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
--- En date de : Mar 16.9.08, Antonios - Constantine Thanellas <[log in to unmask]> a écrit :
> De: Antonios - Constantine Thanellas <[log in to unmask]>
> Objet: Re: [FSL] following different order on VBM analysis steps+in addition
> À: [log in to unmask]
> Date: Mardi 16 Septembre 2008, 11h31
> Hi Gwenaelle,
> It gives me the exact same error that can be found in the
> log files
> fslvbm2d.e25560. See the attached shel.txt file
>
> Antonios-Constantine
>
>
>
> On Mon, 15 Sep 2008 15:44:00 +0000, Gwenaëlle DOUAUD
> <[log in to unmask]> wrote:
>
> >Hi Antonios - Constantine,
> >
> >what is the output in your shell when you're trying
> to run this command:
> >
> >
> >/usr/share/fsl/bin/fsl_reg
> 01_CON_002_S_0295_M06_struc_GM template_GM_init
> 01_CON_002_S_0295_M06_struc_GM_to_T_init -fnirt
> "--config=GM_2_MNI152GM_2mm.cnf"
> >
> >
> >Cheers,
> >Gwenaelle
> >
> >
> >
> >--- En date de : Sam 13.9.08, Antonios - Constantine
> Thanellas
> <[log in to unmask]> a écrit :
> >
> >> De: Antonios - Constantine Thanellas
> <[log in to unmask]>
> >> Objet: Re: [FSL] following different order on VBM
> analysis steps+in addition
> >> À: [log in to unmask]
> >> Date: Samedi 13 Septembre 2008, 18h01
> >> Hi Gwenaelle,
> >> Indeed subtracting these two images gave me a
> blank image.
> >> (so we're talking
> >> about the same image)
> >> Find attached the folowing files:
> >> fslvbm2d.e25560.1.txt.tar.gz ,
> >> fnirt.txt.tar.gz and
> >> log_files.tar.gz (contains all the log files of
> the
> >> analysis)
> >>
> >> Thank you
> >>
> >>
> >> On Fri, 12 Sep 2008 15:59:28 +0000, Gwenaëlle
> DOUAUD
> >> <[log in to unmask]> wrote:
> >>
> >> >Hi Antonios,
> >> >
> >> >the second pass of your template hasn't
> worked
> >> (.msf files are empty and
> >> _to_T_init.nii.gz not created). The template_GM
> and
> >> template_GM_init should
> >> then basically look the same when template_GM
> should look
> >> much more refined...
> >> >
> >> >Could you please send me one fslvbm2d.e25560
> file?
> >> >
> >> >and also, what do you get when you type
> >> "fnirt" in your shell?
> >> >
> >> >Cheers,
> >> >Gwenaelle
> >> >
> >> >
> >> >--- En date de : Ven 12.9.08, Antonios -
> Constantine
> >> Thanellas
> >> <[log in to unmask]> a écrit :
> >> >
> >> >> De: Antonios - Constantine Thanellas
> >> <[log in to unmask]>
> >> >> Objet: Re: [FSL] following different
> order on VBM
> >> analysis steps+in addition
> >> >> À: [log in to unmask]
> >> >> Date: Vendredi 12 Septembre 2008, 9h16
> >> >> Yes Gwenaelle,
> >> >> These files are not created in my struc
> folder,
> >> only some
> >> >> blank msf files
> >> >> for each subject with the names
> >> >> *XXX*_struc_GM_to_T_init_warp.msf
> >> >> Though the analysis continued and
> templates were
> >> created
> >> >> which looked quite
> >> >> normal.
> >> >> The ls-al txt file is attached for your
> >> consideration.
> >> >>
> >> >> Thank you Gwenaelle
> >> >>
> >> >> On Thu, 11 Sep 2008 12:06:15 +0000,
> Gwenaëlle
> >> DOUAUD
> >> >> <[log in to unmask]> wrote:
> >> >>
> >> >> >Hi Antonios - Constantine,
> >> >> >
> >> >> >could you please copy/paste in a text
> file the
> >> output
> >> >> of a ls -al in your
> >> >> struc directory?
