Closed r03ert0 closed 6 years ago
Hi
I think you will need to send me your data so I can try it myself.
Thanks
Emma
On 10 January 2018 at 17:58, Roberto Toro notifications@github.com wrote:
I can't figure out how to get the --trans option to work in msm. This is a test case: I'm doing a first registration, and then using the result .reg.surf file in the --trans option of the same call.
The first call is:
msm -v --levels=2 \ --inmesh=mesh1.sphere.asc --inanat=mesh1.asc --indata=mesh1.data.txt \ --refmesh=mesh2.sphere.asc --refanat=mesh2.asc --refdata=mesh2.data.txt -o L1.
This call works without problem (well, I do get a warning 'newmesh::set_pvalue, warning, index exceeds known pvalues dimension. Appending pvalues' that I have been ignoring...).
From the L1. results, I take L1.sphere.reg.surf.gii as input to --trans, like this:
msm -v --levels=2 \ --inmesh=mesh1.sphere.asc --inanat=mesh1.asc --indata=mesh1.data.txt \ --refmesh=mesh2.sphere.asc --refanat=mesh2.asc --refdata=mesh2.data.txt \ --trans=L1.sphere.reg.surf.gii \ -o L2.
This call fails with the following log and error:
mesh1.data.txt cost.size() 4 AFFINE,DISCRETE,DISCRETE,DISCRETE iters 50,3,3,3 lambda 0,0.1,0.2,0.3 sigmain 2,2,3,2 sigmaref 2,2,1.5,1 datagrid 4,4,5,6 cp gridres 0,2,3,4 sp grid 0,4,5,6 alpha_knn 5,5,5,5 in parse options _simval 1,2,2,2 interations 50,3,3,3 input sigma 2,2,3,2 ref sigma 2,2,1.5,1 lambda 0,0.1,0.2,0.3 _genesis 4,4,5,6 _gridres 0,2,3,4 _sampres 0,4,5,6 opt AFFINE,DISCRETE,DISCRETE,DISCRETE _scale 0 mesh interpolator BARY discrete implementation FastPD regoption 1 potts 0 Initialising level 1 Assertion failed: (px != 0), function operator->, file /Users/cowboy/fsl/extras/include/boost/boost/smart_ptr/shared_ptr.hpp, line 648. Abort trap: 6
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I think actually it might be because you are using the default config that applies an affine step, which isn't needed. Try applying a config file which has only discrete steps.
On 10 January 2018 at 18:03, Emma Robinson emma.robinson01@gmail.com wrote:
Hi
I think you will need to send me your data so I can try it myself.
Thanks
Emma
On 10 January 2018 at 17:58, Roberto Toro notifications@github.com wrote:
I can't figure out how to get the --trans option to work in msm. This is a test case: I'm doing a first registration, and then using the result .reg.surf file in the --trans option of the same call.
The first call is:
msm -v --levels=2 \ --inmesh=mesh1.sphere.asc --inanat=mesh1.asc --indata=mesh1.data.txt \ --refmesh=mesh2.sphere.asc --refanat=mesh2.asc --refdata=mesh2.data.txt -o L1.
This call works without problem (well, I do get a warning 'newmesh::set_pvalue, warning, index exceeds known pvalues dimension. Appending pvalues' that I have been ignoring...).
From the L1. results, I take L1.sphere.reg.surf.gii as input to --trans, like this:
msm -v --levels=2 \ --inmesh=mesh1.sphere.asc --inanat=mesh1.asc --indata=mesh1.data.txt \ --refmesh=mesh2.sphere.asc --refanat=mesh2.asc --refdata=mesh2.data.txt \ --trans=L1.sphere.reg.surf.gii \ -o L2.
This call fails with the following log and error:
mesh1.data.txt cost.size() 4 AFFINE,DISCRETE,DISCRETE,DISCRETE iters 50,3,3,3 lambda 0,0.1,0.2,0.3 sigmain 2,2,3,2 sigmaref 2,2,1.5,1 datagrid 4,4,5,6 cp gridres 0,2,3,4 sp grid 0,4,5,6 alpha_knn 5,5,5,5 in parse options _simval 1,2,2,2 interations 50,3,3,3 input sigma 2,2,3,2 ref sigma 2,2,1.5,1 lambda 0,0.1,0.2,0.3 _genesis 4,4,5,6 _gridres 0,2,3,4 _sampres 0,4,5,6 opt AFFINE,DISCRETE,DISCRETE,DISCRETE _scale 0 mesh interpolator BARY discrete implementation FastPD regoption 1 potts 0 Initialising level 1 Assertion failed: (px != 0), function operator->, file /Users/cowboy/fsl/extras/include/boost/boost/smart_ptr/shared_ptr.hpp, line 648. Abort trap: 6
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that was it! I removed the AFFINE step, and now everything runs properly :)
for reference, this is the conf
file I'm using:
--simval=2,2,2
--sigma_in=4,2,1
--sigma_ref=2,1,1
--lambda=0.1,0.3,0.5
--it=3,3,3
--opt=DISCRETE,DISCRETE,DISCRETE
--CPgrid=2,3,4
--SGgrid=4,5,6
--datagrid=4,5,6
--IN
thank you @ecr05 !
I can't figure out how to get the
--trans
option to work inmsm
. This is a test case: I'm doing a first registration, and then using the result.reg.surf
file in the--trans
option of the same call.The first call is:
This call works without problem (well, I do get a warning 'newmesh::set_pvalue, warning, index exceeds known pvalues dimension. Appending pvalues' that I have been ignoring...).
From the
L1.
results, I takeL1.sphere.reg.surf.gii
as input to--trans
, like this:This call fails with the following log and error: