Whatever you want. 0.00051 will be precise enough. -- 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: mha...@wustl.edu
From: <hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Lisa Kramarenko <lisa.kramare...@gmail.com<mailto:lisa.kramare...@gmail.com>> Date: Monday, May 8, 2017 at 10:40 AM To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Subject: [HCP-Users] Fwd: Fwd: Fwd: Error in fMRI Volume Processing Pipeline 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<mailto: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<mailto: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<tel:(314)%20747-6173> St. Louis, MO 63110Email: mha...@wustl.edu<mailto:mha...@wustl.edu> From: <hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Lisa Kramarenko <lisa.kramare...@gmail.com<mailto:lisa.kramare...@gmail.com>> Date: Monday, May 8, 2017 at 10:11 AM To: "Glasser, Matthew" <glass...@wustl.edu<mailto:glass...@wustl.edu>> Cc: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto: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<mailto:glass...@wustl.edu>> wrote: This tool should help: http://nrg.wustl.edu/software/dicom-browser/ Peace, Matt. From: <hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Lisa Kramarenko <lisa.kramare...@gmail.com<mailto:lisa.kramare...@gmail.com>> Date: Thursday, May 4, 2017 at 9:27 PM To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto: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<mailto: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<mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Lisa Kramarenko <lisa.kramare...@gmail.com<mailto:lisa.kramare...@gmail.com>> Date: Wednesday, May 3, 2017 at 2:04 PM To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto: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<mailto: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<mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Lisa Kramarenko <lisa.kramare...@gmail.com<mailto:lisa.kramare...@gmail.com>> Date: Thursday, April 27, 2017 at 4:46 AM To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto: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_FLIRTBBRAndFreeSurferBBRbased/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_FLIRTBBRAndFreeSurferBBRbased/Scout_gdc_undistorted_warp An error occured while reading file: /media/662A63022A62CE9D/lisa/StudyDirectory/008/rfMRI_REST1/DistortionCorrectionAndEPIToT1wReg_FLIRTBBRAndFreeSurferBBRbased/Scout_gdc_undistorted_warp Image Exception : #22 :: ERROR: Could not open image /media/662A63022A62CE9D/lisa/StudyDirectory/008/rfMRI_REST1/DistortionCorrectionAndEPIToT1wReg_FLIRTBBRAndFreeSurferBBRbased/Scout_gdc_undistorted_warp An error occured while reading file: /media/662A63022A62CE9D/lisa/StudyDirectory/008/rfMRI_REST1/DistortionCorrectionAndEPIToT1wReg_FLIRTBBRAndFreeSurferBBRbased/Scout_gdc_undistorted_warp.nii.gz set -- --path=/media/662A63022A62CE9D/lisa/StudyDirectory --subject=008 --fmriname=rfMRI_REST1 --fmritcs=/media/662A63022A62CE9D/lisa/StudyDirectory/008/unprocessed/3T/rfMRI_REST1/008_3T_rfMRI_REST1.nii.gz --fmriscout=NONE --SEPhaseNeg=NONE --SEPhasePos=NONE --fmapmag=/media/662A63022A62CE9D/lisa/StudyDirectory/008/unprocessed/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<mailto: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<mailto: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<mailto: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<mailto: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<mailto: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
