brain-life / encode Goto Github PK

Hi,

I am starting to take a look at this new version.

As I see it, the output variable [removedFibers] are no longer retained in the new code. Perhaps, we could just remove it from output variable.

I am trying to run app-life on output track.tck generated by brain-life/app-dipy-tracking (multishell tractograph with CSA) app.

When I run LiFE, I get following error message.

{�Error using dtiImportFibersMrtrix (line 76)
Unable to parse header for file ../59a09712682fb20024ca9af8/track.tck


Error in fgRead (line 39)
        fg = dtiImportFibersMrtrix(fgFile);

Error in feConnectomeInit (line 49)
  fg = fgRead(fgFileName);

Error in life (line 10)
fe = feConnectomeInit(config.dwi, ...

Here is the header contained inside the output track.tck.

$ head ../59a09712682fb20024ca9af8/track.tck
mrtrix tracks
count: 0000272259
datatype: Float32LE
file: . 67

It's short, but the structure looks OK? It could be missing some parameters that LiFE needs?

The brain-life/app-dipy-tracking creates track.tck by doing following.

https://github.com/brain-life/app-dipy-tracking/blob/master/main.py#L108

    tractogram = Tractogram(streamlines, affine_to_rasmm=affine)
    save(tractogram, 'track.tck')

It am not sure if this issue needs to be fixed by the tractography app, or the .tck file header parser used by LiFE.

Finding common brain coordinates between P and D connectomes...
Warning: The colorbar TickLength is a scalar quantity. Only the first value will be used. 
> In demo_LiFE>scatterPlotRMSE (line 341)
  In demo_LiFE (line 244) 
[feComputeEvidence] Computing the Earth Mover's distance... 
[feComputeEvidence] Computing the Strength of Evidence... .Error using histc
Edge vector must be monotonically non-decreasing.

Error in hist (line 126)
    nn = histc(y,edgesc,1);

Error in feComputeEvidence (line 84)
    [y(:,inm),xhis] = hist(nullDistributionW(:,inm),linspace(min_x,max_x,se.s.nbins));

Error in demo_LiFE (line 249)
se = feComputeEvidence(prob.rmse,det.rmse);

demo_LiFE is executing fine, but towards the end, while creating plots I get this error. I am not sure why this occurs.

I am trying to troubleshoot an issue that cropped up recently with brain-life/app-life when feConnectomeInit tries to load the dwi data.

Error using sub2ind (line 73)
Out of range subscript.

Error in dwiGet (line 172)


Error in feConnectomeSetDwi (line 47)


Error in feConnectomeInit (line 56)


Error in life (line 10)

I am feeding dtiInit output (dwi_aligned_trilin.nii.gz) with the following dimension.

hayashis@haswell:~/test/encode 1 mrinfo dwi_aligned_trilin.nii.gz
************************************************
Image:               "dwi_aligned_trilin.nii.gz"
************************************************
  Format:            NIfTI-1.1
  Dimensions:        129 x 169 x 121 x 108
  Voxel size:        1.25 x 1.25 x 1.25 x 1
  Dimension labels:  0. left->right (mm)
                     1. posterior->anterior (mm)
                     2. inferior->superior (mm)
                     3. undefined (?)
  Data type:         signed 16 bit integer (little endian)
  Data layout:       [ +0 +1 +2 +3 ]
  Data scaling:      offset = 0, multiplier = 1
  Comments:          Raw Eddy Corrected
  Transform:                    1           0           0         -80
                                0           1           0        -120
                                0           0           1         -60
                                0           0           0           1

Which matches the dwi.nifit.dim that's loaded

K>> dwi.nifti.dim

ans =

   129   169   121   108

The error occurs on https://github.com/vistalab/vistasoft/blob/master/mrDiffusion/dwi/dwiGet.m#L172 where sub2ind is passed roi with overflowing index.

K>> max(feGet(fe,'roi coords'))

ans =

   117   140   122

notice 122 > 121.

I'd like to know why 'fe.roi.coords' could contain index that's greater than the z-size of the image (121)?

K>> find(fe.roi.coords(:,3)==122)

ans =

      201303
      201372
      201443
      206945
      207006
      207066
      212671
      212734
      212796
      218457
      218521
      224269
      224333
      224397
      224461
      224523
      230151
      230217
      230282
      230802
      236628
      236694
      236761
      242665

Please help me troubleshoot this.

@ccaiafa

When we run LiFE, sometimes it fails with the following error message.

checking output
output weights and fibers does not match.. terminating
fe.life.fit.weights839710       1
fe.fg.fibers839711       

When this problem happens, it's usually just 1 fiber that goes missing, but I've seen up to a dozen fibers missing in one occasion.

We don't know why this happens, and often the issue goes away if we rerun the App.. I am trying to investigate the problem but I can't even recreate it when I run it on my laptop. Can you think of any area of the code that might be causing this issue?

The life demo script shows how to output various plots from probabilistic / deterministic / combined steps. However, the fh indices for probabilistic and deterministic steps uses the same indices so the deterministic steps are overriding the graphs for probabilistic steps.

..and..

I just realized that we haven't finished merging Batch_Karst branch (that has a MEX files) to master. I am using Batch_Karst branch code for app-life and ideally, I'd like to switch using the master branch instead.

Can we simply do

git checkout master
git merge Batch_Karst

?

Hi,
I tried to download the demo data but I got an error (see attachment). I registered in the https://scholarworks.iu.edu/ platform with the diego.lozano-soldevilla at neuroelectrics dot com address. Could you please provide an alternative address please?
Best

The indices of the fascicles in Virtual lesion demo are not pased properly.

End of day today. We shoudl fix soon.

