For cortical results, we do not consider MNI coordinates to be sufficiently precise or unambiguous to identify the location of a result. This is partly because many/most current volume registration methods struggle to align tissue types in the face of intersubject variability in folding (this subject has a small extra gyrus, that subject has a sulcus that makes an unusual sudden turn, etc.), but also because aligning based on the anatomy does not align functional cortical areas well in many locations. The purpose of surface-based analysis is to remove this problem from the equation: by mapping individual data onto the same individual's cortical surfaces, we avoid the dependency on volume-based registration for comparing cortical signal across subjects. Since this happens before surface-based registration is involved, that means that surface registration doesn't have to worry about alignment of tissue types while it is aligning data across subjects, which makes the problem easier, and allows the use of features that correspond to functional area boundaries, without being tied to folding geometry.
The flip side of this is that different subjects ultimately have the same functional cortical area at different MNI coordinates. Taking the average across these MNI coordinates is unsatisfying, as the average could even land largely outside of the group average cortical ribbon, and loses the information of what functional area it was really tied to. For this reason, we started the BALSA website (https://balsa.wustl.edu/ , still under development), where people will be able to upload processed data in surface-based formats, so that others can download it and see exactly what part of cortex is implicated by the result. If your reasons for wanting to obtain MNI coordinates are not addressed by this explanation, please explain what your end goal is, so that we can consider how we would do it, given the realities of anatomy and functional location. Tim On Sat, May 26, 2018 at 2:45 PM, [email protected] <[email protected]> wrote: > I don't know if my question goes for your goals. I am struggling in > downloading up datasets and finding MNI coordinates. Does anyone know how > to get the coordinates from the data? It is very important for my study. > Pleaser help me out. Thank you. > > *Sent from my LG X venture, an AT&T 4G LTE smartphone* > > ------ Original message------ > *From: *[email protected] > *Date: *Sat, May 26, 2018 12:00 PM > *To: *[email protected]; > *Cc: * > *Subject:*HCP-Users Digest, Vol 66, Issue 25 > > Send HCP-Users mailing list submissions to [email protected] > <%[email protected]> > > To subscribe or unsubscribe via the World Wide Web, visit > http://lists.humanconnectome.org/mailman/listinfo/hcp-users > or, via email, send a message with subject or body 'help' to > [email protected] > <%[email protected]> > > You can reach the person managing the list at > [email protected] <%[email protected]> > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of HCP-Users digest..." > > > Today's Topics: > > 1. Re: Experiencing downloading problems (Timothy Coalson) > 2. Re: Experiencing downloading problems (Michel Thiebaut) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 25 May 2018 16:05:59 -0500 > From: Timothy Coalson > Subject: Re: [HCP-Users] Experiencing downloading problems > To: "Elam, Jennifer" > Cc: Michel Thiebaut , > "[email protected]" , > "Hileman, Michael" > Message-ID: > > Content-Type: text/plain; charset="utf-8" > > Does aspera start? If so, does it give an error message? Please post that. > > If it doesn't start, check the browser address bar and see if it shows a > puzzle piece or lego block, as it may be preventing the plugin from running > until you tell the browser to allow it. > > Tim > > > On Fri, May 25, 2018 at 5:25 AM, Elam, Jennifer wrote: > > > What browser are you using? > > > > Thanks, > > 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 > > [email protected] <[email protected]> > > www.humanconnectome.org > > > > ------------------------------ > > *From:* Michel Thiebaut > > *Sent:* Friday, May 25, 2018 1:44:34 AM > > > > *To:* Elam, Jennifer > > *Cc:* [email protected] <[email protected]> > > *Subject:* Re: [HCP-Users] Experiencing downloading problems > > > > Hi Jenn, > > > > I tried again this morning