There are 6 files in the subject I am looking at, labeled Warpfield_01 to 06, in additino to Warpfield.nii.gz. All have 3 volumes, with the 2nd volume having the fieldmap/brain image in each. Warpfield images 4-6 look much like the final Warpfield image, whereas Warpfield images 1-3 appear to be roughly inverted versions of 4-6. Would it help for me to attach the images in a separate email? Thanks
__________________________ gaurav patel gauravpa...@gmail.com www.neurofreak.net On May 26, 2015, at 3:19 PM, Glasser, Matthew wrote: > Are there only two of those files? It¹s not really possible for WarpField > to have a warpfield in it (that looks like a field map with a vaguely > brain shape inside it) but for the WarpField_01 and Warpfield_02 not to > have any data in them (did you check all their volumes)? > > Peace, > > Matt. > > On 5/26/15, 10:57 AM, "Juan Sanchez" <sanch...@nyspi.columbia.edu> wrote: > >> Looking at the WarpFields in the >> DistortionCorrectionAndEPIToT1wReg_FLIRTBBRAndFreeSurferBBRbased/FieldMap >> directory, >> the "WarpField" looks good and has data, >> The "WarpField_01" and "WarpField_02" are both empty >> >> >> ________________________________________ >> From: hcp-users-boun...@humanconnectome.org >> [hcp-users-boun...@humanconnectome.org] on behalf of >> hcp-users-requ...@humanconnectome.org >> [hcp-users-requ...@humanconnectome.org] >> Sent: Friday, May 22, 2015 5:24 PM >> To: hcp-users@humanconnectome.org >> Subject: HCP-Users Digest, Vol 30, Issue 26 >> >> Send HCP-Users mailing list submissions to >> hcp-users@humanconnectome.org >> >> To subscribe or unsubscribe via the World Wide Web, visit >> http://lists.humanconnectome.org/mailman/listinfo/hcp-users >> or, via email, send a message with subject or body 'help' to >> hcp-users-requ...@humanconnectome.org >> >> You can reach the person managing the list at >> hcp-users-ow...@humanconnectome.org >> >> When replying, please edit your Subject line so it is more specific >> than "Re: Contents of HCP-Users digest..." >> >> >> Today's Topics: >> >> 1. Re: SBref Distortion Correction (Glasser, Matthew) >> 2. Re: SBref Distortion Correction (Gaurav Patel) >> 3. Re: SBref Distortion Correction (Glasser, Matthew) >> 4. Re: Unresolved: 13-volume mismatch between rsfMRI volumes and >> trigger file? (Greg Burgess) >> >> >> ---------------------------------------------------------------------- >> >> Message: 1 >> Date: Fri, 22 May 2015 19:00:51 +0000 >> From: "Glasser, Matthew" <glass...@wusm.wustl.edu> >> Subject: Re: [HCP-Users] SBref Distortion Correction >> To: Juan Sanchez <sanch...@nyspi.columbia.edu>, >> "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> >> Message-ID: <d184e51f.f52b2%glass...@wusm.wustl.edu> >> Content-Type: text/plain; charset="us-ascii" >> >> An HTML attachment was scrubbed... >> URL: >> http://lists.humanconnectome.org/pipermail/hcp-users/attachments/20150522/ >> 5afce578/attachment-0001.html >> >> ------------------------------ >> >> Message: 2 >> Date: Fri, 22 May 2015 15:28:37 -0400 >> From: Gaurav Patel <gauravpa...@gmail.com> >> Subject: Re: [HCP-Users] SBref Distortion Correction >> Cc: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> >> Message-ID: <c2461f88-23d8-4fd1-a6fe-04a08ff8f...@me.com> >> Content-Type: text/plain; charset="utf-8" >> >> Hi Matt? Juan is working with me at Columbia to get the topups working >> with the HCP pipeline. The echo spacing is the same in both scans, as is >> the geometry we believe, though we still need to confirm that. The >> warpfield images have no information in them that I can tell, as changing >> the scaling of the display doesn't reveal anything. Also the shimming >> should be the same for all scans. The spin echo and gradient echo images >> look like they have the same distortions after they've been rigidly >> realigned, so we're a little puzzled as to why the topup procedure is >> failing. Any help would be appreciated. Thanks! >> >> _________________________ >> gaurav patel >> gauravpa...@gmail.com >> www.neurofreak.net >> >>> On May 22, 2015, at 3:00 PM, Glasser, Matthew <glass...@wusm.wustl.edu> >>> wrote: >>> >>> It helps to reply to the previous e-mail chain so that all of the info >>> on a question is in one place. >>> >>> Are you sure that those warp fields don?t have data in them, just a bad >>> scaling of the display? I don?t think the issue is with the topup >>> configuration (we?ve never had to change that, despite using it on >>> scanners with different field strengths). >>> >>> It would be good to check on what I suggested in the previous response. >>> While it is undoubtably better to use a proper SBRef generated from the >>> MB sequence itself, it should still be possible to do what you are >>> doing. It is important that using a rigid registration of the MB to the >>> SBRef results in a very precise alignment (the images should have >>> exactly the same distortion). >>> >>> Another question, do you know that your scanner used the same shim for >>> all the scans? >>> >>> Peace, >>> >>> Matt. >>> >>> From: Juan Sanchez <sanch...