Hi Eleftherios,
this is actually the same problem than Antonios-Constantine has when he's running FSL-VBM... It has come up several times in the FSL list under various titles (look for fnirt config in the FSL archives). Hopefully Jesper will come up with an answer on how getting/finding these config files (for you the FA one, for Antonios the GM one).
Cheers,
Gwenaelle
--- En date de : Mer 17.9.08, Eleftherios Garyfallidis <[log in to unmask]> a écrit :
> De: Eleftherios Garyfallidis <[log in to unmask]>
> Objet: [FSL] Re : [FSL] tbss_3_postreg problem fix not working]
> À: [log in to unmask]
> Date: Mercredi 17 Septembre 2008, 17h37
> Hi,
>
> When I am running
>
> imaging/local/linux/bin/fsl-4.1.0/bin/fsl_reg
> 070987_dti_FA_FA target
> 070987_dti_FA_FA_to_target -e -FA
>
> inside the FA directory I can see flirt running (using top)
> but then I
> am getting the following errors
>
>
> Cannot find config-file FA_2_FMRIB58_1mm
> ** ERROR (nifti_image_read): failed to find header file for
>
> '070987_dti_FA_FA_to_target_warp'
> ** ERROR:
> nifti_image_open(070987_dti_FA_FA_to_target_warp): bad
> header
> info
> Error: failed to open file 070987_dti_FA_FA_to_target_warp
> Cannot open volume 070987_dti_FA_FA_to_target_warp for
> reading!
> ** ERROR (nifti_image_read): failed to find header file for
>
> '070987_dti_FA_FA_to_target_tmp'
> ** ERROR: nifti_image_open(070987_dti_FA_FA_to_target_tmp):
> bad header info
> Error: failed to open file 070987_dti_FA_FA_to_target_tmp
> ERROR: Could not open image 070987_dti_FA_FA_to_target_tmp
> Image Exception : #22 :: Failed to read volume
> 070987_dti_FA_FA_to_target_tmp
> terminate called after throwing an instance of
> 'RBD_COMMON::BaseException'
> /imaging/local/linux/bin/fsl-4.1.0/bin/fsl_reg: line 144:
> 1522
> Aborted ${FSLDIR}/bin/fslstats ${I2R}_tmp
> -M -P 50
> >${I2R}_warp.msf
>
> and I am getting this errors when I run it above the FA
> directory
>
> Cannot open volume 070987_dti_FA_FA_to_target_warp for
> reading!
> ** ERROR (nifti_image_read): failed to find header file for
>
> '070987_dti_FA_FA_to_target_tmp'
> ** ERROR: nifti_image_open(070987_dti_FA_FA_to_target_tmp):
> bad header info
> Error: failed to open file 070987_dti_FA_FA_to_target_tmp
> ERROR: Could not open image 070987_dti_FA_FA_to_target_tmp
> Image Exception : #22 :: Failed to read volume
> 070987_dti_FA_FA_to_target_tmp
> terminate called after throwing an instance of
> 'RBD_COMMON::BaseException'
> /imaging/local/linux/bin/fsl-4.1.0/bin/fsl_reg: line 144:
> 32569
> Aborted ${FSLDIR}/bin/fslstats ${I2R}_tmp
> -M -P 50
> >${I2R}_warp.msf
> [eg01@l40 tbss]$
> /imaging/local/linux/bin/fsl-4.1.0/bin/fsl_reg
> 070987_dti_FA_FA target 070987_dti_FA_FA_to_target -e -FA
> > log.txt
> ** ERROR (nifti_image_read): failed to find header file for
> 'target'
> ** ERROR: nifti_image_open(target): bad header info
> Error: failed to open file target
> ERROR: Could not open image target
> Image Exception : #22 :: Failed to read volume target
> terminate called after throwing an instance of
> 'RBD_COMMON::BaseException'
> /imaging/local/linux/bin/fsl-4.1.0/bin/fsl_reg: line 124:
> 32718
> Aborted ${FSLDIR}/bin/flirt -ref $REFERENCE
> -in $INPUT
> $INMASK -omat ${I2R}.mat $flirtopts
> Cannot find config-file FA_2_FMRIB58_1mm
> ** ERROR (nifti_image_read): failed to find header file for
>
> '070987_dti_FA_FA_to_target_warp'
> ** ERROR:
> nifti_image_open(070987_dti_FA_FA_to_target_warp): bad
> header
> info
> Error: failed to open file 070987_dti_FA_FA_to_target_warp
> Cannot open volume 070987_dti_FA_FA_to_target_warp for
> reading!
> ** ERROR (nifti_image_read): failed to find header file for
>
> '070987_dti_FA_FA_to_target_tmp'
> ** ERROR: nifti_image_open(070987_dti_FA_FA_to_target_tmp):
> bad header info
> Error: failed to open file 070987_dti_FA_FA_to_target_tmp
> ERROR: Could not open image 070987_dti_FA_FA_to_target_tmp
> Image Exception : #22 :: Failed to read volume
> 070987_dti_FA_FA_to_target_tmp
> terminate called after throwing an instance of
> 'RBD_COMMON::BaseException'
> /imaging/local/linux/bin/fsl-4.1.0/bin/fsl_reg: line 144:
> 32721
> Aborted ${FSLDIR}/bin/fslstats ${I2R}_tmp
> -M -P 50
> >${I2R}_warp.msf
>
> So in both cases I don't see any of the following
>
> Setting subsampling
> Setting reg mode
> Setting lambda
>
> Any ideas?
>
> Cheers,
> Eleftherios
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