I don't know what I lack, please help me!!!

[aidno]

“nomalize volumes”and “check result” when I use this commed, I meet the following error:
`Using single precision for computations.
Input scalar image: E:\matlab lead.dbs\templates\space\MNI_ICBM_2009b_NLIN_ASYM\bb.nii
Reference image: E:\nill\sample_patient_postop_ct2\anat_t1.nii
Transform file does not exist: E:\nill\sample_patient_postop_ct2\glanatInverseComposite.h5
Can’t read initial transform E:\nill\sample_patient_postop_ct2\glanatInverseComposite.h5
错误使用 spm_vol>spm_vol_hdr (line 80)
File “E:\nill\sample_patient_postop_ct2\scrf\bb.nii” does not exist.

出错 spm_vol (line 61)
v = spm_vol_hdr(deblank(P(i,:)));

出错 ea_load_nii (line 39)
nii = spm_vol(fname);

出错 ea_crop_nii (line 49)
nii=ea_load_nii(filename);

出错 ea_refreshscrf>ea_createbbfiles (line 76)
ea_crop_nii([directory,’scrf’,filesep,’bb.nii’]);

出错 ea_refreshscrf>ea_createrefineslice (line 53)
ea_createbbfiles(directory); % needs to unfortunately be done each time since coregistration may have changed.

出错 ea_refreshscrf>ea_loadrefineslice (line 30)
ea_createrefineslice(directory,options,refine);

出错 ea_refreshscrf (line 3)
standardslice=ea_loadrefineslice(directory,options,0);

出错 ea_subcorticalrefine>ea_subcorticalrefine_OpeningFcn (line 66)
ispresent=ea_refreshscrf(options,handles,directory);

出错 gui_mainfcn (line 220)
feval(gui_State.gui_OpeningFcn, gui_hFigure, [], guidata(gui_hFigure), varargin{:});

出错 ea_subcorticalrefine (line 42)
gui_mainfcn(gui_State, varargin{:});

出错 ea_autocoord (line 206)
ea_subcorticalrefine(options);
I have repeat many times, I can’t find soluation via intertet. so, I need help,who can tell me what should I do？
please！！！

[andreashorn]

Hi, apparently ANTs normalization crashes on your system (probably because of a lack of memory).
Use SPM Segment instead – it’s as good and much faster.

Best, Andy

[aidno]

thank you for your answer, but I tried used a Bigger memory, it also report the same error.
`Using single precision for computations.
Input scalar image: E:\matlab lead.dbs\templates\space\MNI_ICBM_2009b_NLIN_ASYM\bb.nii
Reference image: E:\nill\sample_patient_postop_ct\anat_t1.nii
Transform file does not exist: E:\nill\sample_patient_postop_ct\glanatInverseComposite.h5
Can’t read initial transform E:\nill\sample_patient_postop_ct\glanatInverseComposite.h5
错误使用 spm_vol>spm_vol_hdr (line 80)
File “E:\nill\sample_patient_postop_ct\scrf\bb.nii” does not exist.

出错 spm_vol (line 61)
v = spm_vol_hdr(deblank(P(i,:)));

出错 ea_load_nii (line 39)
nii = spm_vol(fname);

出错 ea_crop_nii (line 49)
nii=ea_load_nii(filename);

出错 ea_refreshscrf>ea_createbbfiles (line 76)
ea_crop_nii([directory,’scrf’,filesep,’bb.nii’]);

出错 ea_refreshscrf>ea_createrefineslice (line 53)
ea_createbbfiles(directory); % needs to unfortunately be done each time since coregistration may have changed.

