Re: [HCP-Users] MRI parameters

[Harms, Michael]

Please cc the list, so that others can respond and benefit from the exchange. No, we don't have an issue with TR/TE changing between our structural scans on Siemens scanners.  Is there perhaps a mode of operation of a GE scanner that overrides that sort of behavior, so that it keeps TR/TE completely constant?  If you're operating the scanner in a regime where RF deposition is near its limit, you might have to intentionally "back off" to derive a set of parameters that will basically work for all subjects. 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: Rachel Woodall <rachel.wood...@york.ac.uk> Date: Thursday, November 26, 2015 6:00 AM To: "Harms, Michael" <mha...@wustl.edu> Subject: Re: [HCP-Users] MRI parameters Hi Michael, Apologies, I probably did not make myself very clear. I set up my scan protocol, assuming that the parameters I used would be fixed and the same for every scan.  However, upon checking the DICOM information after the scan, the TR and TE have differed from what was input. I have asked my radiographer whether this would be expected and he said that the differences between the two sets of parameters are trivial and I do not believe (in the absence of the parameters) that you would be able to distinguish one from the other.  All GE systems will modify certain parameters based on a patients weight (especially FSE T2 waited scans where RF deposition is high) and as a consequence the effective TE will vary by a few milliseconds. The nature of my project requires a follow up of the same participants so I am now concerned that the follow up scan will not match the original and what effect this has on the data. Therefore, I wanted to contact someone within the HCP to see if this is also something you have experienced when the image parameters have been checked post-scan. Thanks again for your help. Kind regards, Rachel On 19 November 2015 at 14:39, Harms, Michael <mha...@wustl.edu> wrote: Hi, I'm not following the context for the question.  I've never heard of people varying TR/TE across participants for structural scans.  Is someone suggesting that you do that?    When you set up a protocol on a scanner, you set the TR/TE, so by default, the values will be the same across participants. If you vary TR/TE, you are changing the MR contrast, which can have all kinds of implications. 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: Rachel Woodall <rachel.wood...@york.ac.uk> Date: Thursday, November 19, 2015 8:28 AM To: "Harms, Michael" <mha...@wustl.edu> Subject: Re: [HCP-Users] MRI parameters Dear Michael, Many thanks for your reply. The TR and TE were selected as 7.78ms and 2.98ms for the T1w and 2500ms and 84.9ms for the T2w.  You are suggesting that these parameters should be fixed to prevent any variation, possibly as a result of an individuals weight? Also, what would the implications be of comparing data within and between participants if there is a variation in the TR/TE?  Is there any implication to the HCP pipeline process if the parameters vary? Kind regards, Rachel Woodall On 18 November 2015 at 14:33, Harms, Michael <mha...@wustl.edu> wrote: The particular choice of TR/TE may vary between studies, but for a given study they are typically fixed for all the participants. 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: Rachel Woodall <rachel.wood...@york.ac.uk> Date: Wednesday, November 18, 2015 4:57 AM To: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> Subject: [HCP-Users] MRI parameters Hello, I am using MRI parameters for the structural T1w and T2w scans from the Glasser and Van Essen 2011 paper.  Are these parameters, particularly the TE and TR, fixed or do they/are they expected to vary between participants and scans? Thank you in advance for your help. Kind regards, Rachel -- Rachel Woodall Research Associate University of York Department of Psychology YO10 5DD Email: rachel.wood...@york.ac.uk Tel: 07850 238791 _______________________________________________ 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. -- Rachel Woodall Research Associate University of York Department of Psychology YO10 5DD Email: rachel.wood...@york.ac.uk Tel: 07850 238791   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. -- Rachel Woodall Research Associate University of York Department of Psychology YO10 5DD Email: rachel.wood...@york.ac.uk Tel: 07850 238791   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