Hi Mark,

   Thanks for your quick reply. I followed your instruction and got rid of
the  hash character "#", then run the cmd "bedpost ./" again. But got the
same error messsage:
[haibo@localhost 1_4]$ bedpost ./
subjectdir is /data/licuixia/1_4
making bedpost directory
copying files to bedpost directory
processing data on local host
4 slices processed
5 slices processed
6 slices processed
6 slices processed
7 slices processed
9 slices processed
11 slices processed
12 slices processed
13 slices processed
13 slices processed
14 slices processed
15 slices processed
15 slices processed
16 slices processed
17 slices processed
17 slices processed
18 slices processed
19 slices processed
19 slices processed
20 slices processed
21 slices processed
21 slices processed
22 slices processed
23 slices processed
23 slices processed
24 slices processed
25 slices processed
26 slices processed
26 slices processed
27 slices processed
28 slices processed
29 slices processed
30 slices processed
31 slices processed
32 slices processed
33 slices processed
35 slices processed
Merging outputs into 4D files
DONE
/usr/local/freesurfer/fsl/bin/bedpost: line 293: syntax error: unexpected
end of file

Using "bedpost_datacheck ./" and the cmd dtifit, everything is fine. Bedpost
<indir> files include as followings:
bvals                             li_cui_xia_1_4__ep_b1000_005.img
bvecs                             li_cui_xia_1_4__ep_b1000_006.hdr
data.ecclog                       li_cui_xia_1_4__ep_b1000_006.img
data.nii.gz                       li_cui_xia_1_4__ep_b1000_007.hdr
diff4D.nii.gz                     li_cui_xia_1_4__ep_b1000_007.img
eddy_cor.ecclog                   li_cui_xia_1_4__ep_b1000_008.hdr
eddy_cor.nii.gz                   li_cui_xia_1_4__ep_b1000_008.img
fdt.log                           li_cui_xia_1_4__ep_b1000_009.hdr
li_cui_xia_1_15.hdr               li_cui_xia_1_4__ep_b1000_009.img
li_cui_xia_1_15.img               li_cui_xia_1_4__ep_b1000_010.hdr
li_cui_xia_1_16.hdr               li_cui_xia_1_4__ep_b1000_010.img
li_cui_xia_1_16.img               li_cui_xia_1_4__ep_b1000_011.hdr
li_cui_xia_1_4_bvals              li_cui_xia_1_4__ep_b1000_011.img
li_cui_xia_1_4_bvecs              m_FA.nii.gz
li_cui_xia_1_4__ep_b0.hdr         m_L1.nii.gz
li_cui_xia_1_4__ep_b0.img         m_L2.nii.gz
li_cui_xia_1_4__ep_b1000_000.hdr  m_L3.nii.gz
li_cui_xia_1_4__ep_b1000_000.img  m_MD.nii.gz
li_cui_xia_1_4__ep_b1000_001.hdr  m_S0.nii.gz
li_cui_xia_1_4__ep_b1000_001.img  m_V1.nii.gz
li_cui_xia_1_4__ep_b1000_002.hdr  m_V2.nii.gz
li_cui_xia_1_4__ep_b1000_002.img  m_V3.nii.gz
li_cui_xia_1_4__ep_b1000_003.hdr  nodif_brain_mask.nii.gz
li_cui_xia_1_4__ep_b1000_003.img  nodif_brain.nii.gz
li_cui_xia_1_4__ep_b1000_004.hdr  nodif_brain_overlay.nii.gz
li_cui_xia_1_4__ep_b1000_004.img  nodif.nii.gz
li_cui_xia_1_4__ep_b1000_005.hdr  xfms-bkup

I do not know what happened to me, please give me some advices. BTW, would
you tell me a little detailed info about how to set up the "two masks" or
"connectivity" ,and then how to input the selection into the cmd probtrack.
Thanks in advance.

--haibo