Re: [HCP-Users] gradient unwarp in preFS script

[Harms, Michael]

Hi Greg, Are you trying to re-process the HCP "unprocessed" data through the HCP pipelines?  If so, the grad coefficients from a "stock" Skyra scanner will not be the correct ones for the HCP Connectom scanner (which has a completely different, customized gradient set, from a stock Skyra). In general, we recommend applying the gradient unwarping, as it can only help bring everything into true alignment.  That said, the gradient nonlinearities are a particular issue for the Connectom scanner, and would be less of an issue for say a Trio. 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: mha...@wustl.edu From: <Book>, Gregory <gregory.b...@hhchealth.org> Date: Thursday, October 16, 2014 10:00 AM To: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> Subject: [HCP-Users] gradient unwarp in preFS script I’m continuing to fine-tune our preFS script for our data, and I’m running into trouble with the gradient unwarping step. I’ve obtained the .grad file from our Skyra scanner and running the HCP with it. It runs the gradient unwarp step, but seems to fail right after. If I set the GradientDistortionCoeffs variable in the script to “NONE”, the entire script runs without error.   I’m also wondering if this gradient unwarping step is necessary?       Here is the output from the console:   gradunwarp-INFO: Parsing /opt/HCP/coeff_AS098.grad for harmonics coeffs gradunwarp-INFO: Evaluating spherical harmonics gradunwarp-INFO: on a 60^3 grid gradunwarp-INFO: with extents -300.0mm to 300.0mm gradunwarp-INFO: along x... gradunwarp-INFO: along y... gradunwarp-INFO: along z... gradunwarp-INFO: Evaluating the jacobian multiplier gradunwarp-INFO: Unwarping slice by slice gradunwarp-INFO: Writing output to trilinear.nii.gz Image Exception : #22 :: ERROR: Could not open image /home/pipeline/onrc/data/pipeline/S5452FGE/4/HCPStructural/analysis/T1w/T1w1_GradientDistortionUnwarp/fullWarp_abs terminate called after throwing an instance of 'RBD_COMMON::BaseException' /opt/HCP/HCP/global/scripts/GradientDistortionUnwarp.sh: line 92: 11237 Aborted                 (core dumped) ${FSLDIR}/bin/convertwarp --abs --ref=$WD/trilinear.nii.gz --warp1=$WD/fullWarp_abs.nii.gz --relout --out=$OutputTransform   And the output from the log file: START: GradientDistortionUnwarp . . . . . . . . . 10 . . . . . . . . . 20 . . . . . . . . . 30 . . . . . . . . . 40 . . . . . . . . . 50 . . . . . . . . . 60 . . . . . . . . . 70 . . . . . . . . . 80 . . . . . . . . . 90 . . . . . . . . . 100 . . . . . . . . . 110 . . . . . . . . . 120 . . . . . . . . . 130 . . . . . . . . . 140 . . . . . . . . . 150 . . . . . . . . . 160 . . . . . . . . . 170 . . . . . . . . . 180 . . . . . . . . . 190 . . . . . . . . . 200 . . . . . . . . . 210 . . . . . . . . . 220 . . . . . . . . . 230 . . . . . . . . . 240 . . . . . . . . . 250 . . . . . . . . . 260 . . . . . . . . . 270 . . . . . . . . . 280 . . . . . . . . . 290 . . . . . . . . . 300 . . . . . . . . . 310 . . . . . . . . . 320 set -- --path=/home/pipeline/onrc/data/pipeline/S5452FGE/4/HCPStructural       --subject=analysis       --t1=/home/pipeline/onrc/data/pipeline/S5452FGE/4/HCPStructural/analysis/unprocessed/3T/T1w_MPR1/analysis_3T_T1w_MPR1.nii.gz@       --t2=/home/pipeline/onrc/data/pipeline/S5452FGE/4/HCPStructural/analysis/unprocessed/3T/T2w_SPC1/analysis_3T_T2w_SPC1.nii.gz@       --t1template=/opt/HCP/HCP/global/templates/MNI152_T1_0.7mm.nii.gz       --t1templatebrain=/opt/HCP/HCP/global/templates/MNI152_T1_0.7mm_brain.nii.gz       --t1template2mm=/opt/HCP/HCP/global/templates/MNI152_T1_2mm.nii.gz       --t2template=/opt/HCP/HCP/global/templates/MNI152_T2_0.7mm.nii.gz       --t2templatebrain=/opt/HCP/HCP/global/templates/MNI152_T2_0.7mm_brain.nii.gz       --t2template2mm=/opt/HCP/HCP/global/templates/MNI152_T2_2mm.nii.gz       --templatemask=/opt/HCP/HCP/global/templates/MNI152_T1_0.7mm_brain_mask.nii.gz       --template2mmmask=/opt/HCP/HCP/global/templates/MNI152_T1_2mm_brain_mask_dil.nii.gz       --brainsize=150       --fnirtconfig=/opt/HCP/HCP/global/config/T1_2_MNI152_2mm.cnf       --fmapmag=/home/pipeline/onrc/data/pipeline/S5452FGE/4/HCPStructural/analysis/unprocessed/3T/T1w_MPR1/analysis_3T_FieldMap_Magnitude.nii.gz       --fmapphase=/home/pipeline/onrc/data/pipeline/S5452FGE/4/HCPStructural/analysis/unprocessed/3T/T1w_MPR1/analysis_3T_FieldMap_Phase.nii.gz       --echodiff=2.46       --SEPhaseNeg=NONE       --SEPhasePos=NONE       --echospacing=NONE       --seunwarpdir=NONE \           --t1samplespacing=0.0000065       --t2samplespacing=0.0000023       --unwarpdir=z       --gdcoeffs=/opt/HCP/coeff_AS098.grad       --avgrdcmethod=FIELDMAP       --topupconfig=NONE       --printcom= . /opt/HCP/HCP/Examples/Scripts/SetUpHCPPipeline.sh _________________________________________________ Gregory Book Senior Technology Manager Olin Neuropsychiatry Research Center, Institute of Living, Hartford Hospital 200 Retreat Avenue Hartford, CT 06106 Tel: 860-545-7267 Fax: 860-545-7797 gregory.b...@hhchealth.org http://nidb.sourceforge.net   This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure, or distribution is prohibited. If you are not the intended recipient, or an employee or agent responsible for delivering the message to the intended recipient, please contact the sender by reply e-mail and destroy all copies of the original message, including any attachments. _______________________________________________ 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