Re: [HCP-Users] Myelin Mapping Metrics
Dear Matt, So sorry, I didn't realize metrics were stored in those files (I was looking for a text file like FreeSurfer's aseg.stats). Thank you for the clarification! Sincerely, Anna On 12/20/18 11:26 AM, Glasser, Matthew wrote: > Do you mean GIFTI surface files? > > Matt. > > On 12/20/18, 11:33 AM, "hcp-users-boun...@humanconnectome.org on behalf of > Anna Chen" amc...@ucsd.edu> wrote: > >> Dear experts, >> >> I've processed my data through the HCP structural pipeline >> (prefreesurfer, freesurfer, and postfreesurfer), and was wondering if >> there is a way to extract metrics from the myelin mapping data. I >> noticed here, >> http://brainvis.wustl.edu/wiki/index.php/Caret:Operations/MyelinMapping, >> caret_command was previously used to obtain left and right myelin >> mapping metrics, but these output files don't seem to be produced by the >> current postfreesurfer step. Is there another command I can run to do so? >> >> Sincerely, >> >> Anna >> >> -- >> >> Anna Chen >> Staff Research Associate >> Collaboratory for NeuroImaging Research & Development (CNIRD) >> University of California, San Diego (UCSD) >> 9500 Gilman Dr., #0738; La Jolla, CA 92093-0738 >> Phone: 858-246-0615; Fax: 858-246-0556 >> Email: amc...@ucsd.edu >> >> ___ >> 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. -- Anna Chen Staff Research Associate Collaboratory for NeuroImaging Research & Development (CNIRD) University of California, San Diego (UCSD) 9500 Gilman Dr., #0738; La Jolla, CA 92093-0738 Phone: 858-246-0615; Fax: 858-246-0556 Email: amc...@ucsd.edu ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
Re: [HCP-Users] Myelin Mapping Metrics
Do you mean GIFTI surface files? Matt. On 12/20/18, 11:33 AM, "hcp-users-boun...@humanconnectome.org on behalf of Anna Chen" wrote: >Dear experts, > >I've processed my data through the HCP structural pipeline >(prefreesurfer, freesurfer, and postfreesurfer), and was wondering if >there is a way to extract metrics from the myelin mapping data. I >noticed here, >http://brainvis.wustl.edu/wiki/index.php/Caret:Operations/MyelinMapping, >caret_command was previously used to obtain left and right myelin >mapping metrics, but these output files don't seem to be produced by the >current postfreesurfer step. Is there another command I can run to do so? > >Sincerely, > >Anna > >-- > >Anna Chen >Staff Research Associate >Collaboratory for NeuroImaging Research & Development (CNIRD) >University of California, San Diego (UCSD) >9500 Gilman Dr., #0738; La Jolla, CA 92093-0738 >Phone: 858-246-0615; Fax: 858-246-0556 >Email: amc...@ucsd.edu > >___ >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
Re: [HCP-Users] Myelin Mapping Metrics
Dear experts, I've processed my data through the HCP structural pipeline (prefreesurfer, freesurfer, and postfreesurfer), and was wondering if there is a way to extract metrics from the myelin mapping data. I noticed here, http://brainvis.wustl.edu/wiki/index.php/Caret:Operations/MyelinMapping, caret_command was previously used to obtain left and right myelin mapping metrics, but these output files don't seem to be produced by the current postfreesurfer step. Is there another command I can run to do so? Sincerely, Anna -- Anna Chen Staff Research Associate Collaboratory for NeuroImaging Research & Development (CNIRD) University of California, San Diego (UCSD) 9500 Gilman Dr., #0738; La Jolla, CA 92093-0738 Phone: 858-246-0615; Fax: 858-246-0556 Email: amc...@ucsd.edu ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
Re: [HCP-Users] Myelin mapping with FLAIR
Yes. Do most of your T1w scans look like that? I would get that issue fixed (i.e. acquire the T1w scan sagittally). Matt. From: Barbara Kreilkamp <bakk@googlemail.com<mailto:bakk@googlemail.com>> Date: Friday, November 20, 2015 at 5:37 AM To: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>> Cc: Gaurav Patel <gauravpa...@gmail.com<mailto:gauravpa...@gmail.com>>, "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Subject: Re: [HCP-Users] Myelin mapping with FLAIR Dear Gaurav and Matt, Thank you for your quick response. Unfortunately yes, the T1w scan does not include the cerebellum very well, just the way we managed to acquire the data here at the hospital... So if I understand correctly with this comparison technique we'd be initially targeting a qualitative evaluation? Thank you. Best wishes, Barbara On Fri, Nov 20, 2015 at 12:34 AM, Glasser, Matthew <glass...@wustl.edu<mailto:glass...@wustl.edu>> wrote: I didn¹t see anything obvious from the raw images, but I recommend you run the HCP pipelines on the T1w and T2w data, register the B1 map to the processed data, and map the B1 map onto the surface using the myelin mapping volume to surface algorithm (see the PostFreeSurfer pipeline for how to do it). Then post a comparison between the myelin map and the B1 map. Also, it seemed like the bottom of the T1w image was cut off. Is that typical? Matt. On 11/19/15, 11:18 AM, "hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org> on behalf of Gaurav Patel" <hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org> on behalf of gauravpa...@gmail.com<mailto:gauravpa...@gmail.com>> wrote: >Hi! I'm curious to see how the B1 map will help as well. Its been a >while since our team has thought about this, but I'll show this to our MR >physicist and let you know. We are continuing to pursue obtaining a GE >MPRAGE to see if that would help, but its been slow going. When we do >and are able to run some tests, we'll post the results > >__ > gaurav patel > gauravpa...@gmail.com<mailto:gauravpa...@gmail.com> > www.neurofreak.net<http://www.neurofreak.net> > > > > >On Nov 19, 2015, at 11:27 AM, Barbara Kreilkamp wrote: > >> Dear all, >> >> We've now been able to acquire a sagittal B1-Map from the GE templates >>protocols (GE 3Tesla 750 Discovery). >> I hope this is the right sequence that would tell us where the >>high-intensity artifact in the GE myelin maps come from? >> >> The raw data is here: >> https://app.box.com/s/3t3o77b1ksrhgfs3hgwi1ryodj0hubp0 >> >> These are the related posts (below) and here: >>https://www.mail-archive.com/hcp-users@humanconnectome.org/msg01611.html >> >> The GE physicist has told me that the XETA and CUBE sequence are quite >>different now however as well. >> I wonder if you could please guide me as to whether the B1-Map looks >>usable (unfortunately I have seen some motion/ringing artifact in this >>participant, which we normally don't have an issue with) and in which >>way I could analyze the issue. >> >> Thank you so much, >> Best wishes, >> Barbara >> >> >> >> On 22/06/2015 21:13, Glasser, Matthew wrote: >>> I¹ve not done that, but perhaps someone else has. >>> >>> Peace, >>> >>> Matt. >>> >>> From: Michael Dwyer <mgdw...@bnac.net<mailto:mgdw...@bnac.net>> >>> Date: Monday, June 22, 2015 at 3:12 PM >>> To: Matt Glasser <glass...@wusm.wustl.edu<mailto:glass...@wusm.wustl.edu>> >>> Cc: Gaurav Patel <gauravpa...@gmail.com<mailto:gauravpa...@gmail.com>>, HCP >>> Users >>><HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org>> >>> Subject: Re: [HCP-Users] Myelin mapping with FLAIR >>> >>> Thanks. By the way, have you been able to see any cortical >>>demyelination in neurological diseases like multiple sclerosis with >>>this myelin mapping technique, or only used it on healthy controls and >>>neuropsychiatric disease so far? >>> >>> On Mon, Jun 22, 2015 at 11:26 AM, Glasser, Matthew >>><glass...@wusm.wustl.edu<mailto:glass...@wusm.wustl.edu>> wrote: >>> For the moment one just treats the FLAIR as a T2w scan for the >>>purposes of the pipelines. >>> >>> Peace, >>> >>> Matt. >>> >>> From: >>> <hcp-users-boun...@hum
Re: [HCP-Users] Myelin mapping with FLAIR
