Dear all,

When I used mkbrainmask-sess, an error occurred shown below. I am using the latest FreeSurfer, and the bet command is included in the distribution. Could anyone tell me how to fix it? thanks,

Jia

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mkbrainmask-sess

20041007syhu

$Id: mkbrainmask-sess,v 1.2 2003/10/01 21:54:43 greve Exp $

Linux zion 2.4.22-1.zion #5 SMP Sun Dec 21 12:35:17 CST 2003 i686 i686 i386 GNU/Linux

Tue Nov 23 20:23:19 CST 2004

/nfs/home/jliu/data/scramface/mystudy

-sf sessid_syhu -df sesspar

ProjectDir /nfs/home/jliu/data/scramface/mystudy

------------------------------------------------

------------------------------------------------

/nfs/home/jliu/data/scramface/20041007syhu

Tue Nov 23 20:23:19 CST 2004

/nfs/home/jliu/data/scramface/20041007syhu/bold

mkbrainmask -i 005/f -o masks/brain -thresh 0.1 -umask 2

Scratch Dir is /tmp/mkbrainmask_4734

# ---------- Converting bvolume to .img ------------------ #

mri_convert 005/f_000.bshort /tmp/mkbrainmask_4734/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 from 005/f_000.bshort...

INFO: bvolumeRead: min = 0, max = 885

TR=1.50, TE=30.00, TI=30.00, flip angle=90.00

i_ras = (-1, 0, 0)

j_ras = (0, -0.996195, 0.0871557)

k_ras = (-0, 0.087156, 0.996195)

writing to /tmp/mkbrainmask_4734/f.img...

Analyze Output Matrix

-3.125   0.000  -0.000   100.229;

 0.000  -3.113   0.418   99.376;

 0.000   0.272   4.782  -50.897;

 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/scramface/20041007syhu/bold

bet /tmp/mkbrainmask_4734/f /tmp/mkbrainmask_4734/brain -m -f 0.1

ERROR: bet failed

ERROR: mkbrainmask failed

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