The echo spacing in the Siemens PDF does need to be divided by the ipat/GRAPPA factor. Multi-band has no effect on echo spacing. Peace, Matt. On 3/21/14 11:37 AM, "julia" <[log in to unmask]> wrote: >Hi Michael, > >thanks for the helpful comment. >Does that mean if I have the two parameters 'Echo Spacing' and >'Multiband Acceleration Factor' from the Siemens report at hand I don't >even need the information from the DICOM header (which in not >implemented in my case either)? > >Many thanks, >Julia > > >On 03/13/2014 03:22 PM, Harms, Michael wrote: >> To further add to this (and hopefully not add any confusion), the >>formula >> that Matt supplied for Siemen's acquisitions: >> Echo Spacing = 1 / [(0019,1028) * (0051,100b component #1)] >> where >> 0019 1028: BandwidthPerPixelPhaseEncode -- BW in PE direction (Hz) >> and >> 0051 100b: AcquisitionMatrixText (gives size of *reconstructed* matrix) >> works regardless of whether GRAPPA is used because both variables are >> specified in terms of the *reconstructed* image. >> Note that this is therefore the *effective* echo spacing, which is what >> you want to use in the FSL tools. >> >> The sanity check for all of this for Siemens is simply to compare to the >> ES that Siemen's reports on the Sequence tab of the protocol, keeping in >> mind that the ES that Siemen's reports is the *actual* echo spacing >> (actual time between even and odd echoes), so the ES that is reported on >> the Sequence tab does not change with iPAT factor. >> >> So, if you don't use GRAPPA, the two ES's should simply match. >> If you use GRAPPA, then you need to divide the ES reported on the >>Sequence >> tab by the iPAT factor, and that should then give you the "effective" >>ES, >> and match the value returned by the calculation >> Echo Spacing = 1 / [(0019,1028) * (0051,100b component #1)] >> >> >> 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: [log in to unmask] >> >> >> >> >> On 3/13/14 4:03 AM, "Mark Jenkinson" <[log in to unmask]> >>wrote: >> >>> Hi, >>> >>> That depends on exactly what is extracted as "# of phase encoding >>> samples". >>> If that is equal to the number of voxels in the reconstructed image >>>along >>> the phase encoding direction then you need to divide it by the >>> acceleration factor. If it is equal to the number of k-space lines >>> acquired in the phase encoding direction, then you do not need to >>>divide >>> by the acceleration factor, as this will already be less lines >>>(assuming >>> it is telling you about the number of lines that are actually >>>acquired). >>> >>> So I think the answer will depend on the system you are using and the >>>way >>> that you are extracting the necessary values. >>> >>> All the best, >>> Mark >>> >>> >>> On 13 Mar 2014, at 08:19, Estrid Jakobsen <[log in to unmask]> >>> wrote: >>> >>>> Thanks for all the helpful responses. To clarify, does this mean that >>>> for a GRAPPA sequence, I should calculate the dwell time as described >>>>by >>>> Matt and then divide that by the acceleration factor? As in: >>>> >>>> Dwelltime = (1/(BandwidthPerPixelPhaseEncode * # of phase encoding >>>> samples))/Acceleration factor >>>> >>>> Thanks again! >>>> >>>> Estrid >>>> >>>> >>>> **************** >>>> Estrid Jakobsen >>>> PhD Student, IMPRS NeuroCom >>>> Department of Neurophysics >>>> Max Planck Research Group Neuroanatomy and Connectivity >>>> Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig >>>> +49 341 9940-2423 >>>> >>>> ----- Original Message ----- >>>> From: "Mark Jenkinson" <[log in to unmask]> >>>> To: [log in to unmask] >>>> Sent: Thursday, March 13, 2014 12:32:54 AM >>>> Subject: Re: [FSL] Dwell time calculation for FUGUE >>>> >>>> Hi, >>>> >>>> Just to clarify for the record: >>>> >>>> - The "dwell time" required in FSL is indeed the "effective echo >>>> spacing" and for an unaccelerated sequence is equal to the amount of >>>> time taken between crossings of the k_y axis (in k-space, where >>>>k_x=0). >>>> That is, the time between one crossing and the next. >>>> >>>> - Partial Fourier does not affect this. >>>> >>>> - GRAPPA, or equivalent accelerations that skip lines of k-space, >>>> require the echo spacing to be divided by the acceleration factor >>>>(hence >>>> giving the "effective" echo spacing) >>>> >>>> I hope this helps. >>>> >>>> All the best, >>>> Mark >>>> >>>> >>>> On 12 Mar 2014, at 19:37, Joel Bruss <[log in to unmask]> >>>> wrote: >>>> >>>>> In this case, yes, but thanks for the caution. I'll switch it on my >>>>> end to search for "AcquisitionMatrixText" instead. >>>>> On 03/12/2014 02:27 PM, Harms, Michael wrote: >>>>>> Are you sure that the value of the "PhaseEncodingLines" string is >>>>>>the >>>>>> same >>>>>> as the first value of "AcquisitionMatrixText", in instances of >>>>>>GRAPPA, >>>>>> partial Fourier, etc? >>>>>> >>>>>> 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: [log in to unmask] >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> On 3/12/14 2:05 PM, "Joel Bruss" <[log in to unmask]> wrote: >>>>>> >>>>>>> Thanks for that, Matt. I'd read something similar before but the >>>>>>> DICOM >>>>>>> I have has "Unimplemented" in the 0019,1028 header field. 0051,100b >>>>>>> doesn't exist as well. I had to use the ascii header to grab the >>>>>>> same >>>>>>> information: >>>>>>> >>>>>>> dcmPic=`ls *dcm | sort -t. -k 5 -n | head -1 | tail -1` >>>>>>> BWpe=`strings $dcmPic | grep -A1 "BandwidthPerPixelPhaseEncode" | >>>>>>> head >>>>>>> -2 | tail -1` >>>>>>> dimpe=`strings $dcmPic | grep -A1 "PhaseEncodingLines" | head -1 | >>>>>>> awk >>>>>>> '{print $3}'` >>>>>>> dwellTime=`echo $BWpe $dimpe | awk '{print (1/($1*$2))}'` >>>>>>> >>>>>>> Hope this helps someone else. >>>>>>> >>>>>>> -Joel >>>>>>> >>>>>>> On 03/12/2014 01:58 PM, Matt Glasser wrote: >>>>>>>> For Siemens: >>>>>>>> >>>>>>>> #Echo Spacing or Dwelltime of fMRI image in seconds = >>>>>>>> 1/(BandwidthPerPixelPhaseEncode * # of phase encoding samples): >>>>>>>> DICOM >>>>>>>> field (0019,1028) = BandwidthPerPixelPhaseEncode, DICOM field >>>>>>>> (0051,100b) >>>>>>>> AcquisitionMatrixText first value (# of phase encoding samples) >>>>>>>> >>>>>>>> I believe this accounts for GRAPPA factors and partial fourier >>>>>>>>does >>>>>>>> not >>>>>>>> affect the echo spacing. >>>>>>>> >>>>>>>> Peace, >>>>>>>> >>>>>>>> Matt. >>>>>>>> >>>>>>>> On 3/12/14 1:33 PM, "Estrid Jakobsen" <[log in to unmask]> >>>>>>>>wrote: >>>>>>>> >>>>>>>>> Dear all, >>>>>>>>> >>>>>>>>> I am trying to do fieldmap correction of 7T EPI data using FUGUE, >>>>>>>>> which >>>>>>>>> requires input of a variable, 'dwell time'. If I've understood >>>>>>>>> correctly, >>>>>>>>> this variable actually refers to the 'effective echo spacing' >>>>>>>>> (rather >>>>>>>>> than simply the dwell time listed in the DICOM of the EPI data) >>>>>>>>>but >>>>>>>>> there >>>>>>>>> seem to be several methods to calculate it. >>>>>>>>> >>>>>>>>> 1. DwellTime = (EchoSpacing/GRAPPA)-1 >>>>>>>>> >>>>>>>>> 2. DwellTime = >>>>>>>>>EchoSpacing*((MatrixLines*PartialFourier/GRAPPA)-1) >>>>>>>>> >>>>>>>>> Which of these options (if either) is correct for running FUGUE? >>>>>>>>> >>>>>>>>> Many thanks! >>>>>>>>> >>>>>>>>> Estrid >>>>>> ________________________________ >>>>>> 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. >> >> ________________________________ >> 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.