You can find the MSMAll_hp2000_clean.dtseries.nii file in the regular FIX package.
I think that, due to historical reasons, the “MSMSulc” version of the FIX-cleaned data ended up in both the FIX and FIX-Extended packages. But to avoid file duplication, the “MSMAll” version is only contained in the FIX (and not FIX-Extended) package. 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: Jingwei Li <jingweili.sjtu....@gmail.com<mailto:jingweili.sjtu....@gmail.com>> Date: Thursday, May 11, 2017 at 2:36 AM To: Michael Harms <mha...@wustl.edu<mailto:mha...@wustl.edu>> Cc: "Hodge, Michael" <hod...@wustl.edu<mailto:hod...@wustl.edu>>, "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Subject: Re: [HCP-Users] Download aparc+aseg.nii.gz, aseg.stats, lh/rh.aparc.stats of S1200 new subjects Deal all, Thanks for your explanation. I succeeded to download the lh/rh.aparc.stats, aseg.stats, and aparc+aseg.nii.gz by applying the code you provided me. Now I am facing another downloading issue. In the S1200 manual, it says the FIX_extended package includes the cifti file after ICA-FIX with MSM-all registration, which is rfMRI_REST1_LR_Atlas_MSMAll_hp2000_clean.dtseries.nii for example. We downloaded this package but didn't see this file inside. Therefore I want to download this particular file now. But in the resource, for example https://db.humanconnectome.org/data/experiments/ConnectomeDB_E17905/resources/ for subject 102109, I couldn't find this file as well. Can you show me how to download this file? Thanks, Jingwei On Thu, May 11, 2017 at 1:03 AM, Harms, Michael <mha...@wustl.edu<mailto:mha...@wustl.edu>> wrote: BTW: I thought that the “Expanded FreeSurfer Data” available under “Quick Download” at https://db.humanconnectome.org/data/projects/HCP_1200 contains basically the entire contents of the aseg.stats and {lh,rh}.aparc.stats files. So, all you might need to retrieve is the aparc+aseg.nii.gz files. 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<tel:(314)%20747-6173> St. Louis, MO 63110Email: mha...@wustl.edu<mailto:mha...@wustl.edu> From: <hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>> on behalf of "Hodge, Michael" <hod...@wustl.edu<mailto:hod...@wustl.edu>> Date: Tuesday, May 9, 2017 at 2:32 PM To: Jingwei Li <jingweili.sjtu....@gmail.com<mailto:jingweili.sjtu....@gmail.com>>, "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Subject: Re: [HCP-Users] Download aparc+aseg.nii.gz, aseg.stats, lh/rh.aparc.stats of S1200 new subjects Hi Jingwei, You’ll want to use a mechanism similar to that discussed in this thread: http://www.mail-archive.com/hcp-users@humanconnectome.org/msg04448.html You can use the XNAT REST protocol to iterate over sessions and resources. The files you’re wanting are structural preprocessing file outputs, so you can use something like the following to grep for specific files in the structural preprocessing pipeline output. You’ll probably want to add some redirection to redirect output to files. Regards, Mike #!/bin/bash read -s -p "ENTER PASSWORD: " PW;JSESSIONID=`curl -s -k -u [your_user_name]:$PW https://db.humanconnectome.org/data/JSESSIONID`;export<https://db.humanconnectome.org/data/JSESSIONID;export> JSESSIONID;echo $JSESSIONID for CSVROW in $(curl -s -k --cookie JSESSIONID=$JSESSIONID https://db.humanconnectome.org/data/experiments?xsiType=xnat:mrSessionData\&project=HCP_1200\&columns=ID,label,URI\&format=csv<https://db.humanconnectome.org/data/experiments?xsiType=xnat:mrSessionData%5C&project=HCP_1200%5C&columns=ID,label,URI%5C&format=csv> | grep "experiments"); do LABEL=$(echo $CSVROW | cut -d, -f3) EXP=$(echo $CSVROW | cut -d, -f4) echo "EXPERIMENT=$LABEL" for ROW in $(curl -s -k --cookie JSESSIONID=$JSESSIONID https://db.humanconnectome.org${EXP}/resources/Structural_preproc/files?format=csv<https://db.humanconnectome.org$%7BEXP%7D/resources/Structural_preproc/files?format=csv> | egrep "\/aseg.stats|\/lh.aparc.stats|\/rh.aparc.stats"); do NAME=$(echo $ROW | cut -d, -f1) URI=$(echo $ROW | cut -d, -f3) curl -s -k --cookie JSESSIONID=$JSESSIONID https://db.humanconnectome.org${URI}<https://db.humanconnectome.org$%7BURI%7D> done done From:hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org> [mailto:hcp-users-boun...@humanconnectome.org] On Behalf Of Jingwei Li Sent: Monday, May 8, 2017 10:29 PM To: hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org> Subject: [HCP-Users] Download aparc+aseg.nii.gz, aseg.stats, lh/rh.aparc.stats of S1200 new subjects Dear HCP experts, I understand that the CREST resource mentioned in your wiki page does not contain the files of S1200 new subjects. So I would like to know how to download the aparc+aseg in MNI space, aseg.stats, lh.aparc.stats, and rh.aparc.stats of the S1200 new subjects. I don't want to download the whole structural data package since these are the only files I need. Thank you! Regards, Jingwei _______________________________________________ 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. 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<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. 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