出错 ea_refreshscrf>ea_loadrefineslice (line 30)
ea_createrefineslice(directory,options,refine);

出错 ea_refreshscrf (line 3)
standardslice=ea_loadrefineslice(directory,options,0);

出错 ea_subcorticalrefine>ea_subcorticalrefine_OpeningFcn (line 66)
ispresent=ea_refreshscrf(options,handles,directory);

出错 gui_mainfcn (line 220)
feval(gui_State.gui_OpeningFcn, gui_hFigure, [], guidata(gui_hFigure), varargin{:});

出错 ea_subcorticalrefine (line 42)
gui_mainfcn(gui_State, varargin{:});

出错 ea_autocoord (line 206)
ea_subcorticalrefine(options);

出错 ea_run (line 96)
ea_autocoord(options);

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

出错 gui_mainfcn (line 95)
feval(varargin{:});

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

出错
matlab.graphics.internal.figfile.FigFile/read>@(hObject,eventdata)lead_dbs(‘run_button_Callback’,hObject,eventdata,guidata(hObject))
计算 UIControl Callback 时出错

maybe I lack something, but I don’t know what I lack
I just have two files
the Pre-operative images: anat_t1.nii
Post-operative images: postop_ct.nii
thank you for help!

[aidno]

thank you again, I tried again in another computer, and it’s worked!!
you idea is very useful!
best wish!
adino

[andreashorn]

Great. But again, SPM Segment is just as good and much quicker:
These two papers show it:
https://www.researchgate.net/publication/327908494_Optimization_and_comparative_evaluation_of_nonlinear_deformation_algorithms_for_atlas-based_segmentation_of_DBS_target_nuclei

https://www.researchgate.net/publication/327380509_Lead-DBS_v2_Towards_a_comprehensive_pipeline_for_deep_brain_stimulation_imaging

Probably will make SPM default soon again.

Best, Andy

[aidno]

hi, Andy, sorry I need help again, I have got the 3D of electrode.but the atlas structures just show the SUBCORTICAL ATLASES IN MNI SPACE, I don’t know where to find the subcortical atlases in MNI space? maybe I need download some files?
can you give me more information about this?
thank you very much!

[andreashorn]

Hi Aidno,

just make sure you have a proper installation of Lead-DBS, then it should show the DISTAL atlas by default.
See https://leaddbs.gitbooks.io/leaddbs-manual/content/Installation.html for a guide on how to install Lead-DBS.

Best, Andy

[aidno]

thank you ! I am sure I have a proper installation of Lead-DBS.
I can use LEAD-DBS, but when I click Render 3D, then Run. the Atlas structures Atlasset: will show the SUBCORTICAL ATLASES IN MNI SPACE. but don’t have the subcortical atlases in MNI space.

Best, Adino

[andreashorn]

Not sure why and this has not been reported before. Again, I’m pretty sure that you don’t have all files and should make sure you have a full install. Maybe you just lack some data files. I would redownload, delete the old folder and try again.

Best, Andy

[aidno]

OK, I will try again, thank you!
best, Adino

[aidno]

Hi, Andy
I tried again, but still but don’t have the subcortical atlases in MNI space. you can see the screenshot. Please help me! thank you again!

best, Adino

[andreashorn]

Hi Aidno,

I fear I can’t say much to help you based on the things I know.. We have over 7000 downloads and it usually just works. I’d make sure there is only one single lead-dbs folder on your hard-drive (delete everything older or so). Make sure you have SPM12 on your Matlab path. Also make sure you have ML version >= 2015b.
If that doesn’t help, do you have a Matlab expert somewhere in your institute who could have a look at it?

Best, Andy

[aidno]

Hi, Andy,
I asked three seniors in my institute, they thought maybe because the version of software I using is different from the walkthrough videos. It’s V2.0.0.6 and I used V2.1.0.
I used Windows10, SPM12 is on my Matlab path , and my ML version is R2017a.
I don’t know why it doesn’t work, so, I want to download the Lead-DBS 2.0.6. Can you tell me where I can find the old version? or can you give me a e-mail address, I can show you the screenshot of my problem.
thank you very much!
best, Adino

[andreashorn]

Hi Adino,

it’s surely not the version number, this should be fine.
Regarding screenshots, the best way is to use our Slack user channel:

Slack User Channel

There are also more experts online there than here, maybe someone else has an idea.

Thanks!

Best, Andy

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