Re: [HCP-Users] Q900 task downloads

[Harms, Michael]

Hi Janine, Yes, it does indeed appear to be the case that both the *s4 and *s4_S500_to_S900_extension packages of the task fMRI data include copies of the 2 mm smoothed results as well.  We will investigate and post to the list once that bit of duplication in the packages has been resolved (which may take a week or so).  Meanwhile, if you don’t mind the larger packages, just download the 4 mm smoothed packages and either ignore the 2 mm data, or explore the impact of using the 2 mm level of smoothing instead :) As for your other question, there is single file with the contrasts for each *task* per subject — that is the *s4_MSMAll.dscalar.nii file within the .feat directory for each task.  But, there isn’t one with all the contrasts across all tasks.   Once you’ve downloaded all the task data for a given subject, you can easily create such a file using ‘wb_command -cifti-merge’. 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: <hcp-users-boun...@humanconnectome.org> on behalf of Janine Bijsterbosch <janine.bijsterbo...@ndcn.ox.ac.uk> Date: Monday, January 25, 2016 at 8:19 AM To: Jennifer Elam <jse...@gmail.com> Cc: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> Subject: Re: [HCP-Users] Q900 task downloads Hi Jenn, Thanks so much for your reply! On 25 Jan 2016, at 14:05, Jennifer Elam <jse...@gmail.com> wrote: Hi Janine, The task analysis packages are actually available separately for 2mm and 4mm smoothing levels for grayordinates data. The reason the package sizes have gotten twice as big for S900 subjects is that now both MSM-Sulc and MSM-All registered versions are included in the packages for each task and smoothing level. I thought this was supposed to be the case. However, the 4mm smoothing is twice as large within the S900 data compared to the 2mm smoothing, even though both contain MSM-Sulc and MSM-All. When I downloaded data from a single subject I found that the 4mm download includes four *.feat directories rather than two: ls -1 100307/MNINonLinear/Results/tfMRI_EMOTION/ tfMRI_EMOTION_hp200_s2_level2.feat tfMRI_EMOTION_hp200_s2_level2_MSMAll.feat tfMRI_EMOTION_hp200_s4_level2.feat tfMRI_EMOTION_hp200_s4_level2_MSMAll.feat Perhaps the download accidentally includes both types of smoothing? Thanks!! Best wishes, Janine For previously released subjects (S500 and earlier releases) for which users may have already downloaded/obtained data, we have the S500 to S900 extension package type option to only download the data added for the S900 release (mostly the MSM-All registered version outputs only). Those are the options we have for package download through the DB GUI. You can also download data from DB through REST calls. Usage of REST commands is covered in other posts to the list. Perhaps Mike, Greg, or Matt can answer your other question. Best, Jenn On Mon, Jan 25, 2016 at 6:09 AM, Janine Bijsterbosch <janine.bijsterbo...@ndcn.ox.ac.uk> wrote: Hi, It seems that the task analysis downloads for 4mm smoothing in Q900 contain both 2 and 4mm smoothing (making them twice the size of the 2mm downloads). Is it possible to download only the 4mm smoothing results by any chance please? I was also wondering if there exists a single file per subject that contains all the task contrasts (i.e. similar to the group file HCP_S900_787_tfMRI_ALLTASKS_level3_zstat1_hp200_s4_MSMAll.dscalar.nii)? Thanks so much! Best wishes, Janine ----- Dr Janine Bijsterbosch Postdoctoral Researcher FMRIB Centre, University of Oxford John Radcliffe Hospital Oxford, United Kingdom janine.bijsterbo...@ndcn.ox.ac.uk _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users -- Jennifer Stine Elam, Ph.D. jse...@gmail.com 210-857-1150 _______________________________________________ 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