Dear Gwenaelle,
Thanks,
how have you called this manually edited images? They have to have *exactly* the same name than the ones created by fslvbm1 (*_struc_brain.nii.gz)
Answer:after manually editing the non-brain regions i renamed the files with same extension name for instance "control_004_struc_brain.nii.gz"
If you have correctly named your manually edited brain images, then could you please give me the content of one of your fslvbm2a.e*, fslvbm2b.e*, fslvbm2c.e* and fslvbm2d.e* files
Answer :There is nothing inside the the files "fslvbm2a.e" and "fslvbm2b.e". whereas under "fslvbm2c.e" the following error was reported
** ERROR (nifti_image_read): failed to find header file for 'control_012_struc_GM_to_T'
** ERROR: nifti_image_open(control_012_struc_GM_to_T): bad header info
Error: failed to open file control_012_struc_GM_to_T
ERROR: Could not open image control_012_struc_GM_to_T
Image Exception : #22 :: Failed to read volume control_012_struc_GM_to_T
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
./fslvbm2c: line 13: 17851 Aborted $FSLDIR/bin/fslmerge -t template_4D_GM $mergelist
** ERROR (nifti_image_read): failed to find header file for 'template_4D_GM'
** ERROR: nifti_image_open(template_4D_GM): bad header info
Error: failed to open file template_4D_GM
Cannot open volume template_4D_GM for reading!
** ERROR (nifti_image_read): failed to find header file for 'template_GM'
** ERROR: nifti_image_open(template_GM): bad header info
Error: failed to open file template_GM
ERROR: Could not open file
/usr/local/fsl/bin/fslswapdim: line 105: [: =: unary operator expected
** ERROR (nifti_image_read): failed to find header file for 'template_GM'
** ERROR: nifti_image_open(template_GM): bad header info
Error: failed to open file template_GM
ERROR: Could not open file
/usr/local/fsl/bin/fslswapdim: line 113: [: -gt: unary operator expected
** ERROR (nifti_image_read): failed to find header file for 'template_GM'
** ERROR: nifti_image_open(template_GM): bad header info
Error: failed to open file template_GM
ERROR: Could not open file
/usr/local/fsl/bin/fslswapdim: line 115: [: -gt: unary operator expected
** ERROR (nifti_image_read): failed to find header file for 'template_GM'
** ERROR: nifti_image_open(template_GM): bad header info
Error: failed to open file template_GM
Cannot open volume template_GM for reading!
** ERROR (nifti_image_read): failed to find header file for 'template_GM'
** ERROR: nifti_image_open(template_GM): bad header info
Error: failed to open file template_GM
Cannot open volume template_GM for reading!
ANSWER: and under "fslvbm2d.e" the following error was reported
** 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: 19309 Aborted ${FSLDIR}/bin/flirt -ref $REFERENCE -in $INPUT $INMASK -omat ${I2R}.mat $flirtopts
Part of FSL (build 414)
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 'control_003_struc_GM_to_T_init_warp'
** ERROR: nifti_image_open(control_003_struc_GM_to_T_init_warp): bad header info
Error: failed to open file control_003_struc_GM_to_T_init_warp
ERROR: Could not open image control_003_struc_GM_to_T_init_warp
Image Exception : #22 :: Failed to read volume control_003_struc_GM_to_T_init_warp
An error occured while reading file: control_003_struc_GM_to_T_init_warp
** ERROR (nifti_image_read): failed to find header file for 'control_003_struc_GM_to_T_init_warp'
** ERROR: nifti_image_open(control_003_struc_GM_to_T_init_warp): bad header info
Error: failed to open file control_003_struc_GM_to_T_init_warp
Cannot open volume control_003_struc_GM_to_T_init_warp for reading!
** ERROR (nifti_image_read): failed to find header file for 'control_003_struc_GM_to_T_init_tmp'
** ERROR: nifti_image_open(control_003_struc_GM_to_T_init_tmp): bad header info
Error: failed to open file control_003_struc_GM_to_T_init_tmp
ERROR: Could not open image control_003_struc_GM_to_T_init_tmp
Image Exception : #22 :: Failed to read volume control_003_struc_GM_to_T_init_tmp
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
/usr/local/fsl/bin/fsl_reg: line 144: 19314 Aborted ${FSLDIR}/bin/fslstats ${I2R}_tmp -M -P 50 > ${I2R}_warp.msf
Thanks, it works if i don't do manual editing (i tested by running fslvbm_2_template in a small number of patients without manual editing) but if i use the files with manual extra brain edition it gives the above error. There are two more things which i would like to clarify, even if i manually edit the clearly identifiable non-brain regions, in some cases there are some non-brain regions which are too close to the brain structures which is difficult to clean manually, i am wondering how is this taken care of because i don't know whether these regions will give significant difference on the statistical results. One more clarification when i look at the PV maps of GM after FAST why are the PV values in ventricles are 1.
Thanks again,
Regards
venkateswaran
-----Original Message-----
From: FSL - FMRIB's Software Library on behalf of Gwenaëlle DOUAUD
Sent: Tue 9/15/2009 7:52 AM
To: [log in to unmask]
Subject: [FSL] Re : [FSL] FSL-VBM GM template creation problem
Hi Venkateswaran,
> After
> the first step of template_list creation i ran
> "fslvbm_1_bet -b" and cleaned manually some of the
> left over non brain regions in my data and placed the final
> cleaned files in "struc" directory which is under
> "my_fsl_vbm" directory.
how have you called this manually edited images? They have to have *exactly* the same name than the ones created by fslvbm1 (*_struc_brain.nii.gz)...
> Then i ran the
> second processing step of "fslvbm_2_template -n"
> under "my_fsl_vbm" directory. The processing step
> was complete after few hours when i looked at the
> "struc" directory there was no
> "template_4D_GM" file. When i opened one of the
> text files i.e fslvbm2e.e6190 to see what is in it the
> following error message was displayed
Hmmm, something has gone wrong much earlier in the script... If you have correctly named your manually edited brain images, then could you please give me the content of one of your fslvbm2a.e*, fslvbm2b.e*, fslvbm2c.e* and fslvbm2d.e* files?
> Furthermore I would also like to run VBM on white
> matter images, how to do this.
Please have a look at the archives for this: https://www.jiscmail.ac.uk/cgi-bin/webadmin?S1=fsl
Cheers,
Gwenaelle
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