Hi - no, in my experience running the post-hoc correction should look virtually identical to the on-scanner correction.
Note that this will not be the case for 2D (eg EPI) data because on-scanner can only be done 2D - so that won't match post-hoc 3D correction. Cheers. > On 11 Apr 2018, at 17:51, Kristian Loewe <k...@kristianloewe.com> wrote: > > Hi Michael, > > Thanks for the suggestion! By default, we are using the 3D correction on > the scanner. But I applied the 2D correction to the ND data set > separately to see what it looks like. The result is different from both > the 3D-scanner-correction and the offline-correction but looks > reasonable too. > > Is it the case that for HCP data the scanner-corrected images look > almost exactly the same as the offline-corrected images or is it > ok/normal for them to differ a bit, especially further away from the > isocenter? > > Cheers, > > Kristian > > > On 11.04.2018 15:42, Harms, Michael wrote: >> >> One thought: Are you sure you are using the “3D” (and not the “2D”) >> correction on the scanner? >> >> -- >> Michael Harms, Ph.D. >> >> ----------------------------------------------------------- >> >> Associate Professor of Psychiatry >> >> 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 >> >> On 4/11/18, 8:31 AM, "hcp-users-boun...@humanconnectome.org on behalf of >> Kristian Loewe" <hcp-users-boun...@humanconnectome.org on behalf of >> k...@kristianloewe.com> wrote: >> >> Hi Joo-won and Keith, >> >> I don't think that the table has been moved. Is there any information >> somewhere in the dicom header to double-check this? >> >> I am using the coeff_AS82.grad file for the Prisma data (the second >> command). The first command was what I used for the Verio data. Also, >> I double-checked that I am using the uncorrected volume as input. >> >> I am not sure if I am supposed/allowed to send screenshots of the >> actual data in the subject's native space to the list. I'm going to >> check that. Meanwhile, I asked our local MR team to acquire an >> additional data set using a phantom. The difference between the >> scanner-corrected image and the offline-corrected image is not as >> striking in this case but it's visible. Based on the phantom data, I >> am inclined to say that both corrections work reasonably well, even >> though they are not exactly the same. I also tried the >> offline-correction on some phantom EPI data and it seems to work well >> as it (together with EPI distortion correction) restores the original >> shape of the phantom pretty nicely. >> >> The differences between the correction variants applied to the >> subject's data are actually rather small inside the brain but become >> larger towards the neck, which is to be expected as the distance to >> the magnetic isocenter becomes greater in that direction. >> Nevertheless, I orginally thought that the differences between >> scanner- and offline-corrected images would be smaller than that. >> >> Find attached some plots of the T1 phantom data: >> >> T1_ND*.png - uncorrected images >> T1*.png - scanner-corrected images >> T1_ND_gdc*.png - offline-corrected images >> >> Cheers, >> >> Kristian >> >> >> PS: >> I am sending this email for the second time (apparently the attachment >> was too large). I am not sure if the first email was successfully >> cancelled. I apologize if you are receiving this twice now. >> >> >> Quoting "Kim, Joo-won" <joo-won....@mssm.edu>: >> >>> Hi Kristian, >>> >>> Have you moved table? If you moved the table, you should manually >>> subtract it from qform, sform, and/or affine matrix in the nifty >>> header. >>> >>> Best, >>> Joo-won >>> >>> --- >>> Joo-won Kim, Ph.D. >>> Postdoctoral Fellow >>> Translational and Molecular Imaging Institute >>> Icahn School of Medicine at Mount Sinai >>> >>> >>> From: <hcp-users-boun...@humanconnectome.org> on behalf of Keith >>> Jamison <kjami...@umn.edu> >>> Date: Monday, April 9, 2018 at 10:36 AM >>> To: Kristian Loewe <k...