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
