Thanks a lot, Matt! On Fri, Aug 10, 2018 at 9:27 PM, Glasser, Matthew <[email protected]> wrote:
> So what I take from this is that there are probably bilateral > temporal-occipital differences that are a little bigger on the left than > the right and that statistical thresholding is exaggerating the L/R > differences. Assuming you had a larger sample size and the pattern stayed > the same, the differences would be bilateral. > > Matt. > > From: Darko Komnenić <[email protected]> > Date: Friday, August 10, 2018 at 1:18 PM > To: "Harms, Michael" <[email protected]> > Cc: Matt Glasser <[email protected]>, "Winkler, Anderson (NIH/NIMH) [E]" > <[email protected]>, "[email protected]" < > [email protected]> > > Subject: Re: [HCP-Users] Finding a significant difference only in one > hemisphere > > Hello again everyone, > I am sending the images once again, this time on an inflated surface > (average of the entire sample). As for colors, the last time I used the > third option - "percent" (which was default), but now I changed it to the > second one - percentiles of the absolute value. > We had 17 patients and 25 controls (the reason for this is that we had a > third group as well, from a different patient cohort, and there we had 25 > patients, so we matched the number of people in the control group with that > other patient group). > The map of the significant differences highlighted mostly occipital and > temporal areas in the left hemisphere as more myelinated in the control > sample, and I guess we can sort of see that in the average myelin maps as > well (more red in the occipital areas, a lighter shade of purple in the > superior temporal gyrus)? But, at any rate, it's not a huge effect. > > I'm also including the T1 and T2 protocols in the attachment. > Unfortunately, I was only able to get the T1 protocol in German: "ein" > means "on, "aus" means "off"; some of the parameter names are still in > English even in the T1 file, for those that are in German, you can see > their English translation by looking at the same spot in the T2 file. Sorry > for the inconvenience! > > Looking forward to your feedback! > Best, > Darko > > > > On Wed, Aug 8, 2018 at 9:13 PM, Harms, Michael <[email protected]> wrote: > >> >> >> Hi, >> >> Viewing on the inflated surface would probably be more helpful. >> >> >> >> Also, how many subjects per group? >> >> >> >> Cheers, >> >> -MH >> >> >> >> -- >> >> Michael Harms, Ph.D. >> >> ----------------------------------------------------------- >> >> Associate Professor of Psychiatry >> >> Washington University School of Medicine >> >> Department of Psychiatry, Box 8134 >> >> 660 South Euclid Ave >> <https://maps.google.com/?q=660+South+Euclid+Ave&entry=gmail&source=g>. >> Tel: 314-747-6173 >> >> St. Louis, MO 63110 Email: [email protected] >> >> *From: *Darko Komnenić <[email protected]> >> *Date: *Wednesday, August 8, 2018 at 2:08 PM >> *To: *"Glasser, Matthew" <[email protected]> >> *Cc: *"Harms, Michael" <[email protected]>, "Winkler, Anderson (NIH/NIMH) >> [E]" <[email protected]>, "[email protected]" < >> [email protected]> >> >> *Subject: *Re: [HCP-Users] Finding a significant difference only in one >> hemisphere >> >> >> >> Thanks a lot for the clarifications everyone! >> >> The first two images attached are average myelin maps for controls and >> patients, respectively. >> >> The third image is what I hope to be the effect size map. I added the >> -saveglm flag to palm, and then used command >> -cifti-create-dense-from-template to merge the dpv_cohen files for left >> and right hemisphere. Let me know if this does not work. >> >> Thanks in advance for any comments! >> >> Best, >> >> Darko >> >> >> >> >> >> >> >> On Wed, Aug 8, 2018 at 2:22 AM, Glasser, Matthew <[email protected]> >> wrote: >> >> What is an effect size map? An effect size map is in the case of a >> t-test of difference between two groups is simply the difference in the >> means. A standardized effect size maps is a Cohen’s d, which is helpful if >> you want to compare effect sizes of different measures that are not on the >> same scale. Looking at both the difference between means and the means >> themselves could be helpful in tracking down artifacts. Looking at maps of >> statistical significance is not helpful, despite what you see typically >> done in the neuroimaging literature. >> >> >> >> Matt. >> >> >> >> *From: *<[email protected]> on behalf of "Harms, >> Michael" <[email protected]> >> *Date: *Tuesday, August 7, 2018 at 3:47 PM >> *To: *"Winkler, Anderson (NIH/NIMH) [E]" <[email protected]>, >> Darko Komnenić <[email protected]> >> >> >> *Cc: *"[email protected]" <[email protected]> >> *Subject: *Re: [HCP-Users] Finding a significant difference only in one >> hemisphere >> >> >> >> >> >> A Cohen’s d map of the group difference might be helpful, but even more >> basic would be to just merge the individual myelin maps (-cifti-merge, or >> use wb_shortcuts -cifti-concatenate) and then average them (-cifti-average). >> >> >> >> Cheers, >> >> -MH >> >> >> >> -- >> >> Michael Harms, Ph.D. >> >> ----------------------------------------------------------- >> >> Associate Professor of Psychiatry >> >> Washington University School of Medicine >> >> Department of Psychiatry, Box 8134 >> >> 660 South Euclid Ave >> <https://maps.google.com/?q=660+South+Euclid+Ave&entry=gmail&source=g>. >> Tel: 