ok, now I'm confused. Did recon-all finish or is it still running? What does the end of the recon-all.log file say?
Note that the spatial location of the inflated surfaces relative to the volumes doesn't mean anything
cheers Bruce
On Wed, 6 May 2020, Zeng, Qi wrote:
External Email - Use Caution
Hi Bruce,
After examining the sagittal view of the parietal lobe, it is fine including the area. However, after examining the outputs in surf/, I noticed that after it generated lh.defects, it stopped processing lh.smoothwm and never got a chance to generate rh.defects. Compared to normal subjects that successfully finished, there is a clear mismatch between the inflated.nofix and the brainmask & wm.mgz. Attached below.
Can you help confirm the fact of mismatch and let me know if there is any way to fix this?
Thank you so much ! Best, Qi
On Wed, May 6, 2020 at 10:12 AM Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Qi
it is not obvious from that one image that something is wrong there. What does a saggital view look like with the cursor on that region? Also, can you send an image of the rh.inflated.nofix in 3D mode? Sometime XL defects are fixable automatically, which may be the case for your subjects with very large ventricles, but sometimes not cheers Bruce On Tue, 5 May 2020, Zeng, Qi wrote: > > External Email - Use Caution > > Hi Douglas, > > Compared to the ones without error, the subject surface misses including > left parietal lobe. Is that correct? Attached the comparison. > > Thank you so much! > Best, > Qi > > On Tue, May 5, 2020 at 1:58 PM Douglas N. Greve <dgreve@mgh.harvard.edu> > wrote: > You should load that volume along with the orig.nofix hemisphere > that is giving you problems and look for a large area that > should not be within the surface > > On 5/5/2020 1:23 PM, Zeng, Qi wrote: > > External Email - Use Caution > > Hi Douglas, > > The cerebrum is removed and with no skull attached. > However, compared to others that run normally, it may have > problems with white matter segmentation and missing brainstem > (no clear). Attached the comparison below. Can you help figure > it out? > > > > Thank you so much! > Best, > Qi > > On Tue, May 5, 2020 at 11:36 AM Douglas N. Greve > <dgreve@mgh.harvard.edu> wrote: > You should look at the wm.mgz to see where the > defect is. Probably cerebellum is still attached or > maybe a big piece of skull. > > On 5/4/2020 11:19 PM, Zeng, Qi wrote: > > External Email - Use Caution > > Hi, > > I've conducted longitudinal T1 recon-all. One > subject's last-scan ran into error in the first > independent recon all step: " recon-all -s SUBJ1 > -SUBJ1.nii -all'. > Error: "CORRECTING DEFECT 0 (vertices=14101, convex > hull=2297, v0=1419) XL defect detected...". Log file > attached below. > > I've increased the memory usage limit as some > suggestions did, but no help. Also T1.nii looks > fine, same parameter setting as first scan, also > attached below. Subject first scan and all the other > subjects were finished without errors. Can you help > figure out what has caused it? > > Thank you so much! > Best, > Qi > > -- > > Ph.D. candidate > Icahn School of Medicine at Mount Sinai > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > -- > > Ph.D. candidate > Icahn School of Medicine at Mount Sinai > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > -- > > Ph.D. candidate > Icahn School of Medicine at Mount Sinai > > >_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer--
Ph.D. candidate Icahn School of Medicine at Mount Sinai