Lead-Connectome

[Vinny]

Hi,

I’m using test data from the Human Connectome Project to try out the Lead-Connectome tool. Files were renamed to a format recognized by the Lead-Connectome software and preprocessing appears to have occurred with no problem, i.e., normalization checks revealed good agreement with the MNI template space. However, when attempting to assess structural connectivity using deterministic fibertracking, I get the following error message below in the Matlab command window. Thanks for your help.

*** Performing structural parts of LEAD-Connectome…

————————————————————————
Running job #1
————————————————————————
Running ‘Segment’

SPM12: spm_preproc_run (v6365) 15:26:09 – 01/04/2017
========================================================================
Segment C:\Users\Vinit\Downloads\lead\templates\space\MNI_ICBM_2009b_NLIN_ASYM\t1.nii,1
Failed ‘Segment’
Error using spm_vol>spm_vol_hdr (line 80)
File “C:\Users\Vinit\Downloads\lead\templates\space\MNI_ICBM_2009b_NLIN_ASYM\pca.nii” does not exist.
In file “C:\Users\Vinit\Downloads\spm12\spm_vol.m” (v5958), function “spm_vol_hdr” at line 80.
In file “C:\Users\Vinit\Downloads\spm12\spm_vol.m” (v5958), function “spm_vol” at line 61.
In file “C:\Users\Vinit\Downloads\spm12\spm_preproc_run.m” (v6365), function “run_job” at line 84.
In file “C:\Users\Vinit\Downloads\spm12\spm_preproc_run.m” (v6365), function “spm_preproc_run” at line 41.
In file “C:\Users\Vinit\Downloads\spm12\config\spm_cfg_preproc8.m” (v6798), function “spm_local_preproc_run” at line 418.

The following modules did not run:
Failed: Segment

Error using MATLABbatch system
Job execution failed. The full log of this run can be found in MATLAB command window, starting with the
lines (look for the line showing the exact #job as displayed in this error message)
——————
Running job #1
——————
Error while evaluating UIControl Callback

[ningfei]

Hi Vinny,

Did you upgrade LEAD from an old version without downloading the data updates or the full version? Since this pca.nii file had been added to LEAD some versions before. If so, you can get the file here. Or you may want to download the full data pack here.

Best,
Ningfei

[Vinny]

Hi Ningfei,

I downloaded Lead-DBS on Feb 10, 2017 and it was version 1.6.2. I upgraded to version 1.6.3 and have the brainshift correction feature installed. Thanks for the sending the pca.nii file; I placed it in the appropriate subfolder in the lead folder. However, now I get a new error message when assessing structural connectivity using deterministic fibertracking related to no b0.nii file existing; diff.nii, dti.bval, dti.bvec, and anat_t1 files exist in the patient folder.

Thanks/Vinit

Running job #1
————————————————————————
Running ‘Coregister: Estimate & Reslice’

SPM12: spm_coreg (v6435) 23:57:54 – 01/04/2017
========================================================================
Failed ‘Coregister: Estimate & Reslice’
Error using spm_vol>spm_vol_hdr (line 80)
File “C:\Users\Vinit\Documents\MATLAB\Diffusion-raw\b0.nii” does not exist.
In file “C:\Users\Vinit\Downloads\spm12\spm_vol.m” (v5958), function “spm_vol_hdr” at line 80.
In file “C:\Users\Vinit\Downloads\spm12\spm_vol.m” (v5958), function “spm_vol” at line 61.
In file “C:\Users\Vinit\Downloads\spm12\spm_coreg.m” (v6435), function “spm_coreg” at line 117.
In file “C:\Users\Vinit\Downloads\spm12\config\spm_run_coreg.m” (v5956), function “spm_run_coreg” at line 22.

The following modules did not run:
Failed: Coregister: Estimate & Reslice

Error using MATLABbatch system
Job execution failed. The full log of this run can be found in MATLAB command window, starting with the
lines (look for the line showing the exact #job as displayed in this error message)
——————
Running job #1
——————
Error while evaluating UIControl Callback

[andreashorn]

Hi Vinit,

we should in fact remove the deterministic fiber tracking module from Lead-DBS because it is a very basic, even tensor based method (https://www.mathworks.com/matlabcentral/fileexchange/21130-dti-and-fiber-tracking) that hasn’t been used in a while. It is well possible that the method is broken.
Please try to run the GQI method instead which uses Fang-Cheng Yeh’s / DSI studio’s generalized q-sampling imaging and supports multishell data (such as from HCP). It is also deterministic and performed best in a recent open competition (http://biorxiv.org/content/early/2016/11/07/084137).

For multishell data, this is clearly the method of choice of the ones implemented in Lead-DBS.

Best, Andy

[Vinny]

Thanks Andy. I’ve bolded the subset of files from HCP that I’m using for Lead-Connectome:

anat/ Anatomical scans
T1/T1.nii.gz MPRAGE
T2/T2.nii.gz T2-weighted

diff/ Diffusion scans
raw/ unprocessed data
mri/diff.nii.gz four shells, b-values of b1k, b3k, b5k, and b10k
bvals.txt b-values
bvecs.txt diffusion gradient directions
bvecs_fsl.txt FSL compatible version of diffusion gradient directions

I renamed the files to be compatible for reading by Lead-Connectome but get the error message that the dti.bval file is unable to be read. Is it because the bvec and bval files are in .txt extension rather than .bvec and .bval format?

