Back to PLS HelpPosted on 07/02/13 04:23:44
Number of posts: 8
Hi
I'm having problems loading my image data into the create datamat session. I have 2 conditions GM and WM and 34 subjects from 2 different groups. The filename structure is subjID-condition-group.nii. I enter 2 conditions *GM*.nii and *WM*.nii and then press select subjects. I am presented with 34 entries subjID--group.nii. I select all these and then click create datamat. I am presented with a list of 34 files and I select all of those and then choose my brain mask and click create. It picks up 34 subjects for condition 1 and then stops at condition 2 subject 1 with an error in the matlab window (see below). I can see its looking for PLS-analysis.hdr -why ? PLS-analysis is my working folder. At what point would I have input this as a filename? Could someone please point at the obviously stupid error I'm making :) thanks, Anna
Replies:
I'm Online
Posted on 07/02/13 08:47:59
Number of posts: 291
The raw image can be stored anywhere. However, it is better not to put raw image in your working folder. If you are running fMRI study, images belong to the same run should be kept in the same folder. Please take a look at the examples under:
http://research.baycrest.org/pls/source/Testdata.zip
If it is still not working, please give me more details, like: what are all the folder names and file names for your images, and how you want the datamat to be created, and what is the module (E.R.fMRI? Blocked fMRI?), and which image file names that you are selected for cond1 and which for condition2, etc.
Posted on 07/02/13 09:42:56
Number of posts: 8
Hi Jimmy
thanks for getting back so quick. I can answer some of these right off and then I will go back and create a different folder as you suggested.
I'm doing PLS structural ; condition 1 is grey matter maps *gm*.nii. condition 2 is white matter maps *wm*.nii. I never get asked to load data for condition 2 - was confused by this.
Thanks
Anna
I'm Online
Posted on 07/02/13 09:51:48
Number of posts: 291
You will never get asked to load data for either condition, this is done automatically when you input subject in Structure PLS depending on your file name. Therefore, in Strcture PLS, the file names are critically important. In addition, in Structure PLS, all files with all conditions are stored in the same folder. Please list all the file names in full (not using wildcard * or ?) for all subjects and all conditions if it is still not working. Also please list the condition filters. I will have to reply you by the end of the day.
Posted on 07/02/13 10:27:01
Number of posts: 8
Hi Jimmy
This is much appreciated, I'm sure its something silly I've forgotten to do. Ubuntu OS and Matlab 64 R2012a
Here's the directory structure
PLS-analysis>data>*.nii and my working directory is PLS-analysis>PLS-results
Here's the complete list of filenames
I'm Online
Posted on 07/02/13 16:19:03
Number of posts: 291
I am sure that the following answer will solve your problem:
You must keep the file name consistent. It is okay to use both "-" and "_", since you can put condition filter like *GM*.nii and *HM*.nii. However, when you assign "_" to "ATKPA_HM-NC.nii", you cannot assign "-" to "ATKPA-GM-NC.nii". I have tried, if you rename them to either "ATKPA_HM-NC.nii / ATKPA_GM-NC.nii" or "ATKPA-HM-NC.nii / ATKPA-GM-NC.nii", they will both work; otherwise, exactly the same error message will pop up.
Please check all the file names carefully, and make sure there is no mistake. If you still get problem, please only take 2 or 3 pairs to start, and find wrong file name in the rest files. Eventually, you will be fine.
Good Luck!
Posted on 07/03/13 04:35:31
Number of posts: 8
Of course - thank you so much. I thought I had checked all the filenames but just goes to show that you need a second pair of eyes or get a computer to do the check for you 
. Should work fine now.
Thanks
Anna
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