Re: [HCP-Users] Threshold p value in workbench view
Hi, Let’s step back. Why you want to convert the provided group z-stat maps to p-values? Any such p-value map (converted simplistically from the zstat map) will (1) not account for multiple comparisons over grayordinates, and (2) will not account for the family structure (dependence between subjects). That is why we have not supplied a p-value map. It is possible to work around both issues using, e.g., the PALM tool in FSL, and thereby generate truly meaningful p-values, but that is not something we have internally generated for each of the task contrasts. cheers, -MH -- Michael Harms, Ph.D. --- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave.Tel: 314-747-6173 St. Louis, MO 63110Email: mha...@wustl.edu On 12/28/16, 9:23 AM, "hcp-users-boun...@humanconnectome.org on behalf of Xavier Guell Paradis" wrote: I think I cannot access this link https://wustl.box.com/s/uuxn06pjlnn6ts7nhak0zww53l33fxzf ; the following message appears: "This shared file or folder link has been removed or is unavailable to you. ". Is there an alternative way to access the information in this link? As for this image (https://drive.google.com/file/d/0B76s53K6sr4Qa0Z6MHB3OXRxbW8/view?usp=shar ing), wouldn't this show z values from 0 to 0.05 (instead of p values from 0 to 0.05) if the file I am using is the "tfMRI_ALLTASKS_level3_zstat1" file? I guess it is first necessary to convert z values to p values using the wb_command. Is this explained in the wustl.box link that you sent? Thank you, Xavier. From: Dierker, Donna [do...@wustl.edu] Sent: Wednesday, December 28, 2016 10:11 AM To: Xavier Guell Paradis Subject: Re: [HCP-Users] Threshold p value in workbench view Does this link work? https://drive.google.com/file/d/0B76s53K6sr4Qa0Z6MHB3OXRxbW8/view?usp=shari ng > On Dec 27, 2016, at 5:04 PM, Dierker, Donna wrote: > > See if you can read this link, Xavier: > > https://wustl.box.com/s/uuxn06pjlnn6ts7nhak0zww53l33fxzf > > People also use metric- or cifti-math to convert to log p or 1-p. >Whatever works for you. > > >> On Dec 27, 2016, at 10:39 AM, Xavier Guell Paradis >>wrote: >> >> Dear Sir or Madam, >> When viewing task contrasts in workbench (the file is >>HCP_S900_787_tfMRI_ALLTASKS_level3_zstat1_hp200_s2_MSMSulc.dscalar.nii), >>is there a way to threshold areas of activation for a given p value >>(e.g. areas that, in the task contrast, have achieved a p<0.001)? >> A previous post in this mailing list asked the same question (the post >>was called "thresholding the data to p-value"), but the person that >>replied to the email included a screen capture which is not available in >>the mail archive. Without that screen capture, I cannot understand how >>to threshold data using p values. >> >> Thank you very much, >> Xavier. >> >> >> Xavier Guell Paradis, M.D. >> Visiting Scientist >> Massachusetts Institute of Technology >> McGovern Institute for Brain Research >> Office: 46-4033A >> Phone: (617) 324-4355 >> Email: xavie...@mit.edu >> ___ >> HCP-Users mailing list >> 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 >https://drive.google.com/file/d/0B76s53K6sr4Qa0Z6MHB3OXRxbW8/view?usp=shar >ingnot 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. > > ___ > HCP-Users mailing list > 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. ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.
