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 > ${I2R}_warp.msf
dinos@Spartan:~/Desktop/FSL-VBM-new/GE/M06/struc$
|