[HCP-Users] Subject list for the HCP Q2 release
Hello, I'm trying to replicate some findings from this very interesting Nature Neuroscience paper: https://www.nature.com/articles/nn.4135 The following is in the subject information: > *HCP data.* We used the Q2 HCP data release, which was all the HCP data publicly available at the time that this project began. The full Q2 release contains data on 142 healthy subjects; we restricted our analysis to subjects for whom all six fMRI sessions were available (*n* = 126; 40 males, age 22–35). Unfortunately, I'm unable to find the list of subjects in the Q2 release. More specifically, the subjects that had all six fMRI sessions that were recorded at that time. Can you please help me find these subjects? Sincerely, Manasij ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
[HCP-Users] Some columns in the Movement_Regressors.txt are zeros
I've come across this a few times so I thought I'd report it. Column 6 and 12 in the Movement_Regressors.txt is all zeros. An example of such a file is in 414229\MNINonLinear\Results\tfMRI_LANGUAGE_RL This usually creates problems if I use 3dDeconvolve for regressing out motion. Is this an issue with the movement file? If you know a work around, please let me know. Sincerely, Manasij ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
[HCP-Users] ROI cluster centers to surface grayordinates
Hi, I have a set of ROI cluster center coordinates in MNI space. My goal is to create similar ROI clusters to use with HCP data. I understand there's no true equivalent in terms of surface grayordinates but what would be the best way to find their approximate position on the surface? Is this the information contained in the surf.gii files? Please let me know. Sincerely, Manasij ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
Re: [HCP-Users] Theory of mind animations
It's working. Thank you! On Tue, Dec 5, 2017 at 3:34 PM, Elam, Jennifer <e...@wustl.edu> wrote: > Hi Manasij, > > The 3T Task resources should now be again available for download via > Aspera. > > > 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 > www.humanconnectome.org > > -- > *From:* hcp-users-boun...@humanconnectome.org <hcp-users-bounces@ > humanconnectome.org> on behalf of Elam, Jennifer <e...@wustl.edu> > *Sent:* Tuesday, December 5, 2017 10:03:41 AM > *To:* Manasij Venkatesh > *Cc:* hcp-users@humanconnectome.org; Hileman, Michael > > *Subject:* Re: [HCP-Users] Theory of mind animations > > > Hi Manasij, > > We are having trouble with Aspera downloads for cross-subject resources > such as the task resources and group average dataset. We are looking into > the issue and will let you know when it's working again. Sorry for the > delay. > > > 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 > www.humanconnectome.org > > -- > *From:* Manasij Venkatesh <mana...@umd.edu> > *Sent:* Tuesday, December 5, 2017 9:58:06 AM > *To:* Elam, Jennifer > *Cc:* hcp-users@humanconnectome.org > *Subject:* Re: [HCP-Users] Theory of mind animations > > I noticed there was a previous post about this where you asked to clear > the cache and try a link. But that didn't work either, and gave the same > error. > > > > On Tue, Dec 5, 2017 at 10:02 AM, Manasij Venkatesh <mana...@umd.edu> > wrote: > > Hi Jennifer, > > When I try to download this through Aspera Connect, I get an error: Server > aborted session: No such file or directory (Code: 43). I've tried it on a > few computers with different internet connections. > > Is there any other way to download this? I checked S3, but couldn't find > these folders there either. Please let me know. > > Sincerely, > Manasij > > On Wed, Nov 15, 2017 at 1:25 PM, Elam, Jennifer <e...@wustl.edu> wrote: > > Hi Manasij, > > All the 3T task AVI videos and EPrime scripts for the original HCP Young > Adult are available for download as a single package in ConnectomeDB on > the HCP S1200 Project page > <https://db.humanconnectome.org/data/projects/HCP_1200> under "Task > Resources". Specifically, you are looking for the videos for the SOCIAL > task. > > > 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 > www.humanconnectome.org > > -- > *From:* hcp-users-boun...@humanconnectome.org < > hcp-users-boun...@humanconnectome.org> on behalf of Manasij Venkatesh < > mana...@umd.edu> > *Sent:* Wednesday, November 15, 2017 12:06:32 PM > *To:* hcp-users@humanconnectome.org > *Subject:* [HCP-Users] Theory of mind animations > > Hi, > > Can I get access to the exact videos used for the TOM task paradigm? > > Sincerely, > Manasij > > ___ > 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 > ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
Re: [HCP-Users] Theory of mind animations