@nyspi.columbia.edu> >>> Date: Friday, May 22, 2015 at 8:56 AM >>> To: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> >>> Subject: [HCP-Users] SBref Distortion Correction >>> >>> >>> Let us clarify what we are doing exactly here. We are using spin-echo >>> images with alternating phase-encoding directions in alternating runs >>> (Topup PA and Topup AP, in our case). We also decided to use the >>> corresponding Topup (PA or AP) as SBRef instead of an actual single-band >>> reference image because we had issues obtaining the single-band image >>> and because the tissue contrast in the spin-echo/Topup is pretty good >>> (we tried using as SBRef the first frame of the multiband EPI but the >>> spin-echo/Topup definitely works better, probably because of its >>> improved tissue contrast). Even though using the Topups instead of a B0 >>> map for distortion correction and using the Topup as SBRef instead of >>> the first frame of the multiband EPI result in clear improvements, the >>> resulting undistorted SBRef is not perfectly aligned to the anatomical >>> images. For this reason, we think there's a problem with the procedures >>> creating or applying the WarpField (the topup procedure or the applyward >>> proce >> dure that uses the WarpField to undistort the SBRef). The undistorted >> SBRef in an example subject from the HCP dataset looks noticeably better >> aligned to the anatomical image than ours. Furthermore, the WarpField.nii >> in that example subject looks very similar to the corresponding >> TopupField.nii (like a scaled version of it). In our data, in contrast, >> the TopupField.nii looks probably like it's supposed to look like (with >> some anatomical information) but the WarpField.nii is totally empty in >> some cases! After realizing this is the case, we think that our (main) >> problem may be in the topup procedure (or maybe the input images it uses >> or some later modification to the WarpField.nii). Could you give us any >> suggestions as to how to fix this issue? Maybe we need to adjust some of >> the configuration files that the topup procedure uses? Did you have to >> tweak any parameters to optimize this for your scanner? >>> >>> We're attaching one screencapture with the TopupField.nii and the >>> WarpField.nii, another image showing the T2 anatomical scan, and a third >>> image showing the SBRef (Topup in our case). >>> _______________________________________________ >>> 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 >> -------------- next part -------------- >> An HTML attachment was scrubbed... >> URL: >> http://lists.humanconnectome.org/pipermail/hcp-users/attachments/20150522/ >> d6de269a/attachment-0001.html >> >> ------------------------------ >> >> Message: 3 >> Date: Fri, 22 May 2015 19:32:40 +0000 >> From: "Glasser, Matthew" <glass...@wusm.wustl.edu> >> Subject: Re: [HCP-Users] SBref Distortion Correction >> To: Gaurav Patel <gauravpa...@gmail.com> >> Cc: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> >> Message-ID: <d184ede4.f52e2%glass...@wusm.wustl.edu> >> Content-Type: text/plain; charset="us-ascii" >> >> An HTML attachment was scrubbed... >> URL: >> http://lists.humanconnectome.org/pipermail/hcp-users/attachments/20150522/ >> e4eb61bd/attachment-0001.html >> >> ------------------------------ >> >> Message: 4 >> Date: Fri, 22 May 2015 16:24:08 -0500 >> From: Greg Burgess <gcburg...@gmail.com> >> Subject: Re: [HCP-Users] Unresolved: 13-volume mismatch between rsfMRI >> volumes and trigger file? >> To: Nicola Toschi <tos...@med.uniroma2.it> >> Cc: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> >> Message-ID: <5c42c7cc-d4e7-481a-a9c3-c7957036c...@gmail.com> >> Content-Type: text/plain; charset="us-ascii" >> >> The missing triggers (and corresponding physio samples) are cut off the >> end of the scan. The physio files from the scanner have time stamps >> called LogStartMDHTime and LogStopMDHTime, which can be synchronized with >> the DICOM timestamps to ensure that the physio measurements are correctly >> aligned with the BOLD image. The difference between the LogStartMDHTime >> and LogStopMDHTime covers 1200 TRs. However, that duration does not >> appear to compensate for the fact that the MB sequences collect a SBRef >> volume and five dummy scans prior to the onset of the first MB BOLD >> volume. Therefore, when we included only the samples that occurred >> between LogStartMDHTime and LogStopMDHTime, it consequently cut off (from >> the end of the physio samples) a duration equivalent to the time to >> acquire the SBRef and dummy BOLD scans, which accounts for the 13 missing >> TRs at the end. >> >> --Greg >> ____________________________________________________________________ >> Greg Burgess, Ph.D. >> Staff Scientist, Human Connectome Project >> Washington University School of Medicine >> Department of Anatomy and Neurobiology >> Email: burge...