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
[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
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