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help > Voxel-to-Voxel First Level Analysis Error?
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Nov 15, 2011 05:11 PM | Jason Druzgal
Voxel-to-Voxel First Level Analysis Error?
I'm using the lastest version of the toolbox (13h) to look at
resting state data for a single subject. Everything seems to
proceed smoothly through Setup and Preprocessing. But when I try to
go to the First Level Analysis, I get an error box that says:
Data not prepared for analysis. Press "done" in the Preprocessing window.
Going back to Preprocessing and pressing "done" doesn't address the issue. It's worth noting that when I hit the First Level Analysis tab, the default selection is a Voxel-to-Voxel analysis. If I switch to ROI-to-ROI or Seed-to-Voxel, the error goes away and things appear to proceed normally... the preview results look like what I would expect for the data. However, if I try to switch back to Voxel-to-Voxel, I get the same error again. Any thoughts on the source of the error?
In case it's relevant, I'm running SPM8 with the current patches, Matlab 2010a, and OSX 10.6.8.
Thanks!
Jason Druzgal
Data not prepared for analysis. Press "done" in the Preprocessing window.
Going back to Preprocessing and pressing "done" doesn't address the issue. It's worth noting that when I hit the First Level Analysis tab, the default selection is a Voxel-to-Voxel analysis. If I switch to ROI-to-ROI or Seed-to-Voxel, the error goes away and things appear to proceed normally... the preview results look like what I would expect for the data. However, if I try to switch back to Voxel-to-Voxel, I get the same error again. Any thoughts on the source of the error?
In case it's relevant, I'm running SPM8 with the current patches, Matlab 2010a, and OSX 10.6.8.
Thanks!
Jason Druzgal
Nov 16, 2011 09:11 AM | Alfonso Nieto-Castanon - Boston University
RE: Voxel-to-Voxel First Level Analysis Error?
Hi Jason,
Sorry about this, this seems like a bug in the gui, could you please try the attached patch (simply save the attached file on the conn toolbox folder replacing the file with the same name there) and let me know whether that seems to fix this issue?
Alfonso
Originally posted by Jason Druzgal:
Sorry about this, this seems like a bug in the gui, could you please try the attached patch (simply save the attached file on the conn toolbox folder replacing the file with the same name there) and let me know whether that seems to fix this issue?
Alfonso
Originally posted by Jason Druzgal:
I'm using the lastest version of the toolbox
(13h) to look at resting state data for a single subject.
Everything seems to proceed smoothly through Setup and
Preprocessing. But when I try to go to the First Level Analysis, I
get an error box that says:
Data not prepared for analysis. Press "done" in the Preprocessing window.
Going back to Preprocessing and pressing "done" doesn't address the issue. It's worth noting that when I hit the First Level Analysis tab, the default selection is a Voxel-to-Voxel analysis. If I switch to ROI-to-ROI or Seed-to-Voxel, the error goes away and things appear to proceed normally... the preview results look like what I would expect for the data. However, if I try to switch back to Voxel-to-Voxel, I get the same error again. Any thoughts on the source of the error?
In case it's relevant, I'm running SPM8 with the current patches, Matlab 2010a, and OSX 10.6.8.
Thanks!
Jason Druzgal
Data not prepared for analysis. Press "done" in the Preprocessing window.
Going back to Preprocessing and pressing "done" doesn't address the issue. It's worth noting that when I hit the First Level Analysis tab, the default selection is a Voxel-to-Voxel analysis. If I switch to ROI-to-ROI or Seed-to-Voxel, the error goes away and things appear to proceed normally... the preview results look like what I would expect for the data. However, if I try to switch back to Voxel-to-Voxel, I get the same error again. Any thoughts on the source of the error?
In case it's relevant, I'm running SPM8 with the current patches, Matlab 2010a, and OSX 10.6.8.
Thanks!
Jason Druzgal
Nov 16, 2011 04:11 PM | Jason Druzgal
RE: Voxel-to-Voxel First Level Analysis Error?
Hi Alfonso,
Thanks for the quick reply. The patch seemed to fix the original issue, but generated a new one. When I click the Voxel-to-Voxel analysis, the program seems to be looking for a file that wasn't generated at an earlier step. I now get the following error message in the Matlab command window:
----------------------------------------------------------------
??? Error using ==> load
Unable to read file
/fMRI_Data_Processing/Conn_Test/ET_FUS/results/preprocessing/vvPC_Subject001_Condition001.mat: No
such file or directory.
Error in ==> conn_vol at 3
load(filename);
Error in ==> conn at 1611
CONN_h.menus.m_analyses.Y=conn_vol(filename);
Error in ==> conn_menumanager at 116
feval(MM.MENU{n0}.callback{n1}{1},MM.MENU{n0}.callback{n1}{2:end});
??? Error while evaluating figure WindowButtonUpFcn
----------------------------------------------------------------
When I look through all of the files created by the analysis, there's nothing with a name even close to vvPC_Subject001_Condition001.mat.
