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. > _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
