Hi Merry,
I am afraid you will need to edit the GM_2_MNI152GM_2mm.cnf file. In
the version we released with 4.0 there was an explicit path given for
the --refmask file. If you just remove the explicit path, i.e. makes
sure it reads
--refmask=MNI152_T1_2mm_brain_mask_dil
This has been fixed for the next release.
Good Luck Jesper
On 29 Sep 2008, at 22:52, Merry Mani wrote:
>> 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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