Hi David,
it seems that something is missing from the 2nd step of fslvbm (you should have a Subject.MPRAGE_struc_GM_to_T_init.nii.gz)...
Can you please attach your fslvbm2d file and one of your fslvbm2d.e* and fslvbm2d.o* log file?
Thanks,
Gwenaelle
--- En date de : Jeu 19.3.09, David Lahna <[log in to unmask]> a écrit :
> De: David Lahna <[log in to unmask]>
> Objet: Re: [FSL] Re : [FSL] VBM trouble: no GM_mod_merg file
> À: [log in to unmask]
> Date: Jeudi 19 Mars 2009, 20h37
> Thanks for taking time to help me with this.
>
> For each subject I have these files in struc:
>
> Subject.MPRAGE_struc_brain_mixeltype.nii.gz
> Subject.MPRAGE_struc_brain.nii.gz
> Subject.MPRAGE_struc_brain_pve_0.nii.gz
> Subject.MPRAGE_struc_brain_pve_2.nii.gz
> Subject.MPRAGE_struc_brain_pveseg.nii.gz
> Subject.MPRAGE_struc_brain_seg.nii.gz
> Subject.MPRAGE_struc_cut.nii.gz
> Subject.MPRAGE_struc_GM.nii.gz
> Subject.MPRAGE_struc_GM_to_template_GM.mat
> Subject.MPRAGE_struc_GM_to_template_GM_warp.msf
> Subject.MPRAGE_struc_GM_to_T_init.mat
> Subject.MPRAGE_struc_GM_to_T_init_warp.msf
> Subject.MPRAGE_struc_GM_to_T.mat
> Subject.MPRAGE_struc_GM_to_T.nii.gz
> Subject.MPRAGE_struc.nii
>
>
> While fslvbm3a.e* contains:
>
> The usage of fnirt (as if "fnirt" had been
> entered into the terminal without any arguments)
>
> followed by:
>
> fnirt::fnirt_clp: No file matching --refmask= found
> ** ERROR (nifti_image_read): failed to find header file for
> 'Subject.MPRAGE_struc_GM_to_template_GM_warp'
> ** ERROR:
> nifti_image_open(Subject.MPRAGE_struc_GM_to_template_GM_warp):
> bad header info
> Error: failed to open file
> Subject.MPRAGE_struc_GM_to_template_GM_warp
> ERROR: Could not open image
> Subject.MPRAGE_struc_GM_to_template_GM_warp
> Image Exception : #22 :: Failed to read volume
> Subject.MPRAGE_struc_GM_to_template_GM_warp
> An error occured while reading file:
> Subject.MPRAGE_struc_GM_to_template_GM_warp
> ** ERROR (nifti_image_read): failed to find header file for
> 'Subject.MPRAGE_struc_GM_to_template_GM_warp'
> ** ERROR:
> nifti_image_open(Subject.MPRAGE_struc_GM_to_template_GM_warp):
> bad header info
> Error: failed to open file
> Subject.MPRAGE_struc_GM_to_template_GM_warp
> Cannot open volume
> Subject.MPRAGE_struc_GM_to_template_GM_warp for reading!
> ** ERROR (nifti_image_read): failed to find header file for
> 'Subject.MPRAGE_struc_GM_to_template_GM_tmp'
> ** ERROR:
> nifti_image_open(Subject.MPRAGE_struc_GM_to_template_GM_tmp):
> bad header info
> Error: failed to open file
> Subject.MPRAGE_struc_GM_to_template_GM_tmp
> ERROR: Could not open image
> Subject.MPRAGE_struc_GM_to_template_GM_tmp
> Image Exception : #22 :: Failed to read volume
> Subject.MPRAGE_struc_GM_to_template_GM_tmp
> terminate called after throwing an instance of
> 'RBD_COMMON::BaseException'
> /home/david/Resources/FSL/bin/fsl_reg: line 144: 6409
> Aborted ${FSLDIR}/bin/fslstats ${I2R}_tmp -M
> -P 50 > ${I2R}_warp.msf
> ** ERROR (nifti_image_read): failed to find header file for
> 'Subject.MPRAGE_struc_GM_to_template_GM'
> ** ERROR:
> nifti_image_open(Subject.MPRAGE_struc_GM_to_template_GM):
> bad header info
> Error: failed to open file
> Subject.MPRAGE_struc_GM_to_template_GM
> Cannot open volume Subject.MPRAGE_struc_GM_to_template_GM
> for reading!