I noticed there was a previous post about this where you asked to clear the cache and try a link. But that didn't work either, and gave the same error. On Tue, Dec 5, 2017 at 10:02 AM, Manasij Venkatesh <mana...@umd.edu> wrote: > Hi Jennifer, > > When I try to download this through Aspera Connect, I get an error: Server > aborted session: No such file or directory (Code: 43). I've tried it on a > few computers with different internet connections. > > Is there any other way to download this? I checked S3, but couldn't find > these folders there either. Please let me know. > > Sincerely, > Manasij > > On Wed, Nov 15, 2017 at 1:25 PM, Elam, Jennifer <e...@wustl.edu> wrote: > >> Hi Manasij, >> >> All the 3T task AVI videos and EPrime scripts for the original HCP Young >> Adult are available for download as a single package in ConnectomeDB on >> the HCP S1200 Project page >> <https://db.humanconnectome.org/data/projects/HCP_1200> under "Task >> Resources". Specifically, you are looking for the videos for the SOCIAL >> task. >> >> >> 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 >> www.humanconnectome.org >> >> -- >> *From:* hcp-users-boun...@humanconnectome.org < >> hcp-users-boun...@humanconnectome.org> on behalf of Manasij Venkatesh < >> mana...@umd.edu> >> *Sent:* Wednesday, November 15, 2017 12:06:32 PM >> *To:* hcp-users@humanconnectome.org >> *Subject:* [HCP-Users] Theory of mind animations >> >> Hi, >> >> Can I get access to the exact videos used for the TOM task paradigm? >> >> Sincerely, >> Manasij >> >> ___ >> 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
Re: [HCP-Users] Theory of mind animations
Hi Jennifer, When I try to download this through Aspera Connect, I get an error: Server aborted session: No such file or directory (Code: 43). I've tried it on a few computers with different internet connections. Is there any other way to download this? I checked S3, but couldn't find these folders there either. Please let me know. Sincerely, Manasij On Wed, Nov 15, 2017 at 1:25 PM, Elam, Jennifer <e...@wustl.edu> wrote: > Hi Manasij, > > All the 3T task AVI videos and EPrime scripts for the original HCP Young > Adult are available for download as a single package in ConnectomeDB on > the HCP S1200 Project page > <https://db.humanconnectome.org/data/projects/HCP_1200> under "Task > Resources". Specifically, you are looking for the videos for the SOCIAL > task. > > > 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 > www.humanconnectome.org > > -- > *From:* hcp-users-boun...@humanconnectome.org <hcp-users-bounces@ > humanconnectome.org> on behalf of Manasij Venkatesh <mana...@umd.edu> > *Sent:* Wednesday, November 15, 2017 12:06:32 PM > *To:* hcp-users@humanconnectome.org > *Subject:* [HCP-Users] Theory of mind animations > > Hi, > > Can I get access to the exact videos used for the TOM task paradigm? > > Sincerely, > Manasij > > ___ > 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
[HCP-Users] Regarding the multi-modal parcellation of the cortex
Hi, I've been using your parcellation ( https://www.ncbi.nlm.nih.gov/pubmed/27437579) for analyzing HCP task data. I want to perform similar analysis on data collected in our university but the data I have is in the MNI152 (2mm) template. Is there an equivalent parcellation scheme for this template as well? Please let me know. Sincerely, Manasij ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
[HCP-Users] Task description for EMOTION data
Hi, The task description for the EMOTION data is as follows: *This task was adapted from the one developed by Hariri and colleagues which had shown evidence as a functional localizer (Hariri et al., 2002) with moderate reliability across time (Manuck et al., 2007a). Participants are presented with blocks of trials that either ask them to decide which of two faces presented on the bottom of the screen match the face at the top of the screen, or which of two shapes presented at the bottom of the screen match the shape at the top of the screen. The faces have either angry or fearful expressions. Trials are presented in blocks of 6 trials of the same task (face or shape), with the stimulus presented for 2 s and a 1 s ITI. Each block is preceded by a 3 s task cue (“shape” or “face”), so that each block is 21 s including the cue. Each of the two runs includes 3 face blocks and 3 shape blocks. However, there was a bug in the E-prime script for this task such that the task stopped short of the last three trials of the last task block in each run. To promote comparability across participants, we decided not to fix the bug (given that a number of subjects had already been run before it was detected) as we thought it would have minimal impact on the data. In phase I, we compared this task to one using negative and neutral IAPS pictures (see Supplemental Materials).* A typical EV file looks like this (fear.txt) 32.053181 74.196181 116.338181 The block length indicated is 18, where as the description says 21. My question is if the onset listed here is that of the first trial or of the cue. My confusion is based on 2 things: 1. For the working memory (WM) data, the block lengths include the time of the cue. The onsets are that of the cue. 2. The bug reported says the last 3 trials are cut-off/ missing, and if I do the math it seems this can't be the onset of the cue. I wanted to confirm this. Please let me know. Sincerely, Manasij ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
[HCP-Users] Downloading from the S3 browser
Hi, Is there an easy way to download working memory data for the unrelated subjects group from the S3 browser? I'm having some trouble with Aspera Connect, the connection fails often and I have to restart the whole procedure. The downloading is much faster on the S3 browser, but I can't find an easy way to download just the files I need. Sincerely, Manasij ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