on two computers. > > I'm afraid it still doesn't work. > > > > Best > > > > mich > > > > *Michel Thiebaut de Schotten* > > Associate Professor, PhD, HDR, CNRS > > Sorbonne Universities, UPMC Univ Paris 06 > > Brain Connectivity and Behaviour Group > > Frontlab, Institut du cerveau et la moelle ?pini?re > > H?pital de la Salp?tri?re - ICM > > 47 Bvd de l'H?pital > > > > CS21414 > > 75646 PARIS CEDEX 13 > > > > Skype: michel_thiebaut_de_schotten > > phone: +33 7 83 50 81 60 <+33%207%2083%2050%2081%2060> > > http://www.bcblab.com > > http://toolkit.bcblab.com > > > > > > On Thu, May 24, 2018 at 3:33 PM, Elam, Jennifer wrote: > > > > Hi Mich, > > We believe the issue should be resolved now, please try the download > > again. Thanks for your patience! > > > > 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 > > [email protected] <[email protected]> > > www.humanconnectome.org > > > > ------------------------------ > > *From:* Michel Thiebaut > > *Sent:* Thursday, May 24, 2018 1:39:11 AM > > *To:* Elam, Jennifer > > *Cc:* [email protected] <[email protected]> > > > > *Subject:* Re: [HCP-Users] Experiencing downloading problems > > > > Hi Jenn, > > > > Thanks for getting back to me. I tried to download a single subject this > > morning again on two different computers that I previously used to download > > HCP data, and it didn't work. > > The download just doesn't start in Aspera. > > > > Thanks for letting me know when the redeployment is done. > > > > Kind regards > > > > mich > > > > *Michel Thiebaut de Schotten* > > Associate Professor, PhD, HDR, CNRS > > Sorbonne Universities, UPMC Univ Paris 06 > > Brain Connectivity and Behaviour Group > > Frontlab, Institut du cerveau et la moelle ?pini?re > > H?pital de la Salp?tri?re - ICM > > 47 Bvd de l'H?pital > > > > CS21414 > > 75646 PARIS CEDEX 13 > > > > Skype: michel_thiebaut_de_schotten > > phone: +33 7 83 50 81 60 <+33%207%2083%2050%2081%2060> > > http://www.bcblab.com > > http://toolkit.bcblab.com > > > > > > On Wed, May 23, 2018 at 11:10 PM, Elam, Jennifer wrote: > > > > Hi again Mich, > > > > Go ahead and try a test download, but the developers here have found > > another issue that might be causing the problem. For their fix to go > > through they need to schedule a redeployment of ConnectomeDB, which will > > hopefully happen tomorrow. 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 > > [email protected] <[email protected]> > > www.humanconnectome.org > > > > ------------------------------ > > *From:* [email protected] > > <[email protected]> < > > [email protected] > > <[email protected]>> on behalf of Elam, Jennifer < > > [email protected] <[email protected]>> > > *Sent:* Wednesday, May 23, 2018 11:32:18 AM > > *To:* Michel Thiebaut; [email protected] > > <[email protected]> > > *Subject:* Re: [HCP-Users] Experiencing downloading problems > > > > > > Hi Mich, > > > > Could you try the download again? We had an outage earlier this morning, > > but we are hoping that everything is working now. Let us know how it goes. > > > > > > 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 > > [email protected] <[email protected]> > > www.humanconnectome.org > > > > ------------------------------ > > *From:* [email protected] > > <[email protected]> < > > [email protected] > > <[email protected]>> on behalf of Michel Thiebaut < > > [email protected] <[email protected]>> > > *Sent:* Wednesday, May 23, 2018 4:56:46 AM > > *To:* [email protected] <[email protected]> > > *Subject:* [HCP-Users] Experiencing downloading problems > > > > Dear HCP team, > > > > I've been experiencing downloading issue today. > > I tried to download the 7T Resting-State fMRI FIX-Denoised (Extended), > > however, for some reason, the download doesn't start in Aspera. I also > > tried a single subject without success. > > I usually have no problem. > > Is it happening on your side? > > > > Thanks a lot for letting me know > > Kind regards > > > > mich > > > > > > *Michel Thiebaut de Schotten* > > Associate Professor, PhD, HDR, CNRS > > Sorbonne Universities, UPMC Univ Paris 06 > > Brain Connectivity and Behaviour Group > > Frontlab, Institut du cerveau et la moelle ?pini?re > > H?pital de la Salp?tri?re - ICM > > 47 Bvd de l'H?pital > > > > CS21414 > > 75646 PARIS CEDEX 13 > > > > Skype: michel_thiebaut_de_schotten > > phone: +33 7 83 50 81 60 <+33%207%2083%2050%2081%2060> > > http://www.bcblab.com > > http://toolkit.bcblab.com > > > > _______________________________________________ > > HCP-Users mailing list > > [email protected] <[email protected]> > > http://lists.humanconnectome.org/mailman/listinfo/hcp-users > > > > _______________________________________________ > > HCP-Users mailing list > > [email protected] <[email protected]> > > http://lists.humanconnectome.org/mailman/listinfo/hcp-users > > > > > > > > _______________________________________________ > > HCP-Users mailing list > > [email protected] <[email protected]> > > http://lists.humanconnectome.org/mailman/listinfo/hcp-users > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://lists.humanconnectome.org/pipermail/hcp-users/attachments/20180525/c4f0d224/attachment-0001.html > > ------------------------------ > > Message: 2 > Date: Sat, 26 May 2018 09:52:05 +0200 > From: Michel Thiebaut > Subject: Re: [HCP-Users] Experiencing downloading problems > To: Timothy Coalson > Cc: "[email protected]" , > "Hileman, Michael" > Message-ID: > > Content-Type: text/plain; charset="utf-8" > > Hi Timothy, > > I tried twice this morning after clearing the cache in safari > The first time it didn't work (aspera is opened but the download doesn't > start), the second time it finally started! > > Thanks for the help, > Kind regards, > > mich > > *Michel Thiebaut de Schotten* > Associate Professor, PhD, HDR, CNRS > Sorbonne Universities, UPMC Univ Paris 06 > Brain Connectivity and Behaviour Group > Frontlab, Institut du cerveau et la moelle ?pini?re > H?pital de la Salp?tri?re - ICM > 47 Bvd de l'H?pital CS21414 > 75646 <2141475646> PARIS CEDEX 13 > > Skype: michel_thiebaut_de_schotten > phone: +33 7 83 50 81 60 > <+33%207%2083%2050%2081%2060>http://www.bcblab.comhttp://toolkit.bcblab.com > > > On Fri, May 25, 2018 at 11:05 PM, Timothy Coalson wrote: > > > Does aspera start? If so, does it give an error message? Please post > > that. > > > > If it doesn't start, check the browser address bar and see if it shows a > > puzzle piece or lego block, as it may be preventing the plugin from running > > until you tell the browser to allow it. > > > > Tim > > > > > > On Fri, May 25, 2018 at 5:25 AM, Elam, Jennifer wrote: > > > >> What browser are you using? > >> > >> Thanks, > >> 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 > >> [email protected] <[email protected]> > >> www.humanconnectome.org > >> > >> ------------------------------ > >> *From:* Michel Thiebaut > >> *Sent:* Friday, May 25, 2018 1:44:34 AM > >> > >> *To:* Elam, Jennifer > >> *Cc:* [email protected] <[email protected]> > >> *Subject:* Re: [HCP-Users] Experiencing downloading problems > >> > >> Hi Jenn, > >> > >> I tried again this morning on two computers. > >> I'm afraid it still doesn't work. > >> > >> Best > >> > >> mich > >> > >> *Michel Thiebaut de Schotten* > >> Associate Professor, PhD, HDR, CNRS > >> Sorbonne Universities, UPMC Univ Paris 06 > >> Brain Connectivity and Behaviour Group > >> Frontlab, Institut du cerveau et la moelle ?pini?re > >> H?pital de la Salp?tri?re - ICM > >> 47 Bvd de l'H?pital > >> > >> CS21414 > >> 75646 PARIS CEDEX 13 > >> > >> Skype: michel_thiebaut_de_schotten > >> phone: +33 7 83 50 81 60 <+33%207%2083%2050%2081%2060> > >> http://www.bcblab.com > >> http://toolkit.bcblab.com > >> > >> > >> On Thu, May 24, 2018 at 3:33 PM, Elam, Jennifer wrote: > >> > >> Hi Mich, > >> We believe the issue should be resolved now, please try the download > >> again. Thanks for your patience! > >> > >> 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 > >> [email protected] <[email protected]> > >> www.humanconnectome.org > >> > >> ------------------------------ > >> *From:* Michel Thiebaut > >> *Sent:* Thursday, May 24, 2018 1:39:11 AM > >> *To:* Elam, Jennifer > >> *Cc:* [email protected] <[email protected]> > >> > >> *Subject:* Re: [HCP-Users] Experiencing downloading problems > >> > >> Hi Jenn, > >> > >> Thanks for getting back to me. I tried to download a single subject this > >> morning again on two different computers that I previously used to download > >> HCP data, and it didn't work. > >> The download just doesn't start in Aspera. > >> > >> Thanks for letting me know when the redeployment is done. > >> > >> Kind