tag:blogger.com,1999:blog-1405968300258104460.post2527152344154888303..comments2024-03-27T01:18:24.341-04:00Comments on Andy's Brain Blog: Independent Components Analysis, Part II: Using FSL Example DataAndrew Jahnhttp://www.blogger.com/profile/16435706598096921650noreply@blogger.comBlogger6125tag:blogger.com,1999:blog-1405968300258104460.post-67169793254067271282017-12-29T11:49:10.134-05:002017-12-29T11:49:10.134-05:00Hi Andy,
Thank you for you wonderful videos and t...Hi Andy,<br /><br />Thank you for you wonderful videos and tutorials! Though, I still don't understand how the thresholding works... It seems that in the video you have left it at 0.5 - which according to FSL docs keeps the balance between false positives and negatives equal, but you say most papers use 0.8-0.9? Also the thresholding of spatial maps of z-score you brought it to 2 - 10, was that on top of the already applied threshold during melodic processing?<br /><br />Thank you,<br />M<br />Mhttps://www.blogger.com/profile/03867090914739198365noreply@blogger.comtag:blogger.com,1999:blog-1405968300258104460.post-10732778516988175042017-01-04T10:23:32.818-05:002017-01-04T10:23:32.818-05:00Hey there,
Assuming that your groupICA map was co...Hey there,<br /><br />Assuming that your groupICA map was coregistered to your anatomical, you can warp your anatomical to MNI space, and then apply those transforms to your groupICA map.<br /><br />Best,<br /><br />-AndyAndrew Jahnhttps://www.blogger.com/profile/16435706598096921650noreply@blogger.comtag:blogger.com,1999:blog-1405968300258104460.post-25983443144883832582017-01-01T22:08:21.984-05:002017-01-01T22:08:21.984-05:00Hi Andrew, Thank you for making this blog.
I have...Hi Andrew, Thank you for making this blog.<br /><br />I have a question regarding the visualization of the groupICA result.<br /><br />I have the melodic_IC volume file after the analysis was completed but I don't have a specific *.mat file for running the flirt command. How can I register the result to the standard MNI template?Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-1405968300258104460.post-62283381770878764852016-03-12T17:09:27.369-05:002016-03-12T17:09:27.369-05:00Hi Diana,
I hadn't heard of that, but that is...Hi Diana,<br /><br />I hadn't heard of that, but that is interesting; if true, that would be a reason against collecting a separate resting state scan. I haven't tried it, but I'm curious what other people have found. Can you post the references for the papers where they have done that?<br /><br />-AndyAndrew Jahnhttps://www.blogger.com/profile/16435706598096921650noreply@blogger.comtag:blogger.com,1999:blog-1405968300258104460.post-77611268725605217222016-03-12T04:10:31.320-05:002016-03-12T04:10:31.320-05:00Hi Andy,
thanks for the posts, they are very helpf...Hi Andy,<br />thanks for the posts, they are very helpful!<br />I've a quite conceptual question related to ICA analysis, i would like to know your opinion. Do you think i can do a "resting Ica analysis" on a task related functional dataset? e.g., using fsl melodic without regressing out the task related brain activity. There are some recent papers showing high correspondence between brain functional networks at task and at rest, actually you can retrieve the typical resting networks (e.g., those showed in Smith et al. 2009 PNAS) if you apply concatenated melodic ICA on the whole task related activity . The reason to do that is that I am interested to study changes in the resting state networks of different groups, i have not acquired resting state data but i Have task related fmri. I m not sure if its conceptually valid. <br /><br />Thank you very much, <br /><br />Diana LB. SUSAN CALVINhttps://www.blogger.com/profile/00025324798825395949noreply@blogger.comtag:blogger.com,1999:blog-1405968300258104460.post-39694716883289738952015-11-15T16:35:12.276-05:002015-11-15T16:35:12.276-05:00Hi Andy,
Thank you very much for your insightful ...Hi Andy,<br /><br />Thank you very much for your insightful videos. They have helped me at all those times when I felt I could no longer handle the complexity of neuroimaging data. So, sincerely, thank you again! <br />I also just wanted to check in with you: I am currently running FSL's MELODIC with 2 resting state scans. Specifically, I am using the concatenated, registered, normalized, motion scrubbed res4d images (or the residual functional images obtained after pre-processing and accounting for motion WM/CSF in the GLM model for each scan) as the input to the MELODIC. I have a specific question I have been unable to resolve:<br />My understanding based on the FSL forums is that the res4D image should not be registered during the MELODIC stage (e.g. , see here: https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1511&L=fsl&F=&S=&X=9F00F01E7564947927&Y=shunyata.aishwarya%40gmail.com&P=200122). Thus, in my design file, I set all registrations (from functional to high res (native) structural, then from high res structural to std. space, as 0). <br />When I look at the IC components generated in the html log file, the areas of activation can be clearly identified and are interpretable, but the slices themselves are white. That is to say, the ventricle regions do not appear "dark", as would expect them to. Would you have any suggestions for why this may be the case? I can share some screenshots if you'd like. <br />Thank you again! You are awesome!Ar Bnoreply@blogger.com