Disabling
openMP does cause a bottleneck with that many samples.
The
preprocessing step takes a while, so unless it has an
impact on the particle distribution, I would like run
groom with openMP and run optimization single threaded to
get at least speed up. That should produce identical
results, right?
Thanks
for the parameter suggestions, I will definitely try them.
Unfortunately,
I didn’t get identical results using the commit you
provided with openmp.
Here
is what I did: First executed the groom and run, move
the output*wpts to a new folder and execute the run one
more time. Attached are the parameters in xml.
Is
there anything I am missing?
ShapeWorksGroom
/home/murat/SW/1/shapeworks.groom.xml center isolate
hole_fill antialias fastmarching blur
ShapeWorksRun
/home/murat/SW/1/shapeworks.run.xml
Groom.xml
<antialias_iterations>100</antialias_iterations>
<background>0</background>
<foreground>2</foreground>
<transform_file>/home/murat/SW/1//shapeworks.transform</transform_file>
<inputs>/home/murat/SW/1/def_152-11_to_atlas.nii.gz_inv.nii.gz
/home/murat/SW/1/def_152-10_to_atlas.nii.gz_inv.nii.gz
/home/murat/SW/1/def_152-15_to_atlas.nii.gz_inv.nii.gz
/home/murat/SW/1/def_152-14_to_atlas.nii.gz_inv.nii.gz
/home/murat/SW/1/def_152-18_to_atlas.nii.gz_inv.nii.gz
/home/murat/SW/1/def_152-13_to_atlas.nii.gz_inv.nii.gz
/home/murat/SW/1/def_152-17_to_atlas.nii.gz_inv.nii.gz
/home/murat/SW/1/def_152-19_to_atlas.nii.gz_inv.nii.gz
/home/murat/SW/1/def_152-12_to_atlas.nii.gz_inv.nii.gz</inputs>
<outputs>/home/murat/SW/1/def_152-11_to_atlas_DT.nii.gz_inv_DT.nii.gz
/home/murat/SW/1/def_152-10_to_atlas_DT.nii.gz_inv_DT.nii.gz
/home/murat/SW/1/def_152-15_to_atlas_DT.nii.gz_inv_DT.nii.gz
/home/murat/SW/1/def_152-14_to_atlas_DT.nii.gz_inv_DT.nii.gz
/home/murat/SW/1/def_152-18_to_atlas_DT.nii.gz_inv_DT.nii.gz
/home/murat/SW/1/def_152-13_to_atlas_DT.nii.gz_inv_DT.nii.gz
/home/murat/SW/1/def_152-17_to_atlas_DT.nii.gz_inv_DT.nii.gz
/home/murat/SW/1/def_152-19_to_atlas_DT.nii.gz_inv_DT.nii.gz
/home/murat/SW/1/def_152-12_to_atlas_DT.nii.gz_inv_DT.nii.gz
</outputs>
Run.xml
<?xml
version="1.0" encoding="UTF-8"?>
<iterations_per_split>100</iterations_per_split>
<starting_regularization>1000</starting_regularization>
<ending_regularization>0.1</ending_regularization>
<number_of_particles>1024</number_of_particles>
<optimization_iterations>1000</optimization_iterations>
<procrustes_scaling>0</procrustes_scaling>
<output_points_prefix>/home/murat/SW/1//output_points</output_points_prefix>
<output_transform_file>/home/murat/SW/1//output_transform_file</output_transform_file>
<inputs>/home/murat/SW/1/def_152-11_to_atlas_DT.nii.gz_inv_DT.nii.gz
/home/murat/SW/1/def_152-10_to_atlas_DT.nii.gz_inv_DT.nii.gz
/home/murat/SW/1/def_152-15_to_atlas_DT.nii.gz_inv_DT.nii.gz
/home/murat/SW/1/def_152-14_to_atlas_DT.nii.gz_inv_DT.nii.gz
/home/murat/SW/1/def_152-18_to_atlas_DT.nii.gz_inv_DT.nii.gz
/home/murat/SW/1/def_152-13_to_atlas_DT.nii.gz_inv_DT.nii.gz
/home/murat/SW/1/def_152-17_to_atlas_DT.nii.gz_inv_DT.nii.gz
/home/murat/SW/1/def_152-19_to_atlas_DT.nii.gz_inv_DT.nii.gz
/home/murat/SW/1/def_152-12_to_atlas_DT.nii.gz_inv_DT.nii.gz
</inputs>
From:
shapeworks-users-request@sci.utah.edu
[mailto:shapeworks-users-request@sci.utah.edu]
On Behalf Of Murat Maga
Sent: Thursday, February 18, 2016 10:07 AM
To: Shireen Elhabian; shapeworks-users@sci.utah.edu
Subject: RE: [shapeworks-users] unstable
shapeworks results
Hi
Shireen,
Thanks
a bunch. We are testing it right now, and I will let you
know.
M
From:
Shireen Elhabian [mailto:shireen@sci.utah.edu]
Sent: Thursday, February 18, 2016 9:20 AM
To: shapeworks-users@sci.utah.edu;
Murat Maga
Subject: Re: [shapeworks-users] unstable
shapeworks results
Hi Murat,
Please clone the latest source code of shapeworks (https://github.com/SCIInstitute/shapeworks)
... I have fixed this issue ...you should be able now to
get repeatable results with the same set of shapes and
parameters and with disabling openmp ... you might want
to try this first on a small subset of shape just to
make sure that it actually works ...
best regards
Shireen
On 02/17/2016 10:28 PM, Murat Maga wrote:
Hi
Shireen,
There
are few things going on I think.
First
off using the provided SW studio windows binary we get
repeatable results. But that’s not going to cut it for
us, because I have 500 samples. I don’t have windows
box that has the necessary amount of memory to run all
the samples. At about 200 samples, it is maxing out on
my 32GB RAM.
Therefore
downloaded the latest linux commandline tool (from the
website links) and compiled it. We did not get
repeatable results with or without openMP enabled.
When I execute the script on the same samples with
using the same parameter set back to back, I get
different results. I am not so concerned that the
exact correspondence is not achieved. What I am
concerned is if you rank them by their relative
position to their respective mean (from closest to
farthest) based on procrustes distance, ranking is not
identical in those runs. That is quite concerning, at
least to me.
So
there is something we are missing in Linux causing the
inconsistency, but I can’t quite figure it out. I even
exported the groom and optimize xml files I used on
windows and try on Linux and that didn’t make any
difference.
M
From:
shapeworks-users-request@sci.utah.edu
[mailto:shapeworks-users-request@sci.utah.edu]
On Behalf Of Shireen Elhabian
Sent: Wednesday, February 17, 2016 6:09 PM
To: shapeworks-users@sci.utah.edu
Subject: Re: [shapeworks-users] unstable
shapeworks results
Hi,
1 . In order to get repeatable results, i.e same exact
correspondence model, you might want to disable openmp
at the expense of longer computation time ...
nonetheless, with openmp, you still get similar
correspondence model in terms of representation, yet
not the same exact ordering and positional
information.
2. points in wpts are already procrustes aligned and
can directly be fed to PCA. we are working on an
improved version of SW and will add the exportation of
the eigenmodes and scores ... thanks for bringing this
up ... for the time being, please refer to
ComputeModeLengths.cxx for utilities that would
compute pca modes and scores ...
hope this helps ...
best regards
Shireen
On 02/17/2016 12:07 PM, Murat Maga wrote:
Hi,
I
want to follow up on this. We want to use the PC
scores from the shapeworks analysis as input for our
quantitative trait mapping to find genomic intervals
associated with molar morphology and size. We
successfully used this approach using traditional
landmarks, but I definitely see value using SW.
However, there are couple concerns:
1.
We
are not getting repeatable results (as Ryan
described below) with identical datasets and
parameter xmls. Parameter space is too big to
randomly experiment on our own. We can use
suggestions on what to focus and what might be
driving this randomness.
2.
Although
I can visualize the modes of variation using SW
Studio, I can’t get to the individual eigenvectors
or the PC scores. To overcome this, I am feeding the
wpts files into a Procrustes analysis and doing
alignment and PCA, which is kind of silly, since SW
does it already. It would be good to expose the PC
scores an eigenvectors.
Best
wishes,
Murat
A.
Murat Maga, PhD
Assistant
Professor
UW
Dept. of Pediatrics
Division
of Craniofacial Medicine
&
Member
Seattle
Children’s Research Institute
Center
for Developmental Biology and Regenerative Medicine
From:
shapeworks-users-request@sci.utah.edu
[mailto:shapeworks-users-request@sci.utah.edu]
On Behalf Of Young, Ryan
Sent: Tuesday, February 16, 2016 3:14 PM
To: shapeworks-users@sci.utah.edu
Subject: [shapeworks-users] unstable
shapeworks results
Hello,
I have been using shapeworks to landmark six
different mouse molars. Shapeworks was run twice
on each molar, with identical parameters and
volumes. The results are surprisingly different.
Regressing the distance to the mean shape of each
the landmarks configuration between runs, 5-10
samples are drastically different. See attached
plot. I was wondering if I am running the samples
with enough iterations? I am going to experiment
with increasing the number of iteration to see if
the results stabilize, but would greatly
appreciate any suggestions. The top of the
groom.xml and run.xml files are below.
groom.xml
<?xml version="1.0" encoding="UTF-8"?>
<blur_sigma>0.5</blur_sigma>
<antialias_iterations>50</antialias_iterations>
<background>0</background>
<foreground>2</foreground>
<transform_file>/cm/shared/data/n2_molars/shapeworks/label1//shapeworks.transform</transform_file>
<inputs>/cm/shared/data/n2_molars/shapeworks/label1/def_152-11_to_atlas.nii.gz_inv.nii.gz
run.xml
<?xml version="1.0" encoding="UTF-8"?>
<iterations_per_split>100</iterations_per_split>
<starting_regularization>1000</starting_regularization>
<ending_regularization>0.1</ending_regularization>
<number_of_particles>1024</number_of_particles>
<optimization_iterations>1000</optimization_iterations>
<output_points_prefix>/cm/shared/data/n2_molars/shapeworks/label1//output_points</output_points_prefix>
<output_transform_file>/cm/shared/data/n2_molars/shapeworks/label1//output_transform_file</output_transform_file>
<inputs>/
CONFIDENTIALITY NOTICE: This e-mail
message, including any attachments, is for the sole
use of the intended recipient(s) and may contain
confidential and privileged information protected by
law. Any unauthorized review, use, disclosure or
distribution is prohibited. If you are not the
intended recipient, please contact the sender by reply
e-mail and destroy all copies of the original message.