@kristianloewe.com> >>> Cc: HCP Users <hcp-users@humanconnectome.org> >>> Subject: Re: [HCP-Users] gradient nonlinearity correction question >>> >>> First make sure you're using the right coefficient file, copied >>> directly from the scanner. The Prisma should have a file called >>> coeff_AS82.grad, so the one you used in your *second* command above >>> should be correct. >>> Second is to be absolutely sure your input is the uncorrected volume (*_ND). >>> If you include some matched screenshots of the uncorrected, >>> offline-corrected, and scanner-corrected volumes, we can maybe help >>> evaluate the difference. >>> >>> >>> On Mon, Apr 9, 2018 at 4:09 AM, Kristian Loewe >>> <k...@kristianloewe.com<mailto:k...@kristianloewe.com>> wrote: >>> Thanks Keith, >>> >>> Cropping is turned off by default in the version of dcm2niix that >>> I'm using but I re-ran the conversion with "-x n" anyway. I also >>> used fslreorient2std as per your suggestion. Unfortunately, the >>> result is still the same. Do you have any other ideas? >>> >>> >>> Cheers, >>> >>> Kristian >>> >>> >>> Quoting Keith Jamison <kjami...@umn.edu<mailto:kjami...@umn.edu>>: >>> Some problems can arrise if the NIFTI files are unexpectedly manipulated >>> prior gradient_unwarp. Two things to check: >>> >>> 1. dcm2nii and dcm2niix has options to perform additional processing like >>> reorienting or cropping, some of which may be enabled by default. Make sure >>> those are all DISABLED. (for dcm2niix add "-x n" and for dcm2nii you can >>> add "-x N -r N" >>> 2. We also usually use "fslreorient2std <origT1> <origT1>_new and then >>> gradient_unwarp.py<https://urldefense.proofpoint.com/v2/url?u=http-3A__gradient-5Funwarp.py&d=DwQFaQ&c=shNJtf5dKgNcPZ6Yh64b-A&r=C4genPYC6QtMDghAR1Km4p6emgS7QcLRMzo8A8hTJKk&m=ZMuNtM9D5WoxjxPsNEf3nsA4vd9aenKnJbd7pJY5V6o&s=0fRXneyYj_8irqp1xYKJzBXtTZP9nixP-6_oGvClUEE&e=> >>> on >>> <origT1>_new >>> >>> -Keith >>> >>> >>> On Fri, Apr 6, 2018 at 12:05 PM, Kristian Loewe >>> <k...@kristianloewe.com<mailto:k...@kristianloewe.com>> >>> wrote: >>> Hi, >>> >>> I would like to use gradunwarp for offline gradient nonlinearity >>> correction of some data acquired on our local Siemens scanners. I used >>> dcm2niix to convert the dicom data to nifti format. After applying >>> gradunwarp to a T1 image in nifti format (the one that originally has >>> the _ND suffix), I proceeded to compare the result with the >>> Siemens-corrected T1 image. I expected that they would look very >>> similar but in fact they look quite different. I am wondering if this >>> is to be expected to some degree because of differences in the >>> correction algorithms or what else might be the reason for this. Could >>> it be the case, for example, that the wrong center is being used for >>> some reason? >>> >>> I have tried this for a T1 image acquired on a Verio and another one >>> from a Prisma using >>> >>> >>> gradient_unwarp.py<https://urldefense.proofpoint.com/v2/url?u=http-3A__gradient-5Funwarp.py&d=DwQFaQ&c=shNJtf5dKgNcPZ6Yh64b-A&r=C4genPYC6QtMDghAR1Km4p6emgS7QcLRMzo8A8hTJKk&m=ZMuNtM9D5WoxjxPsNEf3nsA4vd9aenKnJbd7pJY5V6o&s=0fRXneyYj_8irqp1xYKJzBXtTZP9nixP-6_oGvClUEE&e=> >>> T1.nii.gz T1_gdc.nii.gz siemens -g >>> coeff_AS097.grad >>> -n >>> >>> and >>> >>> >>> gradient_unwarp.py<https://urldefense.proofpoint.com/v2/url?u=http-3A__gradient-5Funwarp.py&d=DwQFaQ&c=shNJtf5dKgNcPZ6Yh64b-A&r=C4genPYC6QtMDghAR1Km4p6emgS7QcLRMzo8A8hTJKk&m=ZMuNtM9D5WoxjxPsNEf3nsA4vd9aenKnJbd7pJY5V6o&s=0fRXneyYj_8irqp1xYKJzBXtTZP9nixP-6_oGvClUEE&e=> >>> T1.nii.gz T1_gdc.nii.gz siemens -g coeff_AS82.grad >>> -n >>> >>> respectively. >>> >>> I would really appreciate any help or advice you can provide. >>> >>> Cheers, >>> >>> Kristian >>> >>> >>> Quoting Keith Jamison <kjami...@umn.edu<mailto:kjami...@umn.edu>>: >>> >>>> FYI, when available, you can enable it on the scanner in the >>>> "Resolution->Filter" tab with the "Distortion Correction" checkbox. It's >>>> often used for structural scans like MPRAGE, where you will see two DICOM >>>> folders in the output: <scanname> and <scanname>_ND. ND means "No >>>> Distortion [Correction]".. .A very confusing choice of acronym. You can >>>> then compare the online corrected (not _ND) and offline using gradunwarp. >>>> >>>> -Keith >>>> >>>> >>>> On Wed, Oct 19, 2016 at 4:44 PM, Glasser, Matthew >>>> <glass...