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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