Hi,

OK, to start with don't worry about the volume measurement as it
is well within reason if the boundary correction hasn't been done.
For example, the HarvardOxford atlas has a volume of around
4200 but if you dilate this by one voxel only it becomes more like
7500!

So I'm still not sure what is going on with your images.  It seems
that now the Amygdala is failing but I don't know why and this error
seems like a downstream problem, not the primary cause.  Is this
really the only contents of the *.logs/*.e* files?  If so, can you also
include the output of the *.logs/*.o* files?  If there is more in the 
*.e* files though, just include that.

It would also be helpful to see what happens if you just try running
with "-s L_Amyg" to see if that will work on its own.

Finally, can you also let me know what kind of platform (OS type)
you are running on?

All the best,
	Mark


On 4 Jan 2011, at 15:19, Charlotte Bernard wrote:

> Thanks for your answer.
> I run FIRST without left accumbens. I obtained for all my structures .bvars, .vtk. For the putamen, the thalamus and the pallidum, I have .nii.gz and the file corrected.  But, for the others structures, I have not the .nii.gz and i have a problem with first boundary correction with the option fast. 
> This is what I can read on my shell:
> 
> ** ERROR (nifti_image_read): failed to find header file for 'output_460108-L_Amyg_corr'
> ** ERROR: nifti_image_open(output_460108-L_Amyg_corr): bad header info
> Error: failed to open file output_460108-L_Amyg_corr
> Cannot open volume output_460108-L_Amyg_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
> 
> I don't understand. I know my data are floating data.
> 
> For the volume I mentionned (5036 mm3), it was for the left hippocampus, I used the command: fslstats output_460108 -l 16.5 -u 17.5 - V
> I had use the boundary correction with the option "none". Perhaps it's for that!
> 
> Thanks 
> Charlotte
> 
> 
> > Date: Tue, 4 Jan 2011 11:39:11 +0000
> > From: [log in to unmask]
> > Subject: Re: [FSL] FIRST error
> > To: [log in to unmask]
> > 
> > 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
> > >