Hi All,
I have been having some trouble running bedpost and so I tried to replicate
the subj1 data. When I ran "bedpost subj1" on the sample data, the program
produced all off the expected output files, but ended early with the
following error:
marc-dubins-computer:~/Documents/feeds/examples marc$ bedpost fdt_subj1
subjectdir is /Users/marc/Documents/feeds/examples/fdt_subj1
making bedpost directory
copying files to bedpost directory
processing data on local host
0 slices processed
Merging outputs into 4D files
DONE
/usr/local/fsl/bin/bedpost: line 293: syntax error: unexpected end of file
I also compared the logfiles between the pre-run bedpost (that comes with
the sample data in directory fdt_subj1.bedpost) and my run. My run
appears to have all of the same iterations (4555) but it is written in a
different format.
A few sample lines from the logfile from my run are included here:
Log directory is:
/Users/marc/Documents/feeds/examples/fdt_subj1.bedpost/diff_slices/data_slice_0000
ntpts=65
nvoxels=4555
nparams=5
nsamples=50
1,(data-retend).SumSquare()=2273.97
2,(data-retend).SumSquare()=2362.2
3,(data-retend).SumSquare()=3256.89
4,(data-retend).SumSquare()=2625.69
5,(data-retend).SumSquare()=2818.28
6,(data-retend).SumSquare()=1496.17
7,(data-retend).SumSquare()=1958.92
8,(data-retend).SumSquare()=2266.13
9,(data-retend).SumSquare()=2862.29
10,(data-retend).SumSquare()=4123.55
11,(data-retend).SumSquare()=6445.43
12,(data-retend).SumSquare()=4440.08
13,(data-retend).SumSquare()=5491.9
14,(data-retend).SumSquare()=4489.53
15,(data-retend).SumSquare()=3991.24
16,(data-retend).SumSquare()=3929.16
17,(data-retend).SumSquare()=1442.45
...
...
...
4546,(data-retend).SumSquare()=10456.1
4547,(data-retend).SumSquare()=9000.21
4548,(data-retend).SumSquare()=7957.14
4549,(data-retend).SumSquare()=8924.28
4550,(data-retend).SumSquare()=9028.84
4551,(data-retend).SumSquare()=6496.61
4552,(data-retend).SumSquare()=6921.44
4553,(data-retend).SumSquare()=11905.1
4554,(data-retend).SumSquare()=9663.75
4555,(data-retend).SumSquare()=6759.75
Saving results... finished
Log directory was:
/Users/marc/Documents/feeds/examples/fdt_subj1.bedpost/diff_slices/data_slice_0000
I HAVE ALSO INCLUDED THE DIRECTORY LISTING FOR THE DISTRIBUTED BEDPOST
OUTPUT (WHICH i MOVED TO fdt_subj1safe.bedpost) and the outpt from my run,
which is in fdt_subj1.bedpost
marc-dubins-computer:~/Documents/feeds/examples/fdt_subj1.bedpost marc$ ls -l
total 5208
-rw-r--r-- 1 marc marc 1041 Jun 7 01:15 bvals
-rw-r--r-- 1 marc marc 2988 Jun 7 01:15 bvecs
-rw-r--r-- 1 marc marc 51809 Jun 7 01:30 dyadic_vectors.nii.gz
drwxr-xr-x 7 marc marc 238 Jun 7 01:33 logs
-rw-r--r-- 1 marc marc 17002 Jun 7 01:30 mean_fsamples.nii.gz
-rw-r--r-- 1 marc marc 16604 Jun 7 01:30 mean_phsamples.nii.gz
-rw-r--r-- 1 marc marc 16422 Jun 7 01:30 mean_thsamples.nii.gz
-rw-r--r-- 1 marc marc 846458 Jun 7 01:30 merged_fsamples.nii.gz
-rw-r--r-- 1 marc marc 833680 Jun 7 01:30 merged_phsamples.nii.gz
-rw-r--r-- 1 marc marc 828981 Jun 7 01:30 merged_thsamples.nii.gz
-rw-r--r-- 1 marc marc 16158 Jun 7 01:15 nodif.nii.gz
-rw-r--r-- 1 marc marc 7059 Jun 7 01:15 nodif_brain.nii.gz
-rw-r--r-- 1 marc marc 367 Jun 7 01:15 nodif_brain_mask.nii.gz
drwxr-xr-x 3 marc marc 102 Jun 7 01:30 xfms
marc-dubins-computer:~/Documents/feeds/examples/fdt_subj1.bedpost marc$ cd
../fdt_subj1safe.bedpost/
marc-dubins-computer:~/Documents/feeds/examples/fdt_subj1safe.bedpost marc$
ls -l
total 5216
-rw-r--r-- 1 marc marc 1041 Jun 7 01:14 bvals
-rw-r--r-- 1 marc marc 2988 Jun 7 01:14 bvecs
-rw-r--r-- 1 marc marc 51848 Jun 7 01:14 dyadic_vectors.nii.gz
drwxr-xr-x 6 marc marc 204 Jun 7 01:14 logs
-rw-r--r-- 1 marc marc 16999 Jun 7 01:14 mean_fsamples.nii.gz
-rw-r--r-- 1 marc marc 16582 Jun 7 01:14 mean_phsamples.nii.gz
-rw-r--r-- 1 marc marc 16450 Jun 7 01:14 mean_thsamples.nii.gz
-rw-r--r-- 1 marc marc 847107 Jun 7 01:14 merged_fsamples.nii.gz
-rw-r--r-- 1 marc marc 833863 Jun 7 01:14 merged_phsamples.nii.gz
-rw-r--r-- 1 marc marc 833042 Jun 7 01:14 merged_thsamples.nii.gz
-rw-r--r-- 1 marc marc 16158 Jun 7 01:14 nodif.nii.gz
-rw-r--r-- 1 marc marc 7058 Jun 7 01:14 nodif_brain.nii.gz
-rw-r--r-- 1 marc marc 367 Jun 7 01:14 nodif_brain_mask.nii.gz
drwxr-xr-x 3 marc marc 102 Jun 7 01:14 xfms
Do you know if I have neglected a setting or am doing something else wrong?
Best,
Marc
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