> On Sep 16, 2008, at 6:51 AM, Gwenaëlle DOUAUD wrote:
>> Hi Antonios - Constantine,
>>
>> I can only reproduce the same error message when the reference
>> image (here the template) is not found. Can you see any obvious
>> reasons why it could not be found in your struc directory? If not,
>> please upload your whole VBM directory and I'll have a look...
>> http://www.fmrib.ox.ac.uk/cgi-bin/upload.cgi
>>
>> Cheers,
>> Gwenaelle
>>
Hi Gwenaelle, Antonios-Constantine,
Was this problem solved? I am experiencing the same problem and
would like to know the solution.
For my fslvbm analysis of 50 subjects, fslvbm_2_template -a ran
fine. I get the template_GM.nii.gz and it looks fine.
When I run fslvbm_3_proc, error occurs and the following is what gets
written in fslvbm3a.e1416.1
Part of FSL (build 1)
fnirt
Usage:
fnirt --ref=<some template> --in=<some image>
fnirt --ref=<some template> --in=<some image> --infwhm=8,4,2 --
subsamp=4,2,1 --warpres=8,8,8
Compulsory arguments (You MUST set one or more of):
--ref name of reference image
--in name of input image
Optional arguments (You may optionally specify one or more of):
--aff name of file containing affine transform
--inwarp name of file containing initial non-linear warps
--intin name of file/files containing initial intensity maping
--cout name of output file with field coefficients
--iout name of output image
--fout name of output file with field
--jout name of file for writing out the Jacobian of the field (for
diagnostic or VBM purposes)
--refout name of file for writing out intensity modulated --ref (for
diagnostic purposes)
--intout name of files for writing information pertaining to
intensity mapping
--logout Name of log-file
--config Name of config file specifying command line arguments
--refmask name of file with mask in reference space
--inmask name of file with mask in input image space
--applyrefmask Use specified refmask if set, deafult 1 (true)
--applyinmask Use specified inmask if set, deafult 1 (true)
--imprefm If =1, use implicit masking based on value in --ref image.
Default =1
--impinm If =1, use implicit masking based on value in --in image,
Default =1
--imprefval Value to mask out in --ref image. Default =0.0
--impinval Value to mask out in --in image. Default =0.0
--miter Max # of non-linear iterations, default 5,5,5,5
--subsamp sub-sampling scheme, default 4,2,1,1
--warpres (approximate) resolution (in mm) of warp basis in x-, y-
and z-direction, default 10,10,10
--splineorder Order of spline, 2->Qadratic spline, 3->Cubic spline.
Default=3
--infwhm FWHM (in mm) of gaussian smoothing kernel for input volume,
default 6,4,2,2
--reffwhm FWHM (in mm) of gaussian smoothing kernel for ref volume,
default 4,2,0,0
--regmod Model for regularisation of warp-field [membrane_energy
bending_energy], default bending_energy
--lambda Weight of regularisation, default depending on --ssqlambda
and --regmod switches. See user documetation.
--ssqlambda If set (=1), lambda is weighted by current ssq, default 1
--jacrange Allowed range of Jacobian determinants, default 0.01,100.0
--refderiv If =1, ref image is used to calculate derivatives.
Default =0
--intmod Model for intensity-mapping [none global_linear
global_non_linear local_linear global_non_linear_with_bias
local_non_linear]
--intorder Order of poynomial for mapping intensities, default 5
--biasres Resolution (in mm) of bias-field modelling local
intensities, default 50,50,50
--biaslambda Weight of regularisation for bias-field, default 10000
--estint Estimate intensity-mapping if set, deafult 1 (true)
--numprec Precision for representing Hessian, double or float.
Default double
-v,--verbose Print diagonostic information while running
-h,--help display help info
fnirt::fnirt_clp: No file matching --refmask= found
** ERROR (nifti_image_read): failed to find header file for
'G02_struc_GM_to_template_GM_warp'
** ERROR: nifti_image_open(G02_struc_GM_to_template_GM_warp): bad
header info
Error: failed to open file G02_struc_GM_to_template_GM_warp
ERROR: Could not open image G02_struc_GM_to_template_GM_warp
Image Exception : #22 :: Failed to read volume
G02_struc_GM_to_template_GM_warp
An error occured while reading file: G02_struc_GM_to_template_GM_warp
** ERROR (nifti_image_read): failed to find header file for
'G02_struc_GM_to_template_GM_warp'
** ERROR: nifti_image_open(G02_struc_GM_to_template_GM_warp): bad
header info
Error: failed to open file G02_struc_GM_to_template_GM_warp
Cannot open volume G02_struc_GM_to_template_GM_warp for reading!
** ERROR (nifti_image_read): failed to find header file for
'G02_struc_GM_to_template_GM_tmp'
** ERROR: nifti_image_open(G02_struc_GM_to_template_GM_tmp): bad
header info
Error: failed to open file G02_struc_GM_to_template_GM_tmp
ERROR: Could not open image G02_struc_GM_to_template_GM_tmp
Image Exception : #22 :: Failed to read volume
G02_struc_GM_to_template_GM_tmp
/RCBI/fsl/bin/fsl_reg: line 144: 17593 Bus error $
{FSLDIR}/bin/fslstats ${I2R}_tmp -M -P 50 >${I2R}_warp.msf
** ERROR (nifti_image_read): failed to find header file for
'G02_struc_GM_to_template_GM'
** ERROR: nifti_image_open(G02_struc_GM_to_template_GM): bad header info
Error: failed to open file G02_struc_GM_to_template_GM
Cannot open volume G02_struc_GM_to_template_GM for reading!
I tried to run the following, but I get the same above error.
fsl_reg G02_struc_GM template_GM G02_struc_GM_to_template_GM -fnirt
"--config=GM_2_MNI152GM_2mm.cnf --jout=G02_struc_JAC_nl";
I do get the G02_struc_GM_to_template_GM.mat file created with values
in it . I also get G02_struc_GM_to_template_GM_warp.msf created, but
it is empty.
I tried to add the GM_2_MNI152GM_2mm.cnf in my struc folder and I
tried the command with and without .cnf extension. But so far nothing
has worked.
I would greatly appreciate if anyone could shed some light on this.
Thanks,
-Merry.
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