Hi Salil, I'm posting this to the list since others (i,e Zeke and/or Nick) can better diagnose installation problems. doug

On 03/20/2013 05:21 PM, Salil Soman wrote:

Hi Doug,

Following up on our previous emails, I have been able to get the entire tracula process to work on our sun grid engine using FLT and disabling bbr.

However, if I enable bbr I still get a number of errors, the first of which appears to be

mris_resample: error while loading shared libraries: libboost_program_options.so.5: cannot open shared object file: No such file or directory

The log file and a text file with the lines with the word error are attached.

Any suggestions on how to address this issue would be greatly appreciated.

Best wishes,

Salil

On Wed, Mar 13, 2013 at 9:55 PM, Salil Soman <salsoman@stanford.edu mailto:salsoman@stanford.edu> wrote:

Dear Doug,

Thank you for your email. I apologize for the delay in responding.
At present the file
/mnt/glusterfs/salsoman/output/TRACULA/WCA_0226_T1_FS/dmri/xfms/tmp.bbregister.30396/template.nii
does not exist.

These are the files in the directory
/mnt/glusterfs/salsoman/output/TRACULA/WCA_0226_T1_FS/dmri/xfms/tmp.bbregister.30396:

fslregister  reg.init.dat.fslregister.log
reg.init.dat.fslregister.log.old

the 2 files are attached.

Best wishes,

Salil




On Sun, Mar 10, 2013 at 10:17 AM, Douglas Greve
<greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote:


    Hmmm, I think that these failures are happening because it is
    looking for an input that does not exist. Does
    /mnt/glusterfs/salsoman/output/TRACULA/WCA_0226_T1_FS/dmri/xfms/tmp.bbregister.30396/template.nii
    exist? This was in a temporary directory, and it is likely
    that it was deleted when the script was run.

    doug




    On 3/8/13 8:43 PM, Salil Soman wrote:

...

    Dear Doug,

    Thank you for your email.

    Please find the output attached.

    Best wishes,

    Salil


    On Fri, Mar 8, 2013 at 8:47 AM, Douglas N Greve
    <greve@nmr.mgh.harvard.edu
    <mailto:greve@nmr.mgh.harvard.edu>> wrote:

        Salil, can you run fslregister with --debug as the first
        option, capture the terminal output, and send it to me?
        thanks
        doug



        On 03/07/2013 09:02 PM, Anastasia Yendiki wrote:


            Hi Salil - I'm cc-ing Doug who may be able to help.
            The error happens when bbregister invokes
            fslregister, in this particular line of fslregister:
              set refvol = `stem2fname
            $SUBJECTS_DIR/$subjid/mri/$fsvol`

            When run on brainmask.mgz, it returns "ERROR: could
            not determine file".

            a.y

            On Wed, 6 Mar 2013, Salil Soman wrote:


                Thank you for your email. Changing the mask
                option got me past the error I
                was having initially, but now I get these new errors:

                mri_convert ERROR: could not determine file for
                /mnt/glusterfs/salsoman/output/FS/WCA_0226_T1_FS/mri/ERROR:/mnt/glusterfs/salsoman/output/TRACULA/WCA_0226_T1_FS/dmri/xfms/tmp.bbregis

                ter.30396/fslregister/refvol.fslregister.nii
                mri_convert ERROR: could not determine file for
                /mnt/glusterfs/salsoman/output/FS/WCA_0226_T1_FS/mri/ERROR:/mnt/glusterfs/salsoman/output/TRACULA/WCA_0226_T1_FS/dmri/xfms/tmp.bbregis

                ter.30396/fslregister/refvol.fslregister.nii

                Thank you for your consideration.

                Best wishes,

                -S

                On Wed, Mar 6, 2013 at 1:15 PM, Anastasia Yendiki
                <ayendiki@nmr.mgh.harvard.edu
                <mailto:ayendiki@nmr.mgh.harvard.edu>> wrote:

                Hi Salil - The problem is that you've set dob0 =
                1 but you haven't set
                b0mlist and b0plist, so it doesn't know where to
                find your field maps to do
                the B0 unwarping.

                a.y






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        Douglas N. Greve, Ph.D.
        MGH-NMR Center
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    ---------- Forwarded message ----------
    From: *Salil Soman* <salsoman@stanford.edu
    <mailto:salsoman@stanford.edu>>
    Date: Fri, Mar 8, 2013 at 11:41 AM
    Subject: fslregister output
    To: salsoman@gmail.com <mailto:salsoman@gmail.com>