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.
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