[HCP-Users] humanconnectome.org SSL-certificate renewed
Last week, the HCP's SSL-certificate expired. This affected user access to all secured sites ending in humanconnectome.org and may have tripped a warning from your internet browser that these sites were unsecured or blocked access to certain functions. We now have a new certificate in place and have run the necessary verification steps to get all sites functioning properly. We are sorry for the inconvenience this has caused and have plans in place to prevent such a disruption from happening again. Please let us know if you experience further problems accessing ConnectomeDB or the HCP wiki . Thanks again for your patience! Best, The WU-Minn HCP Consortium Jennifer Elam, Ph.D. Outreach Coordinator, Human Connectome Project Washington University School of Medicine Department of Anatomy and Neurobiology, Box 8108 660 South Euclid Avenue St. Louis, MO 63110 tel:314-362-9387 314-362-9387 mailto:el...@pcg.wustl.edu el...@pcg.wustl.edu http://www.humanconnectome.org www.humanconnectome.org ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
Re: [HCP-Users] The minimal preprocessing pipelines for HCP
This is a good point and something we thought about at the time. The reason we did it this way was to avoid having to generate two separate volume timeseries files (making these is by far the most time-consuming part of the fMRIVolume pipeline). We would have had to make one that was fully distortion corrected, but put into native T1w space with a single resampling step and another (the only one that we currently make) that is put into MNI space with a single resampling step. There was a third way this could have been done (much more complicated, but without the single spline interpolation step in the volume): We could have applied the volume warpfield for each fMRI timeseries volume to the native mesh surfaces to make many copies of them (because of the motion correction there is a unique warpfield for each fMRI volume) and resampled onto the surfaces directly from the original fMRI timeseries. This also would have been more exact because while volumes must be resampled after registration to a voxel grid, surfaces can have the transformations applied to their vertex coordinate positions exactly (in mm). Coding this up would have been a bit of a challenge (and slower), as things like the high local COV exclusion expect the surface not to move around and thus would also have to be computed for every fMRI volume. Perhaps if computers get faster and someone gets bored enough to bother, this will get implemented… Peace, Matt. From: ting xu xutin...@gmail.com Date: Monday, March 2, 2015 at 8:30 PM To: Matt Glasser glass...@wusm.wustl.edu Subject: The minimal preprocessing pipelines for HCP Dear Dr. Glasser, My name is Ting Xu and I am a postdoc from Nathan Kline Institute, New York state. I am writing to enquire about the order of preprocess steps in HCP pipeline. I read the pipeline scripts and noticed that the order of preprocess for surface data is (1) registered native volume to MNI volume using fnirt, (2) applied the fnirt registration to native surface, (3) project data from volume to surface in MNI space, (4) registered the data to fs32k template. There is another way for registration, e.g. project the data from native volume to native surface then register to fs32k template. I was wondering why should we bring the the data to MNI space for both native volume and surface first, and then do the projection in MNI space? Would you please tell me are there any specific reasons behind this? Many thanks for your comments! Warmly regards, Ting -- Xu,Ting Postdoc Nathan Kline Institute, Child Mind Institute Laboratory for Functional Connectome and Development (LFCD), Institute of Psychology, CAS 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 listHCP-Users@humanconnectome.orghttp://lists.humanconnectome.org/mailman/listinfo/hcp-users
[HCP-Users] HCP workbench view
Hello, I'm trying to edit the color of my borders when I am viewing them in Workbench_View. Specifically, I would like to change the border color from black to white for visibility purposes. I've tried opening the features box and changing the coloring setting from name to 'class. This changes the color from black to white sometimes, but other times it stays the same color. Does anyone have a technique for reliably getting the border color to change? Thanks very much for your help. best, Katherine -- Katherine Bryant, MS PhD Candidate in Neuroscience Yerkes National Primate Research Center Emory University ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
Re: [HCP-Users] projecting from volume to R440 template (subcortical and cerebellum)
Not sure if this will help your purposes, but the HCP500-PTN(ParcellationTimeseriesNetmats)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 listHCP-Users@humanconnectome.orghttp://lists.humanconnectome.org/mailman/listinfo/hcp-users