*** Performing structural parts of LEAD-Connectome…
Building DTI files…
Export b0…
Error using load
Unable to read file ‘C:\Users\Vinit\Documents\MATLAB\Diffusion-raw\dti.bval’. No such file or directory.
Error in ea_exportb0 (line 4)
bvals=load([options.root,options.patientname,filesep,options.prefs.bval]);
Error in ea_prepare_dti (line 14)
ea_exportb0(options);
Error in ea_ft_gqi_yeh (line 13)
ea_prepare_dti(options)
Error in ea_perform_ft_proxy (line 6)
eval([options.lc.struc.ft.method,'(options)’]); % triggers the fibertracking function and passes the options
struct to it.
Error in ea_perform_lc (line 13)
ea_perform_ft_proxy(options);
Error in ea_autocoord (line 109)
ea_perform_lc(options);
Error in ea_run (line 95)
ea_autocoord(options);
Error in lead_connectome>runsavebutn_Callback (line 289)
ea_run(‘run’,options);
Error in gui_mainfcn (line 95)
feval(varargin{:});
Error in lead_connectome (line 42)
gui_mainfcn(gui_State, varargin{:});
Error in
matlab.graphics.internal.figfile.FigFile/read>@(hObject,eventdata)lead_connectome(‘runsavebutn_Callback’,hObject,eventdata,guidata(hObject))
Error while evaluating UIControl Callback

[Vinny]

Hi Andy,

I tested Lead-Connectome with diffusion-weighted imaging data from BrainSuite and was able to complete all the steps and obtain the DTI connectivity matrix. For the BrainSuite data, the extensions are .bval and .bvec as opposed to the .txt extension from the HCP for the bval and bvec files. Also, I had renamed from diff.nii to dti.nii and re-ran the HCP data but the same error appeared after trying to export FA. I am not sure if the .txt extension is the issue.

Regards/Vinit

[andreashorn]

Yes, they need to be called .bval and .bvec. Alternatively, you can change these naming conventions to suit your needs in the preferences file ([Tools]->[Edit Prefs file]).

Best, Andy

[Vinny]

Thanks Andy

[peace]

Dear Lead-DBS experts

I’m new to Lead-Connectome. Where could I get more information about the preprocessing sequences implemented in both co-registration and normalization menu?

Such as, head-motion, scrubbing, slice timing etc.

Thanks for considering my request.

Cheers
Larry

[andreashorn]

Hi Larry,

the preprocessing basically follows the pipeline described in
https://www.ncbi.nlm.nih.gov/pubmed/24099851

Motion params are regressed out, slice timing is not corrected for, no scrubbing. WM/CSF signal is regressed out and bandpass-filtering applied within a common window (see paper).
I’d say the rs-fMRI preprocessing pipeline currently is pretty old-school but works for most applications and is really easy to use. Then again also easy to e.g. use fMRIPREP or similar before using lead connectome.
Also we’re much looking for people interested in implementing some additional tools into the pipeline.
Contact me directly if that is interesting.

Best, Andy

[peace]

Hi Andy

Thanks for your quick reply.

Screen Shot 2018-05-17 at 4.40.36 PM
https://drive.google.com/open?id=1ZEPrkbUHHEMWUpIkkAl2w4zAOt8SoTbO

The GUI status appears busy after the preprocessing.

I get the following error messages (“Please export the connectivity matrix first” in the Matlab after performing the graph matrix analysis. .

Exporting coregistration check images to /Volumes/Data/untitled folder/checkreg…
Done.
*** Performing structural parts of LEAD-Connectome…
*** Done.
*** Performing functional parts of LEAD-Connectome…
*** 1 rs-fMRI files to analyze…
*** Done analyzing 1 rs-fMRI files…
Error using ea_error (line 16)
Please export connectivity matrices first.

Error in ea_perform_lc (line 129)
ea_error(‘Please export connectivity matrices first.’);

Error in ea_autocoord (line 179)
ea_perform_lc(options);

Error in ea_run (line 96)
ea_autocoord(options);

Error in lead_connectome>runsavebutn_Callback (line 317)
ea_run(‘run’,options);

Error in gui_mainfcn (line 95)
feval(varargin{:});

Error in lead_connectome (line 42)
gui_mainfcn(gui_State, varargin{:});

Error in
matlab.graphics.internal.figfile.FigFile/read>@(hObject,eventdata)lead_connectome(‘runsavebutn_Callback’,hObject,eventdata,guidata(hObject))
Error while evaluating UIControl Callback.
—

—
Best regards
Larry

[andreashorn]

Yes, please export the connectivity matrix first.

[peace]

Hi Andy

Thanks. How to export it?

Cheers
Larry

[andreashorn]

“Compute Connectivity Matrix” checkbox.

[Author]

Posts