hi Alex-
this is not a problem. you can safely ignore it.
thanks, brian
On Tue, 7 Jun 2005, Fornito, Alexander wrote:
Hi, We've managed to get it working. Your help is very much appeciated!! However, when I run recon-all -stage1, things work fine until it calls nu_correct. I then get a recurring message saying "Not implemented yet in cache_volume_range_has_changed()", before moving on to the next processing stage. Below is a sample of the output. Is this indicative of a problem? Thanks again, Alex
Nu Intensity Correction Tue Jun 7 12:03:52 EST 2005 mri_convert orig nu/nu0.mnc mri_convert orig nu/nu0.mnc reading from orig... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to nu/nu0.mnc... nu_correct -clobber nu/nu0.mnc nu/nu1.mnc [alex@flanders:/data/flanders/work/alex/freesurfer/subjects/186_good/mri/] [2005-06-07 12:04:01] running: /usr/local/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir /var/tmp/nu_correct_14595/ nu/nu0.mnc nu/nu1.imp
Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed()
#...and so on...
Number of iterations: 32 CV of field change: 0.000883872 [alex@flanders:/data/flanders/work/alex/freesurfer/subjects/186_good/mri/] [2005-06-07 12:04:58] running: /usr/local/mni/bin/make_template -quiet -shrink 3 nu/nu0.mnc /var/tmp/nu_correct_14595//template.mnc
Transforming slices:......................................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Transforming slices:................................................................................................................................................................................................................................................................Done nu_correct -clobber nu/nu1.mnc nu/nu2.mnc [alex@flanders:/data/flanders/work/alex/freesurfer/subjects/186_good/mri/] [2005-06-07 12:05:10] running: /usr/local/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir /var/tmp/nu_correct_15016/ nu/nu1.mnc nu/nu2.imp
Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Number of iterations: 3 CV of field change: 0.000947262 [alex@flanders:/data/flanders/work/alex/freesurfer/subjects/186_good/mri/] [2005-06-07 12:05:21] running: /usr/local/mni/bin/make_template -quiet -shrink 3 nu/nu1.mnc /var/tmp/nu_correct_15016//template.mnc
Transforming slices:......................................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Transforming slices:................................................................................................................................................................................................................................................................Done nu_correct -clobber nu/nu2.mnc nu/nu3.mnc [alex@flanders:/data/flanders/work/alex/freesurfer/subjects/186_good/mri/] [2005-06-07 12:05:37] running: /usr/local/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir /var/tmp/nu_correct_15089/ nu/nu2.mnc nu/nu3.imp
Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Number of iterations: 3 CV of field change: 0.000802066 [alex@flanders:/data/flanders/work/alex/freesurfer/subjects/186_good/mri/] [2005-06-07 12:05:49] running: /usr/local/mni/bin/make_template -quiet -shrink 3 nu/nu2.mnc /var/tmp/nu_correct_15089//template.mnc
Transforming slices:......................................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Transforming slices:................................................................................................................................................................................................................................................................Done nu_correct -clobber nu/nu3.mnc nu/nu4.mnc [alex@flanders:/data/flanders/work/alex/freesurfer/subjects/186_good/mri/] [2005-06-07 12:06:01] running: /usr/local/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir /var/tmp/nu_correct_15162/ nu/nu3.mnc nu/nu4.imp
Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Number of iterations: 3 CV of field change: 0.000831802 [alex@flanders:/data/flanders/work/alex/freesurfer/subjects/186_good/mri/] [2005-06-07 12:06:13] running: /usr/local/mni/bin/make_template -quiet -shrink 3 nu/nu3.mnc /var/tmp/nu_correct_15162//template.mnc
Transforming slices:......................................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Transforming slices:................................................................................................................................................................................................................................................................Done mri_convert nu/nu4.mnc nu mri_convert nu/nu4.mnc nu reading from nu/nu4.mnc... DimSizes: 3, 256, 256, 256, 1 DataType: 1 MINC Linear Transform -1.0000 0.0000 0.0000 128.0000 0.0000 0.0000 1.0000 -128.0000 0.0000 -1.0000 0.0000 128.0000 0.0000 0.0000 0.0000 1.0000 Done reading minc TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) Original Data has (1, 1, 1) mm size and (256, 256, 256) voxels. Data is conformed to 1 mm size and 256 voxels for all directions writing to nu...
-----Original Message----- From: Nick Schmansky [mailto:nicks@nmr.mgh.harvard.edu] Sent: Sat 6/4/2005 7:41 AM To: Fornito, Alexander Cc: Freesurfer Mailing List Subject: Re: [Freesurfer] Missing libraries? Alex,
I've just posted a source code bundle of most of the MNI-BIC tools, along with a Makefile for building/installing/testing this software.
The README file is here:
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/mni.srcbuild.README
and the gzip file is here:
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/mni.srcbuild.tar.gz
Although the README says the ideal place to install is at /usr/pubsw/packages/mni/current, I've installed the set in a local home directory, and the segment_subject works for me (on Mac OS X, and Linux CENTOS 4)
However, you may be able to get your existing install working by just adding the environment var DYLD_LIBRARY_PATH. See the README for an example. Your error (not finding a .so file) is indicative of this problem.
Let me know how things go.
Nick
On Fri, 2005-05-27 at 14:38 +1000, Fornito, Alexander wrote:
Hi, We're really stuck on this one... We are running a linux kernel 2.4.26 debian 3.0 (woody). We've installed the freesurfer and the packaged MINC tools in the apporpriate directories and set the appropriate environment variables. We can't get the MNI tools to work through freesurfer, and only some limited MINC tools work if we try to run them on their own (eg., we can use MINC display, but can't do anyting with the images). It seems like there are some libraries missing (see below). Can you tell us why the MINC tools that came packaged with fressurfer aren't working? Is there something else that needs to be installed? If I try to run mri_convert from the GUI after checking the MNI Linear Register option in expert preferences, I get a message saying MNI align not yet implemented. If I run segment_subject I get :
segment_subject 190 cp: cannot stat `/data/flanders/work/alex/freesurfer/subjects/scripts/brain.dat' : No such file or directory /data/flanders/work/alex/freesurfer/subjects/190/scripts /data/flanders/work/ale x/freesurfer/subjects registering 190 mri_convert orig orig/orig.mnc reading from orig... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to orig/orig.mnc... mincinfo: error while loading shared libraries: libvolume_io.so.0: cannot open shared object file: No such file or directory Error executing mincinfo on orig/orig.mnc Error: could not open file "/data/flanders/work/alex/freesurfer/subjects/190/mr i/transforms/talairach.xfm". System message: No such file or directory mri_add_xform_to_header: could not read xform file '/data/flanders/work/alex/fre esurfer/subjects/190/mri/transforms/talairach.xfm'
Any help would be much appreciated!!! Thanks, Alex
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