[HCP-Users] About the .dlabel.nii file for the 180 parcellations in your study
Hi, I've been having some issues importing a *.dlabel.nii file to matlab using ft_read_cifti. The error I obtain is "Invalid file identifier. Use fopen to generate a valid file identifier" but the *.dtseries.nii imports just fine. Has this bug been fixed? After looking at some old posts, I decided to instead use wb_command -cifti-separate Q1-Q6_RelatedParcellation210.CorticalAreas_dil_Final_Final_Areas_Group_Colors.32k_fs_LR.dlabel.nii COLUMN -label CORTEX_LEFT left.label.gii to obtain the cluster labels. This works just fine since I can import this on matlab using the gifti toolbox. My question is about the anatomical names associated with these clusters. I believe these are also contained in the *.dlabel.nii file? How do I separate this information? Sincerely, Manasij ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
Re: [HCP-Users] Understanding surface alignment in HCP
Thank you for your quick response, that was really helpful. I'll use the 180 parcellations as well, but I wish to do some analysis using custom ROIs. A quick follow up question: Suppose I want to do clustering using these geodesic distances, is there a file containing them as well? Sincerely, Manasij On Tue, Jun 6, 2017 at 6:12 PM, Timothy Coalson <tsc...@mst.edu> wrote: > First, you might consider using our 180-area-per-hemisphere functional > parcellation (https://balsa.wustl.edu/study/show/RVVG), which is more > specialized to human cortex than a distance-based clustering would be. > Also keep in mind that vertices being close in 3D doesn't mean they are > related, they can be on the opposite side of a large sulcus - we use > geodesic distance for this purpose (crawling along the surface triangles). > Additional answers inline. > > Tim > > On Tue, Jun 6, 2017 at 4:55 PM, Manasij Venkatesh <mana...@umd.edu> wrote: > >> Hi, >> >> The number of vertices on the surface is of the order of ~60k (excluding >> subcortical regions). I wish to work in an ROI space (say 100 ROIs) by >> clustering the cortical vertices that are near-by. To do so, I need to know >> the co-ordinates of the vertices on the surface. I had the following >> questions regarding this: >> >> 1. Does the data in *.dtseries.nii correspond to the time series of the >> vertices after surface alignment? If so, which is the file containing the >> coordinates of these vertices? >> > > Yes, the coordinates are in ".surf.gii" files. You probably want > midthickness coordinates, but there are also pial and white matter > surfaces. The MNI space versions are in MNINonLinear/fsaverage_LR32k, but > there are also structural space versions (no scaling or stretching from > distortion corrected scan data) in the T1w folder. > > >> 2. Do the vertices across patients correspond to the same region in the >> brain? >> > > That is the purpose of registration, so fs_LR surfaces have this property, > yes. The correspondence is better with MSMAll than with MSMSulc or > FreeSurfer. > > >> If this is true, shouldn't there be one surface file for all subjects >> after alignment? I'm wondering why there's a surface file for each subject. >> > > No, surface registration does not do anything to anatomical shape. After > registration and resampling of a subject's surface, it looks exactly the > same as before, it is simply that when we click on a point on one subject's > surface, we can now find a matching point on another subject's surface. > None of this requires altering the anatomical shape of any subject, so they > all still have individual surfaces. > > One important reason for this is that many functional areas are not > strictly matched to nearby sulci/gyri (also, different subjects have rather > different folding patterns in a fair portion of cortex). Thus, MSMAll > establishes correspondence based on areal features (myelination, visual > areas, rfMRI components, cortical thickness), which causes folding patterns > to not have as good correspondence across subjects as they would with > MSMSulc, which establishes correspondence based only on folding patterns. > > >> Thank you in advance. >> >> Sincerely, >> Manasij >> >> ___ >> 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
[HCP-Users] Understanding surface alignment in HCP
Hi, The number of vertices on the surface is of the order of ~60k (excluding subcortical regions). I wish to work in an ROI space (say 100 ROIs) by clustering the cortical vertices that are near-by. To do so, I need to know the co-ordinates of the vertices on the surface. I had the following questions regarding this: 1. Does the data in *.dtseries.nii correspond to the time series of the vertices after surface alignment? If so, which is the file containing the coordinates of these vertices? 2. Do the vertices across patients correspond to the same region in the brain? If this is true, shouldn't there be one surface file for all subjects after alignment? I'm wondering why there's a surface file for each subject. Thank you in advance. Sincerely, Manasij ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