> >> >> >
> >> >> >Cheers,
> >> >> >Gwenaelle
> >> >> >
> >> >> >
> >> >> >--- En date de : Mer 10.9.08,
> Antonios -
> >> Constantine
> >> >> Thanellas
> >> >> <[log in to unmask]> a écrit
> :
> >> >> >
> >> >> >> De: Antonios - Constantine
> Thanellas
> >> >> <[log in to unmask]>
> >> >> >> Objet: Re: [FSL] following
> different
> >> order on VBM
> >> >> analysis steps+in addition
> >> >> >> À: [log in to unmask]
> >> >> >> Date: Mercredi 10 Septembre
> 2008, 10h39
> >> >> >> Hi Gwenaelle,
> >> >> >> Yes you are right, I'm sorry
> for
> >> wasting your
> >> >> time with
> >> >> >> such a silly mistake
> >> >> >> of mine.
> >> >> >> I run correctly this time the
> >> fslvbm_2_template
> >> >> and it
> >> >> >> created the template
> >> >> >> which looks ok (template_4D_GM
> through
> >> fslview).
> >> >> Though
> >> >> >> some of the log
> >> >> >> files showed some errors and
> i'm not
> >> sure if
> >> >> >> they're important and can
> >> >> >> affect my results.Can you take a
> look at
> >> them
> >> >> please and
> >> >> >> tell me your opinion?
> >> >> >>
> >> >> >> The error files are:
> fslvbm2d.e25560
> >> >> >>
> >> fslvbm2e.e29568
> >> >> >> and a warning message in:
> fslvbm2e.o29568
> >> >> >>
>
> >>
> >> >> fslvbm2c.o23932
> >> >> >>
> >> >> >> For once more thank you
> >> >> >>
> >> >> >> On Tue, 9 Sep 2008 12:56:39
> +0000,
> >> Gwenaëlle
> >> >> DOUAUD
> >> >> >> <[log in to unmask]>
> wrote:
> >> >> >>
> >> >> >> >Hi,
> >> >> >> >
> >> >> >> >the problem is coming from
> what
> >> you've
> >> >> entered in
> >> >> >> your template_list: you
> >> >> >> entered (first line) the name of
> this
> >> image that
> >> >> does not
> >> >> >> exist.
> >> >> >> Subsequently, the first-pass
> template is
> >> not
> >> >> created, then
> >> >> >> the second one...
> >> >> >> >
> >> >> >> >Try rerunning fslvbm_2 with
> the
> >> correct names
> >> >> in the
> >> >> >> template_list, it
> >> >> >> should be fine...
> >> >> >> >
> >> >> >> >Cheers,
> >> >> >> >Gwenaelle
> >> >> >> >
> >> >> >> >PS: The two versions I
> mentioned were
> >> of the
> >> >> >> template_list, not of fslvbm_2.
> >> >> >> >
> >> >> >> >
> >> >> >> >--- En date de : Mar 9.9.08,
> Antonios
> >> -
> >> >> Constantine
> >> >> >> Thanellas
> >> >> >> <[log in to unmask]>
> a écrit
> >> :
> >> >> >> >
> >> >> >> >> De: Antonios -
> Constantine
> >> Thanellas
> >> >> >> <[log in to unmask]>
> >> >> >> >> Objet: Re: [FSL]
> following
> >> different
> >> >> order on VBM
> >> >> >> analysis steps+in addition
> >> >> >> >> À: [log in to unmask]
> >> >> >> >> Date: Mardi 9 Septembre
> 2008,
> >> 14h28
> >> >> >> >> Hello again Gwenaelle,
> >> >> >> >>
> >> >> >> >> I've modifed the
> >> fslvbm_2_template as
> >> >> >> you've
> >> >> >> >> proposed and the run
> was more
> >> >> >> >> normal this time.Though
> the
> >> >> template_GM_4D image
> >> >> >> was not
> >> >> >> >> created.I've
> >> >> >> >> noticed the following
> errors:
> >> >> >> >> 1st) Even though my
> template
> >> list
> >> >> contains 36 (out
> >> >> >> of the
> >> >> >> >> 38 files,since
> >> >> >> >> according to the guides
> the same
> >> amount
> >> >> of
> >> >> >> controls and
> >> >> >> >> patients should be
> >> >> >> >> used) ,it seems that
