Re: [HCP-Users] Spatial normalization of 50 Subjects T1w images

[Harms, Michael]

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: mha...@wustl.edu From: <hcp-users-boun...@humanconnectome.org> on behalf of Dev vasu <vasudevamurthy.devulapa...@gmail.com> Date: Thursday, June 23, 2016 at 10:02 AM To: "Harms, Michael" <mha...@wustl.edu> Cc: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> 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 <mha...@wustl.edu> 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: mha...@wustl.edu From: Dev vasu <vasudevamurthy.devulapa...@gmail.com> Date: Thursday, June 23, 2016 at 8:53 AM To: "Harms, Michael" <mha...@wustl.edu> Cc: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> 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 <mha...@wustl.edu> 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: mha...@wustl.edu From: Dev vasu <vasudevamurthy.devulapa...@gmail.com> Date: Wednesday, June 22, 2016 at 1:03 AM To: "Harms, Michael" <mha...@wustl.edu> Cc: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> 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 <mha...@wustl.edu> 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: mha...@wustl.edu From: Dev vasu <vasudevamurthy.devulapa...@gmail.com> Date: Tuesday, June 21, 2016 at 2:36 PM To: "Harms, Michael" <mha...@wustl.edu> Cc: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> 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 <mha...@wustl.edu> 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: mha...@wustl.edu From: <hcp-users-boun...@humanconnectome.org> on behalf of Dev vasu <vasudevamurthy.devulapa...@gmail.com> Date: Tuesday, June 21, 2016 at 2:02 PM To: "Harms, Michael" <mha...@wustl.edu> Cc: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> 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 <mha...@wustl.edu> 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: mha...@wustl.edu From: <hcp-users-boun...@humanconnectome.org> on behalf of Dev vasu <vasudevamurthy.devulapa...@gmail.com> Date: Tuesday, June 21, 2016 at 1:30 PM To: Stamatios Sotiropoulos <stamatios.sotiropou...@ndcn.ox.ac.uk>, "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org>, "Glasser, Matthew" <glass...@wustl.edu>, Timothy Brown <tbbr...@wustl.edu> 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 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. 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