[MINC-users] xv error (mincview) on Ubuntu / make_model error

[Lisa F. Akiyama]

Hello,

I am using MINC on Ubuntu 10.10.
I am facing two problems at the moment:

1) I get an error saying that the xv command is missing when I try to run
mincview:

todd at neptune-ubuntu:~/Desktop/SF6-noneck-notcoreg/mritotal$ mincview
> 6mth_ucla_little_endian_clean.mnc
> Loading
> slices...........................................................................................................................................Done
> xv: Command not found.
>

Is there a need for me to install xv following steps such as those listed
here?: http://www.halibutdepot.org/xv/building_xv_on_ubuntu.html


2) When running make_model, I get errors saying that it was unable to open
the ...mask.mnc files.
No mask.mnc files are created (only dxyz.mnc's and blur.mnc's have been
created).

todd at neptune-ubuntu:~/Desktop/SF6-noneck-notcoreg/mritotal$ make_model
> 6mth_ucla_little_endian_clean
> Using base filename 6mth_ucla_little_endian_clean
> Note that your input volume *must* be in Talairach space for this to work
> ** Making 6mth_ucla_little_endian_clean_pad.mnc from
> 6mth_ucla_little_endian_clean.mnc by resampling on 2mm grid and padding by
> 16mm
> [autocrop] [todd at neptune-ubuntu:/home/todd/Desktop/SF6-noneck-notcoreg/mritotal]
> [2011-02-09 13:12:46] /usr/local/bic/bin/mincresample -clobber
> 6mth_ucla_little_endian_clean.mnc 6mth_ucla_little_endian_clean_pad.mnc
> -start -83.8711 -98.0312 -89.2422 -step 2 2 2 -nelements 84 99 90
> Transforming
> slices:....................................................................................Done
> ** Building 16mm data for 6mth_ucla_little_endian_clean
> Making byte volume...
> [autocrop] [todd at neptune-ubuntu:/home/todd/Desktop/SF6-noneck-notcoreg/mritotal]
> [2011-02-09 13:12:47] /usr/local/bic/bin/mincreshape -clobber
> tmp_16_blur.mnc 6mth_ucla_little_endian_clean_16_blur.mnc -start 8,8,18
> -count 68,83,54
> Copying
> chunks:....................................................................Done.
> *(from miopen): Unable to open file
> '6mth_ucla_little_endian_clean_mask.mnc'*
> ncvarid: ncid -1: NetCDF: Not a valid ID
> ** Building 8mm data for 6mth_ucla_little_endian_clean
> Making byte volume...
> Transforming
> slices:....................................................................................Done
> Making byte volume dx...Making byte volume dy...Making byte volume
> dz...[autocrop] [todd at neptune-ubuntu:/home/todd/Desktop/SF6-noneck-notcoreg/mritotal]
> [2011-02-09 13:12:48] /usr/local/bic/bin/mincreshape -clobber tmp_8_blur.mnc
> 6mth_ucla_little_endian_clean_8_blur.mnc -start 8,8,13 -count 68,83,64
> Copying
> chunks:....................................................................Done.
> [autocrop] [todd at neptune-ubuntu:/home/todd/Desktop/SF6-noneck-notcoreg/mritotal]
> [2011-02-09 13:12:48] /usr/local/bic/bin/mincreshape -clobber tmp_8_dxyz.mnc
> 6mth_ucla_little_endian_clean_8_dxyz.mnc -start 8,8,13 -count 68,83,64
> Copying
> chunks:....................................................................Done.
> *(from miopen): Unable to open file
> '6mth_ucla_little_endian_clean_mask.mnc'
> ncvarid: ncid -1: NetCDF: Not a valid ID*
> ** Making 6mth_ucla_little_endian_clean_pad4.mnc from
> 6mth_ucla_little_endian_clean.mnc by padding by 4mm
> [autocrop] [todd at neptune-ubuntu:/home/todd/Desktop/SF6-noneck-notcoreg/mritotal]
> [2011-02-09 13:12:48] /usr/local/bic/bin/mincreshape -clobber
> 6mth_ucla_little_endian_clean.mnc 6mth_ucla_little_endian_clean_pad4.mnc
> -start -4,-4,-4 -count 149,177,160
> Copying
> chunks:.....................................................................................................................................................Done.
> ** Building 4mm data for 6mth_ucla_little_endian_clean
> Making byte volume...
> Transforming
> slices:.....................................................................................................................................................Done
> Making byte volume dx...Making byte volume dy...Making byte volume
> dz...[autocrop] [todd at neptune-ubuntu:/home/todd/Desktop/SF6-noneck-notcoreg/mritotal]
> [2011-02-09 13:12:53] /usr/local/bic/bin/mincreshape -clobber tmp_4_blur.mnc
> 6mth_ucla_little_endian_clean_4_blur.mnc -start 9,9,9 -count 132,160,143
> Copying
> chunks:....................................................................................................................................Done.
> [autocrop] [todd at neptune-ubuntu:/home/todd/Desktop/SF6-noneck-notcoreg/mritotal]
> [2011-02-09 13:12:53] /usr/local/bic/bin/mincreshape -clobber tmp_4_dxyz.mnc
> 6mth_ucla_little_endian_clean_4_dxyz.mnc -start 9,9,9 -count 132,160,143
> Copying
> chunks:....................................................................................................................................Done.
> *(from miopen): Unable to open file
> '6mth_ucla_little_endian_clean_mask.mnc'
> ncvarid: ncid -1: NetCDF: Not a valid ID*
> ** Building 2mm data for 6mth_ucla_little_endian_clean
> Making byte volume...
> Transforming
> slices:.....................................................................................................................................................Done
> Making byte volume dx...Making byte volume dy...Making byte volume
> dz...[autocrop] [todd at neptune-ubuntu:/home/todd/Desktop/SF6-noneck-notcoreg/mritotal]
> [2011-02-09 13:12:58] /usr/local/bic/bin/mincreshape -clobber tmp_2_blur.mnc
> 6mth_ucla_little_endian_clean_2_blur.mnc -start 7,7,7 -count 136,164,147
> Copying
> chunks:........................................................................................................................................Done.
> [autocrop] [todd at neptune-ubuntu:/home/todd/Desktop/SF6-noneck-notcoreg/mritotal]
> [2011-02-09 13:12:58] /usr/local/bic/bin/mincreshape -clobber tmp_2_dxyz.mnc
> 6mth_ucla_little_endian_clean_2_dxyz.mnc -start 7,7,7 -count 136,164,147
> Copying
> chunks:........................................................................................................................................Done.
> *(from miopen): Unable to open file
> '6mth_ucla_little_endian_clean_mask.mnc'
> ncvarid: ncid -1: NetCDF: Not a valid ID*
>



Any tips on how to tackle these two problems?

Thank you in advance.


Best,
Lisa