I'm sorry, I made a mistake. It is 0.00051000424 indeed. My question now is only whether to let the digits in the end stay or whether to use 0.00051 as you wrote?
thanks a lot! Lisa On 8 May 2017 at 17:24, Lisa Kramarenko <lisa.kramare...@gmail.com> wrote: > thanks! so should I put in 0.00051 or 0.005100042 (as it is the exact > number coming out of the calculation)? > > On 8 May 2017 at 17:21, Harms, Michael <mha...@wustl.edu> wrote: > >> >> If you meant 0.00051, then yes, that is the right order of magnitude. >> >> -- >> 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 <(314)%20747-6173> >> St. Louis, MO 63110 Email: mha...@wustl.edu >> >> From: <hcp-users-boun...@humanconnectome.org> on behalf of Lisa >> Kramarenko <lisa.kramare...@gmail.com> >> Date: Monday, May 8, 2017 at 10:11 AM >> To: "Glasser, Matthew" <glass...@wustl.edu> >> Cc: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> >> Subject: Re: [HCP-Users] Fwd: Fwd: Error in fMRI Volume Processing >> Pipeline >> >> thank you, it helped! just to verify: the value in the (0019, 1028) is >> 30.637 and in the (0051, 100b) it's 64x64, so that i calculate >> 1/(30.637*64) which results in 0.005100042. does it look correct? >> >> thanks a lot! >> >> On 4 May 2017 at 14:54, Glasser, Matthew <glass...@wustl.edu> wrote: >> >>> This tool should help: http://nrg.wustl.edu/software/dicom-browser/ >>> >>> Peace, >>> >>> Matt. >>> >>> From: <hcp-users-boun...@humanconnectome.org> on behalf of Lisa >>> Kramarenko <lisa.kramare...@gmail.com> >>> Date: Thursday, May 4, 2017 at 9:27 PM >>> To: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> >>> Subject: [HCP-Users] Fwd: Fwd: Error in fMRI Volume Processing Pipeline >>> >>> Thanks so much. I am not sure as to where find the necessary DICOM >>> fields ((0019,1028) for BandwidthPerPixelPhaseEncode and (0051,100b) for # >>> of phase encoding samples). Where should I look for them? >>> Thanks again! >>> >>> On 3 May 2017 at 21:08, Glasser, Matthew <glass...@wustl.edu> wrote: >>> >>>> Indeed you need to provide a dwell time for fMRI. This is the dwell >>>> time of the fMRI scan. If that doesn’t fix things up, please post the >>>> launcher script you are using to call the pipeline. >>>> >>>> Peace, >>>> >>>> Matt. >>>> >>>> From: <hcp-users-boun...@humanconnectome.org> on behalf of Lisa >>>> Kramarenko <lisa.kramare...@gmail.com> >>>> Date: Wednesday, May 3, 2017 at 2:04 PM >>>> To: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> >>>> Subject: [HCP-Users] Fwd: Error in fMRI Volume Processing Pipeline >>>> >>>> I called it as ./GenericfMRIVolumeProcessingPipelineBatch.sh >>>> --runlocal from the folder with the Example scripts, like i previously did >>>> with the structural ones. >>>> >>>> I filled in "NONE" everywhere except for DistortionCorrection="FIELDMAP", >>>> MagnitudeInputName, PhaseInputName (and of course things like >>>> FinalFMRIResolution="2", DeltaTE="2.46"). As I understand the error it >>>> seems that I have to have some value in the Dwell Time? But I thought it's >>>> possible to set in to NONE and it's enough to only provide Magnitude and >>>> Phase? Or do I need Dwell Time regardless? >>>> would it be easier to attach the modified script so you can look at it >>>> first hand? >>>> >>>> Thanks a lot! >>>> >>>> >>>> On 27 April 2017 at 15:06, Glasser, Matthew <glass...