> the script
> >> processes
> >> >> all the
> >> >> >> files
> >> >> >> >> (i've seen that the
> >> >> >> >> same issue has been
> reported in
> >> the fsl
> >> >> list with
> >> >> >> the
> >> >> >> >> title: "VBM
> template
> >> >> >> >> creation with selected
> >> images")
> >> >> >> >>
> >> >> >> >> 2nd) an error
> fslvbm2e.e10389
> >> report
> >> >> which is very
> >> >> >> strange
> >> >> >> >> for the following
> >> >> >> >> reason: It mentions
> that:
> >> >> >> >> ** ERROR
> (nifti_image_read):
> >> failed to
> >> >> find header
> >> >> >> file for
> >> >> >> >>
> >> >>
> '01_CON_002_S_0295_SC_struc_GM_to_T_init'
> >> >> >> >> ** ERROR:
> >> >> >> >>
> >> >> >>
> >> >>
> >>
> nifti_image_open(01_CON_002_S_0295_SC_struc_GM_to_T_init):
> >> >> >> >> bad
> >> >> >> >> header info
> >> >> >> >>
> >> >> >> >> and the strange thing
> is that
> >> >> 01_CON_002_S_0295_SC
> >> >> >> file
> >> >> >> >> does not exist.This
> >> >> >> >> file actually is the
> >> >> 20_CON_002_S_0295_SC.
> >> >> >> >>
> >> >> >> >> In order for this to be
> more
> >> clarified
> >> >> find
> >> >> >> attached the
> >> >> >> >> .txt files that
> >> >> >> >> were created during the
> analysis
> >> + the
> >> >> structure
> >> >> >> of my
> >> >> >> >> folder were the
> >> >> >> >> analysis took place.
> >> >> >> >> Thank you
> >> >> >> >>
> >> >> >> >>
> >> >> >> >> On Mon, 8 Sep 2008
> 14:30:24
> >> +0100,
> >> >> Antonios -
> >> >> >> Constantine
> >> >> >> >> Thanellas
> >> >> >> >>
> <[log in to unmask]>
> >> wrote:
> >> >> >> >>
> >> >> >> >> >Yes Gwenaelle,
> >> >> >> >> >I work with an AMD
> athlon 64
> >> ,3200+,
> >> >> with 1GB
> >> >> >> RAM and a
> >> >> >> >> SATA hard disk. My
> >> >> >> >> >platform is Ubuntu
> 7.10
> >> (gutsy) and i
> >> >> use the
> >> >> >> FSL 4.1.0
> >> >> >> >> version. All my data
> >> >> >> >> > (brain images)
> come though
> >> from a
> >> >> previous
> >> >> >> version of
> >> >> >> >> fsl (FSL 4.0) and
> >> >> >> >> >ubuntu (7.04).
> >> >> >> >> >As i've already
> >> mentioned i
> >> >> bypassed the
> >> >> >> first step
> >> >> >> >> of VBM analysis since i
> >> >> >> >> >had already my
> brain images
> >> >> extracted and i
> >> >> >> confronted
> >> >> >> >> this problem when i
> >> >> >> >> >was trying to run
> the script
> >> >> fslvbm_2_template
> >> >> >> -n.
> >> >> >> >> >Find attached an
> >> fslerroreport that
> >> >> may give
> >> >> >> you some
> >> >> >> >> more info regarding my
> >> >> >> >> >system and my
> environmental
> >> >> variables.
> >> >> >> >> >In case you need
> some more
> >> >> information ,just
> >> >> >> inform me
> >> >> >> >> >Thank you
> >> >> >> >> >
> >> >> >> >> >
> >> >> >> >> >On Mon, 8 Sep 2008
> 12:30:56
> >> +0000,
> >> >> Gwenaëlle
> >> >> >> DOUAUD
> >> >> >> >>
> >> ><[log in to unmask]>
> >> >> wrote:
> >> >> >> >> >
> >> >> >> >> >>Hi Antonios -
> >> Constantine,
> >> >> >> >> >>
> >> >> >> >> >>this is exactly
> the
> >> problem,
> >> >> you're
> >> >> >> right. I
> >> >> >> >> know about this script
> (since
> >> >> >> >> >I've written it
> with
> >> Steve), this
> >> >> is why I
> >> >> >> asked
> >> >> >> >> you the output of
> imglob as
> >> >> >> >> >it was the only
> problem I
> >> could think
> >> >> of :-).