Hi! I'm curious to see how the B1 map will help as well. Its been a while since our team has thought about this, but I'll show this to our MR physicist and let you know. We are continuing to pursue obtaining a GE MPRAGE to see if that would help, but its been slow going. When we do and are able to run some tests, we'll post the results __ gaurav patel gauravpa...@gmail.com www.neurofreak.net On Nov 19, 2015, at 11:27 AM, Barbara Kreilkamp wrote: > Dear all, > > We've now been able to acquire a sagittal B1-Map from the GE templates > protocols (GE 3Tesla 750 Discovery). > I hope this is the right sequence that would tell us where the high-intensity > artifact in the GE myelin maps come from? > > The raw data is here: > https://app.box.com/s/3t3o77b1ksrhgfs3hgwi1ryodj0hubp0 > > These are the related posts (below) and here: > https://www.mail-archive.com/hcp-users@humanconnectome.org/msg01611.html > > The GE physicist has told me that the XETA and CUBE sequence are quite > different now however as well. > I wonder if you could please guide me as to whether the B1-Map looks usable > (unfortunately I have seen some motion/ringing artifact in this participant, > which we normally don't have an issue with) and in which way I could analyze > the issue. > > Thank you so much, > Best wishes, > Barbara > > > > On 22/06/2015 21:13, Glasser, Matthew wrote: >> I’ve not done that, but perhaps someone else has. >> >> Peace, >> >> Matt. >> >> From: Michael Dwyer <mgdw...@bnac.net> >> Date: Monday, June 22, 2015 at 3:12 PM >> To: Matt Glasser <glass...@wusm.wustl.edu> >> Cc: Gaurav Patel <gauravpa...@gmail.com>, HCP Users >> <HCP-Users@humanconnectome.org> >> Subject: Re: [HCP-Users] Myelin mapping with FLAIR >> >> Thanks. By the way, have you been able to see any cortical demyelination in >> neurological diseases like multiple sclerosis with this myelin mapping >> technique, or only used it on healthy controls and neuropsychiatric disease >> so far? >> >> On Mon, Jun 22, 2015 at 11:26 AM, Glasser, Matthew <glass...@wusm.wustl.edu> >> wrote: >> For the moment one just treats the FLAIR as a T2w scan for the purposes of >> the pipelines. >> >> Peace, >> >> Matt. >> >> From: <hcp-users-boun...@humanconnectome.org> on behalf of Michael Dwyer >> <mgdw...@bnac.net> >> Date: Sunday, June 21, 2015 at 8:24 PM >> To: Gaurav Patel <gauravpa...@gmail.com> >> >> Cc: HCP Users <HCP-Users@humanconnectome.org> >> Subject: Re: [HCP-Users] Myelin mapping with FLAIR >> >> Thanks, Gaurav, I would be very grateful for any updates on your progress. >> >> On Sun, Jun 21, 2015 at 3:41 PM, Gaurav Patel <gauravpa...@gmail.com> wrote: >> FYI we're still working on this problem; I'm hoping for a meaningful update >> soon >> >> _ >> gaurav patel >> gauravpa...@gmail.com >> www.neurofreak.net >> >> On Jun 21, 2015, at 3:04 PM, Harms, Michael <mha...@wustl.edu> wrote: >> >>> >>> I don't know. If the myelin mapping isn't working quite as expected with >>> T1/T2w scans on GE, then its really hard to know what to expect if you use >>> FLAIR instead of T2w. >>> >>> 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: Michael Dwyer <mgdw...@bnac.net> >>> Date: Sunday, June 21, 2015 11:17 AM >>> To: "Harms, Michael" <mha...@wustl.edu> >>> Cc: HCP Users <HCP-Users@humanconnectome.org> >>> Subject: Re: [HCP-Users] Myelin mapping with FLAIR >>> >>> Thanks, I saw those. We'll certainly have to deal with those issues if we >>> want to do this. >>> >>> Other than that, though, would you recommend doing anything differently >>> with FLAIR than with T2? >>> >>> Best, >>> Mike >>> >>> On Fri, Jun 19, 2015 at 10:19 PM, Harms, Michael <mha...@wustl.edu> wrote: >>> >>> Take a look also at the recent posts. There are unfortunately some >>> unresolve
Re: [HCP-Users] Myelin mapping with FLAIR
For the moment one just treats the FLAIR as a T2w scan for the purposes of the pipelines. Peace, Matt. From: hcp-users-boun...@humanconnectome.org on behalf of Michael Dwyer mgdw...@bnac.net Date: Sunday, June 21, 2015 at 8:24 PM To: Gaurav Patel gauravpa...@gmail.com Cc: HCP Users HCP-Users@humanconnectome.org Subject: Re: [HCP-Users] Myelin mapping with FLAIR Thanks, Gaurav, I would be very grateful for any updates on your progress. On Sun, Jun 21, 2015 at 3:41 PM, Gaurav Patel gauravpa...@gmail.com wrote: FYI we're still working on this problem; I'm hoping for a meaningful update soon _ gaurav patel gauravpa...@gmail.com www.neurofreak.net On Jun 21, 2015, at 3:04 PM, Harms, Michael mha...@wustl.edu wrote: I don't know. If the myelin mapping isn't working quite as expected with T1/T2w scans on GE, then its really hard to know what to expect if you use FLAIR instead of T2w. 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: Michael Dwyer mgdw...@bnac.net Date: Sunday, June 21, 2015 11:17 AM To: Harms, Michael mha...@wustl.edu Cc: HCP Users HCP-Users@humanconnectome.org Subject: Re: [HCP-Users] Myelin mapping with FLAIR Thanks, I saw those. We'll certainly have to deal with those issues if we want to do this. Other than that, though, would you recommend doing anything differently with FLAIR than with T2? Best, Mike On Fri, Jun 19, 2015 at 10:19 PM, Harms, Michael mha...@wustl.edu wrote: Take a look also at the recent posts. There are unfortunately some unresolved issues about myelin maps acquired on the GE platform not looking the same as they do when derived from Siemens data. 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: Michael Dwyer mgdw...@bnac.net Date: Thursday, June 18, 2015 4:25 PM To: Gordon Xu junqian...@mssm.edu Cc: HCP Users HCP-Users@humanconnectome.org Subject: Re: [HCP-Users] Myelin mapping with FLAIR Thanks for the quick reply! Unfortunately, we have a GE scanner, not a Siemens. Any advice for that? Also any different recommendations for the post-processing when using FLAIR? Best, Mike On Thu, Jun 18, 2015 at 5:04 PM, Xu, Junqian junqian...@mssm.edu wrote: You can take a look at the UK Biobank project FLAIR protocol first and start your site-specific piloting from there. http://users.fmrib.ox.ac.uk/~steve/BiobankPiloting/ On Jun 18, 2015, at 10:56 AM, Michael Dwyer mgdw...@bnac.net wrote: Dear HCP experts, First, I would like to thank you all for a great and informative course last week. I really enjoyed the interleaved lectures and practicals, and everything was extremely well organized I think Matt had mentioned during the course that the T1/T2 myelin mapping could also work with FLAIR. We are acquiring a hi-res 3D-FLAIR clinically on a GE scanner, and I was hoping you could give some pointers on the best way to acquire it. I assume we should avoid pre-scan re-calibration, but is there anything else special we should do? Thanks in advance. Best, Mike -- Michael G. Dwyer, Ph.D. Assistant Professor of Neurology and Biomedical Informatics Director of Technical Imaging Development Buffalo Neuroimaging Analysis Center University at Buffalo 100 High St. Buffalo NY 14203 mgdw...@bnac.net (716) 859-7065 ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users -- Michael G. Dwyer, Ph.D. Assistant Professor of Neurology and Biomedical Informatics Director of Technical Imaging Development Buffalo Neuroimaging Analysis Center University at Buffalo 100 High St. Buffalo NY 14203 mgdw...@bnac.net (716) 859-7065 ___ 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. -- Michael G. Dwyer, Ph.D. Assistant Professor of Neurology
Re: [HCP-Users] Myelin mapping with FLAIR
Thanks. By the way, have you been able to see any cortical demyelination in neurological diseases like multiple sclerosis with this myelin mapping technique, or only used it on healthy controls and neuropsychiatric disease so far? On Mon, Jun 22, 2015 at 11:26 AM, Glasser, Matthew glass...@wusm.wustl.edu wrote: For the moment one just treats the FLAIR as a T2w scan for the purposes of the pipelines. Peace, Matt. From: hcp-users-boun...@humanconnectome.org on behalf of Michael Dwyer mgdw...@bnac.net Date: Sunday, June 21, 2015 at 8:24 PM To: Gaurav Patel gauravpa...@gmail.com Cc: HCP Users HCP-Users@humanconnectome.org Subject: Re: [HCP-Users] Myelin mapping with FLAIR Thanks, Gaurav, I would be very grateful for any updates on your progress. On Sun, Jun 21, 2015 at 3:41 PM, Gaurav Patel gauravpa...@gmail.com wrote: FYI we're still working on this problem; I'm hoping for a meaningful update soon _ gaurav patel gauravpa...@gmail.com www.neurofreak.net On Jun 21, 2015, at 3:04 PM, Harms, Michael mha...@wustl.edu wrote: I don't know. If the myelin mapping isn't working quite as expected with T1/T2w scans on GE, then its really hard to know what to expect if you use FLAIR instead of T2w. 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: Michael Dwyer mgdw...