Hi Andrew, Your videos help me a lot. I try to follow your step to find out ROI analysis in SPM8, but it didn't work. I use the SPM.mat file from one subject's first level design and click Result to represent it, but can not find the ROI analysis option. How can I find that function?
Hello, I'm not sure; you should see it after you've selected your uncorrected p-value threshold and any correction options. Can you view your results without using the ROI analysis option? In other words, has the SPM.mat file been estimated? -Andy
Hi Andy, Thanks for your response. The SPM.mat file has been estimated and define different contrast in it. I can view the result without ROI analysis option. It always represent the general Result view in SPM 8. Did I miss any steps before I followed your video? Thank you very much!!
That's odd; it's a standard SPM option, and it should be there. The only recommendation I can make is to reinstall SPM and see if that changes anything.
Hi Andrew, Your videos are awesome. I am quite new in fMRI preprocessing. I have task fMRI data and I want to extract Automated Anatomical Labelling (AAL) ROIs from fMRI data. After spatial preprocessing in SPM, I am stuck now how to do that. Can you please give me directions? Thanks Atif
Does the initial file you select from results have to be a SPM.mat file? Nothing is able to open when I'm trying to select data for the first entry. neither .mat or .nii files are even accessible to open
Hi Soyee, Are you looking in the right directory? As far as I know, you can only open up SPM.mat files for the Results. If it's located somewhere else, you can navigate to there and open it. Best, -Andy
Hi, JahnThank you for useful videos. I woud like to know how the coordinates extracted by xSPM.XYZ, after some deletion and addition of xyz, could be back to image file. I put the coordinates into marsbar's ROI definition-Build-Voxel function, but the image cretaed by such procedure did not match the SPM's standard brain.
Hi Murano, See the "write NIFTI" function described here; it may be what you want: andysbrainblog.blogspot.com/2015/05/k-means-analysis-with-fmri-data.html -Andy
Hi Andrew, I have been having some trouble with ROIs I created at JIM 7.0 (Xynapse). It does not allow me to use in other software such as MRICron or FSL, since it is not a .VOI file, or just says "unable to open: file size should be divisible by 4". Do you know what could I do to fix it? Many thanks!
Martin Cohn Hey Martin, I don't have any experience with the Xynapse software, so I'm unsure of what the conversion issue is. Your best bet would probably be to contact the developers directly. -Andy
+Omri Raccah Hi Omri, you should be able to use the latest version of Marsbar with SPM, by linking it to the toolbox menu through the steps outlined on the Marsbar website. Is there a specific error you are getting? -Andy
Hi Andrew,
Your videos help me a lot. I try to follow your step to find out ROI analysis in SPM8, but it didn't work. I use the SPM.mat file from one subject's first level design and click Result to represent it, but can not find the ROI analysis option. How can I find that function?
Hello,
I'm not sure; you should see it after you've selected your uncorrected p-value threshold and any correction options. Can you view your results without using the ROI analysis option? In other words, has the SPM.mat file been estimated?
-Andy
Hi Andy,
Thanks for your response.
The SPM.mat file has been estimated and define different contrast in it. I can view the result without ROI analysis option. It always represent the general Result view in SPM 8. Did I miss any steps before I followed your video?
Thank you very much!!
That's odd; it's a standard SPM option, and it should be there. The only recommendation I can make is to reinstall SPM and see if that changes anything.
Hi Andrew,
Your videos are awesome.
I am quite new in fMRI preprocessing. I have task fMRI data and I want to extract Automated Anatomical Labelling (AAL) ROIs from fMRI data. After spatial preprocessing in SPM, I am stuck now how to do that.
Can you please give me directions? Thanks
Atif
Does the initial file you select from results have to be a SPM.mat file? Nothing is able to open when I'm trying to select data for the first entry. neither .mat or .nii files are even accessible to open
Hi Soyee,
Are you looking in the right directory? As far as I know, you can only open up SPM.mat files for the Results. If it's located somewhere else, you can navigate to there and open it.
Best,
-Andy
Hi, JahnThank you for useful videos. I woud like to know how the coordinates extracted by xSPM.XYZ, after some deletion and addition of xyz, could be back to image file. I put the coordinates into marsbar's ROI definition-Build-Voxel function, but the image cretaed by such procedure did not match the SPM's standard brain.
Hi Murano,
See the "write NIFTI" function described here; it may be what you want: andysbrainblog.blogspot.com/2015/05/k-means-analysis-with-fmri-data.html
-Andy
Hi,Thanks. This is what I want. It works well.
Hi Andrew,
I have been having some trouble with ROIs I created at JIM 7.0 (Xynapse). It does not allow me to use in other software such as MRICron or FSL, since it is not a .VOI file, or just says "unable to open: file size should be divisible by 4".
Do you know what could I do to fix it?
Many thanks!
Martin Cohn Hey Martin, I don't have any experience with the Xynapse software, so I'm unsure of what the conversion issue is. Your best bet would probably be to contact the developers directly.
-Andy
Is there a version of Marsbar I can use with spm12?
+Omri Raccah Hi Omri, you should be able to use the latest version of Marsbar with SPM, by linking it to the toolbox menu through the steps outlined on the Marsbar website. Is there a specific error you are getting?
-Andy
+Andrew Jahn thanks Andrew! I was able to figure it out. Very helpful videos btw