Hi,
Sometimes FIRST has problems estimating small structures, or structures
on the edge of the FOV. I suspect that if you only see errors relating to the
Left Accumbens, then it might be a problem for only this structure. Can you
test this by running FIRST (via run_first_all - which is what I am assuming
that you are doing) and specify the option:
-s L_Amyg,L_Caud,L_Hipp,L_Late,L_Pall,L_Puta,L_Thal,R_Amyg,R_Caud,R_Hipp,R_Late,R_Pall,R_Puta,R_Thal,BrStem
If this works then we can try and sort out the accumbens problem separately.
As for the volume question - what image did you run this on, what command
did you use, and what structure were you trying to measure? Without this
information I really cannot comment further.
All the best,
Mark
On 3 Jan 2011, at 16:35, SUBSCRIBE FSL Anonymous wrote:
> Dear FSL users,
>
> I try to understand how to run FIRST. I have two problems:
>
> 1) I have run it on one of my subject to better understand how the method works.
> My problem is that I don't have the file: output_name_all_fast_firstseg.nii.gz and I have this error in the logs:
> ** ERROR (nifti_image_read): failed to find header file for 'output_460108-L_Accu_corr'
> ** ERROR: nifti_image_open(output_460108-L_Accu_corr): bad header info
> Error: failed to open file output_460108-L_Accu_corr
> Cannot open volume output_460108-L_Accu_corr for reading!
> ** ERROR (nifti_image_read): failed to find header file for 'output_460108_all_fast_firstseg'
> ** ERROR: nifti_image_open(output_460108_all_fast_firstseg): bad header info
> Error: failed to open file output_460108_all_fast_firstseg
> ERROR: Could not open image output_460108_all_fast_firstseg
> Image Exception : #22 :: Failed to read volume output_460108_all_fast_firstseg
> Aborted
>
> When I wrote cat *.logs/*.e*, i can read that:
>
> /usr/local/fsl/bin/first_boundary_corr: line 149: printf: 131.0000000000: nombre non valable
> /usr/local/fsl/bin/first_boundary_corr: line 149: printf: 131.0000000000: nombre non valable
> /usr/local/fsl/bin/first_boundary_corr: line 149: printf: 73.0000000000: nombre non valable
> terminate called after throwing an instance of 'NEWMAT::SingularException'
> /usr/local/fsl/bin/first_boundary_corr: line 88: 9426 Abandon flirt -in ${imout}_roi -ref ${imlb} -out ${imout} -interp
>
> I don't understand what I mean. I believe there is a problem with the boundary correction but I don't know how to correct it.
>
> 2) My second problem is with fslstat:
> I run manually each stage of FIRST with the same subject. I had no problem! But I obtained avolume of 5036 mm3. It's big isn't it?
>
> I hope somebody can help me,
> Thanks
> Charlotte
>
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