Hi Bruce, When looking at my top slices in brain ask I noticed that the gray/white matter shows but the darker areas surrounding it are not present (this usually goes to the edge of the brain). Could the large defects be a result of having masked this out on the input file? I multiplied the template with the GM/WM/CSF masks they provided to get the brain extracted so I only see this missing in the very top few slices of the brain.
Thanks, Ajay On Tuesday, December 1, 2015, Bruce Fischl <fis...@nmr.mgh.harvard.edu> wrote: > Hi Falk > > I don't think you need to rerun the qsphere. I'm pretty sure this is a bug > in mris_fix_topology for giant defects, but haven't finished tracking it > down yet > > cheers > Bruce > > > On Tue, 1 Dec 2015, Falk Lüsebrink wrote: > > >> Hi Ajay, >> >> >> >> you should >> >> >> >> cp ?h.orig.nofix ?h.orig >> >> cp ?h.inflated.nofix ?h.inflated >> >> >> >> with ? being l or r depending your hemisphere. After the fixing stage the >> surfaces got damaged somehow, therefore you have to recreate it them. I’m >> not entirely sure about the qsphere. Probably you have to run the -qsphere >> stage again also. >> >> >> >> Best, >> >> Falk >> >> >> >> >> >> Von: Ajay Kurani [mailto:dr.ajay.kur...@gmail.com] >> Gesendet: Montag, 30. November 2015 21:50 >> An: Falk Lüsebrink >> Cc: Freesurfer support list; Bruce Fischl >> Betreff: Re: [Freesurfer] Freesurfer 6.0 - Autorecon2 failure >> (mris_euler_number) using high res (0.5mm isotropic) T1 image >> >> >> >> Hi Falk, >> >> I used the command and got the following error: >> >> Command: ris_topo_fixer -mgz -warning -seed 1234 ICBM lh >> mris_topo_fixer -mgz -warning -seed 1234 ICBM lh >> INFO: assuming .mgz format >> setting seed for random number genererator to 1234 >> reading input >> surface/home/imuser/Downloads/mni_icbm152_nlin_sym_09b_nifti/mni_icbm152_nlin_sym >> _09b/ICBM/surf/lh.orig... >> >> mrisFindNeighbors:/home/imuser/Downloads/mni_icbm152_nlin_sym_09b_nifti/mni_icbm152_nlin_sym >> _09b/ICBM/surf/lh.orig: face[46196].v[0] = 24215, but face 46196 not in >> vertex 24215 face list >> >> mris_topo_fixer -mgz -warning -seed 1234 ICBM rh >> INFO: assuming .mgz format >> setting seed for random number genererator to 1234 >> reading input >> surface/home/imuser/Downloads/mni_icbm152_nlin_sym_09b_nifti/mni_icbm152_nlin_sym >> _09b/ICBM/surf/rh.orig... >> >> mrisFindNeighbors:/home/imuser/Downloads/mni_icbm152_nlin_sym_09b_nifti/mni_icbm152_nlin_sym >> _09b/ICBM/surf/rh.orig: face[35822].v[2] = 18903, but face 35822 not in >> vertex 18903 face list >> >> Any suggestions would be appreciated. >> >> Thanks, >> >> Ajay >> >> >> >> On Mon, Nov 30, 2015 at 2:41 AM, Falk Lüsebrink <falk.luesebr...@ovgu.de> >> wrote: >> >> Hi Ajay, >> >> I ran into the same error processing hires data a while ago using a >> nightly >> build of centos 6 with the hires flag only. Disk space or alike wasn't an >> issue. I ran mris_topo_fixer instead of mris_fix_topology to get working >> surfaces. >> >> Best, >> Falk >> >> -----Ursprüngliche Nachricht----- >> Von: freesurfer-boun...@nmr.mgh.harvard.edu >> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Im Auftrag von Bruce >> Fischl >> Gesendet: Sonntag, 29. November 2015 22:48 >> An: Freesurfer support list >> Betreff: Re: [Freesurfer] Freesurfer 6.0 - Autorecon2 failure >> (mris_euler_number) using high res (0.5mm isotropic) T1 image >> >> Hi Ajay >> >> are you sure you didn't run out of disk space? That error is a sanity >> check >> on the surfaces that should never occur >> >> cheers >> Bruce >> >> On Sun, 29 Nov 2015, Ajay >> Kurani wrote: >> >> > Hello Freesurfer experts, >> > I am trying to run Freesurfer 6.0 beta (downloaded 10/15/15 >> > version) with the -hires flag to process an MNI template image which >> > is 0.5mm isotropic. Stage 1 ran well and on stage 2 there is an error >> > during >> > pocessing: >> > >> > Command run: >> > recon-all -s ICBM -autorecon2 -openmp 8 -3T -hires -expert expert.opts >> > >> > I supplied a skull stripped brain which was nu corrected and so I used >> > the T1.mgz and copied it to brainmask.mgz and nu.mgz in autorecon1 >> > stage. I then ran autorecon2 and it was working well until I was at >> > the -fix stage and ran into the following error: >> > >> > >> > Error: >> > mris_euler_number ./surf/lh.orig >> > mrisFindNeighbors: ./surf/lh.orig: face[46196].v[0] = 24215, but face >> > 46196 not in vertex 24215 face list >> > >> > >> > >> > I am not sure if this is due to the fact that we have a very high >> > resolution image (template) and if there are any modifications needed >> > aside from the hires flag. Are there any suggestions you have? >> > >> > Thanks, >> > Ajay >> > >> > >> >> >> >> >> >> > > 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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