Hi --

A quick (hopefully) question about img2stdcoord.

My aim is to take thresholded group ("2nd level") stats performed on low-res
functional data and get the maxima-coordinates in publishable MNI-coordinates.

Have been attempting to so by with:

/apps/linux/fsl-3.3/bin/img2stdcoord -verbose -img
SWM_dvACC_ivSFTH_covOSPAN_mv_targ_encode2_model2Multistat_t_DblThreshPosNeg_CorrCloggMasked_GMBStemMasked
-std avg152T1_brain -xfm MyFunctionalMask-to-MNI152_dof8.mat xyx.mat

img2stdcoord can read/see all of the files (and reports correct values for
vox dimensions and the like) EXCEPT the file with the coordinates (xyz.mat).

The error message reads "Could not open matrix file xyx.mat"

xyz.mat is just a plain vanilla .ascii format file:

1 2 3
4 5 6

(have also tried real coordinates, double spaces, and the like)

If anyone has some advice, I would be grateful,
Alex Shackman


----------------------------------------------------------
{full output from program}
/apps/linux/fsl-3.2/bin/img2talcoord -verbose -img
SWM_dvACC_ivSFTH_covOSPAN_mv_targ_encode2_model2Multistat_t_DblThreshPosNeg_CorrCloggMasked_GMBStemMasked
-tal avg152T1_brain -vox -xfm MyFunctionalMask-to-MNI152_dof8.mat xyx.mat
Talairach Volume:: SIZE = 91 x 109 x 91
Talairach Volume:: DIMS = 2 x 2 x 2 mm

IMG Volume:: SIZE = 49 x 49 x 49
IMG Volume:: DIMS = 5 x 5 x 5 mm

affmat =
-0.000377 -0.984038 0.000460 205.183000
1.018640 -0.000362 0.005542 -6.167220
-0.005541 0.000446 1.018640 -84.861400
0.000000 0.000000 0.000000 1.000000


talvox2world =
-2.000000 0.000000 0.000000 90.000000
0.000000 2.000000 0.000000 -126.000000
0.000000 0.000000 2.000000 -72.000000
0.000000 0.000000 0.000000 1.000000


Coordinates in Talairach volume (in mm):
Could not open matrix file xyx.mat

------------------------------------
{directory contents}
avg152T1_brain.hdr
avg152T1_brain.img
MyFunctionalMask-to-MNI152_dof8.mat
SWM_dvACC_ivSFTH_covOSPAN_mv_targ_encode2_model2Multistat_t_DblThreshPosNeg_CorrCloggMasked_GMBStemMasked.hdr
SWM_dvACC_ivSFTH_covOSPAN_mv_targ_encode2_model2Multistat_t_DblThreshPosNeg_CorrCloggMasked_GMBStemMasked.img
xyz.mat

all permissions = -rwxrwxrwx

----------------------------------
avwhd
SWM_dvACC_ivSFTH_covOSPAN_mv_targ_encode2_model2Multistat_t_DblThreshPosNeg_CorrCloggMasked_GMBStemMasked
filename
SWM_dvACC_ivSFTH_covOSPAN_mv_targ_encode2_model2Multistat_t_DblThreshPosNeg_CorrCloggMasked_GMBStemMasked

sizeof_hdr     348
data_type
db_name
extents        0
session_error  0
regular        r
hkey_un0
dim0           3
dim1           49
dim2           49
dim3           49
dim4           1
dim5           1
dim6           1
dim7           1
vox_units
cal_units
unused1        0
datatype       16
bitpix         32
pixdim0        0.0000000000
pixdim1        -5.0000000000
pixdim2        5.0000000000
pixdim3        5.0000000000
pixdim4        2.0000000000
pixdim5        1.0000000000
pixdim6        1.0000000000
pixdim7        1.0000000000
vox_offset     0.0000
funused1       0.0000
funused2       0.0000
funused3       0.0000
cal_max        4.7638
cal_min        0.0000
compressed     0
verified       0
glmax          0
glmin          0
descrip        FSL3.2beta
aux_file       none
orient         0
originator
origin1        0
origin2        0
origin3        0
generated
scannum
patient_id
exp_date
exp_time
hist_un0
views          0
vols_added     0
start_field    0
field_skip     0
omax           0
omin           0
smin           0
smin           0
file_type      ANALYZE-7.5
file_code      0
----------------------------------------------------------
avwhd avg152T1_brain
Byte swapping
filename       avg152T1_brain

sizeof_hdr     348
data_type      dsr
db_name        T1.hdr
extents        0
session_error  0
regular        r
hkey_un0       0
dim0           4
dim1           91
dim2           109
dim3           91
dim4           1
dim5           0
dim6           0
dim7           0
vox_units      mm
cal_units
unused1        0
datatype       2
bitpix         8
pixdim0        0.0000000000
pixdim1        -2.0000000000
pixdim2        2.0000000000
pixdim3        2.0000000000
pixdim4        0.0000000000
pixdim5        0.0000000000
pixdim6        0.0000000000
pixdim7        0.0000000000
vox_offset     0.0000
funused1       1715.0446
funused2       0.0000
funused3       0.0000
cal_max        0.0000
cal_min        0.0000
compressed     0
verified       0
glmax          255
glmin          0
descrip        ICBM AVG 152 T1 TAL LIN
aux_file       none
orient         0
originator     .
origin1        46
origin2        64
origin3        37
generated
scannum
patient_id
exp_date
exp_time
hist_un0
views          0
vols_added     0
start_field    0
field_skip     0
omax           0
omin           0
smin           0
smin           0
file_type      ANALYZE-7.5
file_code      0
----------------------------------------------------------
{contents of .xfm}
-0.000377214  -0.984038  0.000459994  205.183
1.01864  -0.000361974  0.00554151  -6.16722
-0.00554134  0.000446339  1.01864  -84.8614
0  0  0  1

----------------------------------------------------------
Alexander J. Shackman
Laboratory for Affective Neuroscience
Waisman Laboratory for Brain Imaging & Behavior
University of Wisconsin-Madison
1202 West Johnson Street
Madison, Wisconsin 53706

Telephone: +1 (608) 358-5025
FAX: +1 (608) 265-2875
EMAIL: [log in to unmask]
http://psyphz.psych.wisc.edu/~shackman