Thanks again,
Jason
Thanks for the quick reply. The patch seemed to fix the original issue, but generated a new one. When I click the Voxel-to-Voxel analysis, the program seems to be looking for a file that wasn't generated at an earlier step. I now get the following error message in the Matlab command window:
----------------------------------------------------------------
??? Error using ==> load
Unable to read file
/fMRI_Data_Processing/Conn_Test/ET_FUS/results/preprocessing/vvPC_Subject001_Condition001.mat: No
such file or directory.
Error in ==> conn_vol at 3
load(filename);
Error in ==> conn at 1611
CONN_h.menus.m_analyses.Y=conn_vol(filename);
Error in ==> conn_menumanager at 116
feval(MM.MENU{n0}.callback{n1}{1},MM.MENU{n0}.callback{n1}{2:end});
??? Error while evaluating figure WindowButtonUpFcn
----------------------------------------------------------------
When I look through all of the files created by the analysis, there's nothing with a name even close to vvPC_Subject001_Condition001.mat.
Thanks again,
Jason
Nov 16, 2011 09:11 PM | Alfonso Nieto-Castanon - Boston University
RE: Voxel-to-Voxel First Level Analysis Error?
Hi Jason,
mmm... so that was not a gui issue after all, it seems as if the voxel-to-voxel preprocessing step had not been run yet. Just to double-check, could you please first go to Setup->Options and make sure that the 'voxel-to-voxel' checkbox is marked, then go to the Preprocessing tab and click 'Done' again (simply answer 'No' when prompted whether to 'Overwrite existing subjects results' to avoid repeating the already-performed analysis steps). This should run the voxel-to-voxel preprocessing step which should take a few minutes per subject. After this is finished, go to the First-level Analysis window and let me know if you are still getting this error message.
Thanks
Alfonso
Originally posted by Jason Druzgal:
mmm... so that was not a gui issue after all, it seems as if the voxel-to-voxel preprocessing step had not been run yet. Just to double-check, could you please first go to Setup->Options and make sure that the 'voxel-to-voxel' checkbox is marked, then go to the Preprocessing tab and click 'Done' again (simply answer 'No' when prompted whether to 'Overwrite existing subjects results' to avoid repeating the already-performed analysis steps). This should run the voxel-to-voxel preprocessing step which should take a few minutes per subject. After this is finished, go to the First-level Analysis window and let me know if you are still getting this error message.
Thanks
Alfonso
Originally posted by Jason Druzgal:
Hi Alfonso,
Thanks for the quick reply. The patch seemed to fix the original issue, but generated a new one. When I click the Voxel-to-Voxel analysis, the program seems to be looking for a file that wasn't generated at an earlier step. I now get the following error message in the Matlab command window:
----------------------------------------------------------------
??? Error using ==> load
Unable to read file
/fMRI_Data_Processing/Conn_Test/ET_FUS/results/preprocessing/vvPC_Subject001_Condition001.mat: No
such file or directory.
Error in ==> conn_vol at 3
load(filename);
Error in ==> conn at 1611
CONN_h.menus.m_analyses.Y=conn_vol(filename);
Error in ==> conn_menumanager at 116
feval(MM.MENU{n0}.callback{n1}{1},MM.MENU{n0}.callback{n1}{2:end});
??? Error while evaluating figure WindowButtonUpFcn
----------------------------------------------------------------
When I look through all of the files created by the analysis, there's nothing with a name even close to vvPC_Subject001_Condition001.mat.
Thanks again,
Jason
Thanks for the quick reply. The patch seemed to fix the original issue, but generated a new one. When I click the Voxel-to-Voxel analysis, the program seems to be looking for a file that wasn't generated at an earlier step. I now get the following error message in the Matlab command window:
----------------------------------------------------------------
??? Error using ==> load
Unable to read file
/fMRI_Data_Processing/Conn_Test/ET_FUS/results/preprocessing/vvPC_Subject001_Condition001.mat: No
such file or directory.
Error in ==> conn_vol at 3
load(filename);
Error in ==> conn at 1611
CONN_h.menus.m_analyses.Y=conn_vol(filename);
Error in ==> conn_menumanager at 116
feval(MM.MENU{n0}.callback{n1}{1},MM.MENU{n0}.callback{n1}{2:end});
??? Error while evaluating figure WindowButtonUpFcn
----------------------------------------------------------------
When I look through all of the files created by the analysis, there's nothing with a name even close to vvPC_Subject001_Condition001.mat.