@bnac.net Date: Sunday, June 21, 2015 11:17 AM To: Harms, Michael mha...@wustl.edu Cc: HCP Users HCP-Users@humanconnectome.org Subject: Re: [HCP-Users] Myelin mapping with FLAIR Thanks, I saw those. We'll certainly have to deal with those issues if we want to do this. Other than that, though, would you recommend doing anything differently with FLAIR than with T2? Best, Mike On Fri, Jun 19, 2015 at 10:19 PM, Harms, Michael mha...@wustl.edu wrote: Take a look also at the recent posts. There are unfortunately some unresolved issues about myelin maps acquired on the GE platform not looking the same as they do when derived from Siemens data. 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: Michael Dwyer mgdw...@bnac.net Date: Thursday, June 18, 2015 4:25 PM To: Gordon Xu junqian...@mssm.edu Cc: HCP Users HCP-Users@humanconnectome.org Subject: Re: [HCP-Users] Myelin mapping with FLAIR Thanks for the quick reply! Unfortunately, we have a GE scanner, not a Siemens. Any advice for that? Also any different recommendations for the post-processing when using FLAIR? Best, Mike On Thu, Jun 18, 2015 at 5:04 PM, Xu, Junqian junqian...@mssm.edu wrote: You can take a look at the UK Biobank project FLAIR protocol first and start your site-specific piloting from there. http://users.fmrib.ox.ac.uk/~steve/BiobankPiloting/ On Jun 18, 2015, at 10:56 AM, Michael Dwyer mgdw...@bnac.net wrote: Dear HCP experts, First, I would like to thank you all for a great and informative course last week. I really enjoyed the interleaved lectures and practicals, and everything was extremely well organized I think Matt had mentioned during the course that the T1/T2 myelin mapping could also work with FLAIR. We are acquiring a hi-res 3D-FLAIR clinically on a GE scanner, and I was hoping you could give some pointers on the best way to acquire it. I assume we should avoid pre-scan re-calibration, but is there anything else special we should do? Thanks in advance. Best, Mike -- Michael G. Dwyer, Ph.D. Assistant Professor of Neurology and Biomedical Informatics Director of Technical Imaging Development Buffalo Neuroimaging Analysis Center University at Buffalo 100 High St. Buffalo NY 14203 mgdw...@bnac.net (716) 859-7065 ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users -- Michael G. Dwyer, Ph.D. Assistant Professor of Neurology and Biomedical Informatics Director of Technical Imaging Development Buffalo Neuroimaging Analysis Center University at Buffalo 100 High St. Buffalo NY 14203 mgdw...@bnac.net (716) 859-7065 ___ 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
Re: [HCP-Users] Myelin mapping with FLAIR
I’ve not done that, but perhaps someone else has. Peace, Matt. From: Michael Dwyer mgdw...@bnac.net Date: Monday, June 22, 2015 at 3:12 PM To: Matt Glasser glass...@wusm.wustl.edu Cc: Gaurav Patel gauravpa...@gmail.com, HCP Users HCP-Users@humanconnectome.org Subject: Re: [HCP-Users] Myelin mapping with FLAIR Thanks. By the way, have you been able to see any cortical demyelination in neurological diseases like multiple sclerosis with this myelin mapping technique, or only used it on healthy controls and neuropsychiatric disease so far? On Mon, Jun 22, 2015 at 11:26 AM, Glasser, Matthew glass...@wusm.wustl.edu wrote: For the moment one just treats the FLAIR as a T2w scan for the purposes of the pipelines. Peace, Matt. From: hcp-users-boun...@humanconnectome.org on behalf of Michael Dwyer mgdw...@bnac.net Date: Sunday, June 21, 2015 at 8:24 PM To: Gaurav Patel gauravpa...@gmail.com Cc: HCP Users HCP-Users@humanconnectome.org Subject: Re: [HCP-Users] Myelin mapping with FLAIR Thanks, Gaurav, I would be very grateful for any updates on your progress. On Sun, Jun 21, 2015 at 3:41 PM, Gaurav Patel gauravpa...@gmail.com wrote: FYI we're still working on this problem; I'm hoping for a meaningful update soon _ gaurav patel gauravpa...@gmail.com www.neurofreak.net On Jun 21, 2015, at 3:04 PM, Harms, Michael mha...@wustl.edu wrote: I don't know. If the myelin mapping isn't working quite as expected with T1/T2w scans on GE, then its really hard to know what to expect if you use FLAIR instead of T2w. 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: Michael Dwyer mgdw...@bnac.net Date: Sunday, June 21, 2015 11:17 AM To: Harms, Michael mha...@wustl.edu Cc: HCP Users HCP-Users@humanconnectome.org Subject: Re: [HCP-Users] Myelin mapping with FLAIR Thanks, I saw those. We'll certainly have to deal with those issues if we want to do this. Other than that, though, would you recommend doing anything differently with FLAIR than with T2? Best, Mike On Fri, Jun 19, 2015 at 10:19 PM, Harms, Michael mha...@wustl.edu wrote: Take a look also at the recent posts. There are unfortunately some unresolved issues about myelin maps acquired on the GE platform not looking the same as they do when derived from Siemens data. 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: Michael Dwyer mgdw...@bnac.net Date: Thursday, June 18, 2015 4:25 PM To: Gordon Xu junqian...@mssm.edu Cc: HCP Users HCP-Users@humanconnectome.org Subject: Re: [HCP-Users] Myelin mapping with FLAIR Thanks for the quick reply! Unfortunately, we have a GE scanner, not a Siemens. Any advice for that? Also any different recommendations for the post-processing when using FLAIR? Best, Mike On Thu, Jun 18, 2015 at 5:04 PM, Xu, Junqian junqian...@mssm.edu wrote: You can take a look at the UK Biobank project FLAIR protocol first and start your site-specific piloting from there. http://users.fmrib.ox.ac.uk/~steve/BiobankPiloting/ On Jun 18, 2015, at 10:56 AM, Michael Dwyer mgdw...@bnac.net wrote: Dear HCP experts, First, I would like to thank you all for a great and informative course last week. I really enjoyed the interleaved lectures and practicals, and everything was extremely well organized I think Matt had mentioned during the course that the T1/T2 myelin mapping could also work with FLAIR. We are acquiring a hi-res 3D-FLAIR clinically on a GE scanner, and I was hoping you could give some pointers on the best way to acquire it. I assume we should avoid pre-scan re-calibration, but is there anything else special we should do? Thanks in advance. Best, Mike -- Michael G. Dwyer, Ph.D. Assistant Professor of Neurology and Biomedical Informatics Director of Technical Imaging Development Buffalo Neuroimaging Analysis Center University at Buffalo 100 High St. Buffalo NY 14203 mgdw...@bnac.net (716) 859-7065 ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users -- Michael G. Dwyer, Ph.D. Assistant Professor of Neurology and Biomedical Informatics Director of Technical Imaging Development Buffalo Neuroimaging Analysis Center University at Buffalo 100 High St. Buffalo NY 14203 mgdw...@bnac.net (716) 859-7065
Re: [HCP-Users] Myelin mapping with FLAIR
Thanks, I saw those. We'll certainly have to deal with those issues if we want to do this. Other than that, though, would you recommend doing anything differently with FLAIR than with T2? Best, Mike On Fri, Jun 19, 2015 at 10:19 PM, Harms, Michael mha...@wustl.edu wrote: Take a look also at the recent posts. There are unfortunately some unresolved issues about myelin maps acquired on the GE platform not looking the same as they do when derived from Siemens data. 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: Michael Dwyer mgdw...@bnac.net Date: Thursday, June 18, 2015 4:25 PM To: Gordon Xu junqian...@mssm.edu Cc: HCP Users HCP-Users@humanconnectome.org Subject: Re: [HCP-Users] Myelin mapping with FLAIR Thanks for the quick reply! Unfortunately, we have a GE scanner, not a Siemens. Any advice for that? Also any different recommendations for the post-processing when using FLAIR? Best, Mike On Thu, Jun 18, 2015 at 5:04 PM, Xu, Junqian junqian...@mssm.edu wrote: You can take a look at the UK Biobank project FLAIR protocol first and start your site-specific piloting from there. http://users.fmrib.ox.ac.uk/~steve/BiobankPiloting/ On Jun 18, 2015, at 10:56 AM, Michael Dwyer mgdw...@bnac.net wrote: Dear HCP experts, First, I would like to thank you all for a great and informative course last week. I really enjoyed the interleaved lectures and practicals, and everything was extremely well organized I think Matt had mentioned during the course that the T1/T2 myelin mapping could also work with FLAIR. We are acquiring a hi-res 3D-FLAIR clinically on a GE scanner, and I was hoping you could give some pointers on the best way to acquire it. I assume we should avoid pre-scan re-calibration, but is there anything else special we should do? Thanks in advance. Best, Mike -- Michael G. Dwyer, Ph.D. Assistant Professor of Neurology and Biomedical Informatics Director of Technical Imaging Development Buffalo Neuroimaging Analysis Center University at Buffalo 100 High St. Buffalo NY 14203 mgdw...@bnac.net (716) 859-7065 ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users -- Michael G. Dwyer, Ph.D. Assistant Professor of Neurology and Biomedical Informatics Director of Technical Imaging Development Buffalo Neuroimaging Analysis Center University at Buffalo 100 High St. Buffalo NY 14203 mgdw...@bnac.net (716) 859-7065 ___ 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. -- Michael G. Dwyer, Ph.D. Assistant Professor of Neurology and Biomedical Informatics Director of Technical Imaging Development Buffalo Neuroimaging Analysis Center University at Buffalo 100 High St. Buffalo NY 14203 mgdw...@bnac.net (716) 859-7065 ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
