Browse Forums

help

502 Subscribers

help > CONN toolbox - Asked to keep re-running Denoising step

Showing 1-7 of 7 posts

CONN toolbox - Asked to keep re-running Denoising step

Hello,

I am analysing resting-state fMRI scans and CONN keeps asking me to re-run the Denoising step even though I have run it already twice and without any errors. Here is the specific error message:

Please complete the first-level ROI-to-ROI or seed-to-voxel step first
(fill any required information and press "Done" in the first-level analysis tab)
or selet a different first-level analysis to continue
Not ready to start first-level Analysis step

Can you help me, please? What am I missing?

Thank you!

RE: CONN toolbox - Asked to keep re-running Denoising step

Not sure about this one, have you tried re-running the Setup step as well? -with the 'do not overwrite' option should suffice. (e.g. this issue may happen for example if one creates a new condition in Setup.Condition and then tries to re-run first-level analyses without first re-running the Setup and Denoising steps, as the first-level analysis step will notice that there is a new condition which has not yet been processed and ask you to re-run Denoising, when in reality you would need to re-run both Setup and Denoising for the information about that new condition to correctly propagate to the first-level analysis tab)

Hope this helps

Alfonso

Originally posted by alfredalfred:

Hello,

I am analysing resting-state fMRI scans and CONN keeps asking me to re-run the Denoising step even though I have run it already twice and without any errors. Here is the specific error message:

Please complete the first-level ROI-to-ROI or seed-to-voxel step first
(fill any required information and press "Done" in the first-level analysis tab)
or selet a different first-level analysis to continue
Not ready to start first-level Analysis step

Can you help me, please? What am I missing?

Thank you!

RE: CONN toolbox - Asked to keep re-running Denoising step

Hi Alfonso,

I did this and it still gives the same mistake. Then I reinstalled conn22 and reran everything from scratch and I still get this message (below is the full error message). I also searched for other messages and checked that all four analyses types are set-up in set-up options (indeed they are). I also checked in the project conn_*/results/preprocessing folder whether files named ROI_Subject*_Condition*.mat exist - and it indeed does.

I really do not know what the problem is so I have also copied the matlab code in the doc file in case that is a help.

Thank you in advance!

Not ready to start first-level Analysis step

Please complete the Denoising step first
(fill any required information and press "Done" in the Denoising tab)
ERROR DESCRIPTION:

Error using matlab.ui.control.UIControl/set
Invalid or deleted object.

Error in conn (line 7550)
set(CONN_h.menus.m_analyses_00{46},'string',CONN_x.Analyses(ianalysis).name);

Error in conn (line 7037)
conn gui_analyses;

Error in conn (line 7285)
conn('gui_analysesgo',1);
CONN22.a
SPM12 + DAiSS DEM FieldMap MEEGtools
Matlab v.2022a
project: CONN22.a
storage: 2995.8Gb available

spm @ C:\Users\dauvermm\Documents\MATLAB\spm12
conn @ C:\Users\dauvermm\Documents\MATLAB\spm12\toolbox\conn22a\conn

Originally posted by Alfonso Nieto-Castanon:

Hi

Not sure about this one, have you tried re-running the Setup step as well? -with the 'do not overwrite' option should suffice. (e.g. this issue may happen for example if one creates a new condition in Setup.Condition and then tries to re-run first-level analyses without first re-running the Setup and Denoising steps, as the first-level analysis step will notice that there is a new condition which has not yet been processed and ask you to re-run Denoising, when in reality you would need to re-run both Setup and Denoising for the information about that new condition to correctly propagate to the first-level analysis tab)

Hope this helps

Alfonso

Originally posted by alfredalfred:

Hello,

I am analysing resting-state fMRI scans and CONN keeps asking me to re-run the Denoising step even though I have run it already twice and without any errors. Here is the specific error message:

Please complete the first-level ROI-to-ROI or seed-to-voxel step first
(fill any required information and press "Done" in the first-level analysis tab)
or selet a different first-level analysis to continue
Not ready to start first-level Analysis step

Can you help me, please? What am I missing?

Thank you!

Attachment: Matlab.docx

RE: CONN toolbox - Asked to keep re-running Denoising step

Hi Alfonso,

I briefly follow up again after I checked that all steps have been completed, such as pre-processing (and it has). I noticedt though that four participants' scans have been identified of having more than 10 outliers. Could this be part of the problem and I need to remove them before running the denoising step again? I am happy send more information if this would help finding the problem.

Thank you!

Originally posted by alfredalfred:

Hi Alfonso,

I did this and it still gives the same mistake. Then I reinstalled conn22 and reran everything from scratch and I still get this message (below is the full error message). I also searched for other messages and checked that all four analyses types are set-up in set-up options (indeed they are). I also checked in the project conn_*/results/preprocessing folder whether files named ROI_Subject*_Condition*.mat exist - and it indeed does.

I really do not know what the problem is so I have also copied the matlab code in the doc file in case that is a help.

Thank you in advance!

Not ready to start first-level Analysis step

Please complete the Denoising step first
(fill any required information and press "Done" in the Denoising tab)
ERROR DESCRIPTION:

Error using matlab.ui.control.UIControl/set
Invalid or deleted object.

