Hi,
You should be specifying an output file name.
If you do not it takes the name to be blank, and I suspect
that it creates problems during the processing and that is
why you see differences in the outputs.
All the best,
Mark
On 15 Oct 2010, at 12:56, Duncan wrote:
> Hello,
>
> I'm trying to look at hippocampal volumes from a range of subjects.
>
> (1) If I run_first_all without specifying an output file name, I get
> different output files to if I run_first_all with an output file
> specified. Can anyone explain why?
> I presume specifying an output filename is the best way to proceed?
> (Details of which files listed below).
>
> (2) If I run fslstats -V on some of these output files, I get quite
> different results.
> Of the three measures that seem to make reasonable sense, can anyone
> advise on the most realistic measure of hippocampal volume?
>
> fslstats NAME-L_Hipp_first.nii.gz -V (obtained from both output and
> non-output run_first_all)
> 3478 4576.762695
> fslstats NAME-L_Hipp_corr.nii.gz -V (obtained from output
> run_first_all only)
> 2665 3506.921387
> fslstats -L_Hipp_corr_grot.nii.gz -V (obtained from non-output
> run_first_all only)
> 1642 2160.737305
>
> Thanks very much in advance,
> Duncan
>
>
> SPECIFIED OUTPUT (-o):
> run_first_all -i IMAGENAME -b -s L_Hipp -o NAME
> image_spgr_axial.img_to_std_sub.mat
>
> GIVES:
> NAME.com
> NAME-L_Hipp_first.nii.gz
> IMAGENAME_spgr_axial_to_std_sub.nii.gz
> NAME-L_Hipp_corr.nii.gz
> NAME-L_Hipp_first.vtk
> NAME-L_Hipp_first.bvars
> NAME.logs
> IMAGENAME_spgr_axial_to_std_sub.mat
>
> NON-SPECIFIED OUTPUT:
> run_first_all -i IMAGENAME -b -s L_Hipp
> image_spgr_axial.img_to_std_sub.mat
>
> GIVES:
> NAME.logs
> -L_Hipp_corr_t1_roi.nii.gz
> -L_Hipp_first.nii.gz
> -L_Hipp_corr_grot.nii.gz
> -L_Hipp_corr_trans_roi.mat
> -L_Hipp_first.vtk
> IMAGENAME_spgr_axial_to_std_sub.mat
> -L_Hipp_corr_lb_roi.nii.gz
> -L_Hipp_first.bvars
> IMAGENAME_spgr_axial_to_std_sub.nii.gz
>
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