@wustl.edu> wrote: >>>> >>>>> How did you call the pipeline? Indeed it seems as though you didn’t >>>>> put “NONE” in all of the places you needed to. Note that you must have a >>>>> field map of some kind for the fMRIVolume pipeline to run. >>>>> >>>>> Peace, >>>>> >>>>> Matt. >>>>> >>>>> From: <hcp-users-boun...@humanconnectome.org> on behalf of Lisa >>>>> Kramarenko <lisa.kramare...@gmail.com> >>>>> Date: Thursday, April 27, 2017 at 4:46 AM >>>>> To: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> >>>>> Subject: [HCP-Users] Error in fMRI Volume Processing Pipeline >>>>> >>>>> Dear users, >>>>> >>>>> I am not sure whether I should turn to you or to the FSL mailing list, >>>>> but I will try my luck here first. I suspect it has something to do with >>>>> filling in values in the GenericfMRIVolumeProcessingPipelineBatch.sh >>>>> script (because of the illegal characters almost spelling "NONE" and it >>>>> complaining that the dwell time is set to NONE). You can see my settings >>>>> on >>>>> the bottom. The error message is this: >>>>> >>>>> "END: Field Map Preprocessing and Gradient Unwarping >>>>> (standard_in) 1: illegal character: N >>>>> (standard_in) 1: illegal character: O >>>>> (standard_in) 1: illegal character: N >>>>> (standard_in) 1: illegal character: N >>>>> (standard_in) 1: illegal character: O >>>>> (standard_in) 1: illegal character: N >>>>> /home/guestuser/Desktop/lisa/Pipelines/global/scripts/epi_reg_dof: >>>>> line 182: [: =: unary operator expected >>>>> Running FAST segmentation >>>>> FLIRT pre-alignment >>>>> Registering fieldmap to structural >>>>> Running BBR with fieldmap >>>>> 0.482078 0.999999 -0.000744 -0.001198 0.000000 0.000738 0.999984 >>>>> -0.005527 0.000000 0.001202 0.005526 0.999984 0.000000 0.157694 2.242522 >>>>> 5.317938 1.000000 >>>>> Making warp fields and applying registration to EPI series >>>>> >>>>> Part of FSL (build 509) >>>>> fugue >>>>> FMRIB's Utility for Geometric Unwarping of EPIs >>>>> Copyright(c) 2000-2008, University of Oxford (Mark Jenkinson) >>>>> >>>>> Usage: >>>>> fugue -i <epi> -p <unwrapped phase map> -d <dwell-to-asym-ratio> -u >>>>> <result> [options] >>>>> fugue -i <unwarped-image> -p <unwrapped phase map> -d >>>>> <dwell-to-asym-ratio> -w <epi-like-result> [options] >>>>> fugue -p <unwrapped phase map> -d <dwell-to-asym-ratio> >>>>> --saveshift=<shiftmap> [options] >>>>> >>>>> Optional arguments (You may optionally specify one or more of): >>>>> -i,--in filename of input volume >>>>> -u,--unwarp apply unwarping and save as filename >>>>> -w,--warp apply forward warp and save as filename >>>>> -p,--phasemap filename for input phase image >>>>> -d,--dwelltoasym set the dwell to asym time ratio >>>>> --dwell set the EPI dwell time per phase-encode line - same as >>>>> echo spacing - (sec) >>>>> --asym set the fieldmap asymmetric spin echo time (sec) >>>>> --savefmap filename for saving fieldmap (rad/s) >>>>> --loadfmap filename for loading fieldmap (rad/s) >>>>> --saveshift filename for saving pixel shift volume >>>>> --loadshift filename for reading pixel shift volume >>>>> -m,--median apply 2D median filtering >>>>> --despike apply a 2D de-spiking filter >>>>> --nofill do not apply gap-filling measure to the fieldmap >>>>> --noextend do not apply rigid-body extrapolation to the fieldmap >>>>> --smooth2 apply 2D Gaussian smoothing of sigma N (in mm) >>>>> -s,--smooth3 apply 3D Gaussian smoothing of sigma N (in mm) >>>>> --poly apply polynomial fitting of order N >>>>> --fourier apply Fourier (sinusoidal) fitting of order N >>>>> --pava apply monotonic enforcement via PAVA >>>>> --despikethreshold specify the threshold for de-spiking >>>>> (default=3.0) >>>>> --unwarpdir specifies direction of warping [x/y/z/x-/y-/z-] >>>>> (default y) >>>>> --phaseconj apply phase conjugate method of unwarping >>>>> --icorr apply intensity correction to unwarping (pixel shift >>>>> method only) >>>>> --icorronly apply intensity correction only (must specify >>>>> output with -u,--unwarp) >>>>> --mask filename for loading valid mask >>>>> --unmaskfmap saves the unmasked fieldmap when using --savefmap >>>>> --unmaskshift saves the unmasked shiftmap when using --saveshift >>>>> --nokspace do not use k-space forward warping >>>>> --nocheck turn off all checking >>>>> -v,--verbose switch on diagnostic messages >>>>> -h,--help display this message >>>>> >>>>> --dwell: Couldn't set_value! valstr="NONE"! >>>>> Image Exception : #22 :: ERROR: Could not open image >>>>> /media/662A63022A62CE9D/lisa/StudyDirectory/008/rfMRI_REST1/ >>>>> DistortionCorrectionAndEPIToT1wReg_FLIRTBBRAndFreeSurferBBRb >>>>> ased/Scout_gdc_undistorted_fieldmaprads2epi_shift >>>>> terminate called after throwing an instance of >>>>> 'RBD_COMMON::BaseException' >>>>> /home/guestuser/Desktop/lisa/Pipelines/global/scripts/epi_reg_dof: >>>>> line 386: 149158 Aborted (core dumped) >>>>> $FSLDIR/bin/convertwarp -r ${vrefhead} -s ${vout}_fieldmaprads2epi_shift >>>>> --postmat=${vout}.mat -o ${vout}_warp --shiftdir=${fdir} --relout >>>>> Image Exception : #22 :: ERROR: Could not open image >>>>> /media/662A63022A62CE9D/lisa/StudyDirectory/008/rfMRI_REST1/ >>>>> DistortionCorrectionAndEPIToT1wReg_FLIRTBBRAndFreeSurferBBRb >>>>> ased/Scout_gdc_undistorted_warp >>>>> An error occured while reading file: /media/662A63022A62CE9D/lisa/S >>>>> tudyDirectory/008/rfMRI_REST1/DistortionCorrectionAndEPIToT1 >>>>> wReg_FLIRTBBRAndFreeSurferBBRbased/Scout_gdc_undistorted_warp >>>>> Image Exception : #22 :: ERROR: Could not open image >>>>> /media/662A63022A62CE9D/lisa/StudyDirectory/008/rfMRI_REST1/ >>>>> DistortionCorrectionAndEPIToT1wReg_FLIRTBBRAndFreeSurferBBRb >>>>> ased/Scout_gdc_undistorted_warp >>>>> An error occured while reading file: /media/662A63022A62CE9D/lisa/S >>>>> tudyDirectory/008/rfMRI_REST1/DistortionCorrectionAndEPIToT1 >>>>> wReg_FLIRTBBRAndFreeSurferBBRbased/Scout_gdc_undistorted_warp.nii.gz >>>>> set -- --path=/media/662A63022A62CE9D/lisa/StudyDirectory >>>>> --subject=008 --fmriname=rfMRI_REST1 >>>>> --fmritcs=/media/662A63022A62CE9D/lisa/StudyDirectory/008/un >>>>> processed/3T/rfMRI_REST1/008_3T_rfMRI_REST1.nii.gz >>>>> --fmriscout=NONE --SEPhaseNeg=NONE --SEPhasePos=NONE >>>>> --fmapmag=/media/662A63022A62CE9D/lisa/StudyDirectory/008/un >>>>> processed/3T/rfMRI_REST1/008_rfMRI_REST1_FieldMap_Magnitude.nii >>>>> --fmapphase=/media/662A63022A62CE9D/lisa/StudyDirectory/008/ >>>>> unprocessed/3T/rfMRI_REST1/008_rfMRI_REST1_FieldMap_Phase.nii >>>>> --fmapgeneralelectric=NONE --echospacing=NONE >>>>> --echodiff=2.46 --unwarpdir=-y --fmrires=2 >>>>> --dcmethod=FIELDMAP --gdcoeffs=NONE --topupconfig=NONE >>>>> --printcom= --biascorrection=NONE --mctype=MCFLIRT >>>>> >>>>> Any ideas of what can be wrong? >>>>> >>>>> Thanks a lot! >>>>> >>>>> Lisa >>>>> >>>>> _______________________________________________ >>>>> 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 >>> >>> >>> ------------------------------ >>> >>> 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
