[MINC-users] install autoreg_model error
Forrest S. Bao
forrest.bao at gmail.com
Wed Sep 27 21:41:49 EDT 2006
Hi guys,
I tried to install the autoreg_model few days ago. But I see many errors
saying
(from miopen): Can't write compressed file
ncredef: ncid -1: Not a netCDF id
ncattput: ncid -1: Not a netCDF id
ncclose: ncid -1: Not a netCDF id
autocrop: crashed while running minc_modify_header (termination status=768)
Due to this problem, the installation of autoreg_model failed.
How can I fix this problem and install it successfully?
Following is the shell record:
mri at MRI:~/fmri/mni_autoreg_model-1.03$ make install
Creating directory /usr/local/mni/share/mni_autoreg
I hope you have several dozen MB free there!
Using base filename average_305
Note that your input volume *must* be in Talairach space for this to work
** Making average_305_pad.mnc from average_305.mnc by resampling on 2mm grid
and padding by 16mm
[autocrop] [mri at MRI:/usr/local/mni/share/mni_autoreg] [2006-09-25 17:12:29]
/usr /local/mni/bin/mincresample -clobber average_305.mnc
average_305_pad.mnc -start -102.095 -142.51 -84.25 -step 2 2 2 -nelements
102 126 94
Transforming
slices:............................................................
..................................Done
(from miopen): Can't write compressed file
ncredef: ncid -1: Not a netCDF id
ncattput: ncid -1: Not a netCDF id
ncclose: ncid -1: Not a netCDF id
autocrop: crashed while running minc_modify_header (termination status=768)
** Building 16mm data for average_305
Making byte volume...
[autocrop] [mri at MRI:/usr/local/mni/share/mni_autoreg] [2006-09-25 17:12:31]
/usr /local/mni/bin/mincreshape -clobber tmp_16_blur.mnc
average_305_16_blur.mnc -sta rt 18,8,8 -count 58,110,86
Copying
chunks:..........................................................Done.
(from miopen): Can't write compressed file
ncredef: ncid -1: Not a netCDF id
ncattput: ncid -1: Not a netCDF id
ncclose: ncid -1: Not a netCDF id
autocrop: crashed while running minc_modify_header (termination status=768)
Transforming
slices:..........................................................Do ne
** Building 8mm data for average_305
Making byte volume...
Transforming
slices:..............................................................................................Done
Making byte volume dx...Making byte volume dy...Making byte volume
dz...[autocrop] [mri at MRI:/usr/local/mni/share/mni_autoreg] [2006-09-25
17:12:34] /usr/local/mni/bin/mincreshape -clobber tmp_8_blur.mnc
average_305_8_blur.mnc -start 13,8,8 -count 68,110,86
Copying
chunks:....................................................................Done.
(from miopen): Can't write compressed file
ncredef: ncid -1: Not a netCDF id
ncattput: ncid -1: Not a netCDF id
ncclose: ncid -1: Not a netCDF id
autocrop: crashed while running minc_modify_header (termination status=768)
[autocrop] [mri at MRI:/usr/local/mni/share/mni_autoreg] [2006-09-25 17:12:34]
/usr/local/mni/bin/mincreshape -clobber tmp_8_dxyz.mnc
average_305_8_dxyz.mnc -start 13,8,8 -count 68,110,86
Copying
chunks:....................................................................Done.
(from miopen): Can't write compressed file
ncredef: ncid -1: Not a netCDF id
ncattput: ncid -1: Not a netCDF id
ncclose: ncid -1: Not a netCDF id
autocrop: crashed while running minc_modify_header (termination status=768)
Transforming
slices:....................................................................Done
** Making average_305_pad4.mnc from average_305.mnc by padding by 4mm
[autocrop] [mri at MRI:/usr/local/mni/share/mni_autoreg] [2006-09-25 17:12:34]
/usr/local/mni/bin/mincreshape -clobber average_305.mnc average_305_pad4.mnc
-start -4,-4,-4 -count 164,228,180
Copying
chunks:....................................................................................................................................................................Done.
(from miopen): Can't write compressed file
ncredef: ncid -1: Not a netCDF id
ncattput: ncid -1: Not a netCDF id
ncclose: ncid -1: Not a netCDF id
autocrop: crashed while running minc_modify_header (termination status=768)
** Building 4mm data for average_305
Making byte volume...
Making byte volume dx...Making byte volume dy...Gradient volume:
..............................................................Making byte
volume dz...
Transforming
slices:....................................................................................................................................................................Done
[autocrop] [mri at MRI:/usr/local/mni/share/mni_autoreg] [2006-09-25 17:12:47]
/usr/local/mni/bin/mincreshape -clobber tmp_4_blur.mnc
average_305_4_blur.mnc -start 9,9,9 -count 146,210,162
Copying
chunks:..................................................................................................................................................Done.
