Hi guys - if the brain is centred on isocentre the gradwarp on a Skyra should be about 1-2mm max within the brain. Cheers, Steve.
On 16 Oct 2014, at 16:16, Harms, Michael <mha...@wustl.edu> wrote: > > In that case, I don't know what the degree of gradient nonlinearity is for a > stock Skyra. But I'd try to get the gradient nonlinearity correction working > nonetheless. You might have to do some more sleuthing to narrow down where > the error is arising before someone here can attempt to assist you. > > Namely, which image is this referring to? > Image Exception : #22 :: ERROR: Could not open image > > > 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 10:11 AM > To: "Harms, Michael" <mha...@wustl.edu>, "hcp-users@humanconnectome.org" > <hcp-users@humanconnectome.org> > Subject: RE: [HCP-Users] gradient unwarp in preFS script > > I’m processing our own raw data, collected on our stock Skyra. Our data was > collected using the HCP sequence recommendation. > -G > > From: Harms, Michael [mailto:mha...@wustl.edu] > Sent: Thursday, October 16, 2014 11:08 AM > To: Book, Gregory; hcp-users@humanconnectome.org > Subject: Re: [HCP-Users] gradient unwarp in preFS script > > > 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. > > > 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 > --------------------------------------------------------------------------- Stephen M. Smith, Professor of Biomedical Engineering Associate Director, Oxford University FMRIB Centre FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK +44 (0) 1865 222726 (fax 222717) st...@fmrib.ox.ac.uk http://www.fmrib.ox.ac.uk/~steve --------------------------------------------------------------------------- Stop the cultural destruction of Tibet _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
