Hi - yes that's all correct. IIRC for that PTN release (as opposed to the previous one) we thought it wasn't worth having subject-specific netmat pconn files, but just put all the information in the text files.
Cheers. > On 1 Jun 2017, at 16:36, Habib Ganjgahi <h.ganjg...@gmail.com> wrote: > > Hi Steve, > > I've extracted the "netmats_3T_HCP820_MSMAll_ICAd15_ts2.tar.gz" file from the > HVP_PTN820 folder but it doesn't contain subject specific pconn files. This > is what i see inside it: > > Mnet1.pconn.nii > > Mnet2.pconn.nii > > hierarchy.png > > netmats1.txt > > netmats2.txt > > each pconn file dimension is 15x15 and each text file is a 820x225 matrix. I > think each row of the matrix corresponds to different subject netmat matrix, > Am i right? if so, is the order of rows as same as the "subjectIDs.txt" file? > > > > Bests, > > Habib > > > On Thu, Jun 1, 2017 at 3:25 PM, Stephen Smith <st...@fmrib.ox.ac.uk > <mailto:st...@fmrib.ox.ac.uk>> wrote: > Probably clearest to use both terms for clarity, e.g. "ICA maps, i.e., > ICA-based parcellations" > > > >> On 1 Jun 2017, at 15:21, Harms, Michael <mha...@wustl.edu >> <mailto:mha...@wustl.edu>> wrote: >> >> >> Would it perhaps be less confusing if the links said “CIFTI Subject-specific >> ICA maps for XXX dimensionality”, rather than “Parcellations” ? >> >> -- >> 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 <mailto:mha...@wustl.edu> >> >> From: <hcp-users-boun...@humanconnectome.org >> <mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Stephen Smith >> <st...@fmrib.ox.ac.uk <mailto:st...@fmrib.ox.ac.uk>> >> Date: Thursday, June 1, 2017 at 9:07 AM >> To: Thomas Nichols <t.e.nich...@warwick.ac.uk >> <mailto:t.e.nich...@warwick.ac.uk>> >> Cc: HCP Users <hcp-users@humanconnectome.org >> <mailto:hcp-users@humanconnectome.org>>, Habib Ganjgahi >> <h.ganjg...@gmail.com <mailto:h.ganjg...@gmail.com>> >> Subject: Re: [HCP-Users] Where are per-subject netmats? >> >> Hi - subject netmats are in the main PTN download. >> Cheers. >> >> >>> On 1 Jun 2017, at 15:05, Thomas Nichols <t.e.nich...@warwick.ac.uk >>> <mailto:t.e.nich...@warwick.ac.uk>> wrote: >>> >>> Hi Jenn, >>> >>> Sorry for the slow reply on this. We tried downloading the links you >>> pointed us to <https://db.humanconnectome.org/data/projects/HCP_1200>: >>>> >>>> The following links contain subject-specific CIFTI maps: subject-specific >>>> versions of the group-ICA parcellations, with various ICA dimensionalities >>>> applied. These are z-statistic maps generated using dual-regression. >>>> >>>> CIFTI Subject-specific Parcellations for 10-, 25-, 50-, >>>> 100-dimensionalities (57GB) >>>> <https://db.humanconnectome.org/app/action/ChooseDownloadResources?project=HCP_Resources&resource=GroupAvg&filePath=HCP_S900_PTNmaps_d15_25_50_100.zip> >>>> CIFTI Subject-specific Parcellations for 200-dimensionality (55GB) >>>> <https://db.humanconnectome.org/app/action/ChooseDownloadResources?project=HCP_Resources&resource=GroupAvg&filePath=HCP_S900_PTNmaps_d200.zip> >>>> CIFTI Subject-specific Parcellations for 300-dimensionality (85GB >>>> <https://db.humanconnectome.org/app/action/ChooseDownloadResources?project=HCP_Resources&resource=GroupAvg&filePath=HCP_S900_PTNmaps_d300.zip>but >>>> they only contain the *dtseries.nii, while in previous releases there >>>> were *pconn.nii files that had the "NetMat" matrices. >>> >>> To be clear, the previous *pconn.nii files had #dim rows, #dim cols, while >>> these *dtseries have #Elm rows and #dim cols. >>> >>> Is there some place that NetMats are currently released? I'm not finding >>> them. I know they're not impossible to recreate but I'd like to minimize >>> effort and chance of error by using the standard released product. >>> >>> -Tom >>> >>> >>> PS: Note that the webpage is incorrectly indicates that the parcellation >>> size is 10, 25, 50 and 100, when instead it is 15, 25, 50 & 100. >>> >>> >>> >>> On Tue, May 16, 2017 at 1:12 PM, Elam, Jennifer <e...@wustl.edu >>> <mailto:e...@wustl.edu>> wrote: >>>> Hi Tom, >>>> Due to size, we have the individual subject parcellations available in >>>> three separate downloads for different dimensionalities under the main PTN >>>> download on this page in the >>>> DB:https://db.humanconnectome.org/data/projects/HCP_1200 >>>> <https://db.humanconnectome.org/data/projects/HCP_1200> >>>> >>>> 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 <mailto:e...@wustl.edu> >>>> www.humanconnectome.org <http://www.humanconnectome.org/> >>>> >>>> From:hcp-users-boun...@humanconnectome.org >>>> <mailto:hcp-users-boun...@humanconnectome.org> >>>> <hcp-users-boun...@humanconnectome.org >>>> <mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Thomas >>>> Nichols <t.e.nich...