Hi Niels,
I am sending you fslinfo (is the same for both input files) and ls -lh outputs in attached files.
The ammount of RAM is 2.9GB in a virtual machine. It is the same RAM that I have in other systems where earlier versions of FSL are running without problems.
data_type INT16
dim1 144
dim2 224
dim3 126
dim4 1
datatype 4
pixdim1 1.199995
pixdim2 1.000000
pixdim3 1.000000
pixdim4 1.000000
cal_max 0.0000
cal_min 0.0000
file_type NIFTI-1+
total 48M
-rwxrwxrwx. 1 root root 286K Oct 6 16:32 A_and_B.gif
-rwxrwxrwx. 1 root root 121K Oct 6 16:31 A_bet.png
-rwxrwxrwx. 1 root root 327K Oct 6 16:43 A_halfwayto_B_brain_mixeltype.nii.gz
-rwxrwxrwx. 1 root root 697K Oct 6 16:43 A_halfwayto_B_brain_pve_0.nii.gz
-rwxrwxrwx. 1 root root 1.1M Oct 6 16:43 A_halfwayto_B_brain_pve_1.nii.gz
-rwxrwxrwx. 1 root root 560K Oct 6 16:43 A_halfwayto_B_brain_pve_2.nii.gz
-rwxrwxrwx. 1 root root 285K Oct 6 16:43 A_halfwayto_B_brain_pveseg.nii.gz
-rwxrwxrwx. 1 root root 143K Oct 6 16:43 A_halfwayto_B_brain_seg.png
-rwxrwxrwx. 1 root root 153 Oct 6 16:32 A_halfwayto_B.mat
-rwxrwxrwx. 1 root root 6.4M Oct 6 16:43 A_halfwayto_B_render.nii.gz
-rwxrwxrwx. 1 root root 373K Oct 6 16:43 A_halfwayto_B_render.png
-rwxrwxrwx. 1 root root 329K Oct 6 16:35 A_halfwayto_scA_brain_mixeltype.nii.gz
-rwxrwxrwx. 1 root root 2.2M Oct 6 16:32 A_halfwayto_scA_brain.nii.gz
-rwxrwxrwx. 1 root root 701K Oct 6 16:35 A_halfwayto_scA_brain_pve_0.nii.gz
-rwxrwxrwx. 1 root root 1.2M Oct 6 16:35 A_halfwayto_scA_brain_pve_1.nii.gz
-rwxrwxrwx. 1 root root 564K Oct 6 16:35 A_halfwayto_scA_brain_pve_2.nii.gz
-rwxrwxrwx. 1 root root 289K Oct 6 16:35 A_halfwayto_scA_brain_pveseg.nii.gz
-rwxrwxrwx. 1 root root 5.4M Oct 6 16:32 A_halfwayto_scA.nii.gz
-rwxrwxrwx. 1 root root 4.7M Oct 6 16:31 A.nii.gz
-rwxrwxrwx. 1 root root 218K Oct 6 16:43 A_to_B_edgepoints.nii.gz
-rwxrwxrwx. 1 root root 880K Oct 6 16:43 A_to_B_flow.nii.gz
-rwxrwxrwx. 1 root root 188 Oct 6 16:32 A_to_B.mat
-rwxrwxrwx. 1 root root 224K Oct 6 16:35 A_to_scA_edgepoints.nii.gz
-rwxrwxrwx. 1 root root 904K Oct 6 16:35 A_to_scA_flow.nii.gz
-rwxrwxrwx. 1 root root 185K Oct 6 16:32 A_valid_mask_with_B.png
-rwxrwxrwx. 1 root root 120K Oct 6 16:31 B_bet.png
-rwxrwxrwx. 1 root root 324K Oct 6 16:40 B_halfwayto_A_brain_mixeltype.nii.gz
-rwxrwxrwx. 1 root root 683K Oct 6 16:40 B_halfwayto_A_brain_pve_0.nii.gz
-rwxrwxrwx. 1 root root 1.1M Oct 6 16:40 B_halfwayto_A_brain_pve_1.nii.gz
-rwxrwxrwx. 1 root root 548K Oct 6 16:40 B_halfwayto_A_brain_pve_2.nii.gz
-rwxrwxrwx. 1 root root 280K Oct 6 16:40 B_halfwayto_A_brain_pveseg.nii.gz
-rwxrwxrwx. 1 root root 144K Oct 6 16:40 B_halfwayto_A_brain_seg.png
-rwxrwxrwx. 1 root root 152 Oct 6 16:32 B_halfwayto_A.mat
-rwxrwxrwx. 1 root root 326K Oct 6 16:37 B_halfwayto_scB_brain_mixeltype.nii.gz
-rwxrwxrwx. 1 root root 2.2M Oct 6 16:35 B_halfwayto_scB_brain.nii.gz
-rwxrwxrwx. 1 root root 690K Oct 6 16:37 B_halfwayto_scB_brain_pve_0.nii.gz
-rwxrwxrwx. 1 root root 1.1M Oct 6 16:37 B_halfwayto_scB_brain_pve_1.nii.gz
-rwxrwxrwx. 1 root root 554K Oct 6 16:37 B_halfwayto_scB_brain_pve_2.nii.gz
-rwxrwxrwx. 1 root root 286K Oct 6 16:37 B_halfwayto_scB_brain_pveseg.nii.gz
-rwxrwxrwx. 1 root root 5.4M Oct 6 16:35 B_halfwayto_scB.nii.gz
-rwxrwxrwx. 1 root root 4.7M Oct 6 16:31 B.nii.gz
-rwxrwxrwx. 1 root root 214K Oct 6 16:40 B_to_A_edgepoints.nii.gz
-rwxrwxrwx. 1 root root 869K Oct 6 16:40 B_to_A_flow.nii.gz
-rwxrwxrwx. 1 root root 189 Oct 6 16:32 B_to_A.mat
-rwxrwxrwx. 1 root root 221K Oct 6 16:37 B_to_scB_edgepoints.nii.gz
-rwxrwxrwx. 1 root root 894K Oct 6 16:37 B_to_scB_flow.nii.gz
-rwxrwxrwx. 1 root root 190K Oct 6 16:32 B_valid_mask_with_A.png
-rwxrwxrwx. 1 root root 0 Oct 8 13:51 ls-lh.txt
-rwxrwxrwx. 1 root root 4.5K Oct 6 16:43 report.html
-rwxrwxrwx. 1 root root 2.7K Oct 6 16:43 report.siena
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