general-discussion > Delay in TR
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Dec 22, 2010  09:12 PM | Claire Han
Delay in TR
Is the delay in TR usually 20ms in fMRI studies? (my TR is 2300ms and TE is 30ms)
Could you guide me on how to calculate the delay in TR?

Thanks,
Claire
Dec 24, 2010  10:12 AM | Pierre Bellec
RE: Delay in TR
Dear Claire,

Sorry for the delay in answering this post. If you converted the datasets from DICOM to MINC using a recent version of DCM2MNC, you will find this information in the header. If you type the following line in a terminal :

mincheader my_vol.mnc | grep delay

You'll get something like :
acquisition:delay_in_TR = 0. ;

Note that you can get the full details of the protocol in the header ;
mincheader my_vol.mnc | more

This command will produce a lot of infos. If you scroll down to the "acquisition" section, you'll get something like :
int acquisition ;
acquisition:parent = "rootvariable" ;
acquisition:varid = "MINC standard variable" ;
acquisition:vartype = "group________" ;
acquisition:version = "MINC Version 1.0" ;
acquisition:acquisition_id = "3" ;
acquisition:start_time = "20100723 163820.093000 " ;
acquisition:series_time = "171133.156000 " ;
acquisition:acquisition_time = "171049.875000 " ;
acquisition:image_time = "171133.156000 " ;
acquisition:scanning_sequence = "*epfid2d1_64" ;
acquisition:series_description = "ep2d_bold_rest" ;
acquisition:protocol = "ep2d_bold_rest" ;
acquisition:receive_coil = "0 " ;
acquisition:transmit_coil = "Body" ;
acquisition:repetition_time = 2. ;
acquisition:echo_time = 0.03 ;
acquisition:echo_number = 1. ;
acquisition:echo_train_length = 1. ;
acquisition:flip_angle = 90. ;
acquisition:slice_thickness = 4. ;
acquisition:num_slices = 33. ;
acquisition:slice_order = "interleaved" ;
acquisition:delay_in_TR = 0. ;
acquisition:num_dyn_scans = 300. ;
acquisition:num_averages = 1. ;
acquisition:imaging_frequency = 123105436. ;
acquisition:imaged_nucleus = "1H" ;
acquisition:window_center = 750. ;
acquisition:window_width = 1621. ;
acquisition:num_phase_enc_steps = 64. ;
acquisition:percent_sampling = 100. ;
acquisition:percent_phase_fov = 100. ;
acquisition:pixel_bandwidth = 2230. ;
acquisition:phase_enc_dir = "COL " ;
acquisition:SAR = 0.15541185184842 ;
acquisition:mr_acq_type = "2D" ;
acquisition:image_type = "ORIGINAL\\PRIMARY\\M\\ND\\MOSAIC" ;

I hope this helps,

Pierre
Dec 26, 2010  04:12 PM | Claire Han
RE: Delay in TR
Thanks for such detailed response, Pierre!
Claire