Hi Franco and all,

When I run LiFE using encode for specific dataset, I found a case in which small number of streamlines got "NaN" weights after fitting.

For example, I got something like

fe.life.fit.weights(1:10)

ans =

     0

0.0102
0
0
0
NaN
0.0086

In this case, streamlines #6 got "NaN" weight.

It is a first time for me to see this phenomenon. Are there anybody who see similar sort of phenomenon?

feOpenLocalCluster still appears in fefgGet(line 209 and 800) and could cause fefgGet crash.

We've been seeing a lot of out-of-memory issue with encode lately.

Out of memory. Type HELP MEMORY for your options.

Error in unique


Error in unique


Error in fefgGet (line 224)


Error in feSet (line 75)


Error in feConnectomeInit (line 52)

This might be happening because we started feeding track.tck output from mrtrix3 act app, which output somewhat more fibers and track.tck file size is slightly larger (1.69GB)

tckinfo.txt
 
***********************************
  Tracks file: "track.tck"
    act:                  5tt.mif
    backtrack:            variable
    count:                675000
    crop_at_gmwmi:        1
    downsample_factor:    3
    fod_power:            0.25
    init_threshold:       variable
    lmax:                 variable
    max_angle:            variable
    max_num_seeds:        15000000
    max_num_tracks:       15000
    max_seed_attempts:    1000
    max_trials:           1000
    method:               variable
    mrtrix_version:       3.0_RC3
    output_step_size:     0.625
    rk4:                  0
    samples_per_step:     4
    sh_precomputed:       1
    source:               variable
    step_size:            variable
    stop_on_all_include:  0
    threshold:            variable
    timestamp:            1550301026.1405482292
    total_count:          675000
    unidirectional:       0

I will benchmark / profile the memory usage, but if @ccaiafa @francopestilli have any hunch as to what might be causing this issue, please let me know!

[feConnectomeInit] fe-structure Memory Storage:1.05 Gb
The size of the sparse tensor Phi is (Na,Nv,Nf) = (129241,190589,500000)
The size of the dictionary D is (Ntheta,Na) = (96,129241)
Index exceeds matrix dimensions.

Error in demo_connectome_encoding (line 163)
fascicles_indices = unique(inds(:,3));

Got error while running the demo_connectome_encoding.m

++ WARNING: nifti_read_buffer(/home/karan/life/Demo_Data_for_Multidimensional_Encoding_of_Brain_Connectomes/STN/sub-FP/dwi/run01_fliprot_aligned_trilin.nii.gz):
data bytes needed = 323042844
data bytes input = 0
number missing = 323042844 (set to 0)
++ WARNING: nifti_read_buffer(/home/karan/life/Demo_Data_for_Multidimensional_Encoding_of_Brain_Connectomes/STN/sub-FP/dwi/run01_fliprot_aligned_trilin.nii.gz):
data bytes needed = 323042844
data bytes input = 0
number missing = 323042844 (set to 0)
++ WARNING: nifti_read_buffer(/home/karan/life/Demo_Data_for_Multidimensional_Encoding_of_Brain_Connectomes/STN/sub-FP/dwi/run01_fliprot_aligned_trilin.nii.gz):
data bytes needed = 323042844
data bytes input = 0
number missing = 323042844 (set to 0)
++ WARNING: nifti_read_buffer(/home/karan/life/Demo_Data_for_Multidimensional_Encoding_of_Brain_Connectomes/STN/sub-FP/dwi/run01_fliprot_aligned_trilin.nii.gz):
data bytes needed = 323042844
data bytes input = 0
number missing = 323042844 (set to 0)
++ WARNING: nifti_read_buffer(/home/karan/life/Demo_Data_for_Multidimensional_Encoding_of_Brain_Connectomes/STN/sub-FP/dwi/run01_fliprot_aligned_trilin.nii.gz):
data bytes needed = 323042844
data bytes input = 0
number missing = 323042844 (set to 0)
++ WARNING: nifti_read_buffer(/home/karan/life/Demo_Data_for_Multidimensional_Encoding_of_Brain_Connectomes/STN/sub-FP/dwi/run01_fliprot_aligned_trilin.nii.gz):
data bytes needed = 323042844
data bytes input = 0
number missing = 323042844 (set to 0)

And warning in the command prompt.

Create a release version with the code of the first submission to NM and delete previously created released

When running feConnectomeEncoding.m in Matlab2014b, the set(s.matlab.desktop.workspace, 'ArraySizeLimitEnabled',false); line (26) throws an error: "Settings group 'workspace' does not contain setting 'ArraySizeLimitEnabled'." The command works fine with 2015a-2016b, and then it's obviously not run for later versions.

If there's no such setting in 2014b and/or you don't care to support this version, a note in the README or an error message indicating an unsupported version would be great! Thanks!

feConnectomeInit help text orders the arguments incorrectly. The function appears to work fine otherwise; the arguments are the same, the example in the help has them in the wrong order.

Update all demo_scripts with the doi address of demo_datasets

Hi!

I downloaded the recommended dataset and ran demo_LiFE.m without making any change to the code or dataset. But I have received the following error

Error using histc
Edge vector must be monotonically non-decreasing.

Error in hist (line 126)
    nn = histc(y,edgesc,1);

Error in feComputeEvidence (line 25)
[se.lesion.hist,   se.lesion.xhist]   = hist(se.lesion.rmse.all,  se.bins);

Error in demo_LiFE (line 252)
se = feComputeEvidence(prob.rmse,det.rmse); 

When I checked the values of "y" and "edgesc", both contained NaNs. Can you please guide what am I doing wrong? I am using MATLAB 2018a on Windows OS. "rmse", "rmsexv", "rrmse" and "w" all are also NaNs.