(from miopen): Can't write compressed file
ncredef: ncid -1: Not a netCDF id
ncattput: ncid -1: Not a netCDF id
ncclose: ncid -1: Not a netCDF id
autocrop: crashed while running minc_modify_header (termination status=768)
[autocrop] [mri at MRI:/usr/local/mni/share/mni_autoreg] [2006-09-25 17:12:47]
/usr/local/mni/bin/mincreshape -clobber tmp_4_dxyz.mnc
average_305_4_dxyz.mnc -start 9,9,9 -count 146,210,162
Copying
chunks:..................................................................................................................................................Done.
(from miopen): Can't write compressed file
ncredef: ncid -1: Not a netCDF id
ncattput: ncid -1: Not a netCDF id
ncclose: ncid -1: Not a netCDF id
autocrop: crashed while running minc_modify_header (termination status=768)
Transforming
slices:..................................................................................................................................................Done
** Building 2mm data for average_305
Making byte volume...
Making byte volume dx...Making byte volume dy...Gradient volume:
..............................................................Making byte
volume dz...
Transforming
slices:....................................................................................................................................................................Done
[autocrop] [mri at MRI:/usr/local/mni/share/mni_autoreg] [2006-09-25 17:13:00]
/usr/local/mni/bin/mincreshape -clobber tmp_2_blur.mnc
average_305_2_blur.mnc -start 7,7,7 -count 150,214,166
Copying
chunks:......................................................................................................................................................Done.
(from miopen): Can't write compressed file
ncredef: ncid -1: Not a netCDF id
ncattput: ncid -1: Not a netCDF id
ncclose: ncid -1: Not a netCDF id
autocrop: crashed while running minc_modify_header (termination status=768)
[autocrop] [mri at MRI:/usr/local/mni/share/mni_autoreg] [2006-09-25 17:13:00]
/usr/local/mni/bin/mincreshape -clobber tmp_2_dxyz.mnc
average_305_2_dxyz.mnc -start 7,7,7 -count 150,214,166
Copying
chunks:......................................................................................................................................................Done.
(from miopen): Can't write compressed file
ncredef: ncid -1: Not a netCDF id
ncattput: ncid -1: Not a netCDF id
ncclose: ncid -1: Not a netCDF id
autocrop: crashed while running minc_modify_header (termination status=768)
Transforming
slices:......................................................................................................................................................Done
[2]+ Done gedit Makefile
mri at MRI:~/fmri/mni_autoreg_model-1.03$ cd ..]
bash: cd: ..]: No such file or directory
mri at MRI:~/fmri/mni_autoreg_model-1.03$ cd ..
mri at MRI:~/fmri$ ls
AIR5.2.5 ebtks-1.6.1 minc-1.2
mni_n3-1.05.tar.gz
AIR5.2.5.tar.gz ebtks-1.6.1.tar.gz minc-1.2.tar.gz
mni_perllib-0.07
bicpl-1.4.3 emma-0.9.7-linux.tar.gz minc-2.0.10
mni_perllib-0.07.tar.gz
bicpl-1.4.3.tar.gz freeglut-2.4.0 minc-2.0.10.tar.gz
N3
classify-1.0.03 freeglut-2.4.0.tar.gz mni_autoreg-0.99.2
netcdf-3.6.1
classify-1.0.03.tar.gz Getopt-Tabular-0.3
mni_autoreg-0.99.2.tar.gz
netcdf-3.6.1.tar.gz
cobra_v031.tar.gz Getopt-Tabular-0.3.tar.gz
mni_autoreg_model-1.03
PIPELINE.zip
Display-1.4.1 glut-3.6.tar.gz mni_autoreg_model-
1.03.tar.gz Register-1.3.6
Display-1.4.1.tar.gz instruction.txt mni-models_average305-
lin-1.0.tar.gz Register-1.3.6.tar.gz
mri at MRI:~/fmri$ cd ..