Re: [HCP-Users] Myelin mapping with FLAIR
Thanks, Gaurav, I would be very grateful for any updates on your progress. On Sun, Jun 21, 2015 at 3:41 PM, Gaurav Patel gauravpa...@gmail.com wrote: FYI we're still working on this problem; I'm hoping for a meaningful update soon _ gaurav patel gauravpa...@gmail.com www.neurofreak.net On Jun 21, 2015, at 3:04 PM, Harms, Michael mha...@wustl.edu wrote: I don't know. If the myelin mapping isn't working quite as expected with T1/T2w scans on GE, then its really hard to know what to expect if you use FLAIR instead of T2w. 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: Michael Dwyer mgdw...@bnac.net Date: Sunday, June 21, 2015 11:17 AM To: Harms, Michael mha...@wustl.edu Cc: HCP Users HCP-Users@humanconnectome.org Subject: Re: [HCP-Users] Myelin mapping with FLAIR Thanks, I saw those. We'll certainly have to deal with those issues if we want to do this. Other than that, though, would you recommend doing anything differently with FLAIR than with T2? Best, Mike On Fri, Jun 19, 2015 at 10:19 PM, Harms, Michael mha...@wustl.edu wrote: Take a look also at the recent posts. There are unfortunately some unresolved issues about myelin maps acquired on the GE platform not looking the same as they do when derived from Siemens data. 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: Michael Dwyer mgdw...@bnac.net Date: Thursday, June 18, 2015 4:25 PM To: Gordon Xu junqian...@mssm.edu Cc: HCP Users HCP-Users@humanconnectome.org Subject: Re: [HCP-Users] Myelin mapping with FLAIR Thanks for the quick reply! Unfortunately, we have a GE scanner, not a Siemens. Any advice for that? Also any different recommendations for the post-processing when using FLAIR? Best, Mike On Thu, Jun 18, 2015 at 5:04 PM, Xu, Junqian junqian...@mssm.edu wrote: You can take a look at the UK Biobank project FLAIR protocol first and start your site-specific piloting from there. http://users.fmrib.ox.ac.uk/~steve/BiobankPiloting/ On Jun 18, 2015, at 10:56 AM, Michael Dwyer mgdw...@bnac.net wrote: Dear HCP experts, First, I would like to thank you all for a great and informative course last week. I really enjoyed the interleaved lectures and practicals, and everything was extremely well organized I think Matt had mentioned during the course that the T1/T2 myelin mapping could also work with FLAIR. We are acquiring a hi-res 3D-FLAIR clinically on a GE scanner, and I was hoping you could give some pointers on the best way to acquire it. I assume we should avoid pre-scan re-calibration, but is there anything else special we should do? Thanks in advance. Best, Mike -- Michael G. Dwyer, Ph.D. Assistant Professor of Neurology and Biomedical Informatics Director of Technical Imaging Development Buffalo Neuroimaging Analysis Center University at Buffalo 100 High St. Buffalo NY 14203 mgdw...@bnac.net (716) 859-7065 ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users -- Michael G. Dwyer, Ph.D. Assistant Professor of Neurology and Biomedical Informatics Director of Technical Imaging Development Buffalo Neuroimaging Analysis Center University at Buffalo 100 High St. Buffalo NY 14203 mgdw...@bnac.net (716) 859-7065 ___ 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. -- Michael G. Dwyer, Ph.D. Assistant Professor of Neurology and Biomedical Informatics Director of Technical Imaging Development Buffalo Neuroimaging Analysis Center University at Buffalo 100 High St. Buffalo NY 14203 mgdw...@bnac.net (716) 859-7065 ___ HCP-Users mailing list HCP-Users@humanconnectome.org http
Re: [HCP-Users] Myelin mapping with FLAIR
I don't know. If the myelin mapping isn't working quite as expected with T1/T2w scans on GE, then its really hard to know what to expect if you use FLAIR instead of T2w. 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: Michael Dwyer mgdw...@bnac.net Date: Sunday, June 21, 2015 11:17 AM To: Harms, Michael mha...@wustl.edu Cc: HCP Users HCP-Users@humanconnectome.org Subject: Re: [HCP-Users] Myelin mapping with FLAIR Thanks, I saw those. We'll certainly have to deal with those issues if we want to do this. Other than that, though, would you recommend doing anything differently with FLAIR than with T2? Best, Mike On Fri, Jun 19, 2015 at 10:19 PM, Harms, Michael mha...@wustl.edu wrote: Take a look also at the recent posts. There are unfortunately some unresolved issues about myelin maps acquired on the GE platform not looking the same as they do when derived from Siemens data. 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: Michael Dwyer mgdw...@bnac.net Date: Thursday, June 18, 2015 4:25 PM To: Gordon Xu junqian...@mssm.edu Cc: HCP Users HCP-Users@humanconnectome.org Subject: Re: [HCP-Users] Myelin mapping with FLAIR Thanks for the quick reply! Unfortunately, we have a GE scanner, not a Siemens. Any advice for that? Also any different recommendations for the post-processing when using FLAIR? Best, Mike On Thu, Jun 18, 2015 at 5:04 PM, Xu, Junqian junqian...@mssm.edu wrote: You can take a look at the UK Biobank project FLAIR protocol first and start your site-specific piloting from there. http://users.fmrib.ox.ac.uk/~steve/BiobankPiloting/ On Jun 18, 2015, at 10:56 AM, Michael Dwyer mgdw...@bnac.net wrote: Dear HCP experts, First, I would like to thank you all for a great and informative course last week. I really enjoyed the interleaved lectures and practicals, and everything was extremely well organized I think Matt had mentioned during the course that the T1/T2 myelin mapping could also work with FLAIR. We are acquiring a hi-res 3D-FLAIR clinically on a GE scanner, and I was hoping you could give some pointers on the best way to acquire it. I assume we should avoid pre-scan re-calibration, but is there anything else special we should do? Thanks in advance. Best, Mike -- Michael G. Dwyer, Ph.D. Assistant Professor of Neurology and Biomedical Informatics Director of Technical Imaging Development Buffalo Neuroimaging Analysis Center University at Buffalo 100 High St. Buffalo NY 14203 mgdw...@bnac.net (716) 859-7065 ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users -- Michael G. Dwyer, Ph.D. Assistant Professor of Neurology and Biomedical Informatics Director of Technical Imaging Development Buffalo Neuroimaging Analysis Center University at Buffalo 100 High St. Buffalo NY 14203 mgdw...@bnac.net (716) 859-7065 ___ 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. -- Michael G. Dwyer, Ph.D. Assistant Professor of Neurology and Biomedical Informatics Director of Technical Imaging Development Buffalo Neuroimaging Analysis Center University at Buffalo 100 High St. Buffalo NY 14203 mgdw...@bnac.net (716) 859-7065 ___ 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
Re: [HCP-Users] Myelin mapping with FLAIR
