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
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[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
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