Back to PLS Helpcheck image orientation using PLS
Posted on 03/21/11 10:03:24
Number of posts: 16
Hi PLSusers:
There are two ways to create datamat file using PLS. One is to create a batch file and the other is to using "session profile for block/e.r fMRI data" to create datamat file.
In "session profile for block/e.r. fMRI data" there is one part where you can check your image orientation (i.e. There is a button "check image orientation" in generating the datamat file box). My question is if we use batch file to create the datamat file, where we can check the image orientation.
Can anyone let me know?
Thank you in advance.
bye
Replies:
Untitled Post
I'm Online
Posted on 03/21/11 10:56:29
Number of posts: 291
If you use batch file to create the datamat file, you can use the following commands to check and change the orientation. As a matter of fact, button in PLSgui to "check image orientation" when generating datamat file use the same commands to do so. Assuming your raw image file name is "scan.img", here're the commands:
Now, check whether your image orientation is in neurological convention. If not, click "Convert to RAS orientation" item under "Edit" command, and make the change. Then go to "File" menu to save the displayed image.
If your image is only in 3D, and you don't want to do this one by one, you can use "collapse_nii_scan" to combine all 3D images in the run to one 4D image. Type: help collapse_nii_scan to learn how to use this command.
nii=load_nii('scan.img');
view_nii(nii);
view_nii(nii);
Now, check whether your image orientation is in neurological convention. If not, click "Convert to RAS orientation" item under "Edit" command, and make the change. Then go to "File" menu to save the displayed image.
If your image is only in 3D, and you don't want to do this one by one, you can use "collapse_nii_scan" to combine all 3D images in the run to one 4D image. Type: help collapse_nii_scan to learn how to use this command.
check image orientation using PLS
Posted on 03/21/11 11:54:32
Number of posts: 16
quote:
If you use batch file to create the datamat file, you can use the following commands to check and change the orientation. As a matter of fact, button in PLSgui to "check image orientation" when generating datamat file use the same commands to do so. Assuming your raw image file name is "scan.img", here're the commands:
Now, check whether your image orientation is in neurological convention. If not, click "Convert to RAS orientation" item under "Edit" command, and make the change. Then go to "File" menu to save the displayed image.
If your image is only in 3D, and you don't want to do this one by one, you can use "collapse_nii_scan" to combine all 3D images in the run to one 4D image. Type: help collapse_nii_scan to learn how to use this command.
Thank you for your reply. I am new to PLS. I am not quite sure if I get it. Do I type the two commands in PuTTy? I do not see the .img file in my folder.
The output from batch file is ..._fMRIsession.mat and ..._fMRIdatamat.mat. I am not sure where I can find the image file?
Sorry...
Thanks.
If you use batch file to create the datamat file, you can use the following commands to check and change the orientation. As a matter of fact, button in PLSgui to "check image orientation" when generating datamat file use the same commands to do so. Assuming your raw image file name is "scan.img", here're the commands:
nii=load_nii('scan.img');
view_nii(nii);
view_nii(nii);
Now, check whether your image orientation is in neurological convention. If not, click "Convert to RAS orientation" item under "Edit" command, and make the change. Then go to "File" menu to save the displayed image.
If your image is only in 3D, and you don't want to do this one by one, you can use "collapse_nii_scan" to combine all 3D images in the run to one 4D image. Type: help collapse_nii_scan to learn how to use this command.
Untitled Post
I'm Online
Posted on 03/21/11 12:01:55
Number of posts: 291
- type the two commands in MATLAB command window
- image files (.img or .nii) are specified in your data_files fields in your batch script file.
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