Take a look also at the recent posts. There are unfortunately some unresolved issues about myelin maps acquired on the GE platform not looking the same as they do when derived from Siemens data. 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: Michael Dwyer mgdw...@bnac.net Date: Thursday, June 18, 2015 4:25 PM To: Gordon Xu junqian...@mssm.edu Cc: HCP Users HCP-Users@humanconnectome.org Subject: Re: [HCP-Users] Myelin mapping with FLAIR Thanks for the quick reply! Unfortunately, we have a GE scanner, not a Siemens. Any advice for that? Also any different recommendations for the post-processing when using FLAIR? Best, Mike On Thu, Jun 18, 2015 at 5:04 PM, Xu, Junqian junqian...@mssm.edu wrote: You can take a look at the UK Biobank project FLAIR protocol first and start your site-specific piloting from there. http://users.fmrib.ox.ac.uk/~steve/BiobankPiloting/ On Jun 18, 2015, at 10:56 AM, Michael Dwyer mgdw...@bnac.net wrote: Dear HCP experts, First, I would like to thank you all for a great and informative course last week. I really enjoyed the interleaved lectures and practicals, and everything was extremely well organized I think Matt had mentioned during the course that the T1/T2 myelin mapping could also work with FLAIR. We are acquiring a hi-res 3D-FLAIR clinically on a GE scanner, and I was hoping you could give some pointers on the best way to acquire it. I assume we should avoid pre-scan re-calibration, but is there anything else special we should do? Thanks in advance. Best, Mike -- Michael G. Dwyer, Ph.D. Assistant Professor of Neurology and Biomedical Informatics Director of Technical Imaging Development Buffalo Neuroimaging Analysis Center University at Buffalo 100 High St. Buffalo NY 14203 mgdw...@bnac.net (716) 859-7065 ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users -- Michael G. Dwyer, Ph.D. Assistant Professor of Neurology and Biomedical Informatics Director of Technical Imaging Development Buffalo Neuroimaging Analysis Center University at Buffalo 100 High St. Buffalo NY 14203 mgdw...@bnac.net (716) 859-7065 ___ 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 listHCP-Users@humanconnectome.orghttp://lists.humanconnectome.org/mailman/listinfo/hcp-users
Re: [HCP-Users] Myelin mapping with FLAIR
You can take a look at the UK Biobank project FLAIR protocol first and start your site-specific piloting from there. http://users.fmrib.ox.ac.uk/~steve/BiobankPiloting/ On Jun 18, 2015, at 10:56 AM, Michael Dwyer mgdw...@bnac.netmailto:mgdw...@bnac.net wrote: Dear HCP experts, First, I would like to thank you all for a great and informative course last week. I really enjoyed the interleaved lectures and practicals, and everything was extremely well organized I think Matt had mentioned during the course that the T1/T2 myelin mapping could also work with FLAIR. We are acquiring a hi-res 3D-FLAIR clinically on a GE scanner, and I was hoping you could give some pointers on the best way to acquire it. I assume we should avoid pre-scan re-calibration, but is there anything else special we should do? Thanks in advance. Best, Mike -- Michael G. Dwyer, Ph.D. Assistant Professor of Neurology and Biomedical Informatics Director of Technical Imaging Development Buffalo Neuroimaging Analysis Center University at Buffalo 100 High St. Buffalo NY 14203 mgdw...@bnac.netmailto:mgdw...@bnac.net (716) 859-7065 ___ HCP-Users mailing list HCP-Users@humanconnectome.orgmailto:HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
Re: [HCP-Users] Myelin Mapping
Okay, thank you to both of you. Best wishes, Barbara Anne On 07/05/2015 03:35, Glasser, Matthew wrote: That’s a good point and would still be true of the current version of the HCP Pipelines. While we don’t rely on FNIRT to align cortex, it is still used to make the initial brain mask, and that could work not as well without FAT sat. You should probably check over your results more carefully if not using FAT sat to see if any subjects need to be excluded (e.g. obvious large very high or very low intensity artifacts in the myelin maps). Peace, Matt. From: Harms, Michael mha...@wustl.edu mailto:mha...@wustl.edu Date: Wednesday, May 6, 2015 at 9:30 PM To: Matt Glasser glass...@wusm.wustl.edu mailto:glass...@wusm.wustl.edu, Barbara Kreilkamp bakk@googlemail.com mailto:bakk@googlemail.com, hcp-users@humanconnectome.org mailto:hcp-users@humanconnectome.org hcp-users@humanconnectome.org mailto:hcp-users@humanconnectome.org Subject: Re: [HCP-Users] Myelin Mapping Separate from FS, we've also found that fat sat in the T1 helps make FNIRT more robust. 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 63110Email: mha...@wustl.edu mailto:mha...@wustl.edu From: Glasser, Matt Glasser glass...@wusm.wustl.edu mailto:glass...@wusm.wustl.edu Date: Wednesday, May 6, 2015 11:57 AM To: Barbara Kreilkamp bakk@googlemail.com mailto:bakk@googlemail.com, hcp-users@humanconnectome.org mailto:hcp-users@humanconnectome.org hcp-users@humanconnectome.org mailto:hcp-users@humanconnectome.org Subject: Re: [HCP-Users] Myelin Mapping Not having FAT saturation is mainly an issue for FreeSurfer which can sometimes get the surface wrong if it gets confused and thinks fat is white matter. I don’t know how much of an issue this is for more recent HCP Pipeline versions though. Peace, Matt. From: Barbara Kreilkamp bakk@googlemail.com mailto:bakk@googlemail.com Date: Wednesday, May 6, 2015 at 11:53 AM To: hcp-users@humanconnectome.org mailto:hcp-users@humanconnectome.org hcp-users@humanconnectome.org mailto:hcp-users@humanconnectome.org Subject: Re: [HCP-Users] Myelin Mapping Thanks, Matt, this is great. You said once 'You will need a T1w and a T2w images acquired in the same scanning session with the same image intensity filters (e.g. pre scan normalize or not) applied to both.' Are these the main issues I have to look out for? As I notice some differences in my acquisition parameters when comparing to other papers. Also, we did not apply FAT saturation, I read somewhere this would be beneficial for myelin mapping. Best wishes and thanks for your help. Barbara Anne On 05/05/2015 23:00, Glasser, Matthew wrote: (1) Use the 1mm templates. (2) You can do this, but it’s important to note that the myelin/iron relationship, which is very close in cortex, may deviate more in subcortical white matter. Also, the myelin content of a white matter region will depend on the density of axons vs other things, ratio of space inside the axon to the space taken up by the myelin wraps, etc, which may produce counterintuitive effects. Also, while one can validly do stats on grey matter myelin on the cortical surface, white matter in the volume is quite tricky (more central regions may be reasonably aligned with nonlinear volume registration, but more cortical regions have the same issue as cortical grey matter and won’t be aligned well). Perhaps a TBSS-like skeleton approach is warranted… (3) Have a look at the references in the beginning of Glasser and Van Essen 2011 Journal of Neuroscience (http://www.jneurosci.org/content/31/32/11597.short) for the validation of various MR contrasts vs histological myelin stains. Also there’s more discussion of this in Glasser at al 2013 Neuroimage, Trends and Properties of Cortex (http://www.sciencedirect.com/science/article/pii/S1053811913003108). Peace, Matt. From: Barbara Kreilkamp bakk@googlemail.com mailto:bakk@googlemail.com Date: Tuesday, May 5, 2015 at 4:46 PM To: hcp-users@humanconnectome.org mailto:hcp-users@humanconnectome.org hcp-users@humanconnectome.org mailto:hcp-users@humanconnectome.org Subject: Re: [HCP-Users] Myelin Mapping Dear Matt and HCP experts, Thanks again for this. I have some further questions: (1) Even if my data is 1x1x1mm^3 should it be registered to the workbench default T1 MNI of 0.7mm or to 1x1x1mm^3? (2) Within HCP: Is it valid to also look at white matter myelin not just cortical myelin? (3) Finally, does anyone know any postmortem validation studies for this technique? Thank you very much, Best wishes, Barbara Anne On 20/02/2015 13:08, Glasser, Matthew wrote: Please use the HCP Minimal Preprocessing Pipelines to create T1w/T2w myelin
Re: [HCP-Users] Myelin Mapping