@warwick.ac.uk <mailto:t.e.nich...@warwick.ac.uk>> >>>> Sent: Tuesday, May 16, 2017 5:16:15 AM >>>> To: HCP Users >>>> Subject: [HCP-Users] Where are per-subject netmats? >>>> >>>> Hi folks, >>>> >>>> When poking through the PTN download for the netmats, we're having trouble >>>> finding the netmat for each subject. >>>> >>>> As per the S1200 release manual >>>> <http://www.humanconnectome.org/documentation/S1200/HCP_S1200_Release_Reference_Manual.pdf>, >>>> pp 99-100, it says when we extract one of the flies like >>>> netmats_3T_HCP820_MSMAll_ICAd*_ts*.tar.gz >>>> we should get a *_netmat1 directory filled with "One netmat file per >>>> subject, computed using full correlation, Z-transformed", and another >>>> variant in *_netmat2. >>>> >>>> Instead, we find that these tar.gz files only have 5 files, in a directory >>>> netmats/3T_HCP820_MSMAll_ICAd*_ts*. Two of these are netmat{1,2}.txt >>>> files, but these are a single column and have a very strange number of >>>> rows (e.g. for d=50 it has 820 rows). (There are also Mnet?.pconn.nii >>>> files, but these are tiny). >>>> >>>> Where can we find the per-subject netmat files that were in previous >>>> releases? >>>> >>>> -Tom >>>> >>>> >>>> -- >>>> __________________________________________________________ >>>> Thomas Nichols, PhD >>>> Professor, Head of Neuroimaging Statistics >>>> Department of Statistics & Warwick Manufacturing Group >>>> University of Warwick, Coventry CV4 7AL, United Kingdom >>>> >>>> Web: http://warwick.ac.uk/tenichols <http://warwick.ac.uk/tenichols> >>>> Email: t.e.nich...@warwick.ac.uk <mailto:t.e.nich...@warwick.ac.uk> >>>> Tel, Stats: +44 24761 51086, WMG: +44 24761 50752 >>>> Fx, +44 24 7652 4532 <tel:024%207652%204532> >>>> >>>> >>>> _______________________________________________ >>>> HCP-Users mailing list >>>> HCP-Users@humanconnectome.org <mailto:HCP-Users@humanconnectome.org> >>>> http://lists.humanconnectome.org/mailman/listinfo/hcp-users >>>> <http://lists.humanconnectome.org/mailman/listinfo/hcp-users> >>> >>> >>> -- >>> __________________________________________________________ >>> Thomas Nichols, PhD >>> Professor of Neuroimaging Statistics >>> Oxford Big Data Institute >>> Li Ka Shing Centre for Health Information and Discovery >>> University of Oxford >>> >>> Interim Contact Info: >>> Web: http://warwick.ac.uk/tenichols <http://warwick.ac.uk/tenichols> >>> Email: t.e.nich...@warwick.ac.uk <mailto:t.e.nich...@warwick.ac.uk> >>> >>> _______________________________________________ >>> HCP-Users mailing list >>> HCP-Users@humanconnectome.org <mailto:HCP-Users@humanconnectome.org> >>> http://lists.humanconnectome.org/mailman/listinfo/hcp-users >>> <http://lists.humanconnectome.org/mailman/listinfo/hcp-users> >> >> --------------------------------------------------------------------------- >> Stephen M. Smith, Professor of Biomedical Engineering >> Head of Analysis, Oxford University FMRIB Centre >> >> FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK >> +44 (0) 1865 222726 <tel:01865%20222726> (fax 222717) >> st...@fmrib.ox.ac.uk <mailto:st...@fmrib.ox.ac.uk> >> http://www.fmrib.ox.ac.uk/~steve <http://www.fmrib.ox.ac.uk/~steve> >> --------------------------------------------------------------------------- >> >> Stop the cultural destruction of Tibet <http://smithinks.net/> >> >> >> >> >> >> _______________________________________________ >> HCP-Users mailing list >> HCP-Users@humanconnectome.org <mailto:HCP-Users@humanconnectome.org> >> http://lists.humanconnectome.org/mailman/listinfo/hcp-users >> <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. > > > --------------------------------------------------------------------------- > Stephen M. Smith, Professor of Biomedical Engineering > Head of Analysis, Oxford University FMRIB Centre > > FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK > +44 (0) 1865 222726 <tel:01865%20222726> (fax 222717) > st...@fmrib.ox.ac.uk <mailto:st...@fmrib.ox.ac.uk> > http://www.fmrib.ox.ac.uk/~steve <http://www.fmrib.ox.ac.uk/~steve> > --------------------------------------------------------------------------- > > Stop the cultural destruction of Tibet <http://smithinks.net/> > > > > > > --------------------------------------------------------------------------- Stephen M. Smith, Professor of Biomedical Engineering Head of Analysis, Oxford University FMRIB Centre FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK +44 (0) 1865 222726 (fax 222717) st...@fmrib.ox.ac.uk http://www.fmrib.ox.ac.uk/~steve <http://www.fmrib.ox.ac.uk/~steve> --------------------------------------------------------------------------- Stop the cultural destruction of Tibet <http://smithinks.net/> _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