314-747-6173 >> >> St. Louis, MO 63110 Email: [email protected] >> >> *From: *"Winkler, Anderson (NIH/NIMH) [E]" <[email protected]> >> *Date: *Tuesday, August 7, 2018 at 3:02 PM >> *To: *Darko Komnenić <[email protected]>, "Harms, Michael" < >> [email protected]> >> *Cc: *"[email protected]" <[email protected]> >> *Subject: *Re: [HCP-Users] Finding a significant difference only in one >> hemisphere >> >> >> >> Hi Darko, >> >> >> >> The option “-saveglm” in PALM should produce Cohen’s d maps. >> >> >> >> All the best, >> >> >> >> Anderson >> >> >> >> >> >> *From: *Darko Komnenić <[email protected]> >> *Date: *Tuesday, August 7, 2018 at 15:25 >> *To: *"Harms, Michael" <[email protected]> >> *Cc: *"[email protected]" <[email protected]> >> *Subject: *Re: [HCP-Users] Finding a significant difference only in one >> hemisphere >> >> >> >> Hi Michael, >> >> I don't seem to have an average myelin map as an output of the analysis. >> Is it just something I can make by merging and averaging individual myelin >> maps in workbench, or should it have been the output of the GLM analysis? >> Sorry for this most likely really basic question. >> >> Thanks in advance! >> >> Best, >> >> Darko >> >> >> >> On Tue, Aug 7, 2018 at 3:53 PM, Harms, Michael <[email protected]> wrote: >> >> >> >> It might be helpful to simply see the average myelin map for each group. >> Do those look appropriate? >> >> >> >> Cheers, >> >> -MH >> >> >> >> -- >> >> Michael Harms, Ph.D. >> >> ----------------------------------------------------------- >> >> Associate Professor of Psychiatry >> >> Washington University School of Medicine >> >> Department of Psychiatry, Box 8134 >> >> 660 South Euclid Ave >> <https://maps.google.com/?q=660+South+Euclid+Ave&entry=gmail&source=g>. >> Tel: 314-747-6173 >> >> St. Louis, MO 63110 Email: [email protected] >> >> *From: *<[email protected]> on behalf of Darko >> Komnenić <[email protected]> >> *Date: *Tuesday, August 7, 2018 at 6:50 AM >> *To: *"Glasser, Matthew" <[email protected]> >> >> >> *Cc: *"[email protected]" <[email protected]> >> *Subject: *Re: [HCP-Users] Finding a significant difference only in one >> hemisphere >> >> >> >> Hi Matt, >> >> I'm not sure what you mean by a simple effect size map. The file overlaid >> on the surfaces here is a file showing the difference between control and >> patient groups, after correction for multiple comparisons. Do I use that to >> make an effect size map, or something else? >> >> Best, >> >> Darko >> >> >> >> On Mon, Aug 6, 2018 at 9:03 PM, Glasser, Matthew <[email protected]> >> wrote: >> >> Can you just make a simple effect size map with + and – and no >> thresholding? >> >> >> >> Matt. >> >> >> >> *From: *Darko Komnenić <[email protected]> >> *Date: *Monday, August 6, 2018 at 12:09 PM >> >> >> *To: *Matt Glasser <[email protected]> >> *Cc: *"[email protected]" <[email protected]> >> *Subject: *Re: [HCP-Users] Finding a significant difference only in one >> hemisphere >> >> >> >> Hi Matt, >> >> here's a screenshot of an unthresholded map. >> >> Thanks in advance! >> >> Best, >> >> Darko >> >> >> >> On Fri, Aug 3, 2018 at 10:12 PM, Glasser, Matthew <[email protected]> >> wrote: >> >> Thresholded maps of statistical significance are essentially >> uninterpretable as to the existence of artifacts. Please provide an >> unthresholded effect size map. >> >> >> >> Peace, >> >> >> >> Matt. >> >> >> >> *From: *Darko Komnenić <[email protected]> >> *Date: *Friday, August 3, 2018 at 12:12 PM >> *To: *Matt Glasser <[email protected]> >> *Cc: *"[email protected]" <[email protected]> >> *Subject: *Re: [HCP-Users] Finding a significant difference only in one >> hemisphere >> >> >> >> Hi Matt, >> >> here's a screenshot >> >> Thanks in advance! >> >> Best, >> >> Darko >> >> >> >> On Thu, Aug 2, 2018 at 10:01 PM, Glasser, Matthew <[email protected]> >> wrote: >> >> How about posting some pics. >> >> >> >> Matt. >> >> >> >> *From: *<[email protected]> on behalf of Darko >> Komnenić <[email protected]> >> *Date: *Thursday, August 2, 2018 at 9:16 AM >> *To: *"[email protected]" <[email protected]> >> *Subject: *[HCP-Users] Finding a significant difference only in one >> hemisphere >> >> >> >> Dear HCP experts, >> >> I ran an analysis comparing cortical myelination between patients and >> controls and found a significant difference between groups, but only in the >> left hemisphere. What's making me doubt my results is that the differences >> are observed in large areas of the left hemisphere, but absolutely nowhere >> in the right, and we have no theoretical reasons to expect such a >> lateralization. >> >> Do you have any ideas what might have gone wrong? I have 17 patients and >> 25 controls, is this maybe too small of a sample? Should I double check >> certain analysis steps? Basically any ideas are welcome, since I really >> cannot interpret these findings at all, it seems. >> >> Thanks in advance! >> >> Best, >> >> Darko >> >> _______________________________________________ >> HCP-Users mailing list >> [email protected] >> http://lists.humanconnectome.org/mailman/listinfo/hcp-users >> >> >> ------------------------------ >> >> The materials in this message are private and may contain Protected >> Healthcare Information or other information of a sensitive nature. 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