Thanks, Matt, this is great. You said once 'You will need a T1w and a T2w images acquired in the same scanning session with the same image intensity filters (e.g. pre scan normalize or not) applied to both.' Are these the main issues I have to look out for? As I notice some differences in my acquisition parameters when comparing to other papers. Also, we did not apply FAT saturation, I read somewhere this would be beneficial for myelin mapping. Best wishes and thanks for your help. Barbara Anne On 05/05/2015 23:00, Glasser, Matthew wrote: (1) Use the 1mm templates. (2) You can do this, but it’s important to note that the myelin/iron relationship, which is very close in cortex, may deviate more in subcortical white matter. Also, the myelin content of a white matter region will depend on the density of axons vs other things, ratio of space inside the axon to the space taken up by the myelin wraps, etc, which may produce counterintuitive effects. Also, while one can validly do stats on grey matter myelin on the cortical surface, white matter in the volume is quite tricky (more central regions may be reasonably aligned with nonlinear volume registration, but more cortical regions have the same issue as cortical grey matter and won’t be aligned well). Perhaps a TBSS-like skeleton approach is warranted… (3) Have a look at the references in the beginning of Glasser and Van Essen 2011 Journal of Neuroscience (http://www.jneurosci.org/content/31/32/11597.short) for the validation of various MR contrasts vs histological myelin stains. Also there’s more discussion of this in Glasser at al 2013 Neuroimage, Trends and Properties of Cortex (http://www.sciencedirect.com/science/article/pii/S1053811913003108). Peace, Matt. From: Barbara Kreilkamp bakk@googlemail.com mailto:bakk@googlemail.com Date: Tuesday, May 5, 2015 at 4:46 PM To: hcp-users@humanconnectome.org mailto:hcp-users@humanconnectome.org hcp-users@humanconnectome.org mailto:hcp-users@humanconnectome.org Subject: Re: [HCP-Users] Myelin Mapping Dear Matt and HCP experts, Thanks again for this. I have some further questions: (1) Even if my data is 1x1x1mm^3 should it be registered to the workbench default T1 MNI of 0.7mm or to 1x1x1mm^3? (2) Within HCP: Is it valid to also look at white matter myelin not just cortical myelin? (3) Finally, does anyone know any postmortem validation studies for this technique? Thank you very much, Best wishes, Barbara Anne On 20/02/2015 13:08, Glasser, Matthew wrote: Please use the HCP Minimal Preprocessing Pipelines to create T1w/T2w myelin maps with the latest code/methods (including bias correction and normalization): https://github.com/Washington-University/Pipelines You will need a T1w and a T2w images acquired in the same scanning session with the same image intensity filters (e.g. pre scan normalize or not) applied to both. For myelin mapping only, a field map is optional (but recommended). Peace, Matt. From: Barbara Kreilkamp bakk@googlemail.com mailto:bakk@googlemail.com Date: Friday, February 20, 2015 at 7:04 AM To: hcp-users@humanconnectome.org mailto:hcp-users@humanconnectome.org hcp-users@humanconnectome.org mailto:hcp-users@humanconnectome.org Subject: [HCP-Users] Myelin Mapping Dear HCP- users, Could you please point me to a tutorial for myelin mapping with Human Connectome Workbench software? Also, is there a way to implement bias-correction for this technique? Thank you very much, Best wishes, Barbara ___ 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
Re: [HCP-Users] Myelin Mapping
Not having FAT saturation is mainly an issue for FreeSurfer which can sometimes get the surface wrong if it gets confused and thinks fat is white matter. I don’t know how much of an issue this is for more recent HCP Pipeline versions though. Peace, Matt. From: Barbara Kreilkamp bakk@googlemail.com Date: Wednesday, May 6, 2015 at 11:53 AM To: hcp-users@humanconnectome.org hcp-users@humanconnectome.org Subject: Re: [HCP-Users] Myelin Mapping Thanks, Matt, this is great. You said once 'You will need a T1w and a T2w images acquired in the same scanning session with the same image intensity filters (e.g. pre scan normalize or not) applied to both.' Are these the main issues I have to look out for? As I notice some differences in my acquisition parameters when comparing to other papers. Also, we did not apply FAT saturation, I read somewhere this would be beneficial for myelin mapping. Best wishes and thanks for your help. Barbara Anne On 05/05/2015 23:00, Glasser, Matthew wrote: (1) Use the 1mm templates. (2) You can do this, but it’s important to note that the myelin/iron relationship, which is very close in cortex, may deviate more in subcortical white matter. Also, the myelin content of a white matter region will depend on the density of axons vs other things, ratio of space inside the axon to the space taken up by the myelin wraps, etc, which may produce counterintuitive effects. Also, while one can validly do stats on grey matter myelin on the cortical surface, white matter in the volume is quite tricky (more central regions may be reasonably aligned with nonlinear volume registration, but more cortical regions have the same issue as cortical grey matter and won’t be aligned well). Perhaps a TBSS-like skeleton approach is warranted… (3) Have a look at the references in the beginning of Glasser and Van Essen 2011 Journal of Neuroscience (http://www.jneurosci.org/content/31/32/11597.short) for the validation of various MR contrasts vs histological myelin stains. Also there’s more discussion of this in Glasser at al 2013 Neuroimage, Trends and Properties of Cortex (http://www.sciencedirect.com/science/article/pii/S1053811913003108). Peace, Matt. From: Barbara Kreilkamp bakk@googlemail.com Date: Tuesday, May 5, 2015 at 4:46 PM To: hcp-users@humanconnectome.org hcp-users@humanconnectome.org Subject: Re: [HCP-Users] Myelin Mapping Dear Matt and HCP experts, Thanks again for this. I have some further questions: (1) Even if my data is 1x1x1mm^3 should it be registered to the workbench default T1 MNI of 0.7mm or to 1x1x1mm^3? (2) Within HCP: Is it valid to also look at white matter myelin not just cortical myelin? (3) Finally, does anyone know any postmortem validation studies for this technique? Thank you very much, Best wishes, Barbara Anne On 20/02/2015 13:08, Glasser, Matthew wrote: Please use the HCP Minimal Preprocessing Pipelines to create T1w/T2w myelin maps with the latest code/methods (including bias correction and normalization): https://github.com/Washington-University/Pipelines You will need a T1w and a T2w images acquired in the same scanning session with the same image intensity filters (e.g. pre scan normalize or not) applied to both. For myelin mapping only, a field map is optional (but recommended). Peace, Matt. From: Barbara Kreilkamp bakk@googlemail.com Date: Friday, February 20, 2015 at 7:04 AM To: hcp-users@humanconnectome.org hcp-users@humanconnectome.org Subject: [HCP-Users] Myelin Mapping Dear HCP- users, Could you please point me to a tutorial for myelin mapping with Human Connectome Workbench software? Also, is there a way to implement bias-correction for this technique? Thank you very much, Best wishes, Barbara ___ 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 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
Re: [HCP-Users] Myelin Mapping