> >> >> >> >> >>
> >> >> >> >> >>It would be
> interesting
> >> for us to
> >> >> know why
> >> >> >> >> you've got such
> problem. So
> >> >> >> >> >could you please
> give me as
> >> much
> >> >> details as
> >> >> >> possible:
> >> >> >> >> e.g., on which machine
> >> >> >> >> >are you working,
> with which
> >> kind of
> >> >> >> environment etc.?
> >> >> >> >> >>
> >> >> >> >> >>To solve your
> problem
> >> for the
> >> >> moment, try
> >> >> >> replacing
> >> >> >> >> `$FSLDIR/bin/imglob
> >> >> >> >> >*_struc.*` by
> >> `$FSLDIR/bin/remove_ext
> >> >> >> *_struc.*`
> >> >> >> >> throughout the
> >> >> >> >> >fslvbm_2_template
> and
> >> fslvbm_3_proc
> >> >> scripts.
> >> >> >> It should
> >> >> >> >> work fine...
> >> >> >> >> >>
> >> >> >> >> >>Cheers,
> >> >> >> >> >>Gwenaelle
> >> >> >> >> >>
> >> >> >> >> >>
>
>
>
>
> dinos@Spartan:~/Desktop/FSL-VBM-new/GE/M06/struc$
> /usr/share/fsl/bin/fsl_reg 01_CON_002_S_0295_M06_struc_GM
> template_GM_init 01_CON_002_S_0295_M06_struc_GM_to_T_init
> -fnirt "--config=GM_2_MNI152GM_2mm.cnf"
>
> 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
> '01_CON_002_S_0295_M06_struc_GM_to_T_init_warp'
> ** ERROR:
> nifti_image_open(01_CON_002_S_0295_M06_struc_GM_to_T_init_warp):
> bad header info
> Error: failed to open file
> 01_CON_002_S_0295_M06_struc_GM_to_T_init_warp
> ERROR: Could not open image
> 01_CON_002_S_0295_M06_struc_GM_to_T_init_warp
> Image Exception : #22 :: Failed to read volume
> 01_CON_002_S_0295_M06_struc_GM_to_T_init_warp
> An error occured while reading file:
> 01_CON_002_S_0295_M06_struc_GM_to_T_init_warp
> ** ERROR (nifti_image_read): failed to find header file for
> '01_CON_002_S_0295_M06_struc_GM_to_T_init_warp'
> ** ERROR:
> nifti_image_open(01_CON_002_S_0295_M06_struc_GM_to_T_init_warp):
> bad header info
> Error: failed to open file
> 01_CON_002_S_0295_M06_struc_GM_to_T_init_warp
> Cannot open volume
> 01_CON_002_S_0295_M06_struc_GM_to_T_init_warp for reading!
> ** ERROR (nifti_image_read): failed to find header file for
> '01_CON_002_S_0295_M06_struc_GM_to_T_init_tmp'
> ** ERROR:
> nifti_image_open(01_CON_002_S_0295_M06_struc_GM_to_T_init_tmp):
> bad header info
> Error: failed to open file
> 01_CON_002_S_0295_M06_struc_GM_to_T_init_tmp
> ERROR: Could not open image
> 01_CON_002_S_0295_M06_struc_GM_to_T_init_tmp
> Image Exception : #22 :: Failed to read volume
> 01_CON_002_S_0295_M06_struc_GM_to_T_init_tmp
> terminate called after throwing an instance of
> 'RBD_COMMON::BaseException'
> /usr/share/fsl/bin/fsl_reg: line 144: 6066 Aborted
> ${FSLDIR}/bin/fslstats ${I2R}_tmp -M -P 50 >
> ${I2R}_warp.msf
> dinos@Spartan:~/Desktop/FSL-VBM-new/GE/M06/struc$
|
