General discussion

[Alexandre]

Thank you! very useful

[Alexandre]

Thank you, it was of great help.

I was going through the stimulation folders and ea_stats file and I could find the VTAs volume. Is there a way to find the VTAs diameter or radius?

Regards,

Alexandre

[rubenscury]

Dear Andreas,
I’m trying to coregister the images but it is not working…the error below appears in the matlab,
I’m using anat_1.ii anat_2.nii postop_ct.nii…..

I’ve already deleted and reinstalled the lead DBS, but the error continues….
Can you help me?
Many thanks

ANTs LINEAR registration done.
Coregistration done.
Tonemapping CT… Done. (2.1754 s)

Exporting coregistration check images to /Users/rubenscury/Desktop/vanilson sn/checkreg…
Tonemapping CT… Done. (0.8466 s)
Images aren’t the same size!
Done.
Undefined function or variable ‘cfg_util_persistent’.

Error in cfg_util (line 433)
[c0, jobs] = cfg_util_persistent;

Error in spm_jobman (line 246)
cjob = cfg_util(‘initjob’, mljob);

Error in ea_docoreg_spm (line 49)
spm_jobman(‘run’,{matlabbatch});

Error in ea_coreg2images (line 37)
affinefile =
ea_docoreg_spm(options,appendcommaone(moving),appendcommaone(fixed),’nmi’,1,commaoneotherfiles,writeoutmat,interp);

Error in ea_coreg_all_mri (line 16)
ea_coreg2images(options,[directory,presentfiles{coregfi}],[directory,presentfiles{1}],[directory,presentfiles{coregfi}]);

Error in ea_checkcoregallmri (line 9)
ea_coreg_all_mri(options,usebrainmask)

Error in ea_autocoord (line 140)
ea_checkcoregallmri(options,0,1); % check and coregister all
preoperative MRIs here.

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

Error in lead_dbs>run_button_Callback (line 187)
ea_run(‘run’,options);

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

Error in lead_dbs (line 43)
gui_mainfcn(gui_State, varargin{:});

Error in
@(hObject,eventdata)lead_dbs(‘run_button_Callback’,hObject,eventdata,guidata(hObject))

Error while evaluating UIControl Callback

[loreent]

Dear lead-dbs team,

I have a general question regarding OSs, hope you can help. I have been running lead-dbs without problems on my local OS (macOS Sierra, v.10.12.6). Recently we have been trying to move the computations using lead-dbs connectome to our computing cluster for resting state analysis, but here the pipeline (Coregister with SPM/ANTs, Normalize with ANTs, functional connectivity processes) crashes.

Based on the error message (see below), I believe this has to do with an incompatibility stemming from the OS of the virtual machine I am using to push jobs onto the cluster, which runs CentOS 7. As far as I can tell, CentOS 7 only supports glibc 2.17. Can you please advise on whether the VM OS could indeed be the source of the problem, and if so, is a CentOS-compatible version available or planned?

Thank you for your help!
Best wishes, Loreen

Here is the error message I received:

Done preprocessing fMRI data.
No timecourses found, processing…
~/lead/ext_libs/ANTs/antsApplyTransforms.glnxa64: /lib64/libc.so.6: version `GLIBC_2.18′ not found (required by ~/lead/ext_libs/support/libstdc++.so.6)

Error using copyfile
cp: der Aufruf von stat für
“~/001/templates/labeling/wrisk_parcel.nii”
ist nicht möglich: Datei oder Verzeichnis nicht gefunden

Error in ea_warp_parcellation (line 65)
copyfile([directory,’templates’,filesep,’labeling’,filesep,’w’,options.lc.general.parcellation,’.nii’],…

Error in ea_extract_timecourses (line 6)
ea_warp_parcellation(options.prefs.pprest,’rest’,options);

Error in ea_createCM_fmri (line 15)
gmtc=ea_extract_timecourses(options);

Error in ea_perform_lc (line 81)
[fMRI_CM, gmtc]=ea_createCM_fmri(options);

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

[rubenscury]

Dear colleagues,

We’ve been working with DBS targeting the cerebellum (dentate nucleus). Does anyone know if there is any atlas in the Lead-DBS that see the cerebellum? If the answer is not, can I import an atlas into the Lead-DBS?

Best
Rubens

[rubenscury]

Dear colleagues,

In order to walk through all lead-dbs tools, what package in Matlab should I download? 1) computational finance, 2) control system, 3) image processing and computer vision, 4) signal processing, 5) computational biology and 6) data analytics?

I did not find this information in the manual,

Regards
Rubens

[andreashorn]

Hi rubenscury,

re the cerebellum – see the labeling folder which has the suit atlas and the yeo cerebellar functional zones atlas.
You can try to use ea_labeling2atlas(‘Cerebellum_SUIT (Diedrichsen 2006)’) to convert the labeling into an atlas – but I’m not 100% sure if it will work. If not need to do manually (just put nifti files in the folders, ignore the atlas_index.mat and gm.nii files that will be built automatically.

Re toolboxes I think you need stats & machinelearning as well as image processing optimally. Most things should work without but some functions need them.

Best, Andy

[Author]

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