dpbaisurfer问题

Submitted by shenlan on

继续请教严老师，第二次彻底格式化重新安装win10 专业版管理员身份运行matlab，按照install指引安装了docker，复制了许可证，中间matlab没有报错信息。随后再次重启matlab，运行dpabisurfer后仍然报错。还请各位严老师及其他各位老师帮忙分析原因，谢谢！

Citing Information:
DPABISurf is a surface-based resting-state fMRI data analysis toolbox evolved from DPABI/DPARSF, as easy-to-use as DPABI/DPARSF. DPABISurf is based on fMRIPprep 1.4.1 (Esteban et al., 2018) (RRID:SCR_016216), and based on FreeSurfer 6.0.1 (Dale et al., 1999) (RRID:SCR_001847), ANTs 2.2.0 (Avants et al., 2008) (RRID:SCR_004757), FSL 5.0.9 (Jenkinson et al., 2002) (RRID:SCR_002823), AFNI 20160207 (Cox, 1996) (RRID:SCR_005927), SPM12 (Ashburner, 2012) (RRID:SCR_007037), PALM alpha112 (Winkler et al., 2016), GNU Parallel (Tange, 2011), MATLAB (The MathWorks Inc., Natick, MA, US) (RRID:SCR_001622), Docker (https://docker.com) (RRID:SCR_016445), and DPABI V4.1 (Yan et al., 2016) (RRID:SCR_010501).
Starting parallel pool (parpool) using the 'local' profile ...
connected to 1 workers.
 
ans = 
 
 Pool - 属性: 
 
            Connected: true
           NumWorkers: 1
              Cluster: local
        AttachedFiles: {}
    AutoAddClientPath: true
          IdleTimeout: 30 minutes (30 minutes remaining)
          SpmdEnabled: true
 
Chris Rorden's dcm2nii :: 2MAY2016 64bit BSD License  :: (upgrade to dcm2niix suggested) 
reading preferences file DCM2NII.INI 
Validating 6475 potential DICOM images. 
Found 6475 DICOM images. 
Converting 6475/6475  volumes: 185 
IM0->20190105_230714newTianjincooperation2BiLeis003a1001.nii 
Saving C:\USERS\SHENLAN\DESKTOP\PDN-SURFER\FUNIMG\1-BILEI\20190105_230714newTianjincooperation2BiLeis003a1001.nii 
Time elapsed 26203ms 
Converting Functional Images:1-bilei OK
Chris Rorden's dcm2nii :: 2MAY2016 64bit BSD License  :: (upgrade to dcm2niix suggested) 
reading preferences file DCM2NII.INI 
Validating 188 potential DICOM images. 
Found 188 DICOM images. 
Converting 188/188  volumes: 1 
IM0->20190105_230714newTianjincooperation2BiLeis004a1001.nii 
Saving C:\USERS\SHENLAN\DESKTOP\PDN-SURFER\T1IMG\1-BILEI\20190105_230714newTianjincooperation2BiLeis004a1001.nii 
Reorienting as C:\USERS\SHENLAN\DESKTOP\PDN-SURFER\T1IMG\1-BILEI\o20190105_230714newTianjincooperation2BiLeis004a1001.nii 
Saving C:\USERS\SHENLAN\DESKTOP\PDN-SURFER\T1IMG\1-BILEI\o20190105_230714newTianjincooperation2BiLeis004a1001.nii 
Cropping NIfTI/Analyze image C:\USERS\SHENLAN\DESKTOP\PDN-SURFER\T1IMG\1-BILEI\o20190105_230714newTianjincooperation2BiLeis004a1001.nii 
Saving C:\USERS\SHENLAN\DESKTOP\PDN-SURFER\T1IMG\1-BILEI\co20190105_230714newTianjincooperation2BiLeis004a1001.nii 
Time elapsed 1453ms 
Converting T1 Images:1-bilei OK
Removing First 10 Time Points: 1-bilei OK
 
Converting DPARSFA to BIDS structure...
Parallel pool using the 'local' profile is shutting down.
Preprocessing with fmriprep, this process is very time consuming, please be patient...
docker: invalid reference format.
See 'docker run --help'.
Organize thickness files...
docker: invalid reference format.
See 'docker run --help'.
docker: invalid reference format.
See 'docker run --help'.
docker: invalid reference format.
See 'docker run --help'.
docker: invalid reference format.
See 'docker run --help'.
Organize area files...
docker: invalid reference format.
See 'docker run --help'.
docker: invalid reference format.
See 'docker run --help'.
docker: invalid reference format.
See 'docker run --help'.
docker: invalid reference format.
See 'docker run --help'.
Organize curv files...
docker: invalid reference format.
See 'docker run --help'.
docker: invalid reference format.
See 'docker run --help'.
docker: invalid reference format.
See 'docker run --help'.
docker: invalid reference format.
See 'docker run --help'.
Starting parallel pool (parpool) using the 'local' profile ...
connected to 4 workers.
错误使用 y_Organize_fmriprep (line 84)
未找到匹配的文件。
 
出错 DPABISurf_run (line 479)
    y_Organize_fmriprep(Cfg);
 
出错 DPABISurf_Pipeline>pushbuttonDPABISurfRun_Callback (line 1693)   
[Error, Cfg]=DPABISurf_run(handles.Cfg);
 
出错 gui_mainfcn (line 95)
        feval(varargin{:});  
 
出错 DPABISurf_Pipeline (line 42)
    gui_mainfcn(gui_State, varargin{:});
 
出错
matlab.graphics.internal.figfile.FigFile/read>@(hObject,eventdata)DPABISurf_Pipeline('pushbuttonDPABISurfRun_Callback',hObject,eventdata,guidata(hObject)) 
计算 UIControl Callback 时出错。
 
 
文件处理进程图片:   
  
 

Hello,

For DPABISurf it says"Before running DPABISurf_Pipeline, you can test the docker environment by running DPABI->DPABISurf->Utilities->Volume-Surface Projector. If the file can be successfully projected to surface, then the software is all set. "

Which file should I load in this window or should one come up by default?

When I try to run the pipeline, I get the error-

Converting DPARSFA to BIDS structure...

Parallel pool using the 'local' profile is shutting down.
Preprocessing with fmriprep, this process is very time consuming, please be patient...
/bin/bash: docker: command not found
Organize thickness files...
/bin/bash: docker: command not found
/bin/bash: docker: command not found
/bin/bash: docker: command not found
 
In the terminal when I test docker installation, it says:
 

>>docker run hello-world

 

Hello from Docker!

This message shows that your installation appears to be working correctly.

Is there any english video tutorial please? or could you suggest how to get docker and DPABISurf to interact correctly?
 
Thank you!
Maithili

image_2020

Wed, 12/16/2020 - 11:37

Permalink

您好，请问docker在windows安装的问题后来您找到方法解决了吗？我遇到和您一样的问题，在按照网页步骤下载docker后，运行dpabisurfer也是遇到了以下的报错，谢谢~
 
docker: invalid reference format.
See 'docker run --help'.

一样的问题，matlab一直报这个错，尝试用docker 测试别的image没有问题，直接用docker调用cgyan/dpabi这个image就会报错，不知哪里出问题了

(base) PS C:\Users\lhldr> docker run -v cgyan/dpabi /bin/bash
docker: invalid reference format.
See 'docker run --help'.

 

YAN Chao-Gan

Tue, 03/12/2024 - 09:52

Permalink

See 'docker run --help'.
docker: invalid reference format.
 
要去检查docker的安装，images是否正确加载，以及路径中不要有空格和中文。
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