Hi - I think this is fixed in the most recent patch release.
Cheers.
On 26 Feb 2009, at 22:09, Roderick McColl wrote:
> Hi all,
>
> Further to my previous email to the group,
>
> I have found that fnirt core dumps when the ref and input are the
> same,
> as below. So I ended up with 24 cores from my 24 FA maps, one each
> for when the ref and input are the same. So its really a problem with
> tbss_2_reg rather than tbss_3_preproc.
>
> Here is an example from the analysis with fnirt error messages.
>
> The two datasets tested are 004_FA and 007_FA.
>
> First is 007_FA to 004_FA, works fine.
> Second is 004_FA to 004_FA, fnirt not happy.
>
> Suggestions appreciated.
>
> -roddy
>
> ----------------------------------------------------------------------------------------------
>
> [roddy@ FA]$ fsl_reg 007_FA_FA 004_FA_FA 007_to_004 -e -FA
> Setting subsampling
> Setting reg mode
> Setting lambda
> Setting subsampling
> Setting reg mode
> Setting lambda
> Setting subsampling
> Setting reg mode
> Setting lambda
> [roddy@ FA]$ fslmaths 007_to_004_warp -sqr -Tmean 007_to_004_tmp
> [roddy@ FA]$ fslstats 007_to_004_tmp -M -P 50
> fslstats 007_to_004_tmp -M -P 50
> 1.850713 0.492692
>
> [roddy@ FA]$ fsl_reg 004_FA_FA 004_FA_FA 004_to_004 -e -FA
> Error occured during estimation at first level of subsampling
> Exception thrown with message: SpMat::DiagPrecond: Cannot condition
> singular matrix
> ** ERROR (nifti_image_read): failed to find header file for
> '004_to_004_warp'
> ** ERROR: nifti_image_open(004_to_004_warp): bad header info
> Error: failed to open file 004_to_004_warp
> Cannot open volume 004_to_004_warp for reading!
> ** ERROR (nifti_image_read): failed to find header file for
> '004_to_004_tmp'
> ** ERROR: nifti_image_open(004_to_004_tmp): bad header info
> Error: failed to open file 004_to_004_tmp
> ERROR: Could not open image 004_to_004_tmp
> Image Exception : #22 :: Failed to read volume 004_to_004_tmp
> terminate called after throwing an instance of
> 'RBD_COMMON::BaseException'
> /usr/local/fsl/bin/fsl_reg: line 144: 23675 Aborted ${FSLDIR}/bin/
> fslstats ${I2R}_tmp -M -P 50 > ${I2R}_warp.msf
>
---------------------------------------------------------------------------
Stephen M. Smith, Professor of Biomedical Engineering
Associate Director, Oxford University FMRIB Centre
FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK
+44 (0) 1865 222726 (fax 222717)
[log in to unmask] http://www.fmrib.ox.ac.uk/~steve
---------------------------------------------------------------------------
|