Thank you very much!
Leonardo Tozzi, MD, PhD Williams PanLab | Postdoctoral Researcher Stanford University | 401 Quarry Rd lto...@stanford.edu<mailto:lto...@stanford.edu> | (650) 5615738 From: "Hodge, Michael" <hod...@wustl.edu> Date: Thursday, May 30, 2019 at 7:24 AM To: "Harms, Michael" <mha...@wustl.edu>, Leonardo Tozzi <lto...@stanford.edu>, "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> Subject: RE: [HCP-Users] Downloading movement regressors from HYA release Hi Leonardo, There was a problem with the resource catalogs for those 5 subjects. I believe the files should now be accessible via the URL you were using. Let me know if that’s not the case. Regards, Mike From: Harms, Michael <mha...@wustl.edu> Sent: Wednesday, May 29, 2019 1:51 PM To: Leonardo Tozzi <lto...@stanford.edu>; hcp-users@humanconnectome.org Cc: Hodge, Michael <hod...@wustl.edu> Subject: Re: [HCP-Users] Downloading movement regressors from HYA release Which specific files (i.e., which runs) is curl not finding for those remaining subjects? Mike Hodge will likely need to investigate further, because I’m able to find the expected files on our local file systems for 101006 at least. It may be something specific to how REST works, with perhaps a small number of files not “in sync” between what exists on the file systems vs. what the database thinks is available (just guessing…). You could simply download the MPP packages for the small number of remaining subjects through ConnectomeDB. Cheers, -MH -- Michael Harms, Ph.D. ----------------------------------------------------------- Associate Professor of Psychiatry 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<mailto:mha...@wustl.edu> From: Leonardo Tozzi <lto...@stanford.edu<mailto:lto...@stanford.edu>> Date: Wednesday, May 29, 2019 at 1:44 PM To: "Harms, Michael" <mha...@wustl.edu<mailto:mha...@wustl.edu>>, "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Subject: Re: [HCP-Users] Downloading movement regressors from HYA release I did and actually some subjects worked, but not these ones: 101006 159441 926862 927359 942658 I still get a “cannot find file” error (10.4.5). Leonardo Tozzi, MD, PhD Williams PanLab | Postdoctoral Researcher Stanford University | 401 Quarry Rd lto...@stanford.edu<mailto:lto...@stanford.edu> | (650) 5615738 From: "Harms, Michael" <mha...@wustl.edu<mailto:mha...@wustl.edu>> Date: Wednesday, May 29, 2019 at 10:39 AM To: Leonardo Tozzi <lto...@stanford.edu<mailto:lto...@stanford.edu>>, "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Subject: Re: [HCP-Users] Downloading movement regressors from HYA release Did you try downloading again, just in case there was a transfer glitch? Because the Movement_RelativeRMS.txt files appear to be present in the database for all 4 rfMRI runs of 101006 (the one subject I checked). Cheers, -MH -- Michael Harms, Ph.D. ----------------------------------------------------------- Associate Professor of Psychiatry 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<mailto:mha...@wustl.edu> From: Leonardo Tozzi <lto...@stanford.edu<mailto:lto...@stanford.edu>> Date: Wednesday, May 29, 2019 at 11:40 AM To: "Harms, Michael" <mha...@wustl.edu<mailto:mha...@wustl.edu>>, "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Subject: Re: [HCP-Users] Downloading movement regressors from HYA release Dear Michael, I have now downloaded the majority of subjects with: curl -o …/${sub}_${run}_Movement_RelativeRMS.txt -u USER:PASS https://db.humanconnectome.org/data/projects/HCP_1200/subjects/${sub}/experiments/${sub}_CREST/files/MNINonLinear/Results/${run}/Movement_RelativeRMS.txt<https://db.humanconnectome.org/data/projects/HCP_1200/subjects/$%7bsub%7d/experiments/$%7bsub%7d_CREST/files/MNINonLinear/Results/$%7brun%7d/Movement_RelativeRMS.txt> However, these subjects still seem to be missing: 101006 127226 148335 159441 188145 204016 285345 316835 368551 926862 927359 942658 Is that normal? Thank you, Leonardo Tozzi, MD, PhD Williams PanLab | Postdoctoral Researcher Stanford University | 401 Quarry Rd lto...@stanford.edu<mailto:lto...@stanford.edu> | (650) 5615738 From: "Harms, Michael" <mha...@wustl.edu<mailto:mha...@wustl.edu>> Date: Wednesday, May 15, 2019 at 9:31 AM To: Leonardo Tozzi <lto...@stanford.edu<mailto:lto...@stanford.edu>>, "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Subject: Re: [HCP-Users] Downloading movement regressors from HYA release Hi, The Movement_RelativeRMS.txt files aren’t part of the specific “${run}_FIX” resource that you tried to reference. If you have access to outputs in our standard file/directory organization (e.g., Amazon S3, Connectome-in-a-Box, or our downloaded “packages”), the Movement_RelativeRMS.txt files can be found at ${subj}/MNINonLinear/Results/${run}. If not, the “CREST” resource (search the previous HCP-User emails) is what we are intending users to use, which is intended to mimic the standard file/directory organization in terms of where files are located. See FAQ 15 here https://wiki.humanconnectome.org/display/PublicData/HCP+Users+FAQ and the archived user list posts referenced therein. Regarding your item (2), I just confirmed that Movement_Regressors.txt exists for all 4 REST runs for all 6 of those subjects at MNINonLinear/Results/${run} in our unpacked packages, and thus should exist in Amazon S3, Connectome-in-a-Box, and via the CREST resource as well. Cheers, -MH -- Michael Harms, Ph.D. ----------------------------------------------------------- Associate Professor of Psychiatry Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave. Tel: 314-747-6173 St. Louis, MO 63110 Email: mha...@wustl.edu<mailto:mha...@wustl.edu> From: <hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Leonardo Tozzi <lto...@stanford.edu<mailto:lto...@stanford.edu>> Date: Tuesday, May 14, 2019 at 3:50 PM To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Subject: [HCP-Users] Downloading movement regressors from HYA release Dear Experts, Similarly to what described in this thread: https://www.mail-archive.com/hcp-users@humanconnectome.org/msg01342.html I have downloaded motion regressors for files from the healthy young adult release with the following command: curl -o …/${sub}_${run}_Movement_ Regressors.txt -u USER:PASSWORD https://db.humanconnectome.org/data/projects/HCP_1200/subjects/${sub}/experiments/${sub}_3T/resources/${run}_FIX/files/${run}/Movement_Regressors.txt<https://db.humanconnectome.org/data/projects/HCP_1200/subjects/$%7bsub%7d/experiments/$%7bsub%7d_3T/resources/$%7brun%7d_FIX/files/$%7brun%7d/Movement_Regressors.txt> However, I have 2 follow-up questions. 1. I would like to download the relative motion file, Movement_RelativeRMS.txt, to do some motion censoring on the resting state data. But if I try the same command with Movement_RelativeRMS.txt instead of Movement_Regressors.txt I get an error saying that the file does not exist. 2. For some subjects, I can’t find even the Movement_Regressors.txt. Is there any reason for this? These are the IDs: '127226' '130114' '169040' '329844' '908860' '971160' Thank you, Leonardo Tozzi, MD, PhD Williams PanLab | Postdoctoral Fellow Stanford University | 401 Quarry Rd lto...@stanford.edu<mailto:lto...@stanford.edu> | (650) 5615738 _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org<mailto: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. 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