CONN GUI crashed (not responding) and the connproject.mat file was corrupted

, ,
1

Hi there,

I’m using CONN GUI to process 300+ rs-fmri data, however, the GUI screen crashed while performing on “checking if data files have been edited or move, press cancel to skip this step” for multiple hours. (The mouse can still move but it’s not responding anymore) It happened several times before, last time I had to close by entering tty and kill Matlab. And when I reopened CONN GUI and loaded the project, it turns out that all the steps that I’ve been performed (preprocesssing, denoising, 1st and 2nd level analysis) were gone in the GUI panel. However, I did perform “project → save” before it got crashed. The processed images are still intact in the CONN project folder, but the connproject.mat somehow got corrupted and cannot link the CONN GUI to the steps that’s been processed before.

I was wondering if there is any way to kill the process while it got stuck but still safely save the connproject.mat? Or if there is any way to save the corrupted connproject.mat, so I don’t have to process all the steps that I’ve been performed again?

Many thanks in advance!

2

Hi,

So the MATLAB save command used in conn can only save up to a certain file size. Chances are with 300+ files that it exceeds it. If you go into the conn MATLAB source code, you can add an argument to the save command to allow you to save larger files. I can try to find it and get back to you.

Steven

3

You would have to add ‘v7.3’ to the save command to deal with large files. If you want I can send you the modified conn.m script that has this included. Please send me a DM with your email if you want it.

Steven

4

Also, this will not impact the saving time, it will still take a while. May I suggest alternatives that scale better for large datasets, like post processing your data with https://xcpengine.readthedocs.io/ and then putting resultant images in a Nilearn glm to run your connectivity analyses?

5

Dear Steven.I am very new to CONN and I need to analyze 400 resting state data.When I have just started uploading the functional and structural images I had the error

Error using spm_sample_vol
Cant open image file.

Error in conn_fileutils (line 359)
 else [varargout{1:nargout}]=spm_sample_vol(varargin{:});

Error in conn_menu>conn_menu_selectslice (line 1254)
 case 3, y=[]; for nv=1:numel(x.vol), ty=reshape(conn_fileutils('spm_sample_vol',x.vol(nv),reshape(x.x(:,:,n),1,[]),reshape(x.y(:,:,n),1,[]),reshape(x.z(:,:,n),1,[]),1),x.dim([1 2])); y=cat(4,y,ty(end:-1:1,end:-1:1)'); end

Error in conn_menu (line 906)
 title=conn_menu_selectslice(data.x1,data.n,data.view); 

Error in conn (line 2942)
 conn_menu('updateimage',CONN_h.menus.m_setup_00{5},vol);
CONN21.a
SPM12 + DAiSS DEM FieldMap MEEGtools conn
Matlab v.2020b
project: CONN21.a
storage: 31.0Gb available
 
spm @ C:\Users\Su\Desktop\spm12
conn @ C:\Users\Su\Desktop\spm12\toolbox\conn

 
SUGGESTIONS:
 
Potential missing data files or incomplete analyses. Try loading your project again (this will check for potential missing files) or re-running some of the analysis steps if some may have not completed correctly
ERROR DESCRIPTION:
 
Error using spm_sample_vol
Cant open image file.

Error in conn_fileutils (line 359)
 else [varargout{1:nargout}]=spm_sample_vol(varargin{:});

Error in conn_menu>conn_menu_selectslice (line 1254)
 case 3, y=[]; for nv=1:numel(x.vol), ty=reshape(conn_fileutils('spm_sample_vol',x.vol(nv),reshape(x.x(:,:,n),1,[]),reshape(x.y(:,:,n),1,[]),reshape(x.z(:,:,n),1,[]),1),x.dim([1 2])); y=cat(4,y,ty(end:-1:1,end:-1:1)'); end

Error in conn_menu (line 906)
 title=conn_menu_selectslice(data.x1,data.n,data.view); 

Error in conn (line 2942)
 conn_menu('updateimage',CONN_h.menus.m_setup_00{5},vol);
CONN21.a
SPM12 + DAiSS DEM FieldMap MEEGtools conn
Matlab v.2020b
project: CONN21.a
storage: 31.0Gb available
 
spm @ C:\Users\Su\Desktop\spm12
conn @ C:\Users\Su\Desktop\spm12\toolbox\conn

 
SUGGESTIONS:
 
Potential missing data files or incomplete analyses. Try loading your project again (this will check for potential missing files) or re-running some of the analysis steps if some may have not completed correctly
Please visit http://www.nitrc.org/forum/forum.php?forum_id=1144 if the page is not automatically loaded

And same stuff repeated for different lines.I do not know what this is and I really have limited time to finish this and start preprocessing.Can you please help?

6

Hi @Su_Karakelle and welcome to neurostars!

This looks like a different issue than the original one. For future posts, please open a new issue rather than commenting on an unrelated post.

I see some issues here:

I would use the most recent CONN version (22a is the most recent stable version, and 23.03.10 is the most recent development release).

You will not be able to store that 400 resting state acquisitions and their preprocessed derivatives with only 31 GB available. Unless, do you have a bigger drive somewhere else?

I unfortunately cannot suggest much besides trying again without seeing how you tried loading your data.

If you have the storage space to process everything, I recommend as an alternative fMRIPrep to XCP_D for resting-state analysis. I find that it scales better for larger datasets than CONN does (and I try to avoid MATLAB applications when possible). In either case, analyzing that much data will take a fairly long time, especially if you are not using a large computing cluster, just a warning.

Best,
Steven