[MINC-users] mincaverage error

[Lisa F. Akiyama]

Hi Vladimir,
Yes, I specified all the file names.
I also re-ran it including the full path in the filelist, but it still gave
me the same error.
I re-ran it without a filelist (just listed all filenames in the command),
but it failed.

Hi Alex,
Yes, I have writing permission and that there is ample free space (over
120GB) in my current location.
I copied all of my input file to a different location, made sure I had the
correct permission and ample space, and re-ran mincaverage, but failed
again.

Another tidbit:
The output file is created (3.2MB), but when I open it in register, it is
just a black image.


Thanks.


Best,
Lisa


On Fri, Mar 4, 2011 at 12:44 PM, Alex Zijdenbos <zijdenbos at gmail.com> wrote:

> Hi Lisa,
>
> On the off-chance that this is the problem - are you sure you have
> write access and free disk space in the location where you are trying
> to write the output file?
>
> -- Alex
>
> On Fri, Mar 4, 2011 at 3:17 PM, Lisa F. Akiyama <lrisa87 at uw.edu> wrote:
> >
> > Hi Andrew,
> >
> > I double checked each minc file (displayed them in register) and they all
> > seemed to be fine...
> >
> > Don't know if this helps at all..., but here are some more information:
> >
> > 1. A correction to what I wrote earlier:
> >
> > > I am trying to run mincaverage on 43 minc files, all which have been N3
> > > intensity nonuniformity normalized, neck portion cropped off,
> mincnorm-ed,
> > > *and linearly (9parameter) registered to a standard template*.
> >
> >
> > 2. I am using the -filelist option. I have a .txt file with each file
> name
> > listed on separate lines. Is this the correct format for the filelist?
> >
> > 3. The version I am using:
> >
> > > > mincaverage -version
> > > program: 2.1.00
> > > libminc: 2.1.00
> > > netcdf : 4.1.1 of May 15 2010 04:10:51 $
> > > HDF5   : 1.8.4
> >
> >
> >
> > Thanks.
> >
> >
> > Best,
> > Lisa
> >
> > On Fri, Mar 4, 2011 at 11:52 AM, Andrew Wood <andrew at biospective.com>
> wrote:
> >
> > > Hi Lisa,
> > >
> > > Is there any chance that the problem is with your input minc files? I
> just
> > > gave minc average a few good minc volumes plus a filename that didn't
> exist
> > > and I got back your error message.
> > >
> > > Andrew
> > >
> > >
> > > On Fri, Mar 4, 2011 at 2:23 PM, Lisa F. Akiyama <lrisa87 at uw.edu>
> wrote:
> > >
> > > > Hi Jared,
> > > >
> > > > I tried re-running mincaverage with the -clobber extention.
> > > > I also ran it using a totally new output filename too, but it still
> gives
> > > > me
> > > > the same error message.
> > > >
> > > > Thanks.
> > > >
> > > >
> > > > Best,
> > > > Lisa
> > > >
> > > >
> > > >
> > > > On Fri, Mar 4, 2011 at 11:05 AM, Jared Rowley <
> jared.rowley at gmail.com
> > > > >wrote:
> > > >
> > > > > Hi Lisa,
> > > > >
> > > > > I think you need to to do mincaverage -clobber.
> > > > >
> > > > > My guess is that the output.mnc already exists and you need to do
> > > > -clobber
> > > > > to overwrite it.
> > > > >
> > > > > Jared
> > > > >
> > > > >
> > > > > On Fri, Mar 4, 2011 at 2:00 PM, Lisa F. Akiyama <lrisa87 at uw.edu>
> > > wrote:
> > > > >
> > > > > > Hello,
> > > > > >
> > > > > > I am trying to run mincaverage on 43 minc files, all which have
> been
> > > N3
> > > > > > intensity nonuniformity normalized, neck portion cropped off, and
> > > > > > mincnorm-ed.
> > > > > > The following is the error that I receive:
> > > > > >
> > > > > > Processing:........................miicv_attach: MINC package
> entry
> > > > point
> > > > > > > *ncvarid: ncid -1: NetCDF: Not a valid ID*
> > > > > >
> > > > > >
> > > > > > When I run mincaverage on individual files and on subsets of the
> 43
> > > > > files,
> > > > > > mincaverage runs fine.
> > > > > > What is the issue?
> > > > > >
> > > > > > Thank you in advance.
> > > > > >
> > > > > >
> > > > > > Best,
> > > > > > Lisa
> > > > > > _______________________________________________
> > > > > > MINC-users at bic.mni.mcgill.ca
> > > > > > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> > > > > >
> > > > >
> > > > >
> > > > >
> > > > > --
> > > > > Jared Rowley
> > > > > Translational Neuroimaging Laboratory
> > > > > McGill Centre for Studies in Aging
> > > > > Douglas Hospital Research Center
> > > > > McGill University
> > > > > 6825 LaSalle Blvd.
> > > > > Montreal, QC Canada
> > > > > H4H 1R3
> > > > > _______________________________________________
> > > > > MINC-users at bic.mni.mcgill.ca
> > > > > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> > > > >
> > > > _______________________________________________
> > > > MINC-users at bic.mni.mcgill.ca
> > > > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> > > >
> > > _______________________________________________
> > > MINC-users at bic.mni.mcgill.ca
> > > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> > >
> > _______________________________________________
> > MINC-users at bic.mni.mcgill.ca
> > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> _______________________________________________
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> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>