regards > >> > >> mich > >> > >> *Michel Thiebaut de Schotten* > >> Associate Professor, PhD, HDR, CNRS > >> Sorbonne Universities, UPMC Univ Paris 06 > >> Brain Connectivity and Behaviour Group > >> Frontlab, Institut du cerveau et la moelle ?pini?re > >> H?pital > >> > >> de la Salp?tri?re - ICM > >> 47 Bvd de l'H?pital > >> > >> CS21414 > >> 75646 PARIS CEDEX 13 > >> > >> Skype: michel_thiebaut_de_schotten > >> phone: +33 7 83 50 81 60 <+33%207%2083%2050%2081%2060> > >> http://www.bcblab.com > >> http://toolkit.bcblab.com > >> > >> > >> On Wed, May 23, 2018 at 11:10 PM, Elam, Jennifer wrote: > >> > >> Hi again Mich, > >> > >> Go ahead and try a test download, but the developers here have found > >> another issue that might be causing the problem. For their fix to go > >> through they need to schedule a redeployment of ConnectomeDB, which will > >> hopefully happen tomorrow. 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 > >> [email protected] <[email protected]> > >> www.humanconnectome.org > >> > >> ------------------------------ > >> *From:* [email protected] > >> <[email protected]> < > >> [email protected] > >> <[email protected]>> on behalf of Elam, Jennifer < > >> [email protected] <[email protected]>> > >> *Sent:* Wednesday, May 23, 2018 11:32:18 AM > >> *To:* Michel Thiebaut; [email protected] > >> <[email protected]> > >> *Subject:* Re: [HCP-Users] Experiencing downloading problems > >> > >> > >> Hi Mich, > >> > >> Could you try the download again? We had an outage earlier this morning, > >> but we are hoping that everything is working now. Let us know how it goes. > >> > >> > >> 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 > >> [email protected] <[email protected]> > >> www.humanconnectome.org > >> > >> ------------------------------ > >> *From:* [email protected] > >> <[email protected]> < > >> [email protected] > >> <[email protected]>> on behalf of Michel Thiebaut < > >> [email protected] <[email protected]>> > >> *Sent:* Wednesday, May 23, 2018 4:56:46 AM > >> *To:* [email protected] <[email protected]> > >> *Subject:* [HCP-Users] Experiencing downloading problems > >> > >> Dear HCP team, > >> > >> I've been experiencing downloading issue today. > >> I tried to download the 7T Resting-State fMRI FIX-Denoised (Extended), > >> however, for some reason, the download doesn't start in Aspera. I also > >> tried a single subject without success. > >> I usually have no problem. > >> Is it happening on your side? > >> > >> Thanks a lot for letting me know > >> Kind regards > >> > >> mich > >> > >> > >> *Michel Thiebaut de Schotten* > >> Associate Professor, PhD, HDR, CNRS > >> Sorbonne Universities, UPMC Univ Paris 06 > >> Brain Connectivity and Behaviour Group > >> Frontlab, Institut du cerveau et la moelle ?pini?re > >> H?pital de la Salp?tri?re - ICM > >> 47 Bvd de l'H?pital > >> > >> CS21414 > >> 75646 PARIS CEDEX 13 > >> > >> Skype: michel_thiebaut_de_schotten > >> phone: +33 7 83 50 81 60 <+33%207%2083%2050%2081%2060> > >> http://www.bcblab.com > >> http://toolkit.bcblab.com > >> > >> _______________________________________________ > >> HCP-Users mailing list > >> [email protected] <[email protected]> > >> http://lists.humanconnectome.org/mailman/listinfo/hcp-users > >> > >> _______________________________________________ > >> HCP-Users mailing list > >> [email protected] <[email protected]> > >> http://lists.humanconnectome.org/mailman/listinfo/hcp-users > >> > >> > >> > >> _______________________________________________ > >> HCP-Users mailing list > >> [email protected] <[email protected]> > >> http://lists.humanconnectome.org/mailman/listinfo/hcp-users > >> > > > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://lists.humanconnectome.org/pipermail/hcp-users/attachments/20180526/a5479b1c/attachment-0001.html > > ------------------------------ > > _______________________________________________ > HCP-Users mailing list > [email protected]http://lists.humanconnectome.org/mailman/listinfo/hcp-users > > > End of HCP-Users Digest, Vol 66, Issue 25 > ***************************************** > > _______________________________________________ > HCP-Users mailing list > [email protected] > http://lists.humanconnectome.org/mailman/listinfo/hcp-users > _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
