Re: [Freesurfer] mri_convert error during make_average_subject

and can you send us the output? On Mon, 3 Feb 2014, Jonathan Holt wrote:

All, [1]+  Exit 1 nohup make_average_subject --subjects s_090803sk.long.SKtemplate/ s_091202sk.long.SKtemplate/ >&test.log

On Mon, Feb 3, 2014 at 3:28 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Jon

  can you include your entire command line so we can see it?

  thanks
  Bruce


  On Mon, 3 Feb 2014, Jonathan Holt wrote:

        Bruce,
        I tried again on a set of different subjects, it
        error'd out once again. I
        have write permission, this is the same directory
        I've been using for quite
        some time, and I am positive there is space on the
        drive.

        These are the last 50 or so lines of the output
        before it stops:

mghWrite(/net/data4/ALSSCI/FreeSurfer201211/FreeSurfer/LONG_STUDY_2/average

        /tmp/make_average_vol-tmp-28460/orig-s_090803sk.long.SKtemplate/.mgh,
        -1):
        could not open file
        ---------------------------------
        Applying LTAtransformInterp (resample_type 1)
        writingto/net/data4/ALSSCI/FreeSurfer201211/FreeSurfer/LONG_STUDY_2/average/tmp/ma
        ke
        _average_vol-tmp-28460/orig-s_090803sk.long.SKtemplate/.mgh...
        ERROR: failurewriting/net/data4/ALSSCI/FreeSurfer201211/FreeSurfer/LONG_STUDY_2/average/t
        mp/make
        _average_vol-tmp-28460/orig-s_090803sk.long.SKtemplate/.mgh
        /net/data4/ALSSCI/FreeSurfer201211/FreeSurfer/LONG_STUDY_2


        I'm confused as to why it's looking for a nameless
        .mgh file, or perhaps
        that is normal. This is my first usage for
        make_average_subject.

        Jon


        On Sat, Feb 1, 2014 at 5:54 PM, Bruce Fischl
        <fischl@nmr.mgh.harvard.edu>
        wrote:
              Hi Jon

              usually that means that either the partition
        is full or you
              don't have permission. If that's not the case
        you will need to
              give us more details
              Bruce
              On Sat, 1 Feb 2014, Jonathan Holt wrote:

              Hello FS experts,

              I’m trying to make an average subject and I
        had an
              unfortunate error during the mri_convert
        stage,
              specifically an mghWrite error. I failed to
        save the
              output so I cannot recall the exact details,
        are there any
              specific things I should be looking out for to
        prevent
              this?

              best,

              Jon
        _______________________________________________
        Freesurfer mailing list
        Freesurfer@nmr.mgh.harvard.edu
        https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer





        The information in this e-mail is intended only for
        the person to whom
        it is
        addressed. If you believe this e-mail was sent to
        you in error and the
        e-mail
        contains patient information, please contact the
        Partners Compliance
        HelpLine at
        http://www.partners.org/complianceline . If the
        e-mail was sent to you
        in error
        but does not contain patient information, please
        contact the sender
        and properly
        dispose of the e-mail.