Unable to reload the protocol

Discussions
1

Hi team,
I’ve run into an urgent problem: after a MATLAB crash, my protocol no longer loads fully. The imaging data still loads, but all EEG data fails to load—only the “review raw file” items remain. Could you please advise on what I should do to recover or fix this? Thank you!

Additionally, I found that the data loads correctly when sorted by condition, but not when sorted by subjects.

protocol.mat (263.1 KB)
Here is the data protocol generate by brainstorm

4

Right-click on the top node in the Brainstorm database explorer, then on Reload

Check if there are any message in the Matlab command window

5

Thanks for your guidance. Below is the MATLAB Command Window output (apologies—my MATLAB language is set to Simplified Chinese):

警告: Cannot open anatomy file 'G:\brainstorm_db\Test_001\anat\01gaoyibo_2021ft\subjectimage_3DT1.mat'.

位置：db_parse_subject/io_getAnatomyInfo (第 273 行)
位置: db_parse_subject (第 157 行)
位置: db_parse_subject (第 138 行)
位置: db_load_subjects (第 125 行)
位置: db_reload_database (第 74 行)
位置: panel_protocols>ReloadNode (第 720 行)
位置: panel_protocols (第 46 行)
位置: tree_callbacks>@(h,ev)panel_protocols('ReloadNode',bstNodes(1)) (第 2723 行)
警告: Cannot open anatomy file
'G:\brainstorm_db\Test_001\anat\01gaoyibo_2021ft\subjectimage_second_post_seeg_spm_reslice_masked_spm_volct.mat'.
位置：db_parse_subject/io_getAnatomyInfo (第 273 行)
位置: db_parse_subject (第 157 行)
位置: db_parse_subject (第 138 行)
位置: db_load_subjects (第 125 行)
位置: db_reload_database (第 74 行)
位置: panel_protocols>ReloadNode (第 720 行)
位置: panel_protocols (第 46 行)
位置: tree_callbacks>@(h,ev)panel_protocols('ReloadNode',bstNodes(1)) (第 2723 行)
警告: Cannot open anatomy file 'G:\brainstorm_db\Test_001\anat\04liushuhan\subjectimage_251015_2142.mat'.
位置：db_parse_subject/io_getAnatomyInfo (第 273 行)
位置: db_parse_subject (第 157 行)
位置: db_parse_subject (第 138 行)
位置: db_load_subjects (第 125 行)
位置: db_reload_database (第 74 行)
位置: panel_protocols>ReloadNode (第 720 行)
位置: panel_protocols (第 46 行)
位置: tree_callbacks>@(h,ev)panel_protocols('ReloadNode',bstNodes(1)) (第 2723 行)
警告: Cannot open anatomy file
'G:\brainstorm_db\Test_001\anat\04liushuhan\subjectimage_postCT_spm_reslice_masked_spm_volct.mat'.
位置：db_parse_subject/io_getAnatomyInfo (第 273 行)
位置: db_parse_subject (第 157 行)
位置: db_parse_subject (第 138 行)
位置: db_load_subjects (第 125 行)
位置: db_reload_database (第 74 行)
位置: panel_protocols>ReloadNode (第 720 行)
位置: panel_protocols (第 46 行)
位置: tree_callbacks>@(h,ev)panel_protocols('ReloadNode',bstNodes(1)) (第 2723 行)
警告: Cannot open anatomy file 'G:\brainstorm_db\Test_001\anat\05liuyinglu_2016ft\subjectimage_anatomy3_volatlas.mat'.
位置：db_parse_subject/io_getAnatomyInfo (第 273 行)
位置: db_parse_subject (第 157 行)
位置: db_parse_subject (第 138 行)
位置: db_load_subjects (第 125 行)
位置: db_reload_database (第 74 行)
位置: panel_protocols>ReloadNode (第 720 行)
位置: panel_protocols (第 46 行)
位置: tree_callbacks>@(h,ev)panel_protocols('ReloadNode',bstNodes(1)) (第 2723 行)
警告: Cannot open anatomy file 'G:\brainstorm_db\Test_001\anat\05liuyinglu_2016ft\subjectimage_cobra_volatlas.mat'.
位置：db_parse_subject/io_getAnatomyInfo (第 273 行)
位置: db_parse_subject (第 157 行)
位置: db_parse_subject (第 138 行)
