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Thank you, Tim. I let it run longer and it completed this time and I got the desired output. I must have been impatient and cancelled it too early before! I doubled the speed by running it on my two processors. I think I'm going to try to parallelize to other computers as well. I have still only successfully run it on the subj1 sample data. For my data, it does not create datastart and dataend, retstart and retend for my first and last slices. I will try running it on some of my other data and see what happens. Thanks again, Marc On 6/9/07, Tim Behrens <[log in to unmask]> wrote: > > Marc, > This is exactly what a single slice output should look like. When all the > slices are finished they are merged together into files called merged_... > > > You are looking for a directory that doesn't look like this! > > > T > > On 9 Jun 2007, at 00:21, Marc Dubin wrote: > > Hi Tim, > > In follow up to my previous email, I also wanted to let you know that the > bedpost output is very different than the output for the sample data ( > subj1.bedpost). > > > For example, for the data_slice_0010 directory, I get: > > > 975111 Jun 6 01:45 S0_samples.nii.gz > 971621 Jun 6 01:45 d_samples.nii.gz > 183 Jun 6 01:45 dataend > 183 Jun 6 01:45 datastart > 1010243 Jun 6 01:45 f_samples.nii.gz > 627 Jun 8 19:16 fdt.log > 429 Jun 6 01:36 logfile > 995138 Jun 6 01:45 ph_samples.nii.gz > 318 Jun 6 01:45 retend > 318 Jun 6 01:45 retstart > 991613 Jun 6 01:45 th_samples.nii.gz > > I don't get any mean_*, merged_* or nodif_* files. > > > Best, > Marc > > > > > > > > nifti_image_read(/Users/marcDocuments/Dir.bedpost/ > diff_slices/data_slice_0010/ > On 6/7/07, Tim Behrens <[log in to unmask]> wrote: > > > > Hi - the syntax error always occurs (see previous postings here). The > > debugging-style logging also always occurs - it is fine, except for taking > > up disk space etc. Both of these "features" are cleaned up for the next > > release. > > > > > > T > > > > > > > > On 7 Jun 2007, at 14:43, Marc Dubin wrote: > > > > Tim, > > > > Thank you for your help. I will start by trying to find the slice that's > > causing problems. However, I think I may be doing something wrong in bedpost > > in general because when I try to run it on the sample data in fdt_subj1, the > > program ends with a syntax error (293). I have just made a more detailed > > posting about his. I understand that you are busy and will patiently await > > your reply whenever you have time. In the meantime, if I solve my own > > problem I will be sure to let the group know. > > > > Thanks again, > > Marc > > > > On 6/7/07, Tim Behrens < [log in to unmask]> wrote: > > > > > > It sounds like a single slice has crashed and not finished. > > > > > > Could you look in the slice directories to see which one has crashed > > > (the outputs will not be in the directory), and see if there is > > > anything different about the data from that slice. if not, can you > > > send us that slice (data_slice_blah and nodif_brain_mask_slice...) > > > and the bvecs and bvals by uploading them to > > > http://www.fmrib.ox.ac.uk/cgi-bin/upload.cgi > > > and telling us the number. > > > > > > I will take a look as soon as I can, but I'm afraid I am flying to > > > HBM very soon, so I cannot guarantee to do it before getting back. > > > > > > T > > > > > > > > > > > > On 6 Jun 2007, at 23:40, Marc Dubin wrote: > > > > > > > Hello, > > > > > > > > When I run bedpost on my macbook pro intel core 2 duo 2.16 Ghz, > > > > on my 30 slice data with 26 diffusion directions, it appears to > > > finish > > > > in about 2 hours (appears that all outpt is there in the directory > > > > structure) > > > > and then enter an infinite loop, printing to screen "29 slices > > > > process" about > > > > every half hour. Does anyone know if it's done or still doing > > > > something important? > > > > > > > > Best, > > > > Marc > > > > > > > > > > > -- > > 646 831 8886 > > [log in to unmask] > > > > > > > > > -- > 646 831 8886 > [log in to unmask] > > > -- 646 831 8886 [log in to unmask]