The error you're getting is rather strange. It is coming from FSL's bet program (of which mkbrainmask is just a frontend). For some reason the wrong version of bet is being called. Can you track down exactly what is being called when you run bet. You can't just do a which, because it may be a symbolic link. What version of FSL are you using?
doug
Jia Liu wrote:
Dear group-
When I tried mkbrainmask-sess with my data, I encountered an error (see below), and the program aborted. Could any one tell me how to fix this problem? I am using the newest version available from FreeSurfer download site. Thanks,
jia
zion:/nfs/home/jliu/data/test/mystudy> mkbrainmask-sess -sf sessid_re001_2 -df sesspar
/nfs/home/jliu/data/test/20040527rd
Sun Mar 13 16:49:50 CST 2005
/nfs/home/jliu/data/test/20040527rd/bold
mkbrainmask -i 005/f -o masks/brain -thresh 0.1 -umask 2
Scratch Dir is /tmp/mkbrainmask_22219
# ---------- Converting bvolume to .img ------------------ #
mri_convert 005/f_000.bshort /tmp/mkbrainmask_22219/f.img
Reading 005/f_000.bshort ...
Reading 005/f_001.bshort ...
Reading 005/f_002.bshort ...
Reading 005/f_003.bshort ...
Reading 005/f_004.bshort ...
Reading 005/f_005.bshort ...
Reading 005/f_006.bshort ...
Reading 005/f_007.bshort ...
Reading 005/f_008.bshort ...
Reading 005/f_009.bshort ...
Reading 005/f_010.bshort ...
Reading 005/f_011.bshort ...
Reading 005/f_012.bshort ...
Reading 005/f_013.bshort ...
Reading 005/f_014.bshort ...
Reading 005/f_015.bshort ...
Reading 005/f_016.bshort ...
Reading 005/f_017.bshort ...
Reading 005/f_018.bshort ...
Reading 005/f_019.bshort ...
Reading 005/f_020.bshort ...
reading from 005/f_000.bshort...
INFO: bvolumeRead: min = 0, max = 1480
TR=1.50, TE=32.00, TI=32.00, flip angle=90.00
i_ras = (-1, 0, 0)
j_ras = (0, -0.990268, 0.139173)
k_ras = (-0, 0.139173, 0.990268)
writing to /tmp/mkbrainmask_22219/f.img...
Analyze Output Matrix
-3.125 0.000 -0.000 104.375;
0.000 -3.095 0.668 146.084;
0.000 0.435 4.753 -44.536;
0.000 0.000 0.000 1.000;
INFO: set hdr.hist.orient to 3
# ---------- Using FSL's BET to Extract Brain------------------ #
This program has not been compiled for this data type
/nfs/home/jliu/data/test/20040527rd/bold
bet /tmp/mkbrainmask_22219/f /tmp/mkbrainmask_22219/brain -m -f 0.1
ERROR: bet failed
ERROR: mkbrainmask failed
Exit 1
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