Re: [HCP-Users] PreFreeSurferPipeline

[Harms, Michael]

FWIW, while you should use DICOM field (0019, 1018) as Matt said, I believe that the correct formula to come close to that would be: DwellTime = 1 / (PixelBandwidthInReadOutDirection * nReadOut * 2) where  PixelBandwidthInReadOutDirection = DICOM (0018,0095) nReadOut = MatrixSize in the READOUT direction and the factor 2 is to account for the 2x oversampling that is automatically applied. I believe that you can get nReadOut as the 2nd element of (0051 100b). Not sure if that formula handles all possibilities, but try it and see if the ensuing result isn't closer to what is contained in (0019, 1018). (It matches for HCP data, acquired with iPAT = 2). 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: <Glasser>, Matt Glasser <glass...@wusm.wustl.edu> Date: Tuesday, November 25, 2014 10:47 AM To: Matthew George Liptrot <matthew.lipt...@di.ku.dk>, "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> Subject: Re: [HCP-Users] PreFreeSurferPipeline I would probably try to upsample rather than downsample to take advantage of your 0.9mm T1w (we’ve not tried 0.9mm before, but given how much better 0.8mm is than 1mm, it would probably be worth it).  You could see if things run smoothly if you just use the 0.8mm template, or otherwise could create 0.9mm versions by downsampling one of the higher resolutions.   Just take the value in seconds directly from DICOM field (0019,1018).  Which in your case would be 0.0000098 and 0.0000026. Peace, Matt. From: Matthew George Liptrot <matthew.lipt...@di.ku.dk> Date: Tuesday, November 25, 2014 at 9:40 AM To: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> Subject: [HCP-Users] PreFreeSurferPipeline Hi, I’ve been adapting the extremely useful HCP pipelines for application to our own data, and would like some advice regarding the PreFreeSurferPipeline. The HCP T1w and T2w data are at 0.7mm resolution, whereas our T1w is 0.9mm, and T2w is 1.0mm (both isotropic). Would it be best to register both to the 1mm MNI template? For the Readout Distortion Correction, using Siemens Gradient Echo Field Maps (Siemens Verio 3T), I need to specify the “T1wSampleSpacing” and “T2wSampleSpacing”, which I presume is the dwell-time. In the example script (PreFreeSurferPipelineBatch.sh), values of 7.4 (T1) and 2.1 (T2) microsecs are pre-coded, and reference DICOM field (0019,1018). In our images, this field contains the values 9800 (T1) and 2600 (T2), which would imply that they are specified in nanoseconds. Also, if I use the formula DwellTime = 1 / (PixelBandwidth * NumberPhaseEncodeSteps), then I get 19.7 (T1) and 5.6 (T2) microseconds. I get PixelBandwidth from DICOM (0018,0095), and NumberPhaseEncodeSteps from DICOM (0018,0089). Which is correct? Why aren’t they the same (GRAPPA correction, maybe?) Many thanks in advance for any pointers Cheers, M@ --  Matthew George Liptrot Department of Computer Science University of Copenhagen &  Section for Cognitive Systems Department of Applied Mathematics and Computer Science Technical University of Denmark http://about.me/matthewliptrot _______________________________________________ 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. 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