位置: db_load_subjects (第 125 行)
位置: db_reload_database (第 74 行)
位置: panel_protocols>ReloadNode (第 720 行)
位置: panel_protocols (第 46 行)
位置: tree_callbacks>@(h,ev)panel_protocols('ReloadNode',bstNodes(1)) (第 2723 行)
警告: Cannot open anatomy file 'G:\brainstorm_db\Test_001\anat\05liuyinglu_2016ft\subjectimage_hammers_volatlas.mat'.
位置：db_parse_subject/io_getAnatomyInfo (第 273 行)
位置: db_parse_subject (第 157 行)
位置: db_parse_subject (第 138 行)
位置: db_load_subjects (第 125 行)
位置: db_reload_database (第 74 行)
位置: panel_protocols>ReloadNode (第 720 行)
位置: panel_protocols (第 46 行)
位置: tree_callbacks>@(h,ev)panel_protocols('ReloadNode',bstNodes(1)) (第 2723 行)
警告: Cannot open anatomy file
'G:\brainstorm_db\Test_001\anat\05liuyinglu_2016ft\subjectimage_julichbrain_volatlas.mat'.
位置：db_parse_subject/io_getAnatomyInfo (第 273 行)
位置: db_parse_subject (第 157 行)
位置: db_parse_subject (第 138 行)
位置: db_load_subjects (第 125 行)
位置: db_reload_database (第 74 行)
位置: panel_protocols>ReloadNode (第 720 行)
位置: panel_protocols (第 46 行)
位置: tree_callbacks>@(h,ev)panel_protocols('ReloadNode',bstNodes(1)) (第 2723 行)
警告: Cannot open anatomy file 'G:\brainstorm_db\Test_001\anat\05liuyinglu_2016ft\subjectimage_lpba40_volatlas.mat'.
位置：db_parse_subject/io_getAnatomyInfo (第 273 行)
位置: db_parse_subject (第 157 行)
位置: db_parse_subject (第 138 行)
位置: db_load_subjects (第 125 行)
位置: db_reload_database (第 74 行)
位置: panel_protocols>ReloadNode (第 720 行)
位置: panel_protocols (第 46 行)
位置: tree_callbacks>@(h,ev)panel_protocols('ReloadNode',bstNodes(1)) (第 2723 行)
警告: Cannot open anatomy file 'G:\brainstorm_db\Test_001\anat\05liuyinglu_2016ft\subjectimage_mori_volatlas.mat'.
位置：db_parse_subject/io_getAnatomyInfo (第 273 行)
位置: db_parse_subject (第 157 行)
位置: db_parse_subject (第 138 行)
位置: db_load_subjects (第 125 行)
位置: db_reload_database (第 74 行)
位置: panel_protocols>ReloadNode (第 720 行)
位置: panel_protocols (第 46 行)
位置: tree_callbacks>@(h,ev)panel_protocols('ReloadNode',bstNodes(1)) (第 2723 行)
警告: Cannot open anatomy file 'G:\brainstorm_db\Test_001\anat\05liuyinglu_2016ft\subjectimage_thalamus_volatlas.mat'.
位置：db_parse_subject/io_getAnatomyInfo (第 273 行)
位置: db_parse_subject (第 157 行)
位置: db_parse_subject (第 138 行)
位置: db_load_subjects (第 125 行)
位置: db_reload_database (第 74 行)
位置: panel_protocols>ReloadNode (第 720 行)
位置: panel_protocols (第 46 行)
位置: tree_callbacks>@(h,ev)panel_protocols('ReloadNode',bstNodes(1)) (第 2723 行)
警告: Cannot open anatomy file
'G:\brainstorm_db\Test_001\anat\05liuyinglu_2016ft\subjectimage_tissues_cat12_volatlas.mat'.
位置：db_parse_subject/io_getAnatomyInfo (第 273 行)
位置: db_parse_subject (第 157 行)
位置: db_parse_subject (第 138 行)
位置: db_load_subjects (第 125 行)
位置: db_reload_database (第 74 行)
位置: panel_protocols>ReloadNode (第 720 行)
位置: panel_protocols (第 46 行)
位置: tree_callbacks>@(h,ev)panel_protocols('ReloadNode',bstNodes(1)) (第 2723 行)
警告: Cannot open anatomy file
'G:\brainstorm_db\Test_001\anat\10wujiyuan_2022tt\subjectimage_postCT_spm_reslice_masked_spm_volct.mat'.
位置：db_parse_subject/io_getAnatomyInfo (第 273 行)
位置: db_parse_subject (第 157 行)
位置: db_parse_subject (第 138 行)
位置: db_load_subjects (第 125 行)
位置: db_reload_database (第 74 行)
位置: panel_protocols>ReloadNode (第 720 行)
