Dear Matthew,
Dear Wolf,
thank you very much, that did the trick! Of course, upon closer inspection, that information was in the fslmaths help as well… Thank you for the support!
Best regards,
Christian
> ------------------------------
>
> Date: Fri, 6 Jul 2018 15:47:43 +0000
> From: Matthew Webster <[log in to unmask]>
> Subject: Re: Generating a mean slab?
>
> Dear Christian,
> The Zmean option ( in conjunction with the -roi option isn’t quite doing what you want ). The roi option zeroes out data but doesn’t change the image size - hence the means being lower in magnitude. You can fix this by multiplying by the ratio of the total number of slices to the roi slices.
>
> Hope this helps,
> Kind Regards
> Matthew
> --------------------------------
> Dr Matthew Webster
> FMRIB Centre
> John Radcliffe Hospital
> University of Oxford
>
> On 5 Jul 2018, at 22:07, Christian Rubbert <[log in to unmask]<mailto:[log in to unmask]>> wrote:
>
> Dear Wolf,
>
> thank you! You were right about fslmaths -r on Zmean/Zmax/Zmin, partly, those looks closer to what I am expecting.
>
> Still, Zmean should be way closer to to 1000-range than to 50ies. When I look at the slabs, air around the skull has voxel values of around -1000 in the min slabs (good), around -50 in the mean slabs (not ok) and 0 in the max slabs (also not ok, should also be around -1000). It’s strange that the values seem to be capped at 0 for min/max. I just tried setting the datatype to „double", but to no avail.
>
> $ fslstats dcm-in_5_Tilt_1.nii.gz -r
> -1025.914429 1093.793823
>
> $ for i in 5mm/slab_*; do echo -n "${i}: "; fslstats $i -r; done
> 5mm/slab_max_00.nii.gz: 0.000000 362.568481
> 5mm/slab_max_05.nii.gz: 0.000000 909.484619
> 5mm/slab_max_10.nii.gz: 0.000000 1308.794922
> 5mm/slab_max_15.nii.gz: 0.000000 1552.649048
> 5mm/slab_max_20.nii.gz: 0.000000 1593.271240
> 5mm/slab_max_25.nii.gz: 0.000000 1617.283569
> 5mm/slab_max_30.nii.gz: 0.000000 1472.851929
> 5mm/slab_max_35.nii.gz: 0.000000 1367.153687
> 5mm/slab_max_40.nii.gz: 0.000000 1286.210938
> 5mm/slab_max_45.nii.gz: 0.000000 1217.777954
> 5mm/slab_max_50.nii.gz: 0.000000 1261.649536
> 5mm/slab_max_55.nii.gz: 0.000000 1335.314819
> 5mm/slab_max_60.nii.gz: 0.000000 1354.703125
> 5mm/slab_max_65.nii.gz: 0.000000 1416.141479
> 5mm/slab_max_70.nii.gz: 0.000000 1439.741455
> 5mm/slab_max_75.nii.gz: 0.000000 1344.748657
> 5mm/slab_max_80.nii.gz: 0.000000 1319.691528
> 5mm/slab_max_85.nii.gz: 0.000000 1384.317993
> 5mm/slab_max_90.nii.gz: 0.000000 1377.896851
>
> 5mm/slab_mean_00.nii.gz: -53.744469 5.405800
> 5mm/slab_mean_05.nii.gz: -53.782631 19.646496
> 5mm/slab_mean_10.nii.gz: -53.870125 31.961800
> 5mm/slab_mean_15.nii.gz: -53.855896 46.077209
> 5mm/slab_mean_20.nii.gz: -53.908989 55.081894
> 5mm/slab_mean_25.nii.gz: -53.894180 62.276062
> 5mm/slab_mean_30.nii.gz: -53.936626 63.511929
> 5mm/slab_mean_35.nii.gz: -54.039600 58.815556
> 5mm/slab_mean_40.nii.gz: -54.030624 60.064259
> 5mm/slab_mean_45.nii.gz: -54.010727 58.766396
> 5mm/slab_mean_50.nii.gz: -53.992157 56.839329
> 5mm/slab_mean_55.nii.gz: -53.993927 55.504997
> 5mm/slab_mean_60.nii.gz: -53.894657 54.894573
> 5mm/slab_mean_65.nii.gz: -53.971203 53.766869
> 5mm/slab_mean_70.nii.gz: -53.986263 51.587803
> 5mm/slab_mean_75.nii.gz: -53.878334 45.685486
> 5mm/slab_mean_80.nii.gz: -53.845192 44.340462
> 5mm/slab_mean_85.nii.gz: -53.730179 44.319714
> 5mm/slab_mean_90.nii.gz: -53.631649 39.829578
>
> 5mm/slab_min_00.nii.gz: -1024.874634 0.000000
> 5mm/slab_min_05.nii.gz: -1025.274658 0.000000
> 5mm/slab_min_10.nii.gz: -1025.711304 0.000000
> 5mm/slab_min_15.nii.gz: -1027.105225 0.000000
> 5mm/slab_min_20.nii.gz: -1025.801880 0.000000
> 5mm/slab_min_25.nii.gz: -1027.944580 0.000000
> 5mm/slab_min_30.nii.gz: -1026.449585 0.000000
> 5mm/slab_min_35.nii.gz: -1025.554443 0.000000
> 5mm/slab_min_40.nii.gz: -1024.709229 0.000000
> 5mm/slab_min_45.nii.gz: -1024.415649 0.000000
> 5mm/slab_min_50.nii.gz: -1024.604858 0.000000
> 5mm/slab_min_55.nii.gz: -1024.377441 0.000000
> 5mm/slab_min_60.nii.gz: -1024.880981 0.000000
> 5mm/slab_min_65.nii.gz: -1025.405396 0.000000
> 5mm/slab_min_70.nii.gz: -1025.158447 0.000000
> 5mm/slab_min_75.nii.gz: -1024.826782 0.000000
> 5mm/slab_min_80.nii.gz: -1025.350464 0.000000
> 5mm/slab_min_85.nii.gz: -1027.145752 0.000000
> 5mm/slab_min_90.nii.gz: -1027.430054 0.000000
>
> Any clues?
>
> Thank you!
>
> Best regards,
> Christian
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