Dear all, I've acquired the T1w and T2w images on the GE scanner, additionally, as advised we've acquired a B1 field map. I've been trying to use the HCP tools for volume to surface registration of the B1 map, but so far have had no success. I found an mri_vol2surf co-registration algorithm used within recon-all that I wanted to adapt (found no related commands in the PostFreesurferPipelineBatch.sh or SetUpHCPPipeline.sh), but it does not seem to work.
I wonder if you could please help out? This is what I tried: flirt -in REF066p_FieldMap.nii.gz -ref T1w/T1w_acpc_dc_restore.nii.gz -dof 6 -out REF066p_FieldMap_coreg.nii.gz mri_convert -rt nearest -rl T1w/T1w_acpc_dc_restore.nii.gz REF066p_FieldMap_coreg.nii.gz REF066p_FieldMap_coreg_resliced.nii.gz mri_vol2surf --mov REF066p_FieldMap_coreg_resliced.nii.gz --hemi lh --noreshape --interp trilinear --o REF066p_FieldMap_coreg_resliced.lh.mgz --projfrac 0.3 --regheader REF066p --cortex mri_vol2surf --mov REF066p_FieldMap_coreg_resliced.nii.gz --hemi rh --noreshape --interp trilinear --o REF066p_FieldMap_coreg_resliced.rh.mgh --projfrac 0.3 --regheader REF066p --cortex Thank you very much, Best wishes, Barbara On Tue, Dec 1, 2015 at 4:29 PM, Gaurav Patel <[email protected]> wrote: > Just a warning from another GE user, we have not been able to replicate > the myelin maps in Glasser/Van Essen with standard GE sequences on our > MR750 (see previous threads on this forum about that). If you do have > success we'd love to know how. We now have approval to run a GE prototype > of the MPRAGE on our scanner, so hopefully soon we'll see if that solves > the problem. > > __________________________ > gaurav patel > [email protected] > www.neurofreak.net > > > > > On Nov 27, 2015, at 1:15 PM, Harms, Michael wrote: > > > > > 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: [email protected] > > > > From: Rachel Woodall <[email protected]> > > Date: Thursday, November 26, 2015 6:00 AM > > To: "Harms, Michael" <[email protected]> > > 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 <[email protected]> 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: [email protected] > >> > >> From: Rachel Woodall <[email protected]> > >> Date: Thursday, November 19, 2015 8:28 AM > >> To: "Harms, Michael" <[email protected]> > >> 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 <[email protected]> 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: [email protected] > >>> > >>> From: Rachel Woodall <[email protected]> > >>> Date: Wednesday, November 18, 2015 4:57 AM > >>> To: "[email protected]" <[email protected]> > >>> 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: [email protected] > >>> Tel: 07850 238791 > >>> _______________________________________________ > >>> 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. > >> > >> > >> > >> -- > >> Rachel Woodall > >> > >> Research Associate > >> University of York > >> Department of Psychology > >> YO10 5DD > >> > >> Email: [email protected] > >> 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: [email protected] > > 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 > > [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