位置: panel_protocols (第 46 行)
位置: tree_callbacks>@(h,ev)panel_protocols('ReloadNode',bstNodes(1)) (第 2723 行)
警告: Cannot open anatomy file
'G:\brainstorm_db\Test_001\anat\21hujingran_2021tt\subjectimage_postCT_spm_reslice_masked_spm_volct.mat'.
位置：db_parse_subject/io_getAnatomyInfo (第 273 行)
位置: db_parse_subject (第 157 行)
位置: db_parse_subject (第 138 行)
位置: db_load_subjects (第 125 行)
位置: db_reload_database (第 74 行)
位置: panel_protocols>ReloadNode (第 720 行)
位置: panel_protocols (第 46 行)
位置: tree_callbacks>@(h,ev)panel_protocols('ReloadNode',bstNodes(1)) (第 2723 行)
警告: Cannot open anatomy file
'G:\brainstorm_db\Test_001\anat\24muxueting_2023tt\subjectimage_muxuetin_2023tt_postseeg_spm_reslice_masked_spm_volct.mat'.
位置：db_parse_subject/io_getAnatomyInfo (第 273 行)
位置: db_parse_subject (第 157 行)
位置: db_parse_subject (第 138 行)
位置: db_load_subjects (第 125 行)
位置: db_reload_database (第 74 行)
位置: panel_protocols>ReloadNode (第 720 行)
位置: panel_protocols (第 46 行)
位置: tree_callbacks>@(h,ev)panel_protocols('ReloadNode',bstNodes(1)) (第 2723 行)
警告: Cannot open anatomy file 'G:\brainstorm_db\Test_001\anat\25liuxingnan_2023tt\subjectimage_anat.mat'.
位置：db_parse_subject/io_getAnatomyInfo (第 273 行)
位置: db_parse_subject (第 157 行)
位置: db_parse_subject (第 138 行)
位置: db_load_subjects (第 125 行)
位置: db_reload_database (第 74 行)
位置: panel_protocols>ReloadNode (第 720 行)
位置: panel_protocols (第 46 行)
位置: tree_callbacks>@(h,ev)panel_protocols('ReloadNode',bstNodes(1)) (第 2723 行)
警告: Cannot open anatomy file
'G:\brainstorm_db\Test_001\anat\25liuxingnan_2023tt\subjectimage_tissues_segment_volatlas_02.mat'.
位置：db_parse_subject/io_getAnatomyInfo (第 273 行)
位置: db_parse_subject (第 157 行)
位置: db_parse_subject (第 138 行)
位置: db_load_subjects (第 125 行)
位置: db_reload_database (第 74 行)
位置: panel_protocols>ReloadNode (第 720 行)
位置: panel_protocols (第 46 行)
位置: tree_callbacks>@(h,ev)panel_protocols('ReloadNode',bstNodes(1)) (第 2723 行)
警告: Cannot open file
'G:\brainstorm_db\Test_001\data\000yanghanjie_2021ft\Epileptogenicity_volume\brainstormstudy.mat' : ignoring study
位置：db_parse_study (第 79 行)
位置: db_parse_study (第 174 行)
位置: db_parse_study (第 174 行)
位置: db_load_studies (第 141 行)
位置: db_reload_database (第 77 行)
位置: panel_protocols>ReloadNode (第 720 行)
位置: panel_protocols (第 46 行)
位置: tree_callbacks>@(h,ev)panel_protocols('ReloadNode',bstNodes(1)) (第 2723 行)
警告: Cannot open file
'G:\brainstorm_db\Test_001\data\000yanghanjie_2021ft\Epileptogenicity_volume_02\brainstormstudy.mat' : ignoring study
位置：db_parse_study (第 79 行)
位置: db_parse_study (第 174 行)
位置: db_parse_study (第 174 行)
位置: db_load_studies (第 141 行)
位置: db_reload_database (第 77 行)
位置: panel_protocols>ReloadNode (第 720 行)
位置: panel_protocols (第 46 行)
位置: tree_callbacks>@(h,ev)panel_protocols('ReloadNode',bstNodes(1)) (第 2723 行)
警告: Cannot open file 'G:\brainstorm_db\Test_001\data\08sunheze_2015ft\Epileptogenicity_volume\brainstormstudy.mat' :
ignoring study
位置：db_parse_study (第 79 行)
位置: db_parse_study (第 174 行)
位置: db_parse_study (第 174 行)
位置: db_load_studies (第 141 行)
位置: db_reload_database (第 77 行)
位置: panel_protocols>ReloadNode (第 720 行)
位置: panel_protocols (第 46 行)
位置: tree_callbacks>@(h,ev)panel_protocols('ReloadNode',bstNodes(1)) (第 2723 行)

