Hi Jesper,
Will it still be possible for me to process my fairly large slice thickness data (5 mm) with the tbss tools - namely FNIRT? Or should I stick with the earlier version of FSL that did register my data with the old IRTK?
Thank you for your assistance,
Nader
Nader Metwalli
Bioengineering Ph.D. Candidate
The Wallace H. Coulter Department of Biomedical Engineering,
Georgia Institute of Technology / Emory University,
Atlanta, GA, U.S.A.
Tel: (404) 712 4439
----- Original Message -----
From: "Jesper Andersson" <[log in to unmask]>
To: [log in to unmask]
Sent: Saturday, November 8, 2008 6:28:23 AM GMT -05:00 US/Canada Eastern
Subject: Re: [FSL] FNIRT makes my MAC hang
Hi Nader,
> Error occurred when preparing to fnirt
> Exception thrown with message: FslSplines::Spline1D::Spline1D:
> knot-spacing has
> to be > 0
this seems to be the crucial one. Everything else is just knock-on. It
seems that when initializing the fields fnirt somehow thinks the
knot-spacing should be zero. Looking at the code I can see that this could
happen, but only if the voxel-size is very large in the reference image.
Could you please download an example of your CON files and then email me
(off the mailbase) the reference number.
Best regards Jesper
> ** ERROR (nifti_image_read): failed to find header file for
> 'CON_N001_dti_data_FA_FA_to_target_warp'
> ** ERROR: nifti_image_open(CON_N001_dti_data_FA_FA_to_target_warp): bad
> header
> info
> Error: failed to open file CON_N001_dti_data_FA_FA_to_target_warp
> Cannot open volume CON_N001_dti_data_FA_FA_to_target_warp for reading!
> ** ERROR (nifti_image_read): failed to find header file for
> 'CON_N001_dti_data_FA_FA_to_target_tmp'
> ** ERROR: nifti_image_open(CON_N001_dti_data_FA_FA_to_target_tmp): bad
> header
> info
> Error: failed to open file CON_N001_dti_data_FA_FA_to_target_tmp
> ERROR: Could not open image CON_N001_dti_data_FA_FA_to_target_tmp
> Image Exception : #22 :: Failed to read volume
> CON_N001_dti_data_FA_FA_to_target_tmp
> terminate called after throwing an instance of 'RBD_COMMON::BaseException'
> /usr/local/fsl/bin/fsl_reg: line 144: 4832 Abort trap
> ${FSLDIR}/bin/fslstats ${I2R}_tmp -M -P 50 >${I2R}_warp.msf
>
> I double checked my processing steps as per the FSL TBSS page and my FA
> images
> open with fslview fine..
>
> Any help is greatly appreciated.
>
> Thanks,
> Nader
> --
> Nader S. Metwalli
> Bioengineering PhD candidate
> The Wallace H. Coulter Department of Biomedical Engineering,
> Georgia Institute of Technology / Emory University,
> Atlanta, GA 30332-0535
> U.S.A.
>
>
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