@pcg.wustl.edu >> >>> On May 15, 2015, at 3:46 PM, Nicola Toschi <tos...@med.uniroma2.it> >>> wrote: >>> >>> Dear List, >>> >>> I have not yet been able to find an explanation to this (I have >>> searched the list and bug reports): >>> >>> For every subject I have checked in the 100 "unrelated" dataset, there >>> are only 1187 trigger "up" sections in the physio log file (but 1200 >>> rs-fMRI volumes). However, the temporal length of the physio logs is, as >>> expected, 1200 x TR. >>> >>> All physio logs I have looked at end like in the attached picture - >>> there are about 10 seconds of 0's. >>> >>> Could anyone help in figuring out which way the misalignment went? >>> >>> Thanks a lot in advance! >>> >>> Nicola >>> >>> <mime-attachment.jpg> >>> ________________________________________________________________ >>> Prof. Nicola Toschi >>> Associate Professor in Medical Physics >>> Medical Physics Section, Department of Biomedicine and Prevention >>> Faculty of Medicine, University of Rome "Tor Vergata" >>> Via Montpellier 1 - 00133 Rome, Italy >>> tos...@med.uniroma2.it >>> >>> Visiting Assistant Professor in Radiology, Assistant in Neurology >>> Athinoula A. Martinos Center for Biomedical Imaging, Department of >>> Radiology >>> Harvard Medical School >>> 149 Thirteenth Street, Suite 2301, Charlestown, MA 02129 >>> nic...@nmr.mgh.harvard.edu >>> >>> >>> >>> >>> >>> >>> -------- Forwarded Message -------- >>> Subject: Re: [HCP-Users] 13-volume mismatch between rsfMRI volumes >>> and trigger file? >>> Date: Thu, 14 May 2015 22:59:52 +0200 >>> From: Nicola Toschi <tos...@med.uniroma2.it> >>> To: Glasser, Matthew <glass...@wusm.wustl.edu>, >>> hcp-users@humanconnectome.org <hcp-users@humanconnectome.org> >>> >>> Hi, >>> >>> thanks for your quick reply. >>> >>> I had noticed a bug report (also mentioned in the wiki), but a) it >>> refers to a 1 or 1.5 second mismatch (not 13 volumes i.e. roughly 10 >>> seconds), b) the wiki says that the files have been realigned. >>> >>> >>> https://www.mail-archive.com/hcp-users%40humanconnectome.org/msg00217.htm >>> l >>> >>> Any pointers are much appreciated! >>> >>> Thanks a lot - Nicola >>> >>> On 05/14/2015 10:52 PM, Glasser, Matthew wrote: >>>> I believe there has been a reported bug in this, so have a search of >>> the >>>> mailing list archive for it. >>>> >>>> Peace, >>>> >>>> Matt. >>>> >>>> On 5/14/15, 3:48 PM, "Nicola Toschi" <tos...@med.uniroma2.it> wrote: >>>> >>>>> Dear HCP Staff, >>>>> >>>>> I have been looking at the trigger logs (column 1 of the >>> *Physio_log.txt >>>>> files) in rsfMRI data (both sessions) for the 100 unrelated subjects. >>>>> >>>>> While the total temporal length of the physio logs matches the total >>>>> length of the fMRI data (1200 * TR), in all physio logs I >>> consistently >>>>> found 1187 (instead of 1200) triggers (i.e. sections with consecutive >>>>> 1's). >>>>> >>>>> Could there be a 13 - volume shift? Or am I missing something (more >>>>> likely)? >>>>> >>>>> Thanks in advance! >>>>> >>>>> Nicola >>>>> >>>>> >>>>> _______________________________________________ >>>>> 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 >> -------------- next part -------------- >> An HTML attachment was scrubbed... >> URL: >> http://lists.humanconnectome.org/pipermail/hcp-users/attachments/20150522/ >> 91c3061d/attachment.html >> -------------- next part -------------- >> A non-text attachment was scrubbed... >> Name: mime-attachment.jpg >> Type: image/jpeg >> Size: 99605 bytes >> Desc: not available >> Url : >> http://lists.humanconnectome.org/pipermail/hcp-users/attachments/20150522/ >> 91c3061d/attachment.jpg >> >> ------------------------------ >> >> _______________________________________________ >> HCP-Users mailing list >> HCP-Users@humanconnectome.org >> http://lists.humanconnectome.org/mailman/listinfo/hcp-users >> >> >> End of HCP-Users Digest, Vol 30, Issue 26 >> ***************************************** >> >> _______________________________________________ >> 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 _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
