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