@wustl.edu<mailto:glass...@wustl.edu>> >>>> wrote: >>>> >>>>> Some do for some sequences, but because it is not uniformly applied and >>>>> because they are likely not to use optimal interpolation algorithms, we >>>>> prefer to do offline correction. >>>>> >>>>> Peace, >>>>> >>>>> Matt. >>>>> >>>>> From: >>>>> <hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>> >>>>> on behalf of >>>>> Antonin >>> Skoch < >>>>> a...@ikem.cz<mailto:a...@ikem.cz>> >>>>> Date: Wednesday, October 19, 2016 at 4:27 PM >>>>> To: >>>>> "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" >>>>> <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> >>>>> Subject: [HCP-Users] gradient nonlinearity correction question >>>>> >>>>> Dear experts, >>>>> >>>>> during the set-up of gradunwarp scripts, it came to my mind, why scanner >>>>> vendors standardly do not perform gradient nonlinearity correction >>> directly >>>>> on the scanner as part of on-line image reconstruction system (i.e. ICE >>> in >>>>> Siemens)? >>>>> >>>>> Regards, >>>>> >>>>> Antonin Skoch >>>>> >>>>> >>>>> _______________________________________________ >>>>> HCP-Users mailing list >>>>> HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org> >>>>> http://lists.humanconnectome.org/mailman/listinfo/hcp-users<https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.humanconnectome.org_mailman_listinfo_hcp-2Dusers&d=DwMFaQ&c=shNJtf5dKgNcPZ6Yh64b-A&r=C4genPYC6QtMDghAR1Km4p6emgS7QcLRMzo8A8hTJKk&m=ZMuNtM9D5WoxjxPsNEf3nsA4vd9aenKnJbd7pJY5V6o&s=VlS5YxgBaQ-pKX4I4w1y6G0q0a0dP60J_gDUReDB9sE&e=> >>>>> >>>>> >>>>> ------------------------------ >>>>> >>>>> 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<https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.humanconnectome.org_mailman_listinfo_hcp-2Dusers&d=DwMFaQ&c=shNJtf5dKgNcPZ6Yh64b-A&r=C4genPYC6QtMDghAR1Km4p6emgS7QcLRMzo8A8hTJKk&m=ZMuNtM9D5WoxjxPsNEf3nsA4vd9aenKnJbd7pJY5V6o&s=VlS5YxgBaQ-pKX4I4w1y6G0q0a0dP60J_gDUReDB9sE&e=> >>>>> >>>> >>>> _______________________________________________ >>>> HCP-Users mailing list >>>> HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org> >>>> http://lists.humanconnectome.org/mailman/listinfo/hcp-users<https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.humanconnectome.org_mailman_listinfo_hcp-2Dusers&d=DwMFaQ&c=shNJtf5dKgNcPZ6Yh64b-A&r=C4genPYC6QtMDghAR1Km4p6emgS7QcLRMzo8A8hTJKk&m=ZMuNtM9D5WoxjxPsNEf3nsA4vd9aenKnJbd7pJY5V6o&s=VlS5YxgBaQ-pKX4I4w1y6G0q0a0dP60J_gDUReDB9sE&e=> >>> >>> >>> >>> _______________________________________________ >>> HCP-Users mailing list >>> HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org> >>> http://lists.humanconnectome.org/mailman/listinfo/hcp-users<https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.humanconnectome.org_mailman_listinfo_hcp-2Dusers&d=DwMFaQ&c=shNJtf5dKgNcPZ6Yh64b-A&r=C4genPYC6QtMDghAR1Km4p6emgS7QcLRMzo8A8hTJKk&m=ZMuNtM9D5WoxjxPsNEf3nsA4vd9aenKnJbd7pJY5V6o&s=VlS5YxgBaQ-pKX4I4w1y6G0q0a0dP60J_gDUReDB9sE&e=> >>> >>> >>> >>> >>> _______________________________________________ >>> HCP-Users mailing list >>> HCP-Users@humanconnectome.org >>> http://lists.humanconnectome.org/mailman/listinfo/hcp-users<https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.humanconnectome.org_mailman_listinfo_hcp-2Dusers&d=DwQFaQ&c=shNJtf5dKgNcPZ6Yh64b-A&r=C4genPYC6QtMDghAR1Km4p6emgS7QcLRMzo8A8hTJKk&m=ZMuNtM9D5WoxjxPsNEf3nsA4vd9aenKnJbd7pJY5V6o&s=VlS5YxgBaQ-pKX4I4w1y6G0q0a0dP60J_gDUReDB9sE&e=> >> >> >> >> _______________________________________________ >> 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 --------------------------------------------------------------------------- Stephen M. Smith, Professor of Biomedical Engineering Head of Analysis, 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 <http://www.fmrib.ox.ac.uk/~steve> --------------------------------------------------------------------------- Stop the cultural destruction of Tibet <http://smithinks.net/> _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