>
> -----Original Message-----
> From: FSL - FMRIB's Software Library on behalf of
> Gwenaëlle DOUAUD
> Sent: Thu 3/19/2009 12:02 PM
> To: [log in to unmask]
> Subject: [FSL] Re : [FSL] VBM trouble: no GM_mod_merg file
>
> Hi David,
>
> this is presumably not at the fslvbm3b that you got some
> troubles... What are all the outputs (related to just one of
> your exam, that will be enough) that you can find in your
> struc/ directory? Also, what do you get in one of your
> fslvbm3a.e* of struc/?
>
> Cheers,
> Gwenaelle
>
>
> --- En date de : Jeu 19.3.09, David Lahna
> <[log in to unmask]> a écrit :
>
> > De: David Lahna <[log in to unmask]>
> > Objet: [FSL] VBM trouble: no GM_mod_merg file
> > À: [log in to unmask]
> > Date: Jeudi 19 Mars 2009, 19h37
> > I am trying to do a VBM analysis.
> > "fslvbm_1_bet -N" and
> "fslvbm_2_template
> > -n" appear to work appropriately
> > (template_GM_4D looks good) but fslvbm_3_proc does not
> > generate a
> > GM_mod_merg file.
> >
> > Here is the contents of my stats folder:
> > design.con
> > fslvbm3b
> > fslvbm3b.o18784
> >
> > design.mat
> > fslvbm3b.e18784
> > template_GM.nii.gz
> >
> >
> > and the contents of fslvbm3b.e18784 :
> >
> > ** ERROR (nifti_image_read): failed to find header
> file for
> > 'GM_merg'
> >
> > ** ERROR: nifti_image_open(GM_merg): bad header info
> >
> > Error: failed to open file GM_merg
> >
> > Cannot open volume GM_merg for reading!
> >
> > ** ERROR (nifti_image_read): failed to find header
> file for
> > 'GM_mod_merg'
> >
> > ** ERROR: nifti_image_open(GM_mod_merg): bad header
> info
> >
> > Error: failed to open file GM_mod_merg
> >
> > Cannot open volume GM_mod_merg for reading!
> >
> > ** ERROR (nifti_image_read): failed to find header
> file for
> > 'GM_mod_merg_s2'
> >
> > ** ERROR: nifti_image_open(GM_mod_merg_s2): bad header
> info
> >
> > Error: failed to open file GM_mod_merg_s2
> >
> > ERROR: Could not open image GM_mod_merg_s2
> >
> > ERROR: Program failed
> >
> >
> >
> > An exception has been thrown
> >
> > Failed to read volume GM_mod_merg_s2
> >
> >
> >
> > Exiting
> >
> > ** ERROR (nifti_image_read): failed to find header
> file for
> > 'GM_mod_merg'
> >
> > ** ERROR: nifti_image_open(GM_mod_merg): bad header
> info
> >
> > Error: failed to open file GM_mod_merg
> >
> > Cannot open volume GM_mod_merg for reading!
> >
> > ** ERROR (nifti_image_read): failed to find header
> file for
> > 'GM_mod_merg_s3'
> >
> > ** ERROR: nifti_image_open(GM_mod_merg_s3): bad header
> info
> >
> > Error: failed to open file GM_mod_merg_s3
> >
> > ERROR: Could not open image GM_mod_merg_s3
> >
> > ERROR: Program failed
> >
> >
> >
> > An exception has been thrown
> >
> > Failed to read volume GM_mod_merg_s3
> >
> >
> >
> > Exiting
> >
> > ** ERROR (nifti_image_read): failed to find header
> file for
> > 'GM_mod_merg'
> >
> > ** ERROR: nifti_image_open(GM_mod_merg): bad header
> info
> >
> > Error: failed to open file GM_mod_merg
> >
> > Cannot open volume GM_mod_merg for reading!
> >
> > ** ERROR (nifti_image_read): failed to find header
> file for
> > 'GM_mod_merg_s4'
> >
> > ** ERROR: nifti_image_open(GM_mod_merg_s4): bad header
> info
> >
> > Error: failed to open file GM_mod_merg_s4
> >
> > ERROR: Could not open image GM_mod_merg_s4
> >
> > ERROR: Program failed
> >
> >
> >
> > An exception has been thrown
> >
> > Failed to read volume GM_mod_merg_s4
> >
> >
> >
> > Exiting
> >
> > I have probably made a silly error somewhere. Any help
> > would be much
> > appreciated, thanks.
