Hi,
I would generally recommend that you update to FSL version 5, regardless of this issue, as 4.1.9 is now quite an old version and there are lots of improvements and new options in version 5.
It is hard to say why this is failing, although limited FOV can cause this.
If that does not seem to be the problem then upload the data (of just the subject that fails) to:
https://oxfile.ox.ac.uk/oxfile/work/extBox?id=68312615463381F4C
All the best,
Mark
On 1 Jul 2014, at 03:37, SUBSCRIBE FSL Xinfa_Shi <[log in to unmask]> wrote:
> Hi ,
>
> I execute the following commands to segment brain stem :
>
> run_first_all -i CON01 -s BrStem -o CON01
> run_first_all -i CON02 -s BrStem -o CON02
>
> And the first command is normal while the second one doesn't get BrainStem with the following error :
>
> shixinfa@shixinfa:/media/E/FIRST$ cat CON01.logs/*.e*
> shixinfa@shixinfa:/media/E/FIRST$ cat CON02.logs/*.e*
> Segmentation fault (core dumped)
> ** ERROR (nifti_image_read): failed to find header file for 'CON02-BrStem_corr'
> ** ERROR: nifti_image_open(CON02-BrStem_corr): bad header info
> ERROR: failed to open file CON02-BrStem_corr
> ERROR: Could not open image CON02-BrStem_corr
> Image Exception : #22 :: Failed to read volume CON02-BrStem_corr
> terminate called after throwing an instance of 'RBD_COMMON::BaseException'
> Aborted (core dumped)
> ** ERROR (nifti_image_read): failed to find header file for 'CON02-BrStem_first'
> ** ERROR: nifti_image_open(CON02-BrStem_first): bad header info
> ERROR: failed to open file CON02-BrStem_first
> ERROR: Could not open image CON02-BrStem_first
> Image Exception : #22 :: Failed to read volume CON02-BrStem_first
> terminate called after throwing an instance of 'RBD_COMMON::BaseException'
> Aborted (core dumped)
> ** ERROR (nifti_image_read): failed to find header file for 'CON02_all_fast_origsegs'
> ** ERROR: nifti_image_open(CON02_all_fast_origsegs): bad header info
> ERROR: failed to open file CON02_all_fast_origsegs
> ERROR: Could not open image CON02_all_fast_origsegs
> Image Exception : #22 :: Failed to read volume CON02_all_fast_origsegs
> Aborted
>
> Could you tell me how to correct it ? And I have 36 subjects , how I should do to avoid the error ? My version of FSL is 4.1.9 , and if I upgrade it to 5.0 ,may it avoid the error ?
>
> Thand you in advance .
>
> Xin-Fa Shi .
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