Re: [HCP-Users] projecting from volume to R440 template (subcortical and cerebellum)

[Glasser, Matthew]

So Steve Smith told me off list that was the old way it was done, but the guys who made it are doing something faster now that is not equivalent.  I had hoped they would respond with their own explanation, but here is what he said: "Either use the Saad script to get group-surface written into MNI space (that's used in the PTN released thumbnails) or use dual-regression per subject to get volume maps.  We had discussed doing that latter (and then averaging over subjects) for the PTN release but it never got done yet - maybe we should make sure that gets done for the next PTN release." Peace, Matt. From: Yizhou Ma <maxxx...@umn.edu> Date: Friday, March 6, 2015 at 11:11 AM To: Matt Glasser <glass...@wusm.wustl.edu> Cc: Timothy Coalson <tsc...@mst.edu>, "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> Subject: Re: [HCP-Users] projecting from volume to R440 template (subcortical and cerebellum) Thank you for the info Dr. Glasser. Glad to know how melodic_IC_sum.nii.gz is generated. I think it might be helpful to put this info into the "HCP500_GroupICA+NodeTS+Netmats_Summary" document. Best, Cherry On Tue, Mar 3, 2015 at 8:04 PM, Glasser, Matthew <glass...@wusm.wustl.edu> wrote: A better way to put it is any volume-based group average cortical result is not an accurate representation of the underlying subjects’ data.  The results that Mike was talking about are generated by taking the group CIFTI ICA results and dual regressing them into each individual’s CIFTI dense timeseries (for stage one of dual regression) and then the resulting individual subject component timecourses into each subject’s volume timeseries to make individual subject component spatial maps in the volume.  This is accurate as far as getting individual subject volume maps (because we don’t apply any volume-based smoothing), however as soon as you try to average these maps across subjects (to create melodic_IC_sum.nii.gz) you aren’t aligning like with like any more and hence get an inaccurate result.   Peace, Matt. From: Yizhou Ma <maxxx...@umn.edu> Date: Tuesday, March 3, 2015 at 7:15 PM To: Timothy Coalson <tsc...@mst.edu> Cc: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> Subject: Re: [HCP-Users] projecting from volume to R440 template (subcortical and cerebellum) Hi Timothy, Thank you for your reply. So sounds like that the file Atlas_ROIs.2.nii.gz for whichever subject can get me the same result? I'd also like to follow up on Dr. Harms' suggestion on using melodic_IC_sum.nii.gz. Given the discussion on the inaccuracy in group level surface/volume mapping, it seems that melodic_IC_sum.nii.gz is not an accurate representation of the HCP maps in the MNI space, thus it is "for reporting purposes"? Thanks, Cherry On Tue, Mar 3, 2015 at 7:06 PM, Timothy Coalson <tsc...@mst.edu> wrote: It isn't impossible to get the data into the grayordinate space we use, though the volume to surface mapping part could be problematic because of alignment/group average issues.  As long as the data is nonlinearly registered to MNI152 space, you are really only missing the volume subcortical label file to be able to create a cifti file in our grayordinate space.  I think you can get this file by downloading a single subject's dataset from connectomedb (download images, structural preprocessed?). There will be an enhancement added to wb_command that will allow you to create this volume label file from an existing cifti file, rather than downloading it. Tim On Mon, Mar 2, 2015 at 2:13 PM, Yizhou Ma <maxxx...@umn.edu> wrote: Thank you for your suggestion Dr. Harms. It seems that it is the only way to compare subcortical networks at this moment. On Mon, Mar 2, 2015 at 12:21 PM, Harms, Michael <mha...@wustl.edu> wrote: Not sure if this will help your purposes, but the "HCP500-PTN" (Parcellation+Timeseries+Netmats) distribution includes the following: melodic_IC_sum.nii.gz:  ICA spatial maps projected from the surface into the volume, for reporting purposes. MNI152 space. I don't think we have any group ICA maps derived originally in the volume space since the group ICA was done using the FIX-cleaned CIFTI time series as inputs. 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  63110 Email: mha...@wustl.edu From: Yizhou Ma <maxxx...@umn.edu> Date: Sunday, March 1, 2015 10:23 PM To: Matt Glasser <glass...@wusm.wustl.edu> Cc: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> Subject: Re: [HCP-Users] projecting from volume to R440 template (subcortical and cerebellum) Thank you for your reply Dr. Glasser. I've read this recommendation elsewhere on the forum and your point is well taken. Yet in our case the purpose is a bit different. We are not trying to do any analysis but to compare the HCP ICA maps with classical maps that have been generated in the volumetric space. Although this may not be accurate, it'll offer us some insight into the HCP maps. On Sun, Mar 1, 2015 at 10:09 PM, Glasser, Matthew <glass...@wusm.wustl.edu> wrote: I would recommend mapping your individual subject data onto individual subject surfaces and then registering on the surface.  Volume to surface mapping onto a group average surface from a group average volume is not particularly accurate in comparison.  Once you average cortical data in the volume, you lose the ability to do accurate spatial localization to cortical areas.  Instead data can be easily mapped onto locations centimeters away in 2D from the correct location on the folded cortical sheet.  Also, group average surfaces are very blurry in many cortical regions because different people have different folding patterns that cannot be registered (e.g. some people can have two gyri where others have only one).  Thus, it’s really better to do your cortical analysis on the surface to begin with, as we do in the HCP with CIFTI.   Peace, Matt. From: Yizhou Ma <maxxx...@umn.edu> Date: Sunday, March 1, 2015 at 9:27 PM To: Timothy Coalson <tsc...@mst.edu> Cc: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> Subject: Re: [HCP-Users] projecting from volume to R440 template (subcortical and cerebellum) Hi, I am still looking forward to getting help on this issue. Is an "Atlas_ROIs.2.nii.gz" or similar files provided for volume to surface mapping onto R440 group template? If not, will there be any in the future? Thanks, Cherry _______________________________________________ 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   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 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.   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