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

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/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

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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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