Hi Anastasia,
Thanks so much for your message. You were right about the recon directory, the contents had been accidentally moved elsewhere (sorry!) and once I moved them back and reran the script everything worked like a charm without any errors. However, it looks like I'm now stuck at the next processing stage (fsl's bedpostX). I pasted the output with the error message below. FYI: I'm unfortunately forced to run the bedpostX on a single Linux box (64-bit dual core with 8GB of RAM) which I hope is OK?
Thanks so much for all your help,

Ansgar

==================================================
trac-all -bedp -c scripts/dmrirc_single_subject_1only
INFO: SUBJECTS_DIR is /home/ajfurst/Data/WRIISC
INFO: Diffusion root is /home/ajfurst/Data/WRIISC/TRACULA
Actual FREESURFER_HOME /usr/local/freesurfer
ln -sf /home/ajfurst/Data/WRIISC/TRACULA/015/dlabel/diff/anat_brain_mask.bbr.nii.gz /home/ajfurst/Data/WRIISC/TRACULA/015/dmri/nodif_brain_mask.nii.gz
ln -sf /home/ajfurst/Data/WRIISC/TRACULA/015/dmri/dwi.nii.gz /home/ajfurst/Data/WRIISC/TRACULA/015/dmri/data.nii.gz
WARN: Running FSL's bedbost locally - this might take a while
WARN: It is recommended to run this step on a cluster
bedpostx_seychelles /home/ajfurst/Data/WRIISC/TRACULA/015/dmri
subjectdir is /home/ajfurst/Data/WRIISC/TRACULA/015/dmri
Making bedpostx directory structure
Queuing preprocessing stages
Queuing parallel processing stage
0 slices processed
5 slices processed
6 slices processed
7 slices processed
8 slices processed
9 slices processed
9 slices processed
10 slices processed
11 slices processed
11 slices processed
12 slices processed
12 slices processed
13 slices processed
14 slices processed
14 slices processed
14 slices processed
15 slices processed
15 slices processed
16 slices processed
16 slices processed
16 slices processed
17 slices processed
17 slices processed
17 slices processed
18 slices processed
18 slices processed
18 slices processed
18 slices processed
19 slices processed
19 slices processed
19 slices processed
19 slices processed
20 slices processed
20 slices processed
20 slices processed
20 slices processed
21 slices processed
21 slices processed
21 slices processed
21 slices processed
21 slices processed
22 slices processed
22 slices processed
22 slices processed
22 slices processed
23 slices processed
23 slices processed
23 slices processed
23 slices processed
23 slices processed
24 slices processed
24 slices processed
24 slices processed
24 slices processed
24 slices processed
24 slices processed
25 slices processed
25 slices processed
25 slices processed
25 slices processed
25 slices processed
26 slices processed
26 slices processed
26 slices processed
26 slices processed
26 slices processed
26 slices processed
27 slices processed
27 slices processed
27 slices processed
27 slices processed
27 slices processed
28 slices processed
28 slices processed
28 slices processed
28 slices processed
28 slices processed
28 slices processed
29 slices processed
29 slices processed
29 slices processed
29 slices processed
29 slices processed
29 slices processed
30 slices processed
30 slices processed
30 slices processed
30 slices processed
30 slices processed
30 slices processed
31 slices processed
31 slices processed
31 slices processed
31 slices processed
31 slices processed
32 slices processed
32 slices processed
32 slices processed
32 slices processed
32 slices processed
32 slices processed
33 slices processed
33 slices processed
33 slices processed
33 slices processed
33 slices processed
33 slices processed
34 slices processed
34 slices processed
34 slices processed
34 slices processed
34 slices processed
35 slices processed
35 slices processed
35 slices processed
35 slices processed
35 slices processed
35 slices processed
36 slices processed
36 slices processed
36 slices processed
36 slices processed
36 slices processed
37 slices processed
37 slices processed
37 slices processed
37 slices processed
37 slices processed
38 slices processed
38 slices processed
38 slices processed
38 slices processed
38 slices processed
39 slices processed
39 slices processed
39 slices processed
39 slices processed
39 slices processed
40 slices processed
40 slices processed
40 slices processed
40 slices processed
41 slices processed
41 slices processed
41 slices processed
41 slices processed
41 slices processed
42 slices processed
42 slices processed
42 slices processed
42 slices processed
43 slices processed
43 slices processed
43 slices processed
43 slices processed
44 slices processed
44 slices processed
44 slices processed
44 slices processed
45 slices processed
45 slices processed
45 slices processed
46 slices processed
46 slices processed
46 slices processed
46 slices processed
47 slices processed
47 slices processed
47 slices processed
48 slices processed
48 slices processed
49 slices processed
49 slices processed
49 slices processed
50 slices processed
50 slices processed
51 slices processed
51 slices processed
52 slices processed
53 slices processed
Queuing post processing stage
58 slices processed
For some reason the bedpostX process DOES NOT appear
to have successfully completed. Please examine your
results carefully.
/usr/local/freesurfer/bin/bedpostx_seychelles: line 281: kill: (12792) - No such process
===================================================

On Thu, Sep 22, 2011 at 5:17 AM, Anastasia Yendiki <ayendiki@nmr.mgh.harvard.edu> wrote:

Hi Ansgar - Currently there's no way to specify multiple scans for the same subject as dicom files, sorry. You can concatenate the DWIs from the 2 scans in one nifti file, and also concatenate the bvecs/bvals from the two scans, and pass the concatenation to dmrirc.

As for your error, it looks like maybe the freesurfer recon wasn't found, so it skipped some steps (diffusion-to-anatomical registration and mask creation). Does the freesurfer recon dir /home/ajfurst/Data/WRIISC/014/ exist?

a.y