Back to PLS HelpERROR: no common coords among datamats!
Posted on 10/04/09 08:37:43
Number of posts: 22
Hi all,
I'm getting the following error when attempting to run a simple mean-centered PLS:
ERROR: no common coords among datamats!
I have three groups and I only get this error with one of the groups, which seems strange given that all individuals in all groups have been registered to the same (MNI152) standard space template (I'm assuming the error message relates to common co-ordinates?). Can anyone tell me where I might be going wrong.
Any assistance would be greatly appreciated.
Many thanks in advance,
Dan.
Replies:
Untitled Post
Posted on 10/04/09 11:56:49
Number of posts: 394
Hi Dan,
It seems like one or more subject's image may have gotten messed up when warping to template or when its read into PLS to create the data matrices. I assume you are doing event-related fMRI? If so, you run a quick script to identify the potential subject(s) who have a problem
in matlab in the directory where your data reside type (exclude stuff after % since its comments):
d=dir('*fMRIdatamat.mat) %creates a struc array with the file names for all subjects
for i=1:numel(d) %loop across subjects
load(d(i).name) %load in each subject's datamat
disp(d(i).name) % display the file name so you know who is in
length(st_coords) %this is a vector that tells you how many brain voxels PLS thinks there is per volume for this subject
pause %pause the loop, you will need hit any key to continue
end %end the loop
you should compare the st_coords across subjects. Most will be fairly close with 500-600 elements different. What you are looking for is the subject who has a length = 0 or very tiny compare to the rest.
FYI, st_coords comes from a binary mask that is used to eliminate the zeros from the data matrix and read in only brain data. The coords are the actual matrix location for each voxel that has data.
If this is not the problem, then you may need to check the image orientation for each subject, but we can do this if this loop solution does not work.
Randy
It seems like one or more subject's image may have gotten messed up when warping to template or when its read into PLS to create the data matrices. I assume you are doing event-related fMRI? If so, you run a quick script to identify the potential subject(s) who have a problem
in matlab in the directory where your data reside type (exclude stuff after % since its comments):
d=dir('*fMRIdatamat.mat) %creates a struc array with the file names for all subjects
for i=1:numel(d) %loop across subjects
load(d(i).name) %load in each subject's datamat
disp(d(i).name) % display the file name so you know who is in
length(st_coords) %this is a vector that tells you how many brain voxels PLS thinks there is per volume for this subject
pause %pause the loop, you will need hit any key to continue
end %end the loop
you should compare the st_coords across subjects. Most will be fairly close with 500-600 elements different. What you are looking for is the subject who has a length = 0 or very tiny compare to the rest.
FYI, st_coords comes from a binary mask that is used to eliminate the zeros from the data matrix and read in only brain data. The coords are the actual matrix location for each voxel that has data.
If this is not the problem, then you may need to check the image orientation for each subject, but we can do this if this loop solution does not work.
Randy
Untitled Post
Posted on 10/05/09 07:42:17
Number of posts: 22
quote:
Hi Dan,
It seems like one or more subject's image may have gotten messed up when warping to template or when its read into PLS to create the data matrices. I assume you are doing event-related fMRI? If so, you run a quick script to identify the potential subject(s) who have a problem
in matlab in the directory where your data reside type (exclude stuff after % since its comments):
d=dir('*fMRIdatamat.mat) %creates a struc array with the file names for all subjects
for i=1:numel(d) %loop across subjects
load(d(i).name) %load in each subject's datamat
disp(d(i).name) % display the file name so you know who is in
length(st_coords) %this is a vector that tells you how many brain voxels PLS thinks there is per volume for this subject
pause %pause the loop, you will need hit any key to continue
end %end the loop
you should compare the st_coords across subjects. Most will be fairly close with 500-600 elements different. What you are looking for is the subject who has a length = 0 or very tiny compare to the rest.
FYI, st_coords comes from a binary mask that is used to eliminate the zeros from the data matrix and read in only brain data. The coords are the actual matrix location for each voxel that has data.
If this is not the problem, then you may need to check the image orientation for each subject, but we can do this if this loop solution does not work.
Randy
Randy,Hi Dan,
It seems like one or more subject's image may have gotten messed up when warping to template or when its read into PLS to create the data matrices. I assume you are doing event-related fMRI? If so, you run a quick script to identify the potential subject(s) who have a problem
in matlab in the directory where your data reside type (exclude stuff after % since its comments):
d=dir('*fMRIdatamat.mat) %creates a struc array with the file names for all subjects
for i=1:numel(d) %loop across subjects
load(d(i).name) %load in each subject's datamat
disp(d(i).name) % display the file name so you know who is in
length(st_coords) %this is a vector that tells you how many brain voxels PLS thinks there is per volume for this subject
pause %pause the loop, you will need hit any key to continue
end %end the loop
you should compare the st_coords across subjects. Most will be fairly close with 500-600 elements different. What you are looking for is the subject who has a length = 0 or very tiny compare to the rest.
FYI, st_coords comes from a binary mask that is used to eliminate the zeros from the data matrix and read in only brain data. The coords are the actual matrix location for each voxel that has data.
If this is not the problem, then you may need to check the image orientation for each subject, but we can do this if this loop solution does not work.
Randy
This were worked a treat, thanks.
You were spot on - it turns out that one of my timeseries had been corrupted during the registration process.
Thanks again,
Dan.
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