External Email - Use Caution I posted a reply with the dwi_orig.nii screenshots on Friday, but they did not show up on the list.
Yes, the dwi_orig.nii images appear the same as the dwi.nii.gz images. Also, I ran them through TrackVis/DTK and they came out correct, so it seems to be something within Tracula that is not working for me as expected. On Fri, Sep 21, 2018 at 12:27 PM Yendiki, Anastasia < ayend...@mgh.harvard.edu> wrote: > Thank you. Can you also send screenshots of your original DWIs, if they > don't look like this? > ------------------------------ > *From:* freesurfer-boun...@nmr.mgh.harvard.edu < > freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Matthew Grecsek < > m...@grecsek.com> > *Sent:* Friday, September 21, 2018 10:27:37 AM > *To:* Freesurfer support list > *Subject:* Re: [Freesurfer] Freesurfer 6.0 - Tracula - Segmentation fault > > > External Email - Use Caution > > Hi Anastasia, > > Please see attached screenshots from dwi.nii.gz. The first 4 are rotated > 90 degrees around y axis and the last 2 are top and bottom. > > Thanks, > > -Matt > > On Thu, Sep 20, 2018 at 7:19 PM Yendiki, Anastasia < > ayend...@mgh.harvard.edu> wrote: > > Hi Matt - I am asking about the raw diffusion images. You sent a > screenshot of an FA map that looked truncated, with slices missing from the > bottom of the brain (which explains why the error happened for the ILF, > which would go through that missing part of the brain). Does > dmri/dwi.nii.gz look like that? > > > Best, > > a.y > ------------------------------ > *From:* freesurfer-boun...@nmr.mgh.harvard.edu < > freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Matthew Grecsek < > m...@grecsek.com> > *Sent:* Thursday, September 20, 2018 2:00:11 PM > *To:* Freesurfer support list > *Subject:* Re: [Freesurfer] Freesurfer 6.0 - Tracula - Segmentation fault > > > External Email - Use Caution > > If you are referring to the T1 raw images, no they appear normal and the > standard Freesurfer pipeline generates correct volumes. > > If you are referring to the DTI raw images off the scanner, they also > don't appear to have brain parts missing, although some appear more noisy > and pixelated than others. > > This is a mTBI subject with no other anatomical brain anomalies scanned > with a Siemens 3T. > > > ------------------------------------------------ > Re: [Freesurfer] Freesurfer 6.0 - Tracula - Segmentation fault > Yendiki, Anastasia Wed, 19 Sep 2018 13:20:02 -0700 > > > > Do the raw images look like that too? > > From: > <freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu > <freesurfer-boun...@nmr.mgh.harvard.edu>>> > on behalf of Matthew Grecsek <m...@grecsek.com<mailto:m...@grecsek.com > <m...@grecsek.com>>> > Reply-To: Freesurfer support list > <freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu > <freesurfer@nmr.mgh.harvard.edu>>> > Date: Wednesday, September 19, 2018 at 4:07 PM > To: Freesurfer support list > <freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu > <freesurfer@nmr.mgh.harvard.edu>>> > Subject: Re: [Freesurfer] Freesurfer 6.0 - Tracula - Segmentation fault > > External Email - Use Caution > > Yes, a part of the brain appears missing. See attached screenshot. > > I did not use a configuration file, I simply accepted all defaults and kicked > off the process with -s and -i flags. > > ------------------------------------------------ > Re: [Freesurfer] Freesurfer 6.0 - Tracula - Segmentation fault > Yendiki, Anastasia Wed, 19 Sep 2018 09:02:47 -0700 > > Hi Matt – It looks like some sort of registration issue. When you display the > FA map (dmri/dtifit_FA) and structural segmentation in diffusion space > (label/diff/aparc+aseg), do they look fine? Is there any part of the brain > that > is cut off from any of the images? Also, can you attach your config file? > Thanks! > > a.y > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. >
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