Hi Darko, hi all, Are these average images using the exact same color scale? It’d help if the surface geometries were the same (e.g., the same inflated for all). But assuming that the color scale is the same, and trying to see over the geometry differences, looks like the averages between the two groups aren’t that massively different, or at least not that asymmetric, correct?
Then taking this together with the Cohen’s d maps, for me this raises the possibility that there could be a large outlier in one hemisphere – perhaps a subject who moved a bit too much laterally between collection of T1 and T2? Or maybe a subject whose right pial reconstruction wasn’t correct and led to a much thinner cortex, thus with the myelin profile taken too far away from the others (i.e., the mid-thickness too off)? I guess you might want to investigate on a per-subject and per vertex basis... For example, take some vertices where the difference between L and R is large and check how the values vary between subjects, see if there are too influential observations, then open the images for this/these subjects and see if something went wrong along the pipeline… You can also open the residuals and see if there are large outliers with a lot of spatial spread. These are just suggestions… hope they could help anyway… All the best, Anderson From: "Glasser, Matthew" <glass...@wustl.edu> Date: Wednesday, August 8, 2018 at 17:05 To: "Harms, Michael" <mha...@wustl.edu>, Darko Komnenić <komnen...@gmail.com> Cc: "Winkler, Anderson (NIH/NIMH) [E]" <anderson.wink...@nih.gov>, "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> Subject: Re: [HCP-Users] Finding a significant difference only in one hemisphere Also please post the T1w and T2w image protocols and make sure to use the second scaling option for the percentiles (which takes percentiles of the absolute value so that positive and negative colors mean the same thing—this probably should be the default. Matt. From: "Harms, Michael" <mha...@wustl.edu<mailto:mha...@wustl.edu>> Date: Wednesday, August 8, 2018 at 2:13 PM To: Darko Komnenić <komnen...@gmail.com<mailto:komnen...@gmail.com>>, Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>> Cc: "Winkler, Anderson (NIH/NIMH) [E]" <anderson.wink...@nih.gov<mailto:anderson.wink...@nih.gov>>, "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Subject: Re: [HCP-Users] Finding a significant difference only in one hemisphere 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. Tel: 314-747-6173 St. Louis, MO 63110 Email: mha...@wustl.edu<mailto:mha...@wustl.edu> From: Darko Komnenić <komnen...@gmail.com<mailto:komnen...@gmail.com>> Date: Wednesday, August 8, 2018 at 2:08 PM To: "Glasser, Matthew" <glass...@wustl.edu<mailto:glass...@wustl.edu>> Cc: "Harms, Michael" <mha...@wustl.edu<mailto:mha...@wustl.edu>>, "Winkler, Anderson (NIH/NIMH) [E]" <anderson.wink...@nih.gov<mailto:anderson.wink...@nih.gov>>, "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> 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 <glass...@wustl.edu<mailto:glass...@wustl.edu>> 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: <hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>> on behalf of "Harms, Michael" <mha...@wustl.edu<mailto:mha...@wustl.edu>> Date: Tuesday, August 7, 2018 at 3:47 PM To: "Winkler, Anderson (NIH/NIMH) [E]" <anderson.wink...@nih.gov<mailto:anderson.wink...@nih.gov>>, Darko Komnenić <komnen...@gmail.com<mailto:komnen...@gmail.com>> Cc: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> 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: mha...@wustl.edu<mailto:mha...@wustl.edu> From: "Winkler, Anderson (NIH/NIMH) [E]" <anderson.wink...@nih.gov<mailto:anderson.wink...@nih.gov>> Date: Tuesday, August 7, 2018 at 3:02 PM To: Darko Komnenić <komnen...@gmail.com<mailto:komnen...@gmail.com>>, "Harms, Michael" <mha...@wustl.edu<mailto:mha...@wustl.edu>> Cc: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> 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 <komnen...@gmail.com<mailto:komnen...@gmail.com>> Date: Tuesday, August 7, 2018 at 15:25 To: "Harms, Michael" <mha...@wustl.edu<mailto:mha...@wustl.edu>> Cc: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> 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 <mha...@wustl.edu<mailto:mha...@wustl.edu>> 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: mha...@wustl.edu<mailto:mha...@wustl.edu> From: <hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Darko Komnenić <komnen...@gmail.com<mailto:komnen...@gmail.com>> Date: Tuesday, August 7, 2018 at 6:50 AM To: "Glasser, Matthew" <glass...@wustl.edu<mailto:glass...@wustl.edu>> Cc: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> 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 <glass...@wustl.edu<mailto:glass...@wustl.edu>> wrote: Can you just make a simple effect size map with + and – and no thresholding? Matt. From: Darko Komnenić <komnen...@gmail.com<mailto:komnen...@gmail.com>> Date: Monday, August 6, 2018 at 12:09 PM To: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>> Cc: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> 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 <glass...@wustl.edu<mailto:glass...@wustl.edu>> 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 <komnen...@gmail.com<mailto:komnen...@gmail.com>> Date: Friday, August 3, 2018 at 12:12 PM To: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>> Cc: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> 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 <glass...@wustl.edu<mailto:glass...@wustl.edu>> wrote: How about posting some pics. Matt. From: <hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Darko Komnenić <komnen...@gmail.com<mailto:komnen...@gmail.com>> Date: Thursday, August 2, 2018 at 9:16 AM To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> 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 HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org> 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. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. 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