Back to PLS HelpPosted on 02/07/16 08:55:33
Number of posts: 4
Dear PLS experts,
I applied PLS on processed fMRI data from AFNI.
I went to "session profile for block fMRI data" and specified two conditions V and A, relative Ref. scan onset as 0 and 1 respectively, and number of reference scans as 1 and 1.
In "datamat matrix, I entered two *.img files of processed beta images for each of two conditions. So, the column appeared as "sub1_V.img sub1_A.img". Finally, I specified the onsets as 0 for V and 1 for A and lengths as 1 for both V and A condition. This is where the error occurred and it said "All onsets filed must be filled out". Could anyone helped me out with the appropriate way to set up the parameter for processed image data. Thanks!
Sincerely,
Veda
Replies:
Posted on 02/08/16 07:41:35
Number of posts: 394
Dear PLS experts,
I applied PLS on processed fMRI data from AFNI.
I went to "session profile for block fMRI data" and specified two conditions V and A, relative Ref. scan onset as 0 and 1 respectively, and number of reference scans as 1 and 1.
In "datamat matrix, I entered two *.img files of processed beta images for each of two conditions. So, the column appeared as "sub1_V.img sub1_A.img". Finally, I specified the onsets as 0 for V and 1 for A and lengths as 1 for both V and A condition. This is where the error occurred and it said "All onsets filed must be filled out". Could anyone helped me out with the appropriate way to set up the parameter for processed image data. Thanks!
Sincerely,
Veda
Hi Veda - I am a bit confused on how you moved the data from AFNI into PLS. You indicated a block design but it seems you fit an HRF to the data in AFNI and export the beta-images to PLS? PLS can work with the time series images rather than beta, so you don't need to do the HRF fit. All you need to specify for block PLS is the block onset and number of TRs/block. The code does the rest
Posted on 02/08/16 07:52:11
Number of posts: 4
Hi Randy,
Thank you for the reply.
I also tried to feed the time series (360 scans) and specified the onsets and lengths as follows:
condition A / onsets: 0; length:180
condition B / onsets:180; length:180
It still gave me the same error "all the onsets field must be filled out". But, I already did it, didn't I?
Veda
Posted on 02/08/16 07:55:47
Number of posts: 394
try 1 and 181 for the onsets rather than 0 and 180
Posted on 02/08/16 08:02:43
Number of posts: 4
It did not work either but I am pretty sure the file has 360 scans.
Should I provide any other information or send my file to you?
Posted on 02/08/16 08:10:11
Number of posts: 4
BTW, this problem only occurred when I specified two conditions.
If I only specified one condition and set the onsets as 0 (or 1) and length as 180. That worked. However, I do need more than one condition.
Posted on 02/08/16 08:48:09
Number of posts: 394
BTW, this problem only occurred when I specified two conditions.
If I only specified one condition and set the onsets as 0 (or 1) and length as 180. That worked. However, I do need more than one condition.
can you send a screenshot of what you are entering into the GUI? I am not sure why the error is coming up. Also, perhaps you can double-check the NIFIT file for a subject that there are indeed 360 volumes
send the screenshot to my email: rmcintosh@research.baycrest.org
I'm Online
Posted on 02/08/16 11:02:00
Number of posts: 229
Hi Veda..
it looks like you are using 4D nii files from AFNI..
Please run the "expand_nii_scan" script to put each subject's data into a new directory as single nii files..
nancy
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