[HCP-Users] Restricted access
Hello, I applied for (and was granted) access to the restricted HCP database; however, when I log onto https://db.humanconnectome.org/data/projects/HCP_1200 I no longer see an option to download the restricted data. Please help! Best, Jodi Jodi Gilman, Ph.D. Associate Professor, Harvard Medical School Center for Addiction Medicine Massachusetts General Hospital 101 Merrimac St. Boston, MA 02114 Tel.:617-643-7293 Fax:617-643-1998 ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
Re: [HCP-Users] PALM Viewing results
Thank you Tim. I agree about effect size maps being better, but reviewers always want to know what is significant (they are set in their ways!!) So maybe we can do both; an effect size map and then .95-1 in the corr p map? On Mar 16, 2018, at 4:59 PM, Timothy Coalson <tsc...@mst.edu<mailto:tsc...@mst.edu>> wrote: Since the extent that passes significance tests is dependent on number of subjects and other statistical power considerations, we instead recommend viewing the effect size (beta) map. You can overlay outlines of what passed the significance threshold by making that into a label file with wb_command -*-math and -*-label-import, then setting the label layer to draw only the outlines of labels. However, it is also possible to do it the way you described in workbench. There is also a thresholding option in the palette settings, so that you can see an underlay through non-significant regions (T1w and/or sulc as a reference of the anatomical locations, or maybe the HCP MMP v1.0 or its borders as a reference of the functional locations). Tim On Fri, Mar 16, 2018 at 9:45 AM, Gilman, Jodi <jgilm...@mgh.harvard.edu<mailto:jgilm...@mgh.harvard.edu>> wrote: Hi, In documentation for randomise, when viewing the 1-p results in FSLView the min/max display range should be set to 0.95/1.0 so that values less than 0.95 (equivalent to p>0.05) are not shown. If these are corrected values (i.e. corrp) then the visible areas correspond to the statistically significant regions. Is this the same for viewing PALM results in Workbench? All the values seem to be between 0-1, so that makes sense to me... Thanks so much, Jodi The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ HCP-Users mailing list HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org> http://lists.humanconnectome.org/mailman/listinfo/hcp-users ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
[HCP-Users] PALM Viewing results
Hi, In documentation for randomise, when viewing the 1-p results in FSLView the min/max display range should be set to 0.95/1.0 so that values less than 0.95 (equivalent to p>0.05) are not shown. If these are corrected values (i.e. corrp) then the visible areas correspond to the statistically significant regions. Is this the same for viewing PALM results in Workbench? All the values seem to be between 0-1, so that makes sense to me... Thanks so much, Jodi The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
[HCP-Users] NIH toolbox measures
Hi Jenn, I have a question about the scores from NIH toolbox on the domains of negative affect, psychological well-being, social relationships, and stress and self-efficacy. I see that the scores available for download are all unadjusted; I do not see a column for any adjusted scores on these measures. Would you recommend using the unadjusted scores? Or, is there a formula to adjust them? The NIH Toolbox scoring PDF states: "For the NIH Toolbox General Life Satisfaction Survey, higher scores are indicative of more general life satisfaction. Scores 1 SD or more below the mean (T ≤ 40) suggest low levels of general life satisfaction and scores 1 SD or more above the mean (T ≥ 60) suggest high level” Is this true for unadjusted as well? Thanks, Jodi Jodi Gilman, Ph.D. Assistant Professor, Harvard Medical School Center for Addiction Medicine Massachusetts General Hospital 101 Merrimac St. Boston, MA 02114 Tel.:617-643-7293 Fax:617-643-1998 The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
Re: [HCP-Users] Behavior data
Thank you, this is super helpful! On Feb 9, 2018, at 12:30 PM, Elam, Jennifer <e...@wustl.edu<mailto:e...@wustl.edu>> wrote: Hi Jodi, Have you tried the S1200 Reference Manual<https://www.humanconnectome.org/storage/app/media/documentation/s1200/HCP_S1200_Release_Reference_Manual.pdf> Chapter 5 (p.177 and following) on the Behavioral measures details? Also, many references are in the Barch et al. 2013<http://www.sciencedirect.com/science/article/pii/S1053811913005272> paper, but they should largely be the same as those in the Ref Manual. Let me know if there's something specific you can't track down. Best, Jenn Jennifer Elam, Ph.D. Scientific Outreach, Human Connectome Project Washington University School of Medicine Department of Neuroscience, Box 8108 660 South Euclid Avenue St. Louis, MO 63110 314-362-9387 e...