25.687;
 0.028  -0.276  -0.961  -31.406;
 0.000   0.000   0.000   1.000;
register: file /home/eleung1/Vaina/N002/TrioTim-35006-20070211-180738-596000/feat/005_n002-global-fsl.feat/reg/freesurfer/anat2exf.register.dat written
tkregister2 --targ /home/eleung1/freesurfer/fsl/etc/standard/avg152T1_brain.img --mov /home/eleung1/Vaina/N002/TrioTim-35006-20070211-180738-596000/feat/005_n002-global-fsl.feat/example_func.nii.gz --fslreg /home/eleung1/Vaina/N002/TrioTim-35006-20070211-180738-596000/feat/005_n002-global-fsl.feat/reg/example_func2standard.mat --reg /home/eleung1/Vaina/N002/TrioTim-35006-20070211-180738-596000/feat/005_n002-global-fsl.feat/reg/freesurfer/std2exf.register.dat --noedit
-----------------------------------------------------------------
INFO: could not find /home/eleung1/freesurfer/fsl/etc/standard/avg152T1_brain.mat file for direction cosine info.
INFO: use Analyze 7.5 hdr->hist.orient value: 0, transverse unflipped (default).
INFO: if not valid, please provide the information in /home/eleung1/freesurfer/fsl/etc/standard/avg152T1_brain.mat file
-----------------------------------------------------------------
-----------------------------------------------------------------
INFO: could not find /home/eleung1/freesurfer/fsl/etc/standard/avg152T1_brain.mat file for direction cosine info.
INFO: use Analyze 7.5 hdr->hist.orient value: 0, transverse unflipped (default).
INFO: if not valid, please provide the information in /home/eleung1/freesurfer/fsl/etc/standard/avg152T1_brain.mat file
-----------------------------------------------------------------
-----------------------------------------------------------------
INFO: could not find /home/eleung1/freesurfer/fsl/etc/standard/avg152T1_brain.mat file for direction cosine info.
INFO: use Analyze 7.5 hdr->hist.orient value: 0, transverse unflipped (default).
INFO: if not valid, please provide the information in /home/eleung1/freesurfer/fsl/etc/standard/avg152T1_brain.mat file
-----------------------------------------------------------------
---- FSL registration matrix --------
 0.925   0.038   0.025  -10.083;
-0.016   0.373  -1.040   104.961;
-0.071   0.914   0.396  -43.195;
 0.000   0.000   0.000   1.000;
---------------------------------------
target  volume /home/eleung1/freesurfer/fsl/etc/standard/avg152T1_brain.img
movable volume /home/eleung1/Vaina/N002/TrioTim-35006-20070211-180738-596000/feat/005_n002-global-fsl.feat/example_func.nii.gz
reg file       /home/eleung1/Vaina/N002/TrioTim-35006-20070211-180738-596000/feat/005_n002-global-fsl.feat/reg/freesurfer/std2exf.register.dat
LoadVol        0
$Id: tkregister2.c,v 1.49.2.4 2006/03/27 21:48:16 greve Exp $
Diagnostic Level -1
INFO: using NIfTI-1 sform 
INFO: loading target /home/eleung1/freesurfer/fsl/etc/standard/avg152T1_brain.img
INFO: target does not conform to COR format, so I'm going to
reslice to COR. This will not affect the final registration.
