Back to PLS HelpPosted on 02/02/07 12:26:23
Number of posts: 100
Date: 01-09-07 13:39
hi ~
i get the following message while trying to create a datamat structure for single subject analysis (i've gotten it with other subjects as well) :
Scans 3065 for the condition 4 of run1 are not included due to out of bound
??? Error using ==> vertcat
CAT arguments dimensions are not consistent.
Error in ==> fmri_get_datamat at 466
datamat = [datamat; evt_datamat(:)'];
Error in ==> fmri_create_datamat_ui>RunGenDatamat at 1517
fmri_get_datamat(session_file,i,options.BrainRegionFile, ...
Error in ==> fmri_create_datamat_ui at 71
RunGenDatamat;
??? Error using ==> fmri_create_datamat_ui('RUN_BUTTON');
Error using ==> vertcat
CAT arguments dimensions are not consistent.
??? Error using ==> waitfor
Error while evaluating uicontrol Callback
any ideas what's wrong? i am using a binary mask to select voxels - nothiing unusual about the particular time point 3065 that i can see...
thanks very much!
agatha
Replies:
Posted on 02/02/07 12:26:46
Number of posts: 100
Date: 01-09-07 14:33
I think that they are 2 messages.
> i get the following message while trying to create a datamat
> structure for single subject analysis (i've gotten it with
> other subjects as well) :
>
> Scans 3065 for the condition 4 of run1 are not included due to
> out of bound
First message: The above message is normal. Please check:
http://www.rotman-baycrest.on.ca/pls/FAQ.txt
...
Q: When I generate fMRI datamat, I got something like this: Scans 147 for
the condition 3 of run1 are not included due to out of bound. Do you
have any idea what this means?
A: When you enter onset data, make sure they are in the range.
In most case, you encounter this problem because the onset
data you input exceeds the maximum range. The minmum value
is started from 0. However, The maximum value you can enter is:
Number_of_Scans - Temporal_Window_Size_if_fMRI - 1. E.g.: If you
have 180 files, and window size is 8, the maximum value in onset
data is 171.
...
> ??? Error using ==> vertcat
> CAT arguments dimensions are not consistent.
>
> Error in ==> fmri_get_datamat at 466
> datamat = [datamat; evt_datamat(:)'];
>
> Error in ==> fmri_create_datamat_ui>RunGenDatamat at 1517
>
> fmri_get_datamat(session_file,i,options.BrainRegionFile, ...
>
> Error in ==> fmri_create_datamat_ui at 71
> RunGenDatamat;
>
> ??? Error using ==> fmri_create_datamat_ui('RUN_BUTTON');
> Error using ==> vertcat
> CAT arguments dimensions are not consistent.
>
> ??? Error using ==> waitfor
> Error while evaluating uicontrol Callback
Second message above is an error message. I need to look into your data in order to figure out what goes wrong, since I can not duplicate this problem with my data here.
Posted on 02/02/07 12:27:10
Number of posts: 100
Date: 01-09-07 14:58
Thank Jimmy ~ indeed that's very sensible :)
Yes that works. I am currently running out of memory in Matlab, however, so I still can't run the analysis. I expect that this is simply a constraint that I'll have to modify by decreasing the number of events ('subject') in my analysis - I currently have 84 !!!
Thanks for all your help!
agatha
Posted on 02/02/07 12:27:29
Number of posts: 100
Date: 01-09-07 23:12
Agatha, you may find the latest update of interest for your problem. Jimmy has written a single precision version of PLS that saves ENORMOUS amount of CPU overhead. You will need to be running MATLAB R14 for this to work. You will also need to recreate the datamats. I have tested this on an VBM MRI dataset with 330 subjects and it works like a charm.
From WhatsNew
Version 5.0701031 January 3, 2007
Integrated single precision math operation feature of
MATLAB 7 (R14) above into the program. If MATLAB is
running on 64-bit system, a window will be popped out
to ask user for the system's processor. If the answer
is "Don't know" or "Intel processor", double precision
will be used according to MATLAB Bug Report ID 268001.
(If you are using RRI Linux cluster, "telesto" is the
only 64-bit system with non-Intel processor, which
supports single precision math operation)
Posted on 06/13/17 07:29:49
Number of posts: 7
Dear PLS experts,
I have a problem concernign the "out of bouds" message during datamat session files creation. I have checked for first subjects and the scans seem sufficient according to the FAQ and advices on the forum
.........
Q: When I generate fMRI datamat, I got something like this: Scans 147 for
the condition 3 of run1 are not included due to out of bound. Do you
have any idea what this means?
A: When you enter onset data, make sure they are in the range.
In most case, you encounter this problem because the onset
data you input exceeds the maximum range. The minmum value
is started from 0. However, The maximum value you can enter is:
Number_of_Scans - Temporal_Window_Size_if_fMRI - 1. E.g.: If you
have 180 files, and window size is 8, the maximum value in onset
data is 171.
..............
So, I have an event-related design, specifying a window size of 4 to check activation patterns of each trial. For the first subject, Matlab displayed this message : "Scans 1066 for the condition 4 of run1 are not included due to out of bound." So I have checked the subject folder and have 1072 files. So 1072-4-1 = 1067, but the last onset for this subject is 1066. Most of my subjects have an exclcusion of their last onset and I don't understand why or how to deal with that problem. Should I exclude these trials or reduce the temporal window ?
Thanks a lot in advance for your help,
Kind regards,
Marine
Posted on 06/13/17 07:54:44
Number of posts: 394
Dear PLS experts,
I have a problem concernign the "out of bouds" message during datamat session files creation. I have checked for first subjects and the scans seem sufficient according to the FAQ and advices on the forum
.........
Q: When I generate fMRI datamat, I got something like this: Scans 147 for
the condition 3 of run1 are not included due to out of bound. Do you
have any idea what this means?
A: When you enter onset data, make sure they are in the range.
In most case, you encounter this problem because the onset
data you input exceeds the maximum range. The minmum value
is started from 0. However, The maximum value you can enter is:
Number_of_Scans - Temporal_Window_Size_if_fMRI - 1. E.g.: If you
have 180 files, and window size is 8, the maximum value in onset
data is 171.
..............
So, I have an event-related design, specifying a window size of 4 to check activation patterns of each trial. For the first subject, Matlab displayed this message : "Scans 1066 for the condition 4 of run1 are not included due to out of bound." So I have checked the subject folder and have 1072 files. So 1072-4-1 = 1067, but the last onset for this subject is 1066. Most of my subjects have an exclcusion of their last onset and I don't understand why or how to deal with that problem. Should I exclude these trials or reduce the temporal window ?
Thanks a lot in advance for your help,
Kind regards,
Marine
Hi Marine - I wouldn't worry too much about it unless there are few trials for that condition. It amounts to one less trial that goes into the average for that task.
Posted on 06/13/17 08:24:55
Number of posts: 7
Dear Professor McIntosh,
Thank you very much for the very fast reply, I have many trials (maximum 32 and at least 20 according to subject's performance) for each of the 6 conditions, so I suppose that I can feel less stressed to continue my analyses :-)
Thanks again and have a nice day :-)
Marine
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