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 [EMAIL PROTECTED]:/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 [EMAIL PROTECTED]:/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 [EMAIL PROTECTED]:/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 [EMAIL PROTECTED]:/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 [EMAIL PROTECTED]:/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 [EMAIL PROTECTED]:/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 [EMAIL PROTECTED]:/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 [EMAIL PROTECTED]:/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:[EMAIL PROTECTED] 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 > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