Thanks again,
Jason
Nov 17, 2011 12:11 AM | Jason Druzgal
RE: Voxel-to-Voxel First Level Analysis Error?
Hi Alfonso,
I tried your suggestion and still got the same error message.
Thanks,
Jason
I tried your suggestion and still got the same error message.
Thanks,
Jason
Nov 17, 2011 09:11 PM | Alfonso Nieto-Castanon - Boston University
RE: Voxel-to-Voxel First Level Analysis Error?
Hi Jason,
Very sorry about these issues, I am still not able to replicate your error condition, could you please send me your conn_*.mat file and also the file named conn_process.m in the conn toolbox folder to see if there is anything strange in the project definition and check that you have the latest version of the software?
Thanks
Alfonso
Originally posted by Jason Druzgal:
Very sorry about these issues, I am still not able to replicate your error condition, could you please send me your conn_*.mat file and also the file named conn_process.m in the conn toolbox folder to see if there is anything strange in the project definition and check that you have the latest version of the software?
Thanks
Alfonso
Originally posted by Jason Druzgal:
Hi Alfonso,
I tried your suggestion and still got the same error message.
Thanks,
Jason
I tried your suggestion and still got the same error message.
Thanks,
Jason
Nov 17, 2011 10:11 PM | Jason Druzgal
RE: Voxel-to-Voxel First Level Analysis Error?
Hi Alfonso,
Thanks for taking the time to look into this error. I just verified that my version 13h is up to date. And the two files you requested are in the zipped folder attached to this note.
Thanks again,
Jason
Thanks for taking the time to look into this error. I just verified that my version 13h is up to date. And the two files you requested are in the zipped folder attached to this note.
Thanks again,
Jason
Nov 18, 2011 05:11 AM | Alfonso Nieto-Castanon - Boston University
RE: Voxel-to-Voxel First Level Analysis Error?
Hi Jason,
I believe the source of this elusive problem might be that you have used a patch that was designed for a previous version of the toolbox (the conn_process.m file that you sent me is part of conn12, which did not implement the voxel-to-voxel analyses; I believe this is the reason why the toolbox is not running the voxel-to-voxel preprocessing steps, resulting in the errors that you were observing). If you could please try unzipping again the conn13h.zip file and overwriting the files in your current conn toolbox folder I believe that should fix this issue. Please let me know if this works. (as a side note, in general each release of the toolbox incorporates all of the appropriate patches up to that date, in particular for version conn13h the only patch that you might need is the conn_designmatrix.m patch dated 11/10/11 and available from the forum -and this will be incorporated in the next release of the toolbox conn13i which should come out soon)
Best
Alfonso
Originally posted by Jason Druzgal:
I believe the source of this elusive problem might be that you have used a patch that was designed for a previous version of the toolbox (the conn_process.m file that you sent me is part of conn12, which did not implement the voxel-to-voxel analyses; I believe this is the reason why the toolbox is not running the voxel-to-voxel preprocessing steps, resulting in the errors that you were observing). If you could please try unzipping again the conn13h.zip file and overwriting the files in your current conn toolbox folder I believe that should fix this issue. Please let me know if this works. (as a side note, in general each release of the toolbox incorporates all of the appropriate patches up to that date, in particular for version conn13h the only patch that you might need is the conn_designmatrix.m patch dated 11/10/11 and available from the forum -and this will be incorporated in the next release of the toolbox conn13i which should come out soon)
Best
Alfonso
Originally posted by Jason Druzgal:
Hi Alfonso,
Thanks for taking the time to look into this error. I just verified that my version 13h is up to date. And the two files you requested are in the zipped folder attached to this note.
Thanks again,
Jason
Thanks for taking the time to look into this error. I just verified that my version 13h is up to date. And the two files you requested are in the zipped folder attached to this note.
Thanks again,
Jason
Nov 18, 2011 05:11 PM | Jason Druzgal
RE: Voxel-to-Voxel First Level Analysis Error?
Hi Alfonso,
I just scrapped my installation and reinstalled the 13h version. That fixed the problem. Incidentally, before doing the deletion I checked the Updates option under the Help tab one more time. Despite the older version of conn_process.m in the folder, I got the message saying I was up to date with 13h. Not sure how the program evaluates the current version, but that message may give a false sense of security. I appreciate you taking the time to help me sort that out.
Many thanks,
Jason
I just scrapped my installation and reinstalled the 13h version. That fixed the problem. Incidentally, before doing the deletion I checked the Updates option under the Help tab one more time. Despite the older version of conn_process.m in the folder, I got the message saying I was up to date with 13h. Not sure how the program evaluates the current version, but that message may give a false sense of security. I appreciate you taking the time to help me sort that out.
Many thanks,
Jason