Hi there,
As a trial, I'm trying to run "fslvbm_2_template -n" on 9 subjects. Their T1 images were brain-extracted by a protocol besides that executed by "fsl_vbm_bet." From previous exchanges on the listserv, I've learned that I should do the following:
- Create a "struc" directory, in which I should input the subjects' non-brain-extracted T1 images (*_struc.nii.gz) and brain-extracted T1 images (*_struc_brain.nii.gz).
- I've also learned the importance of a correspondence between the contents of the template_list and those of the "struc" directory.
The contents of the template_list:
n_001_T1.nii.gz
n_002_T1.nii.gz
n_003_T1.nii.gz
n_004_T1.nii.gz
p_001_T1.nii.gz
p_002_T1.nii.gz
p_003_T1.nii.gz
p_004_T1.nii.gz
The contents of the "struc" directory:
n_001_T1_struc.nii.gz
n_002_T1_struc.nii.gz
n_003_T1_struc.nii.gz
n_004_T1_struc.nii.gz
n_005_T1_struc.nii.gz
n_001_T1_struc_brain.nii.gz
n_002_T1_struc_brain.nii.gz
n_003_T1_struc_brain.nii.gz
n_004_T1_struc_brain.nii.gz
n_005_T1_struc_brain.nii.gz
p_001_T1_struc.nii.gz
p_002_T1_struc.nii.gz
p_003_T1_struc.nii.gz
p_004_T1_struc.nii.gz
p_001_T1_struc_brain.nii.gz
p_002_T1_struc_brain.nii.gz
p_003_T1_struc_brain.nii.gz
p_004_T1_struc_brain.nii.gz
"fslvbm_2_template -n" doesn't create template_GM_4D, but yields the following error message (fslvbm2d.e20921):
** ERROR (nifti_image_read): failed to find header file for 'template_GM_init'
** ERROR: nifti_image_open(template_GM_init): bad header info
Error: failed to open file template_GM_init
ERROR: Could not open image template_GM_init
Image Exception : #22 :: Failed to read volume template_GM_init
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
/usr/local/fsl/bin/fsl_reg: line 124: 21001 Aborted ${FSLDIR}/bin/flirt -ref $REFERENCE -in $INPUT $INMASK -omat ${I2R}.mat $flirtopts
Part of FSL (build 416)
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 --ref= found
** ERROR (nifti_image_read): failed to find header file for 'template_GM_init'
** ERROR: nifti_image_open(template_GM_init): bad header info
Error: failed to open file template_GM_init
ERROR: Could not open image template_GM_init
Image Exception : #22 :: Failed to read volume template_GM_init
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
/usr/local/fsl/bin/fsl_reg: line 144: 21003 Aborted ${FSLDIR}/bin/applywarp -i $INPUT -o $I2R -r $REFERENCE -w ${I2R}_warp
** ERROR (nifti_image_read): failed to find header file for 'n_001_T1_struc_GM_to_T_init_warp'
** ERROR: nifti_image_open(n_001_T1_struc_GM_to_T_init_warp): bad header info
Error: failed to open file n_001_T1_struc_GM_to_T_init_warp
Cannot open volume n_001_T1_struc_GM_to_T_init_warp for reading!
** ERROR (nifti_image_read): failed to find header file for 'n_001_T1_struc_GM_to_T_init_tmp'
** ERROR: nifti_image_open(n_001_T1_struc_GM_to_T_init_tmp): bad header info
Error: failed to open file n_001_T1_struc_GM_to_T_init_tmp
ERROR: Could not open image n_001_T1_struc_GM_to_T_init_tmp
Image Exception : #22 :: Failed to read volume n_001_T1_struc_GM_to_T_init_tmp
A similar problem was discussed in "FSL-VBM GM template creation problem" on the listserv, but to my knowledge, I've followed the advice that was given.
I'd really appreciate some guidance on this issue.
Michael
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