@wustl.edu<mailto:e...@wustl.edu> www.humanconnectome.org<http://www.humanconnectome.org/> From: hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org> <hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Gilman, Jodi <jgilm...@mgh.harvard.edu<mailto:jgilm...@mgh.harvard.edu>> Sent: Friday, February 9, 2018 11:21:19 AM To: hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org> Subject: [HCP-Users] Behavior data Is there a list of references for all of the behavioral measures collected? I am trying to track them down but it is a lot of work. If these were all in one place, that would be so amazing… Thanks, Jodi Jodi Gilman, Ph.D. Assistant Professor, Harvard Medical School Center for Addiction Medicine Massachusetts General Hospital 101 Merrimac St. Boston, MA 02114 Tel.:617-643-7293 Fax:617-643-1998 The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ HCP-Users mailing list HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org> http://lists.humanconnectome.org/mailman/listinfo/hcp-users ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
[HCP-Users] Behavior data
Is there a list of references for all of the behavioral measures collected? I am trying to track them down but it is a lot of work. If these were all in one place, that would be so amazing… Thanks, Jodi Jodi Gilman, Ph.D. Assistant Professor, Harvard Medical School Center for Addiction Medicine Massachusetts General Hospital 101 Merrimac St. Boston, MA 02114 Tel.:617-643-7293 Fax:617-643-1998 The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
Re: [HCP-Users] group comparison in myelin maps
Hi Matt, We concatenated the myelin maps into one .dscalar.nii map for each group. I cannot open them, however, I think I am missing other files that I need. Which other files do I need to generate? A volume file? Thanks, Jodi Jodi Gilman, Ph.D. Assistant Professor, Harvard Medical School Center for Addiction Medicine Massachusetts General Hospital 101 Merrimac St. Boston, MA 02114 Tel.:617-643-7293 Fax:617-643-1998 On Dec 14, 2017, at 1:14 PM, Gilman, Jodi <jgilm...@mgh.harvard.edu<mailto:jgilm...@mgh.harvard.edu>> wrote: Thank you, Matt. Do you have an example of a -cifti-concatenate script? I keep getting errors, I don’t think I’m getting the syntax correct. Thanks!! Jodi Gilman, Ph.D. Assistant Professor, Harvard Medical School Center for Addiction Medicine Massachusetts General Hospital 101 Merrimac St. Boston, MA 02114 Tel.:617-643-7293 Fax:617-643-1998 On Dec 14, 2017, at 1:11 PM, Glasser, Matthew <glass...@wustl.edu<mailto:glass...@wustl.edu>> wrote: That would be reasonable. I would probably use the myelin maps without _BC if you are looking for differences in myelin content across groups. Peace, Matt. From: <hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>> on behalf of "Gilman, Jodi" <jgilm...@mgh.harvard.edu<mailto:jgilm...@mgh.harvard.edu>> Date: Thursday, December 14, 2017 at 10:21 AM To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Subject: [HCP-Users] group comparison in myelin maps I’m trying to compare 2 groups to see if there are differences in myelination. Here are the steps that seem logical to me, would be great to see if I’m going about this correctly: 1. Create a merged file of the MSMAll .dscalar maps for each group separately (using wb_shortcuts -cifti-concatenate)? 2. Run a permutation test to compare the groups Does that sound right? Thanks, Jodi Jodi Gilman, Ph.D. Assistant Professor, Harvard Medical School Center for Addiction Medicine Massachusetts General Hospital 101 Merrimac St. Boston, MA 02114 Tel.: 617-643-7293 Fax:617-643-1998 The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ HCP-Users mailing list HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org> http://lists.humanconnectome.org/mailman/listinfo/hcp-users ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
[HCP-Users] Best structural image for VBM?
Hello, I am interested in doing a VBM analysis- which structural images would be best for this? I am currently using 3T_T1w_MPR1.nii.gz, which look very good. But I’d like to confirm that these are best. Thanks, Jodi The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
[HCP-Users] group comparison in myelin maps
I’m trying to compare 2 groups to see if there are differences in myelination. Here are the steps that seem logical to me, would be great to see if I’m going about this correctly: 1. Create a merged file of the MSMAll .dscalar maps for each group separately (using wb_shortcuts -cifti-concatenate)? 2. Run a permutation test to compare the groups Does that sound right? Thanks, Jodi Jodi Gilman, Ph.D. Assistant Professor, Harvard Medical School Center for Addiction Medicine Massachusetts General Hospital 101 Merrimac St. Boston, MA 02114 Tel.:617-643-7293 Fax:617-643-1998 The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
