Dear Sir, Can we observe the distribution of vestibulospinal tracts (vestibular circuitry ) from thalamus through vestibular cortex through workbench?, I have DTI data and i can evaluate the functional and structural connectivity but i would like to construct track orientation distribution in each voxel.
Thanks Vasudev On 23 June 2016 at 17:20, Harms, Michael <[email protected]> wrote: > > Not as the pipeline is currently constituted. > > Sorry. > > -- > 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: <[email protected]> on behalf of Dev vasu < > [email protected]> > Date: Thursday, June 23, 2016 at 10:02 AM > > To: "Harms, Michael" <[email protected]> > Cc: "[email protected]" <[email protected]> > Subject: Re: [HCP-Users] Spatial normalization of 50 Subjects T1w images > > Dear Sir, > > In some subjects T2 FLAIR images are missing, is it still possible to run > HCP structural preprocessing pipeline without T2w images?, if not is there > any alternative. > > > Thanks > Vasudev > > > On 23 June 2016 at 16:34, Harms, Michael <[email protected]> wrote: > >> >> Hi, >> After you run the data through the HCP pipelines you will have >> surface-based maps of cortical thickness for each subject. You can then >> use the PALM tool (FSL) to look for statistically significant differences >> in thickness between subject groups. >> >> 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: Dev vasu <[email protected]> >> Date: Thursday, June 23, 2016 at 8:53 AM >> >> To: "Harms, Michael" <[email protected]> >> Cc: "[email protected]" <[email protected]> >> Subject: Re: [HCP-Users] Spatial normalization of 50 Subjects T1w images >> >> Dear Sir, >> >> >> Now i have obtained 30 Healthy controls from the same scanner along with >> 50 subjects with Bilateral Vestibulopathy , I would like to use HCP >> pipelines for 1. Batch processing and also i would like to investigate the >> voxel-based cortical thickness ( as opposed to VBM , as you have cited in >> earlier mails ), could you please let me know how could i perform >> voxel-based cortical thickness, could you please suggest me some methods. >> >> >> >> Thanks >> Vasudev >> >> On 22 June 2016 at 15:51, Harms, Michael <[email protected]> wrote: >> >>> >>> Hi, >>> No, we don’t have any such phantom measurements available. And there >>> are a lot more issues at play in terms of differences between scanners than >>> just differing magnetic inhomogeneities anyway. >>> >>> 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: Dev vasu <[email protected]> >>> Date: Wednesday, June 22, 2016 at 1:03 AM >>> >>> To: "Harms, Michael" <[email protected]> >>> Cc: "[email protected]" <[email protected]> >>> Subject: Re: [HCP-Users] Spatial normalization of 50 Subjects T1w images >>> >>> Dear sir, >>> >>> >>> In order to avoid magnetic homogenities of different scanners, can i >>> take into consideration Field maps from HCP data and some Phantom >>> measurements ( like ACR Phantom Measurements ) ?, If so does HCP provides >>> data for Phantom Measurements ?. >>> >>> >>> >>> Thanks >>> Vasudev >>> >>> On 21 June 2016 at 21:53, Harms, Michael <[email protected]> wrote: >>> >>>> >>>> Hi, >>>> I’m sorry, but there is no way to model or account for the effect of >>>> possible scanner differences if you don’t have at least some of each group >>>> of subjects collected on each scanner. In your current situation, you have >>>> no mechanism to attempt to disentangle the effects of vestibulopathy vs. >>>> scanner. >>>> >>>> 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: Dev vasu <[email protected]> >>>> Date: Tuesday, June 21, 2016 at 2:36 PM >>>> >>>> To: "Harms, Michael" <[email protected]> >>>> Cc: "[email protected]" <[email protected]> >>>> Subject: Re: [HCP-Users] Spatial normalization of 50 Subjects T1w >>>> images >>>> >>>> Dear Sir, >>>> >>>> The vestibulopathy subject scans are from scanner outside HCP, we here >>>> in LMU Munich use Siemens Skyra 3T scanner, in such case how to neutralize >>>> or eliminate the differences which may occur due to scanner differences ?. >>>> >>>> >>>> Thanks >>>> Vasudev >>>> >>>> >>>> On 21 June 2016 at 21:29, Harms, Michael <[email protected]> wrote: >>>> >>>>> >>>>> Hi, >>>>> I would use a measure that relates in a concrete way to the underlying >>>>> neuroanatomy, such as cortical thickness. >>>>> >>>>> There may be a bigger issue here, which is that I’m now guessing that >>>>> your vestibulopathy subjects are coming from scans collected from outside >>>>> HCP? If so, you have a major confound, because you will be attempting to >>>>> compare two groups that were collected on completely different scanners. >>>>> In which case, any difference you find could be attributed to just scanner >>>>> difference effects. >>>>> >>>>> 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: <[email protected]> on behalf of Dev vasu < >>>>> [email protected]> >>>>> Date: Tuesday, June 21, 2016 at 2:02 PM >>>>> To: "Harms, Michael" <[email protected]> >>>>> Cc: "[email protected]" <[email protected]> >>>>> Subject: Re: [HCP-Users] Spatial normalization of 50 Subjects T1w >>>>> images >>>>> >>>>> Dear Professor, >>>>> >>>>> I was advised to do VBM, I understand questions pertaining to >>>>> biological validity of VBM and interpretation issues. I would like to >>>>> investigate the cortical regional differences between health controls and >>>>> controls with vestibulopathy , If you have any other suggestion pertaining >>>>> to this task i would really appreciate your response. >>>>> >>>>> >>>>> >>>>> Thanks >>>>> Vasudev >>>>> >>>>> On 21 June 2016 at 20:47, Harms, Michael <[email protected]> wrote: >>>>> >>>>>> Hi, >>>>>> If I may, why VBM? VBM is prone to a number of interpretational >>>>>> issues, as opposed to say cortical thickness, which is already available >>>>>> for you as part of the HCP processing. >>>>>> >>>>>> 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: <[email protected]> on behalf of Dev vasu < >>>>>> [email protected]> >>>>>> Date: Tuesday, June 21, 2016 at 1:30 PM >>>>>> To: Stamatios Sotiropoulos <[email protected]>, " >>>>>> [email protected]" <[email protected]>, >>>>>> "Glasser, Matthew" <[email protected]>, Timothy Brown < >>>>>> [email protected]> >>>>>> Subject: [HCP-Users] Spatial normalization of 50 Subjects T1w images >>>>>> >>>>>> Dear Sir , >>>>>> >>>>>> >>>>>> I am using HCP data ( 50 subjects ) + 50 patients with bilateral >>>>>> vestibular paresis to examine the Regional differences in cortical >>>>>> organization between healthy controls and patients for which i am using >>>>>> VBM, For spatial registration of 50 HCP subjects i would like to know if >>>>>> HCP offers some customized templates for registration or do i have to >>>>>> perform affine transformation and non linear registration, please kindly >>>>>> let me know . >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> Thanks >>>>>> Vasudev >>>>>> >>>>>> _______________________________________________ >>>>>> 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 >>>>> >>>>> >>>>> ------------------------------ >>>>> >>>>> 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. >>>> >>> >>> >>> ------------------------------ >>> >>> 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 > [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