Error in conn (line 7550)
set(CONN_h.menus.m_analyses_00{46},'string',CONN_x.Analyses(ianalysis).name);

Error in conn (line 7037)
conn gui_analyses;

Error in conn (line 7285)
conn('gui_analysesgo',1);
CONN22.a
SPM12 + DAiSS DEM FieldMap MEEGtools
Matlab v.2022a
project: CONN22.a
storage: 2995.8Gb available

spm @ C:\Users\dauvermm\Documents\MATLAB\spm12
conn @ C:\Users\dauvermm\Documents\MATLAB\spm12\toolbox\conn22a\conn

Originally posted by Alfonso Nieto-Castanon:

Hi

Not sure about this one, have you tried re-running the Setup step as well? -with the 'do not overwrite' option should suffice. (e.g. this issue may happen for example if one creates a new condition in Setup.Condition and then tries to re-run first-level analyses without first re-running the Setup and Denoising steps, as the first-level analysis step will notice that there is a new condition which has not yet been processed and ask you to re-run Denoising, when in reality you would need to re-run both Setup and Denoising for the information about that new condition to correctly propagate to the first-level analysis tab)

Hope this helps

Alfonso

Originally posted by alfredalfred:

Hello,

I am analysing resting-state fMRI scans and CONN keeps asking me to re-run the Denoising step even though I have run it already twice and without any errors. Here is the specific error message:

Please complete the first-level ROI-to-ROI or seed-to-voxel step first
(fill any required information and press "Done" in the first-level analysis tab)
or selet a different first-level analysis to continue
Not ready to start first-level Analysis step

Can you help me, please? What am I missing?

Thank you!

RE: CONN toolbox - Asked to keep re-running Denoising step

Hi alfredalfred,

I am analysing fmri data using CONN and meet the same issue with you. I have rerun SETUP and DENOISING steps, but when I try to run the first-level it also shows:

Not ready to start first-level Analysis step

Please complete the Denoising step first
(fill any required information and press "Done" in the Denoising tab)

I wonder if you have solved this problem? I would be very grateful if you reply to me.

Best,

Originally posted by alfredalfred:

Hi Alfonso,

I briefly follow up again after I checked that all steps have been completed, such as pre-processing (and it has). I noticedt though that four participants' scans have been identified of having more than 10 outliers. Could this be part of the problem and I need to remove them before running the denoising step again? I am happy send more information if this would help finding the problem.

Thank you!

Originally posted by alfredalfred:

Hi Alfonso,

I did this and it still gives the same mistake. Then I reinstalled conn22 and reran everything from scratch and I still get this message (below is the full error message). I also searched for other messages and checked that all four analyses types are set-up in set-up options (indeed they are). I also checked in the project conn_*/results/preprocessing folder whether files named ROI_Subject*_Condition*.mat exist - and it indeed does.

I really do not know what the problem is so I have also copied the matlab code in the doc file in case that is a help.

Thank you in advance!

Not ready to start first-level Analysis step

Please complete the Denoising step first
(fill any required information and press "Done" in the Denoising tab)
ERROR DESCRIPTION:

Error using matlab.ui.control.UIControl/set
Invalid or deleted object.

Error in conn (line 7550)
set(CONN_h.menus.m_analyses_00{46},'string',CONN_x.Analyses(ianalysis).name);

Error in conn (line 7037)
conn gui_analyses;

Error in conn (line 7285)
conn('gui_analysesgo',1);
CONN22.a
SPM12 + DAiSS DEM FieldMap MEEGtools
Matlab v.2022a
project: CONN22.a
storage: 2995.8Gb available

spm @ C:\Users\dauvermm\Documents\MATLAB\spm12
conn @ C:\Users\dauvermm\Documents\MATLAB\spm12\toolbox\conn22a\conn

Originally posted by Alfonso Nieto-Castanon:

Hi

Not sure about this one, have you tried re-running the Setup step as well? -with the 'do not overwrite' option should suffice. (e.g. this issue may happen for example if one creates a new condition in Setup.Condition and then tries to re-run first-level analyses without first re-running the Setup and Denoising steps, as the first-level analysis step will notice that there is a new condition which has not yet been processed and ask you to re-run Denoising, when in reality you would need to re-run both Setup and Denoising for the information about that new condition to correctly propagate to the first-level analysis tab)

Hope this helps

Alfonso

Originally posted by alfredalfred:

Hello,

I am analysing resting-state fMRI scans and CONN keeps asking me to re-run the Denoising step even though I have run it already twice and without any errors. Here is the specific error message:

Please complete the first-level ROI-to-ROI or seed-to-voxel step first
(fill any required information and press "Done" in the first-level analysis tab)
or selet a different first-level analysis to continue
Not ready to start first-level Analysis step

Can you help me, please? What am I missing?

Thank you!

RE: CONN toolbox - Asked to keep re-running Denoising step

Hi!

I'm encountering the same problem, I've ran the Setup multiple times, even with different projects, and it still gives me this error and won't let me access the Denoising tab. I'm using conn22.v2407.

It is strange, because in the past I have preprocessed images exactly the same way (at least to my knowledge) and I never got this error.

Did anybody find a solution?

Thank you!

Maria

RE: CONN toolbox - Asked to keep re-running Denoising step

Hello,

Finally it worked when I checked all the boxes in "enabled analysis" in the "options" tab. However, I had tried this before without success, reading the results of a previous post, but somehow this time it worked. I report this just in case it is useful for anybody with the same problem.

Thank you!