7

It looks like my Protocol got corrupted after I ran SPM12 in the same MATLAB session where Brainstorm was open.
If there are steps to rebuild the database/index, or a recommended recovery workflow, I’d greatly appreciate guidance.

Thanks in advance!

8

image
image1027×1195 91.9 KB

Hi Brainstorm team,

After opening my protocol, clicking any data node triggers an error:

Error in gui_layout.m
Line 699: Index exceeds number of array elements. Index must not exceed 0.

Call stack:
> gui_layout.m>PositionFigure at 699
> gui_layout.m>TileWindows    at 597
> gui_layout.m>Update         at 50
> gui_layout.m at 33
> bst_figures.m>CreateFigure  at 232
> bst_figures.m at 59
> view_timeseries.m at 149
> tree_callbacks.m at 274
> bst_call.m at 28
> panel_protocols.m>CreatePanel/protocolTreeClicked_Callback at 125
> bst_call.m at 28
> panel_protocols.m>@(h,ev)bst_call(@protocolTreeClicked_Callback,h,ev) at 75

This now happens for every file I click. The data are very important to me—any advice on how to repair or recover would be greatly appreciated.

Environment: Brainstorm [version/build], MATLAB [version/update], OS [Windows/macOS/Linux].
(Notes: my MATLAB UI is in Simplified Chinese; the message reads “索引超过元素组的数量，索引不能超过 0”.)

Thank you so much!

Best regards,

9

The issue seems to be related to the position of the figures in your screen(s).

Try changing the Window layout options to None

Please provide the following information, so we can better assist you:

  1. Brainstorm version
  2. Matlab version
  3. Java version
  4. OS and version
  5. Number of screens and their configuration (mirror, horizontal extended, vertical extended, other)

You can find the first four points in the main Brainstorm window, in the menu Help > System info

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