Thank you Matt. Freesurfer did a good job in segmentation, so I'm happy. Cheers, Barbara Anne On 06/05/2015 17:57, Glasser, Matthew wrote: Not having FAT saturation is mainly an issue for FreeSurfer which can sometimes get the surface wrong if it gets confused and thinks fat is white matter. I don’t know how much of an issue this is for more recent HCP Pipeline versions though. Peace, Matt. From: Barbara Kreilkamp bakk@googlemail.com mailto:bakk@googlemail.com Date: Wednesday, May 6, 2015 at 11:53 AM To: hcp-users@humanconnectome.org mailto:hcp-users@humanconnectome.org hcp-users@humanconnectome.org mailto:hcp-users@humanconnectome.org Subject: Re: [HCP-Users] Myelin Mapping Thanks, Matt, this is great. You said once 'You will need a T1w and a T2w images acquired in the same scanning session with the same image intensity filters (e.g. pre scan normalize or not) applied to both.' Are these the main issues I have to look out for? As I notice some differences in my acquisition parameters when comparing to other papers. Also, we did not apply FAT saturation, I read somewhere this would be beneficial for myelin mapping. Best wishes and thanks for your help. Barbara Anne On 05/05/2015 23:00, Glasser, Matthew wrote: (1) Use the 1mm templates. (2) You can do this, but it’s important to note that the myelin/iron relationship, which is very close in cortex, may deviate more in subcortical white matter. Also, the myelin content of a white matter region will depend on the density of axons vs other things, ratio of space inside the axon to the space taken up by the myelin wraps, etc, which may produce counterintuitive effects. Also, while one can validly do stats on grey matter myelin on the cortical surface, white matter in the volume is quite tricky (more central regions may be reasonably aligned with nonlinear volume registration, but more cortical regions have the same issue as cortical grey matter and won’t be aligned well). Perhaps a TBSS-like skeleton approach is warranted… (3) Have a look at the references in the beginning of Glasser and Van Essen 2011 Journal of Neuroscience (http://www.jneurosci.org/content/31/32/11597.short) for the validation of various MR contrasts vs histological myelin stains. Also there’s more discussion of this in Glasser at al 2013 Neuroimage, Trends and Properties of Cortex (http://www.sciencedirect.com/science/article/pii/S1053811913003108). Peace, Matt. From: Barbara Kreilkamp bakk@googlemail.com mailto:bakk@googlemail.com Date: Tuesday, May 5, 2015 at 4:46 PM To: hcp-users@humanconnectome.org mailto:hcp-users@humanconnectome.org hcp-users@humanconnectome.org mailto:hcp-users@humanconnectome.org Subject: Re: [HCP-Users] Myelin Mapping Dear Matt and HCP experts, Thanks again for this. I have some further questions: (1) Even if my data is 1x1x1mm^3 should it be registered to the workbench default T1 MNI of 0.7mm or to 1x1x1mm^3? (2) Within HCP: Is it valid to also look at white matter myelin not just cortical myelin? (3) Finally, does anyone know any postmortem validation studies for this technique? Thank you very much, Best wishes, Barbara Anne On 20/02/2015 13:08, Glasser, Matthew wrote: Please use the HCP Minimal Preprocessing Pipelines to create T1w/T2w myelin maps with the latest code/methods (including bias correction and normalization): https://github.com/Washington-University/Pipelines You will need a T1w and a T2w images acquired in the same scanning session with the same image intensity filters (e.g. pre scan normalize or not) applied to both. For myelin mapping only, a field map is optional (but recommended). Peace, Matt. From: Barbara Kreilkamp bakk@googlemail.com mailto:bakk@googlemail.com Date: Friday, February 20, 2015 at 7:04 AM To: hcp-users@humanconnectome.org mailto:hcp-users@humanconnectome.org hcp-users@humanconnectome.org mailto:hcp-users@humanconnectome.org Subject: [HCP-Users] Myelin Mapping Dear HCP- users, Could you please point me to a tutorial for myelin mapping with Human Connectome Workbench software? Also, is there a way to implement bias-correction for this technique? Thank you very much, Best wishes, Barbara ___ 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
Re: [HCP-Users] Myelin Mapping
That’s a good point and would still be true of the current version of the HCP Pipelines. While we don’t rely on FNIRT to align cortex, it is still used to make the initial brain mask, and that could work not as well without FAT sat. You should probably check over your results more carefully if not using FAT sat to see if any subjects need to be excluded (e.g. obvious large very high or very low intensity artifacts in the myelin maps). Peace, Matt. From: Harms, Michael mha...@wustl.edu Date: Wednesday, May 6, 2015 at 9:30 PM To: Matt Glasser glass...@wusm.wustl.edu, Barbara Kreilkamp bakk@googlemail.com, hcp-users@humanconnectome.org hcp-users@humanconnectome.org Subject: Re: [HCP-Users] Myelin Mapping Separate from FS, we've also found that fat sat in the T1 helps make FNIRT more robust. 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: Glasser, Matt Glasser glass...@wusm.wustl.edu Date: Wednesday, May 6, 2015 11:57 AM To: Barbara Kreilkamp bakk@googlemail.com, hcp-users@humanconnectome.org hcp-users@humanconnectome.org Subject: Re: [HCP-Users] Myelin Mapping Not having FAT saturation is mainly an issue for FreeSurfer which can sometimes get the surface wrong if it gets confused and thinks fat is white matter. I don’t know how much of an issue this is for more recent HCP Pipeline versions though. Peace, Matt. From: Barbara Kreilkamp bakk@googlemail.com Date: Wednesday, May 6, 2015 at 11:53 AM To: hcp-users@humanconnectome.org hcp-users@humanconnectome.org Subject: Re: [HCP-Users] Myelin Mapping Thanks, Matt, this is great. You said once 'You will need a T1w and a T2w images acquired in the same scanning session with the same image intensity filters (e.g. pre scan normalize or not) applied to both.' Are these the main issues I have to look out for? As I notice some differences in my acquisition parameters when comparing to other papers. Also, we did not apply FAT saturation, I read somewhere this would be beneficial for myelin mapping. Best wishes and thanks for your help. Barbara Anne On 05/05/2015 23:00, Glasser, Matthew wrote: (1) Use the 1mm templates. (2) You can do this, but it’s important to note that the myelin/iron relationship, which is very close in cortex, may deviate more in subcortical white matter. Also, the myelin content of a white matter region will depend on the density of axons vs other things, ratio of space inside the axon to the space taken up by the myelin wraps, etc, which may produce counterintuitive effects. Also, while one can validly do stats on grey matter myelin on the cortical surface, white matter in the volume is quite tricky (more central regions may be reasonably aligned with nonlinear volume registration, but more cortical regions have the same issue as cortical grey matter and won’t be aligned well). Perhaps a TBSS-like skeleton approach is warranted… (3) Have a look at the references in the beginning of Glasser and Van Essen 2011 Journal of Neuroscience (http://www.jneurosci.org/content/31/32/11597.short) for the validation of various MR contrasts vs histological myelin stains. Also there’s more discussion of this in Glasser at al 2013 Neuroimage, Trends and Properties of Cortex (http://www.sciencedirect.com/science/article/pii/S1053811913003108). Peace, Matt. From: Barbara Kreilkamp bakk@googlemail.com Date: Tuesday, May 5, 2015 at 4:46 PM To: hcp-users@humanconnectome.org hcp-users@humanconnectome.org Subject: Re: [HCP-Users] Myelin Mapping Dear Matt and HCP experts, Thanks again for this. I have some further questions: (1) Even if my data is 1x1x1mm^3 should it be registered to the workbench default T1 MNI of 0.7mm or to 1x1x1mm^3? (2) Within HCP: Is it valid to also look at white matter myelin not just cortical myelin? (3) Finally, does anyone know any postmortem validation studies for this technique? Thank you very much, Best wishes, Barbara Anne On 20/02/2015 13:08, Glasser, Matthew wrote: Please use the HCP Minimal Preprocessing Pipelines to create T1w/T2w myelin maps with the latest code/methods (including bias correction and normalization): https://github.com/Washington-University/Pipelines You will need a T1w and a T2w images acquired in the same scanning session with the same image intensity filters (e.g. pre scan normalize or not) applied to both. For myelin mapping only, a field map is optional (but recommended). Peace, Matt. From: Barbara Kreilkamp bakk@googlemail.com Date: Friday, February 20, 2015 at 7:04 AM To: hcp-users@humanconnectome.org hcp-users@humanconnectome.org Subject: [HCP-Users] Myelin Mapping Dear HCP- users, Could you please point me to a tutorial
Re: [HCP-Users] Myelin Mapping