Ttarg: --------------------
-1.000   0.000   0.000   128.000;
 0.000   0.000   1.000  -128.000;
 0.000  -1.000   0.000   128.000;
 0.000   0.000   0.000   1.000;
INFO: loading movable /home/eleung1/Vaina/N002/TrioTim-35006-20070211-180738-596000/feat/005_n002-global-fsl.feat/example_func.nii.gz
INFO: using NIfTI-1 sform 
Tmov: --------------------
-3.125   0.000   0.000   100.000;
 0.000   0.000   2.200  -60.500;
 0.000  -3.125   0.000   100.000;
 0.000   0.000   0.000   1.000;
mkheaderreg = 0, float2int = 0
FSLOUTPUTTYPE NIFTI_GZ 
fsl2TkReg: mov det = -21.4844, ref det = -8
---- Input registration matrix (computed) --------
 1.078  -0.008   0.048  -2.561;
-0.011  -0.832   0.339  -17.144;
 0.079  -0.361  -0.944  -36.034;
 0.000   0.000   0.000   1.000;
---------------------------------------
---- Input registration matrix --------
 1.078  -0.008   0.048  -2.561;
-0.011  -0.832   0.339  -17.144;
 0.079  -0.361  -0.944  -36.034;
 0.000   0.000   0.000   1.000;
subject = subject-unknown
RegMat ---------------------------
 1.078   0.048   0.008  -2.561;
-0.011   0.339   0.832  -17.144;
 0.079  -0.944   0.361  -36.034;
 0.000   0.000   0.000   1.000;
register: file /home/eleung1/Vaina/N002/TrioTim-35006-20070211-180738-596000/feat/005_n002-global-fsl.feat/reg/freesurfer/std2exf.register.dat written
mri_matrix_multiply -fsl -im /home/eleung1/Vaina/N002/TrioTim-35006-20070211-180738-596000/feat/005_n002-global-fsl.feat/reg/freesurfer/exf2anat.fsl.mat -iim /home/eleung1/Vaina/N002/TrioTim-35006-20070211-180738-596000/feat/005_n002-global-fsl.feat/reg/example_func2standard.mat -om /home/eleung1/Vaina/N002/TrioTim-35006-20070211-180738-596000/feat/005_n002-global-fsl.feat/reg/freesurfer/std2anat.fsl.mat
-------------------------------------------------------
tkregister2 --targ /home/eleung1/freesurfer/subjects/n002/mri/brain.mgz --mov /home/eleung1/freesurfer/fsl/etc/standard/avg152T1_brain.img --reg /home/eleung1/Vaina/N002/TrioTim-35006-20070211-180738-596000/feat/005_n002-global-fsl.feat/reg/freesurfer/anat2std.register.dat --fslreg /home/eleung1/Vaina/N002/TrioTim-35006-20070211-180738-596000/feat/005_n002-global-fsl.feat/reg/freesurfer/std2anat.fsl.mat --noedit
---- FSL registration matrix --------
 1.056  -0.165   0.055   47.751;
 0.016  -0.127  -1.000   224.821;
 0.230   0.883  -0.068   10.423;
 0.000   0.000   0.000   1.000;
---------------------------------------
target  volume /home/eleung1/freesurfer/subjects/n002/mri/brain.mgz
movable volume /home/eleung1/freesurfer/fsl/etc/standard/avg152T1_brain.img
reg file       /home/eleung1/Vaina/N002/TrioTim-35006-20070211-180738-596000/feat/005_n002-global-fsl.feat/reg/freesurfer/anat2std.register.dat
LoadVol        0
$Id: tkregister2.c,v 1.49.2.4 2006/03/27 21:48:16 greve Exp $
Diagnostic Level -1
INFO: loading target /home/eleung1/freesurfer/subjects/n002/mri/brain.mgz
Ttarg: --------------------
-1.000   0.000   0.000   128.000;
 0.000   0.000   1.000  -128.000;
 0.000  -1.000   0.000   128.000;
 0.000   0.000   0.000   1.000;
INFO: loading movable /home/eleung1/freesurfer/fsl/etc/standard/avg152T1_brain.img
Tmov: --------------------
-2.000   0.000   0.000   91.000;
 0.000   0.000   2.000  -91.000;
 0.000  -2.000   0.000   109.000;
 0.000   0.000   0.000   1.000;
mkheaderreg = 0, float2int = 0
FSLOUTPUTTYPE NIFTI_GZ 
fsl2TkReg: mov det = -8, ref det = -1
---- Input registration matrix (computed) --------
 0.908  -0.175   0.038   1.200;
-0.044  -0.134   0.988  -7.548;
-0.233  -1.077  -0.086  -7.170;
 0.000   0.000   0.000   1.000;
---------------------------------------
---- Input registration matrix --------
 0.908  -0.175   0.038   1.200;
-0.044  -0.134   0.988  -7.548;
-0.233  -1.077  -0.086  -7.170;
 0.000   0.000   0.000   1.000;
subject = subject-unknown
RegMat ---------------------------
 0.908  -0.175   0.038   1.200;
-0.044  -0.134   0.988  -7.548;
-0.233  -1.077  -0.086  -7.170;
 0.000   0.000   0.000   1.000;
register: file /home/eleung1/Vaina/N002/TrioTim-35006-20070211-180738-596000/feat/005_n002-global-fsl.feat/reg/freesurfer/anat2std.register.dat written
To visually check your results, run:
tkregister2 --s n002 --mov /home/eleung1/Vaina/N002/TrioTim-35006-20070211-180738-596000/feat/005_n002-global-fsl.feat/example_func.nii.gz --reg /home/eleung1/Vaina/N002/TrioTim-35006-20070211-180738-596000/feat/005_n002-global-fsl.feat/reg/freesurfer/anat2exf.register.dat --fslreg /home/eleung1/Vaina/N002/TrioTim-35006-20070211-180738-596000/feat/005_n002-global-fsl.feat/reg/freesurfer/exf2anat.fsl.mat --surf orig --tag
Tue Feb 20 11:43:48 EST 2007
reg-feat2anat done
  

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-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
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