mri at MRI:~$ ls
004.HDR 010_RTIP.mnc 112-1.MNC
004.IMG 011.HDR 112-2.MNC
004.MNC 011.IMG
1.2.840.113619.2.134.1762897138.1708.1154955905.102
004_RTIP_MC.log 011.MNC
1.2.840.113619.2.134.1762897138.1708.1154955905.117
004_RTIP_MC.mnc 011_RTIP_MC.log 8-10
004_RTIP.mnc 011_RTIP_MC.mnc a
005.HDR 011_RTIP.mnc b
005.IMG 014.HDR cobra-20030803-185544
005.MNC 014.IMG cobra-20030803-191004
005_RTIP_MC.log 014.MNC cobra-20030803-191700
005_RTIP_MC.mnc 014_RTIP_MC.log cobra-20030803-192529
005_RTIP.mnc 014_RTIP_MC.mnc cobra-20030803-192817
0068_bold_signal_MC.log 014_RTIP.mnc cobra-20030803-192953
0068_bold_signal_MC.mnc 015.HDR cobra-20030803-193842
0068_bold_signal.mnc 015.IMG Desktop
006.HDR 015.MNC Examples
006.IMG 015_RTIP_MC.log fmri
006.MNC 015_RTIP_MC.mnc fmri_bin
006_RTIP_MC.log 015_RTIP.mnc fmri.tar.gz
006_RTIP_MC.mnc 017.HDR
freesurfer-Linux-centos4-stable-pub-v3.0.3-full.tar.gz
006_RTIP.mnc 017.IMG huangliqiu_contrast
007.HDR 017.MNC
huang_pi_chun_20051017_090041_12_mri_1x1x1_toRet.mnc
007.IMG 017_RTIP_MC.log INFO-1.MNC
007.MNC 017_RTIP_MC.mnc INFO-2.MNC
007_RTIP_MC.log 017_RTIP.mnc lv06.mnc
007_RTIP_MC.mnc 018.HDR lv07.mnc
007_RTIP.mnc 018.IMG lv08.mnc
008.HDR 018.MNC lv09.mnc
008.IMG 018_RTIP_MC.log lv1t.mnc
008.MNC 018_RTIP_MC.mnc mni_autoreg-0.1l
008_RTIP_MC.log 018_RTIP.mnc mni_autoreg-0.9.tar.tar
008_RTIP_MC.mnc 019.HDR total_i.xfm
008_RTIP.mnc 019.IMG total.xfm
009.HDR 019.MNC vfsCombinedEye2.m
009.IMG 019_RTIP_MC.log vfsCombinedEye.m
009.MNC 019_RTIP_MC.mnc xingfeng_matlab
009_RTIP_MC.log 019_RTIP.mnc zhangzhiying
009_RTIP_MC.mnc 020.HDR
zhang_zhi_ying_f_31_20060813_130148_16_mri.mnc
009_RTIP.mnc 020.IMG
zhang_zhi_ying_f_31_20060813_130148_1x1x1_mri.mnc
010.HDR 020.MNC
zhang_zhi_ying_f_31_20060813_130148_21_mri.mnc
010.IMG 020_RTIP_MC.log
zhang_zhi_ying_f_31_20060813_130148_3_mri.mnc
010.MNC 020_RTIP_MC.mnc zhenggang
010_RTIP_MC.log 020_RTIP.mnc
010_RTIP_MC.mnc 111.MNC
mri at MRI:~$ mritotal zhang_zhi_ying_f_31_20060813_130148_1x1x1_mri.mnc
Usage: mritotal [options] input_volume output_transform
mritotal -help
Incorrect number of arguments
mri at MRI:~$ mritotal zhang_zhi_ying_f_31_20060813_130148_1x1x1_mri.mnc
111.xfm
Loading configuration file
/usr/local/mni/bin/../etc/mni_autoreg/mritotal.cfg
Loading protocol default (protocol file =
/usr/local/mni/bin/../etc/mni_autoreg/mritotal.default.cfg)
source = zhang_zhi_ying_f_31_20060813_130148_1x1x1_mri.mnc
model = /usr/local/mni/bin/../share/mni_autoreg/average_305
transform = 111.xfm
protocol = default:
linear fit only
subsample heuristically
crop heuristically
blur with 16 and 8 mm FHWM kernels
pad/unpad correctly (encroach on original volume)
default objective function = cross-correlation
Subsampling/cropping data:
[mritotal] [mri at MRI:/home/mri] [2006-09-25 17:14:21]
/usr/local/mni/bin/autocrop
zhang_zhi_ying_f_31_20060813_130148_1x1x1_mri.mnc
/var/tmp/mritotal_5597//zhang_zhi_ying_f_31_20060813_130148_1x1x1_mri_crop.mnc
-step -1.875024 -1.875 2 -extend 0,0 0,0 0,0
[autocrop] [mri at MRI:/home/mri] [2006-09-25 17:14:22]
/usr/local/mni/bin/mincresample
zhang_zhi_ying_f_31_20060813_130148_1x1x1_mri.mnc
/var/tmp/mritotal_5597//zhang_zhi_ying_f_31_20060813_130148_1x1x1_mri_crop.mnc
-start 116.839072 97.947 -31.2595 -step -1.875024 -1.875 2 -nelements 129
128 54
Transforming
slices:......................................................Done
(from miopen): Can't write compressed file
ncredef: ncid -1: Not a netCDF id
ncattput: ncid -1: Not a netCDF id
ncclose: ncid -1: Not a netCDF id
autocrop: crashed while running minc_modify_header (termination status=768)
mritotal: crashed while running autocrop (termination status=768)
--
Forrest Sheng Bao
Dept. of Medical Imaging, Clinical School of Medical College
Nanjing University
Home Page: http://forrest.bao.googlepages.com
MSN: bsh1984 at hotmail.com
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Skype: forrestbao
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