Re: [HCP-Users] Threshold p value in workbench view
I think I cannot access this link https://wustl.box.com/s/uuxn06pjlnn6ts7nhak0zww53l33fxzf ; the following message appears: "This shared file or folder link has been removed or is unavailable to you. ". Is there an alternative way to access the information in this link? As for this image (https://drive.google.com/file/d/0B76s53K6sr4Qa0Z6MHB3OXRxbW8/view?usp=sharing), wouldn't this show z values from 0 to 0.05 (instead of p values from 0 to 0.05) if the file I am using is the "tfMRI_ALLTASKS_level3_zstat1" file? I guess it is first necessary to convert z values to p values using the wb_command. Is this explained in the wustl.box link that you sent? Thank you, Xavier. From: Dierker, Donna [do...@wustl.edu] Sent: Wednesday, December 28, 2016 10:11 AM To: Xavier Guell Paradis Subject: Re: [HCP-Users] Threshold p value in workbench view Does this link work? https://drive.google.com/file/d/0B76s53K6sr4Qa0Z6MHB3OXRxbW8/view?usp=sharing > On Dec 27, 2016, at 5:04 PM, Dierker, Donna wrote: > > See if you can read this link, Xavier: > > https://wustl.box.com/s/uuxn06pjlnn6ts7nhak0zww53l33fxzf > > People also use metric- or cifti-math to convert to log p or 1-p. Whatever > works for you. > > >> On Dec 27, 2016, at 10:39 AM, Xavier Guell Paradis wrote: >> >> Dear Sir or Madam, >> When viewing task contrasts in workbench (the file is >> HCP_S900_787_tfMRI_ALLTASKS_level3_zstat1_hp200_s2_MSMSulc.dscalar.nii), is >> there a way to threshold areas of activation for a given p value (e.g. areas >> that, in the task contrast, have achieved a p<0.001)? >> A previous post in this mailing list asked the same question (the post was >> called "thresholding the data to p-value"), but the person that replied to >> the email included a screen capture which is not available in the mail >> archive. Without that screen capture, I cannot understand how to threshold >> data using p values. >> >> Thank you very much, >> Xavier. >> >> >> Xavier Guell Paradis, M.D. >> Visiting Scientist >> Massachusetts Institute of Technology >> McGovern Institute for Brain Research >> Office: 46-4033A >> Phone: (617) 324-4355 >> Email: xavie...@mit.edu >> ___ >> HCP-Users mailing list >> 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 > https://drive.google.com/file/d/0B76s53K6sr4Qa0Z6MHB3OXRxbW8/view?usp=sharingnot > 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. > > ___ > HCP-Users mailing list > 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. ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
Re: [HCP-Users] Threshold p value in workbench view
See if you can read this link, Xavier: https://wustl.box.com/s/uuxn06pjlnn6ts7nhak0zww53l33fxzf People also use metric- or cifti-math to convert to log p or 1-p. Whatever works for you. > On Dec 27, 2016, at 10:39 AM, Xavier Guell Paradis wrote: > > Dear Sir or Madam, > When viewing task contrasts in workbench (the file is > HCP_S900_787_tfMRI_ALLTASKS_level3_zstat1_hp200_s2_MSMSulc.dscalar.nii), is > there a way to threshold areas of activation for a given p value (e.g. areas > that, in the task contrast, have achieved a p<0.001)? > A previous post in this mailing list asked the same question (the post was > called "thresholding the data to p-value"), but the person that replied to > the email included a screen capture which is not available in the mail > archive. Without that screen capture, I cannot understand how to threshold > data using p values. > > Thank you very much, > Xavier. > > > Xavier Guell Paradis, M.D. > Visiting Scientist > Massachusetts Institute of Technology > McGovern Institute for Brain Research > Office: 46-4033A > Phone: (617) 324-4355 > Email: xavie...@mit.edu > ___ > HCP-Users mailing list > 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. ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
[HCP-Users] Threshold p value in workbench view
Dear Sir or Madam, When viewing task contrasts in workbench (the file is HCP_S900_787_tfMRI_ALLTASKS_level3_zstat1_hp200_s2_MSMSulc.dscalar.nii), is there a way to threshold areas of activation for a given p value (e.g. areas that, in the task contrast, have achieved a p<0.001)? A previous post in this mailing list asked the same question (the post was called "thresholding the data to p-value"), but the person that replied to the email included a screen capture which is not available in the mail archive. Without that screen capture, I cannot understand how to threshold data using p values. Thank you very much, Xavier. Xavier Guell Paradis, M.D. Visiting Scientist Massachusetts Institute of Technology McGovern Institute for Brain Research Office: 46-4033A Phone: (617) 324-4355 Email: xavie...@mit.edu ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
