Hi.
I have a question about the slice thickness and gap information of the brain dataset.
We already know the slice thickness of the knee dataset, which is 3mm, and no gap between slices. But how about the brain dataset. We found that the neighbor slices are quite different in content. Could you offer the slice thickness and gap information about the brain dataset?
Thanks in advance.
Hello, you can find the slice information in the ‘ismrmrd_header’ field. You can use the ISMRMRD Python package to parse it.
I checked with a few people and to my knowledge no slice gaps are in the data set, but some files I checked did have bigger slices than the knee data set (5 mm brain vs. 3 mm knee).
Okay, thank you again!
Hi, could you please point me to where the slice thickness is in the ISMRMRD header?
For example copied below is (a) a list of all dictionary keys in the flattened XML and (b) the XML string read from file_brain_AXFLAIR_200_6002471.h5:
Thank you!
(a)
{http://www.w3.org/2001/XMLSchema-instance}schemaLocation studyInformation_studyTime measurementInformation_measurementID measurementInformation_patientPosition measurementInformation_protocolName measurementInformation_frameOfReferenceUID acquisitionSystemInformation_systemVendor acquisitionSystemInformation_systemModel acquisitionSystemInformation_systemFieldStrength_T acquisitionSystemInformation_relativeReceiverNoiseBandwidth acquisitionSystemInformation_receiverChannels acquisitionSystemInformation_coilLabel_coilNumber acquisitionSystemInformation_coilLabel_coilName acquisitionSystemInformation_institutionName experimentalConditions_H1resonanceFrequency_Hz encoding_encodedSpace_matrixSize_x encoding_encodedSpace_matrixSize_y encoding_encodedSpace_matrixSize_z encoding_encodedSpace_fieldOfView_mm_x encoding_encodedSpace_fieldOfView_mm_y encoding_encodedSpace_fieldOfView_mm_z encoding_reconSpace_matrixSize_x encoding_reconSpace_matrixSize_y encoding_reconSpace_matrixSize_z encoding_reconSpace_fieldOfView_mm_x encoding_reconSpace_fieldOfView_mm_y encoding_reconSpace_fieldOfView_mm_z encoding_trajectory encoding_encodingLimits_kspace_encoding_step_1_minimum encoding_encodingLimits_kspace_encoding_step_1_maximum encoding_encodingLimits_kspace_encoding_step_1_center encoding_encodingLimits_kspace_encoding_step_2_minimum encoding_encodingLimits_kspace_encoding_step_2_maximum encoding_encodingLimits_kspace_encoding_step_2_center encoding_encodingLimits_average_minimum encoding_encodingLimits_average_maximum encoding_encodingLimits_average_center encoding_encodingLimits_slice_minimum encoding_encodingLimits_slice_maximum encoding_encodingLimits_slice_center encoding_encodingLimits_contrast_minimum encoding_encodingLimits_contrast_maximum encoding_encodingLimits_contrast_center encoding_encodingLimits_phase_minimum encoding_encodingLimits_phase_maximum encoding_encodingLimits_phase_center encoding_encodingLimits_repetition_minimum encoding_encodingLimits_repetition_maximum encoding_encodingLimits_repetition_center encoding_encodingLimits_set_minimum encoding_encodingLimits_set_maximum encoding_encodingLimits_set_center encoding_encodingLimits_segment_minimum encoding_encodingLimits_segment_maximum encoding_encodingLimits_segment_center encoding_parallelImaging_accelerationFactor_kspace_encoding_step_1 encoding_parallelImaging_accelerationFactor_kspace_encoding_step_2 encoding_parallelImaging_calibrationMode sequenceParameters_TR sequenceParameters_TE sequenceParameters_TI sequenceParameters_flipAngle_deg sequenceParameters_sequence_type sequenceParameters_echo_spacing userParameters_userParameterDouble
(b)