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
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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>
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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>
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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.
>
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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>
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------------------------------
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.html
>
> 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.
>
>
>
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