Dear FSL friends,
I have some weird output compared to these one mentioned in your documentation.Some are missing, some are extra? Furthermore when I look at the log file it seems to be that the GUI calculates not exactly what I set in.
So my output files are looking like these:
d_stdsamples.nii.gz (extra)
dsamples.nii.gz (extra)
dyads1.nii.gz
dyads2.nii.gz
f1samples.nii.gz (extra)
f2samples.nii.gz (extra)
logfile
mean_d_stdsamples.nii.gz (extra)
mean_dsamples.nii.gz
mean_f1samples.nii.gz
mean_f2samples.nii.gz
mean_S0samples.nii.gz
ph1samples.nii.gz (extra)
ph2samples.nii.gz (extra)
th1sample.nii.gz (extra)
th2samples.nii.gz (extra)
compared to these from your FDT documentary:
merged_th1samples (missing)
merged_th2samples (missing)
merged_ph1samples (missing)
merged_ph2samples (missing)
merged_f1samples (missing)
merged_f2samples (missing)
mean_th1samples (missing)
mean_th2samples (missing)
mean_ph1samples (missing)
mean_ph2samples (missing)
mean_f1samples
mean_f2samples
mean_dsamples
mean_S0samples
dyads1
dyads2
dyads1_dispersion (missing)
dyads2_dispersion (missing)
nodif_brain_mask (missing)
I used FDT GUI with the default scheme: fibres 2 ; weight 1; burn in 1000.
The command started by GUI in the terminal looks like this:
bedpostx /Users/wichmann/Desktop/Max/.../preprocessing/bedpostx/bedpostx_b0500 --nf=2 --fudge=1.0 --bi=1000
/Applications/FSL/bin/bedpostx /Users/wichmann/.../preprocessing/bedpostx/bedpostx_b0500 --nf=2 --fudge=1.0 --bi=1000
subjectdir is /Users/wichmann/.../preprocessing/bedpostx/bedpostx_b0500
Making bedpostx directory structure
Queuing preprocessing stages
Queuing parallel processing stage
----- Bedpostx Monitor -----
1 slices processed out of 62
2 slices processed out of 62
.
.
.
So it looks quite similar to that what I set in the GUI.
But then I do not understand the outputs? I do have some additional outputs and some are missing. I also read that for example the output d_stdsamples.nii.gz belongs to the model2 (multishell) which I didnt supply.
Due to that weirdness I looked at the logfile protocol which is also strange?
I do not understand it at all. First it is said --nf=3 and also --nf=2, then there a extra parameter set like --nj, --se, --model, --cnonlinear.
logfile:
/Applications/FSL/bin/xfibres --data=/Users/wichmann/.../preprocessing/bedpostx/bedpostx_b0500/data_slice_0015 --mask=/Users/wichmann/.../preprocessing/bedpostx/bedpostx_b0500/nodif_brain_mask_slice_0015 -b /Users/wichmann/.../preprocessing/bedpostx/bedpostx_b0500/bvals -r /Users/wichmann/.../preprocessing/bedpostx/bedpostx_b0500/bvecs --forcedir --logdir=/Users/wichmann/Desktop/.../preprocessing/bedpostx/bedpostx_b0500.bedpostX/diff_slices/data_slice_0015 --nf=3 --fudge=1 --bi=1000 --nj=1250 --se=25 --model=2 --cnonlinear --nf=2 --fudge=1.0 --bi=1000
Thank you
Best
Max
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