Dear Matt and HCP experts, Thanks again for this. I have some further questions: (1) Even if my data is 1x1x1mm^3 should it be registered to the workbench default T1 MNI of 0.7mm or to 1x1x1mm^3? (2) Within HCP: Is it valid to also look at white matter myelin not just cortical myelin? (3) Finally, does anyone know any postmortem validation studies for this technique? Thank you very much, Best wishes, Barbara Anne On 20/02/2015 13:08, Glasser, Matthew wrote: Please use the HCP Minimal Preprocessing Pipelines to create T1w/T2w myelin maps with the latest code/methods (including bias correction and normalization): https://github.com/Washington-University/Pipelines You will need a T1w and a T2w images acquired in the same scanning session with the same image intensity filters (e.g. pre scan normalize or not) applied to both. For myelin mapping only, a field map is optional (but recommended). Peace, Matt. From: Barbara Kreilkamp bakk@googlemail.com mailto:bakk@googlemail.com Date: Friday, February 20, 2015 at 7:04 AM To: hcp-users@humanconnectome.org mailto:hcp-users@humanconnectome.org hcp-users@humanconnectome.org mailto:hcp-users@humanconnectome.org Subject: [HCP-Users] Myelin Mapping Dear HCP- users, Could you please point me to a tutorial for myelin mapping with Human Connectome Workbench software? Also, is there a way to implement bias-correction for this technique? Thank you very much, Best wishes, Barbara ___ 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 http://lists.humanconnectome.org/mailman/listinfo/hcp-users
Re: [HCP-Users] Myelin Mapping
Please use the HCP Minimal Preprocessing Pipelines to create T1w/T2w myelin maps with the latest code/methods (including bias correction and normalization): https://github.com/Washington-University/Pipelines You will need a T1w and a T2w images acquired in the same scanning session with the same image intensity filters (e.g. pre scan normalize or not) applied to both. For myelin mapping only, a field map is optional (but recommended). Peace, Matt. From: Barbara Kreilkamp bakk@googlemail.com Date: Friday, February 20, 2015 at 7:04 AM To: hcp-users@humanconnectome.org hcp-users@humanconnectome.org Subject: [HCP-Users] Myelin Mapping Dear HCP- users, Could you please point me to a tutorial for myelin mapping with Human Connectome Workbench software? Also, is there a way to implement bias-correction for this technique? Thank you very much, Best wishes, Barbara ___ 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 listHCP-Users@humanconnectome.orghttp://lists.humanconnectome.org/mailman/listinfo/hcp-users
Re: [HCP-Users] Myelin Mapping
after the talk? On 20 February 2015 at 13:42, Glasser, Matthew glass...@wusm.wustl.edu wrote: If I recall correctly, they withdrew their SFN 2014 presentation. I don’t know the reason for that. Peace, Matt. From: Seán Froudist Walsh froud...@tcd.ie Date: Friday, February 20, 2015 at 7:27 AM To: Matt Glasser glass...@wusm.wustl.edu Cc: Barbara Kreilkamp bakk@googlemail.com, hcp-users@humanconnectome.org hcp-users@humanconnectome.org Subject: Re: [HCP-Users] Myelin Mapping I wonder if you have an opinion on the talk by Stefano Sandrone from Marco Catani's group at OHBM 2014 that showed that this measure doesn't correlate with expected myelin patterns in white matter? On 20 February 2015 at 13:08, Glasser, Matthew glass...@wusm.wustl.edu wrote: Please use the HCP Minimal Preprocessing Pipelines to create T1w/T2w myelin maps with the latest code/methods (including bias correction and normalization): https://github.com/Washington-University/Pipelines You will need a T1w and a T2w images acquired in the same scanning session with the same image intensity filters (e.g. pre scan normalize or not) applied to both. For myelin mapping only, a field map is optional (but recommended). Peace, Matt. From: Barbara Kreilkamp bakk@googlemail.com Date: Friday, February 20, 2015 at 7:04 AM To: hcp-users@humanconnectome.org hcp-users@humanconnectome.org Subject: [HCP-Users] Myelin Mapping Dear HCP- users, Could you please point me to a tutorial for myelin mapping with Human Connectome Workbench software? Also, is there a way to implement bias-correction for this technique? Thank you very much, Best wishes, Barbara ___ 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 -- 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
Re: [HCP-Users] Myelin Mapping
No it was a subsequent presentation on the same topic at a different meeting. Peace, Matt. From: Seán Froudist Walsh froud...@tcd.ie Date: Friday, February 20, 2015 at 7:48 AM To: Matt Glasser glass...@wusm.wustl.edu Cc: Barbara Kreilkamp bakk@googlemail.com, hcp-users@humanconnectome.org hcp-users@humanconnectome.org Subject: Re: [HCP-Users] Myelin Mapping after the talk? On 20 February 2015 at 13:42, Glasser, Matthew glass...@wusm.wustl.edu wrote: If I recall correctly, they withdrew their SFN 2014 presentation. I don’t know the reason for that. Peace, Matt. From: Seán Froudist Walsh froud...@tcd.ie Date: Friday, February 20, 2015 at 7:27 AM To: Matt Glasser glass...@wusm.wustl.edu Cc: Barbara Kreilkamp bakk@googlemail.com, hcp-users@humanconnectome.org hcp-users@humanconnectome.org Subject: Re: [HCP-Users] Myelin Mapping I wonder if you have an opinion on the talk by Stefano Sandrone from Marco Catani's group at OHBM 2014 that showed that this measure doesn't correlate with expected myelin patterns in white matter? On 20 February 2015 at 13:08, Glasser, Matthew glass...@wusm.wustl.edu wrote: Please use the HCP Minimal Preprocessing Pipelines to create T1w/T2w myelin maps with the latest code/methods (including bias correction and normalization): https://github.com/Washington-University/Pipelines You will need a T1w and a T2w images acquired in the same scanning session with the same image intensity filters (e.g. pre scan normalize or not) applied to both. For myelin mapping only, a field map is optional (but recommended). Peace, Matt. From: Barbara Kreilkamp bakk@googlemail.com Date: Friday, February 20, 2015 at 7:04 AM To: hcp-users@humanconnectome.org hcp-users@humanconnectome.org Subject: [HCP-Users] Myelin Mapping Dear HCP- users, Could you please point me to a tutorial for myelin mapping with Human Connectome Workbench software? Also, is there a way to implement bias-correction for this technique? Thank you very much, Best wishes, Barbara ___ 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 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 listHCP-Users@humanconnectome.orghttp://lists.humanconnectome.org/mailman/listinfo/hcp-users
Re: [HCP-Users] Myelin Mapping
Dear Matt, Thank you for your quick reply. Best wishes, Barbara Anne On Fri, Feb 20, 2015 at 1:49 PM, Glasser, Matthew glass...@wusm.wustl.edu wrote: No it was a subsequent presentation on the same topic at a different meeting. Peace, Matt. From: Seán Froudist Walsh froud...@tcd.ie Date: Friday, February 20, 2015 at 7:48 AM To: Matt Glasser glass...@wusm.wustl.edu Cc: Barbara Kreilkamp bakk@googlemail.com, hcp-users@humanconnectome.org hcp-users@humanconnectome.org Subject: Re: [HCP-Users] Myelin Mapping after the talk? On 20 February 2015 at 13:42, Glasser, Matthew glass...@wusm.wustl.edu wrote: If I recall correctly, they withdrew their SFN 2014 presentation. I don’t know the reason for that. Peace, Matt. From: Seán Froudist Walsh froud...@tcd.ie Date: Friday, February 20, 2015 at 7:27 AM To: Matt Glasser glass...@wusm.wustl.edu Cc: Barbara Kreilkamp bakk@googlemail.com, hcp-users@humanconnectome.org hcp-users@humanconnectome.org Subject: Re: [HCP-Users] Myelin Mapping I wonder if you have an opinion on the talk by Stefano Sandrone from Marco Catani's group at OHBM 2014 that showed that this measure doesn't correlate with expected myelin patterns in white matter? On 20 February 2015 at 13:08, Glasser, Matthew glass...@wusm.wustl.edu wrote: Please use the HCP Minimal Preprocessing Pipelines to create T1w/T2w myelin maps with the latest code/methods (including bias correction and normalization): https://github.com/Washington-University/Pipelines You will need a T1w and a T2w images acquired in the same scanning session with the same image intensity filters (e.g. pre scan normalize or not) applied to both. For myelin mapping only, a field map is optional (but recommended). Peace, Matt. From: Barbara Kreilkamp bakk@googlemail.com Date: Friday, February 20, 2015 at 7:04 AM To: hcp-users@humanconnectome.org hcp-users@humanconnectome.org Subject: [HCP-Users] Myelin Mapping Dear HCP- users, Could you please point me to a tutorial for myelin mapping with Human Connectome Workbench software? Also, is there a way to implement bias-correction for this technique? Thank you very much, Best wishes, Barbara ___ 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 -- 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
