tag:blogger.com,1999:blog-1405968300258104460.post5775210016755111486..comments2024-03-27T01:18:24.341-04:00Comments on Andy's Brain Blog: Resting State Analysis, Parts V and VI: Creating Correlation Maps and Z-MapsAndrew Jahnhttp://www.blogger.com/profile/16435706598096921650noreply@blogger.comBlogger11125tag:blogger.com,1999:blog-1405968300258104460.post-26418376152021099072018-06-03T11:06:50.614-04:002018-06-03T11:06:50.614-04:00I believe this will give me the same results?
3dT...I believe this will give me the same results?<br /><br />3dTcorr1D -Fisher sub001_3dtimedata+tlrc. sub001_timeCourse.txt<br /><br />Correct me if I am wrong. Thanks.umeshksinglahttps://www.blogger.com/profile/11991235748278934110noreply@blogger.comtag:blogger.com,1999:blog-1405968300258104460.post-41359079193403647252017-01-28T14:13:38.284-05:002017-01-28T14:13:38.284-05:00Thanks Andy,
So, I think, we can obtain correlat...Thanks Andy, <br /><br />So, I think, we can obtain correlation values to the whole of the brain as follows: <br /><br />3dfim+ -input errts.${subj}+tlrc -mask mask_group+tlrc -fim_thr 0 -polort 0 -ideal_file timeCourse.txt -out Correlation -bucket vmPFC_Corr<br /><br />-fim_thr option works tricky. Even if we specify a mask, 3dfim+ automatically generates another mask to exclude low intensity voxels. Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-1405968300258104460.post-70270338621077661162017-01-28T13:17:34.089-05:002017-01-28T13:17:34.089-05:00Hey there,
You're absolutely right; I hadn...Hey there,<br /><br />You're absolutely right; I hadn't used that option before, but I can see how you may want to use it if you want to know all of the correlations at each voxel. Thanks for pointing that out!<br /><br />-AndyAndrew Jahnhttps://www.blogger.com/profile/16435706598096921650noreply@blogger.comtag:blogger.com,1999:blog-1405968300258104460.post-81671274079345646382017-01-27T23:20:21.472-05:002017-01-27T23:20:21.472-05:00Hi Andy,
I was wondering if I could ask you a qu...Hi Andy, <br /><br />I was wondering if I could ask you a question about 3dfim+. Don't you need to specify -fim_thr 0? 3dfim+ automatically exclude low intensity voxels. Therefore, correlations to low intensity voxels are not calculated and, as a result, an output image may look like cracked. <br /><br />Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-1405968300258104460.post-42267544450833433822016-07-10T13:28:31.021-04:002016-07-10T13:28:31.021-04:00Hey there,
That's a good point; I was followi...Hey there,<br /><br />That's a good point; I was following the steps on Gang Chen's page, but you're right in saying that the data is detrended twice. I'll write to Gang and see what he has to say. Also see this AFNI message board thread about different ways to detrend and calculate the same correlation coefficient: https://afni.nimh.nih.gov/afni/community/board/read.php?1,42274,42276#msg-42276<br /><br />Best,<br /><br />-AndyAndrew Jahnhttps://www.blogger.com/profile/16435706598096921650noreply@blogger.comtag:blogger.com,1999:blog-1405968300258104460.post-6194617718632194662016-07-08T00:37:15.156-04:002016-07-08T00:37:15.156-04:00Hi Andy,
Thank you for many useful posts. Why we...Hi Andy, <br /><br />Thank you for many useful posts. Why we need to run 3dfim+ with -polort 2? Since errts.${subj}+tlrc would be detrended signals, should not we detrend again?<br />Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-1405968300258104460.post-69180985198933063952016-05-31T14:31:38.453-04:002016-05-31T14:31:38.453-04:00Hi Megan,
How big is the size of your seed region...Hi Megan,<br /><br />How big is the size of your seed region? If it is very large (say, a sphere with greater than a 10mm radius), the timecourses that are being averaged together may be so different that the average timecourse doesn't correlate well with any of them.<br /><br />You can check this by creating a seed region that is a small sphere, or even just a single voxel; that should show stronger correlations radiating around that seed, along with any other voxels in the brain that happen to correlate with it. If that still doesn't look right, let me know.<br /><br />Best,<br /><br />-AndyAndrew Jahnhttps://www.blogger.com/profile/16435706598096921650noreply@blogger.comtag:blogger.com,1999:blog-1405968300258104460.post-42955872338717733242016-05-31T09:25:09.424-04:002016-05-31T09:25:09.424-04:00Hi Andy,
I have managed to get through everything...Hi Andy, <br />I have managed to get through everything - thank you so much for taking the time to make and post these tutorials. I have a question. When I open up my "Corr_subj{$subj}_Z" image in afni, the region that the seed was placed should correlate highly (all the way, you might say) with itself. But, when I open the image there is no correlation around my seed, which has me worried I did something wrong. Sorry, I am not very good with scripting, is it that the script is "muting" these region so the correlation doesn't show? Or, in fact, is something going wrong?<br />Thanks!<br />Meghan MDavisnoreply@blogger.comtag:blogger.com,1999:blog-1405968300258104460.post-36559614156789169252014-03-10T13:44:48.768-04:002014-03-10T13:44:48.768-04:00Thanks! I look forward to checking back soon!Thanks! I look forward to checking back soon!Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-1405968300258104460.post-1138244660137632482014-03-10T12:42:25.175-04:002014-03-10T12:42:25.175-04:00Thanks, I'm glad they're useful! And yes, ...Thanks, I'm glad they're useful! And yes, I am planning on doing a similar series of tutorials for FSL; I can't say when, exactly, but probably within the next month.<br /><br />-AndyAndrew Jahnhttps://www.blogger.com/profile/16435706598096921650noreply@blogger.comtag:blogger.com,1999:blog-1405968300258104460.post-31967906147661436762014-03-10T10:33:22.674-04:002014-03-10T10:33:22.674-04:00all of your postings are very useful, so thank you...all of your postings are very useful, so thank you for them! Will you soon be posting about the same resting state analysis using FSL?Anonymousnoreply@blogger.com