Note that the scenes we’ve assembled for “StructuralQC” include a check of the FNIRT registration. You can find the scripts necessary to generate those scenes here:
https://github.com/Washington-University/StructuralQC cheers, -MH -- Michael Harms, Ph.D. ----------------------------------------------------------- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave.Tel: 314-747-6173 St. Louis, MO 63110Email: mha...@wustl.edu On 12/1/16, 1:04 PM, "hcp-users-boun...@humanconnectome.org on behalf of Gaurav Patel" <hcp-users-boun...@humanconnectome.org on behalf of gauravpa...@gmail.com> wrote: We've been noticing similar masking issues with our non-HCP data acquired on a GE MR750, and have found that fat sat in our sequence was turned off, so we will attempt to do the same and report whether that changes things. __________________________ gaurav patel gauravpa...@gmail.com www.neurofreak.net On Dec 1, 2016, at 2:01 PM, Julien Dubois wrote: > It looks like the Freesurfer pipeline does not make use of the MNI space >registration from the last Prefreesurfer step. > Hence, to correct for the suboptimal MNI registration due to the fat sat >discrepancy, my plan of action is to: > 1) generate a "no fat sat" T1w template > 2) re-run AtlasRegistrationToMNI152_FLIRTandFNIRT.sh (last step of the >PreFreesurfer pipeline) > 3) re-run the PostFreesurfer pipeline > Does that sound reasonable? > > If 2) doesn't work well, I'll look into using the T2w image for MNI >space registration instead. > > - Julien > > > Julien Dubois, PhD > Postdoctoral Scientist > Department of Neurosurgery, Cedars-Sinai Medical Center, Los Angeles > Department of the Humanities and Social Sciences, California Institute >of Technology, Pasadena > Tel: +1 (310)423-8377 > Web: http://nigiri.caltech.edu/~jdubois > > > On Thu, Dec 1, 2016 at 10:24 AM, Glasser, Matthew <glass...@wustl.edu> >wrote: > If you have a decent number of subjects that go through the pipelines >okay, you can just generate another average template after MNI >registration. Else, there isn’t any particular reason why a T1w-based >MNI registration is better than a T2w-based registration. We probably >should make a flag that automatically allows you to base the brain mask >and atlas registration on the T2w image. > > Peace, > > Matt. > > From: Julien Dubois <jcrdub...@gmail.com> > Date: Thursday, December 1, 2016 at 11:49 AM > > To: Matt Glasser <glass...@wustl.edu> > Cc: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> > Subject: Re: [HCP-Users] Distorted MNI space result (T?w_restore) -- >maybe due to "bad" initial brain mask? > > Thank you Matt. > > I actually don't think the brain extraction is the culprit, after >spending more time with the intermediate outputs. Indeed, >T1w/T1w_acpc_dc_restore_brain.nii.gz actually looks quite good. > > The issue mostly arises at the fnirt step in >AtlasRegistrationToMNI152_FLIRTandFNIRT.sh. And indeed, it is clear that >the template from the HCP pipelines (MNI152_T1_2mm.nii.gz) is very dark >between the brain and the skull, while my input image >(T1w/T1w_acpc_dc_restore.nii.gz) is not. The best solution will thus >consist in using a template with fat sat off. > > Any idea where I might find such a template? I'll look around, but if >you have suggestions, let me know. > > - Julien > > Julien Dubois, PhD > Postdoctoral Scientist > Department of Neurosurgery, Cedars-Sinai Medical Center, Los Angeles > Department of the Humanities and Social Sciences, California Institute >of Technology, Pasadena > Tel: +1 (310)423-8377 > Web: http://nigiri.caltech.edu/~jdubois > > > On Wed, Nov 30, 2016 at 5:41 PM, Glasser, Matthew <glass...@wustl.edu> >wrote: > If you had a volume template in MNI space that had fat sat off, it might >register better. Alternatively you might modify the pipelines to use the >brain mask from the T2w scan and to do the atlas registration from the >T2w scan. > > Peace, > > Matt. > > From: Julien Dubois <jcrdub...@gmail.com> > Date: Wednesday, November 30, 2016 at 5:51 PM > To: Matt Glasser <glass...@wustl.edu> > Cc: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> > Subject: Re: [HCP-Users] Distorted MNI space result (T?w_restore) -- >maybe due to "bad" initial brain mask? > > I am not sure -- I am checking with the people who acquired that data. > I have had similar issues before with in-house data which does not have >fat sat turned on. > Do you recommend a tweak to the PreFreeSurfer pipeline if fat sat is not >turned on? > > I now see that you recommmend fat sat in the HCP T1 protocol [“Fat >suppr. = Water excit. Fast”] to reduce signal from bone marrow and scalp >fat > > - Julien > > Julien Dubois, PhD > Postdoctoral Scientist > Department of Neurosurgery, Cedars-Sinai Medical Center, Los Angeles > Department of the Humanities and Social Sciences, California Institute >of Technology, Pasadena > Tel: +1 (310)423-8377 > Web: http://nigiri.caltech.edu/~jdubois > > > On Wed, Nov 30, 2016 at 2:18 PM, Glasser, Matthew <glass...@wustl.edu> >wrote: > Out of curiosity, does this data not have fat sat on the T1w scan? > > Peace, > > Matt. > > From: <hcp-users-boun...@humanconnectome.org> on behalf of Julien Dubois ><jcrdub...@gmail.com> > Date: Wednesday, November 30, 2016 at 2:51 PM > To: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> > Subject: [HCP-Users] Distorted MNI space result (T?w_restore) -- maybe >due to "bad" initial brain mask? > > Dear Matt > > I am processing some non-HCP data with the minimal pipelines (v3.5.0). I >don't think that the problem that I am encountering is due to using an >older version of the Pipelines. > > I just looked at one of the subjects, and the MNI normalized T?w_restore >(under MNINonLinear/) are quite distorted (though the initial brain was >perfectly good looking). In particular, the left parietal area is "cut", >as per this screenshot showing the resulting T2w_restore overlaid on the >1mm template ("${HCPPIPEDIR_Templates}/MNI152_T2_1mm.nii.gz") > > <image.png> > > Upon inspecting the various outputs generated during PreFreesurfer, I >can see that the initial brain mask includes some non-brain matter in the >left parietal cortex (screenshot below) . This might be the source of the >distorted output. How can I solve this issue? > <image.png> > > My input T1w & T2w are 1mm isotropic and I am using the 1mm templates. I >am not applying gradient non-linearity or distortion correction. > > > All the files generated by the Pipelines (PreFS, FS, and PostFS) are >available here, and so are the two screenshots if they don't show up >properly in this email. > > Thank you in advance for your help, > - Julien > > > > _______________________________________________ > 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. > > > > > > 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. > > > > > > 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 ________________________________ 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
