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 <[email protected]> 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, "[email protected] on behalf of > Gaurav Patel" <[email protected] on behalf of > [email protected]> 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 > > [email protected] > > 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/[email protected]/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 <[email protected]> > >>> Date: Monday, June 22, 2015 at 3:12 PM > >>> To: Matt Glasser <[email protected]> > >>> Cc: Gaurav Patel <[email protected]>, HCP Users > >>><[email protected]> > >>> 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 > >>><[email protected]> wrote: > >>> For the moment one just treats the FLAIR as a T2w scan for the > >>>purposes of the pipelines. > >>> > >>> Peace, > >>> > >>> Matt. > >>> > >>> From: <[email protected]> on behalf of Michael > >>>Dwyer <[email protected]> > >>> Date: Sunday, June 21, 2015 at 8:24 PM > >>> To: Gaurav Patel <[email protected]> > >>> > >>> Cc: HCP Users <[email protected]> > >>> 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 <[email protected]> > >>>wrote: > >>> FYI we're still working on this problem; I'm hoping for a meaningful > >>>update soon > >>> > >>> _________________________ > >>> gaurav patel > >>> [email protected] > >>> www.neurofreak.net > >>> > >>> On Jun 21, 2015, at 3:04 PM, Harms, Michael <[email protected]> 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: [email protected] > >>>> > >>>> From: Michael Dwyer <[email protected]> > >>>> Date: Sunday, June 21, 2015 11:17 AM > >>>> To: "Harms, Michael" <[email protected]> > >>>> Cc: HCP Users <[email protected]> > >>>> 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 <[email protected]> > >>>>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: [email protected] > >>>> > >>>> From: Michael Dwyer <[email protected]> > >>>> Date: Thursday, June 18, 2015 4:25 PM > >>>> To: Gordon Xu <[email protected]> > >>>> Cc: HCP Users <[email protected]> > >>>> 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 <[email protected]> > >>>>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 <[email protected]> > 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 > >>>>> [email protected] > >>>>> (716) 859-7065 > >>>>> _______________________________________________ > >>>>> HCP-Users mailing list > >>>>> [email protected] > >>>>> 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 > >>>> [email protected] > >>>> (716) 859-7065 > >>>> _______________________________________________ > >>>> HCP-Users mailing list > >>>> [email protected] > >>>> 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 > >>>> [email protected] > >>>> (716) 859-7065 > >>>> _______________________________________________ > >>>> HCP-Users mailing list > >>>> [email protected] > >>>> 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 > >>>> [email protected] > >>>> 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 > >>> [email protected] > >>> (716) 859-7065 > >>> _______________________________________________ > >>> HCP-Users mailing list > >>> [email protected] > >>> 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 > >>> [email protected] > >>> (716) 859-7065 > >>> > >>> > >>> 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 > >>> [email protected] > >>> http://lists.humanconnectome.org/mailman/listinfo/hcp-users > >>> > >> > >> > >> _______________________________________________ > >> 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 > > > _______________________________________________ > 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
