Hi David,
Can you visualize these tracts individually?
type in freeview -v lh.ccg_PP_avg33_mni_flt/path.pd.nii.gz
and to visualize the merged you could try
freeview -tv merged_avg33_mni_flt.nii.gz
If both of these do not work you can try running dmri_mergepaths
seperately using the following command and see if that works for you:
dmri_mergepaths --indir <main input dir> --in <path to all the
path.pd.nii.gz files> --out <path to outputdir/merged_avg32_mni_flt.mgz>
--ctab /usr/local/freesurfer/dev/FreeSurferColorLUT.txt --thresh .15
You should have a copy of this command in your log file you can copy paste
that on to the terminal as well.
Can you try these things to see if it solves your problem?
-Priti
Everything looks to be running fine. Wether I look at the merged file with
freeview or fslview, I still have only one tract. Here's an extract of the
outputs :
Input files: lh.ccg_PP_avg33_mni_flt/path.pd.nii.gz
lh.unc_AS_avg33_mni_flt/path.pd.nii.gz
rh.ccg_PP_avg33_mni_flt/path.pd.nii.gz
rh.unc_AS_avg33_mni_flt/path.pd.nii.gz
Lower threshold for display: 0.150000
Merging volume 1 of 4...
Threshold: 111 Name: Left Cingulum - Cingulate Gyrus
Merging volume 2 of 4...
Threshold: 74.85 Name: Left Uncinate Fasciculus
Merging volume 3 of 4...
Threshold: 87.9 Name: Right Cingulum - Cingulate Gyrus
Merging volume 4 of 4...
Threshold: 57.6 Name: Right Uncinate Fasciculus
Done in 0.621 sec.
dmri_mergepaths done
It remains the same if I take a very low threshold (0.001).
David
Am 24.08.2011 um 16:49 schrieb ayendiki@nmr.mgh.harvard.edu:
Yes, it should be a concatenation of all existing pathway
reconstructions
under dpath/... If you open it with trackvis --tv, you should be able to
see a 3d view of all the pathways. Sometimes the default threshold might
be too high for some pathways and you might need to adjust it
individually
in freeview to be able to see them.
Does the output of dmri_mergepaths show you that it's found multiple
pathways or just ccg?
Yes, there are no more malloc issues, thanks for the update.
However I still have aays question, related to the merged_avg33_mni
file. It
still only contains the first path that was passed as an input to
dmri_mergepaths. If I understand correctly I should see all generated
paths, thresholded and merged into this file ?
David
Am 23.08.2011 um 21:28 schrieb Anastasia Yendiki:
Hi David - Thanks for catching this. There was something wrong with
the
new snow leopard build of dmri_mergepaths. (The original from the 5.1
distribution didn't have this problem). Sorry about that!
I've now updated the snow leopard tar file, so if you download it
again
you should not get this error any more.
As before it's here:
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/macos-snow-leopard-intel/dmri_5.1_snow_leopard.tar.gz
Let me know how it goes,
a.y
On Tue, 23 Aug 2011, David Coynel wrote:
Hi Anastasia,
Thanks for your answer. Unfortunately I overwrote the executables (I
could still retrieve them from the website distribution ?).
Interestingly this message does not show up when selecting only a
subset of the pathways, as for example ( lh.ccg rh.ccg lh.unc rh.unc
),
however the merged_avg33_mni file only appears to contain the first
pathway (lh.ccg).
David
Am 23.08.2011 um 17:06 schrieb Anastasia Yendiki:
Hi David - Glad to hear things are working! I can look into
dmri_mergepaths and see if something is wrong with the snow leopard
build.
Have you by any chance kept the original leopard build of it? If you
haven't overwritten it, it'd be useful to run the same thing with
that
version and see if it works. Thanks!
a.y
On Tue, 23 Aug 2011, David Coynel wrote:
Dear Anastasia,
Thanks a lot for the upload. The procedure now runs perfectly,
except
for that last message at the end of trac-all -path :
Merging volume 18 of 18...
Threshold: 68.1 Name: Right Uncinate Fasciculus
dmri_mergepaths(26008) malloc: *** mmap(size=18446744073709543424)
failed (error code=12)
*** error: can't allocate region
*** set a breakpoint in malloc_error_break to debug
Done in 2.433 sec.
dmri_mergepaths done
#-------------------------------------
trac-paths finished without error at Do 18 Aug 2011 11:39:42 CEST
This however does not seem to affect the pipeline, as all the
expected outputs seem to be present and valid.
Dr. David Coynel
Division of Cognitive Neuroscience
University of Basel
Birmannsgasse 8
4055 Basel - Switzerland
david.coynel@unibas.ch
tel: +41(0)612.670.240
Am 17.08.2011 um 23:44 schrieb Anastasia Yendiki:
Hi all - By popular demand we've posted the dmri_* executables
compiled on
snow leopard here:
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/macos-snow-leopard-intel/dmri_5.1_snow_leopard.tar.gz
This is not the entire FS distribution, just the commands that are
called
by trac-all. If you are a mac user with snow leopard and have been
running
into memory issues with the leopard version, you can download
this,
copy
the new files into your $FREESURFER_HOME/bin, and try rerunning
the
part
of the analysis that had errored out.
Let us know if there are any problems,
a.y
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