Hi, I’ve been adapting the extremely useful HCP pipelines for application to our own data, and would like some advice regarding the PreFreeSurferPipeline.
1. 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? 2. 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 <http://about.me/matthewliptrot> 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 <http://about.me/matthewliptrot> _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
