Nick, I tried my best to align the monkey brain with Talairach brain. The midline cut looks much better than the previous one. But the horizontal cutting plane does not look good. I repeated the process several times and it is always at the level of STG/STS as attached. Is there any way to get around this problem? It does not have to be automatic. I don't mind intensive manual labor.
Thanks, Kazu -----Original Message----- From: Nick Schmansky [mailto:[EMAIL PROTECTED] Sent: Fri 1/26/2007 2:26 PM To: Tanji, Kazuyo (NIH/NIMH) [F] Cc: Freesurfer Mailing List Subject: RE: [Freesurfer] -noaseg Kazu, I should have mentioned this earlier, but when using the -noaseg flag, the talairach transform needs to be correct in order for mri_fill to properly cut the hemispheres vertically and the pons and cerebellum horizontally. It is obvious from your images that mri_fill is not cutting in this direction (and yes, the cerebellum should not appear in the filled.mgz, but it should appear in brainmask.mgz). I'm guessing that the transform, which is one of the early steps in recon-all, is off. Follow the instructions here: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach to align the monkey brain with the (human) talairach brain, as best as you can. Use this command: tkregister --mgz -s <subjid> --fstal which excludes the '--surf orig' option (since you don't yet have the orig surface). Once you feel you have a proper alignment (it can take awhile playing around with tkregister2 to get this, but it doesnt have to be perfect), then you can restart recon-all: recon-all -s <subjid> -autorecon2-wm -noaseg The cc and pons points were saved from the prior run, so they dont need to be specified. You will see them in the recon-all.log file. Actually, once the mri_fill step of recon-all creates the new filled.mgz, you may want to inspect it to make sure it cuts correctly, otherwise the topology fixing step will get stuck again on the huge defect. Nick On Fri, 2007-01-26 at 10:04 -0500, Tanji, Kazuyo (NIH/NIMH) [F] wrote: > Nick, > > Thanks for the suggestion. I saw 2 abnormal perpendicular lines inside white > matter volume (as attached). Does it result from failure in defining cutting > planes? Also I thought at this stage the cerebellum should not be displayed > anymore. Is there ways to correct those manually? > > Best, > Kazu > > > -----Original Message----- > From: Nick Schmansky [mailto:[EMAIL PROTECTED] > Sent: Thu 1/25/2007 5:12 PM > To: Tanji, Kazuyo (NIH/NIMH) [F] > Subject: RE: [Freesurfer] -noaseg > > Kazu, > > In looking at the log, it appears to be stuck on correcting a defect > which has 27024 vertices, which is a huge number. This indicates > something is wrong with an earlier stage. > > Type: > > tkmedit <subj> orig.mgz -aux filled.mgz > > and make sure that the filled.mgz volume looks like it is properly > representing the white matter voxels (use Ctrl 1 and Ctrl 2 to flip > between volumes). > > Also: > > tksurfer <subj> lh orig > > will bring-up the tessellated 'filled' volume. Look for obvious > problems, like dimples or holes. > > You may need to edit the white matter to fix problems. See: > > http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/WhiteMatterEdits > > Also make sure your skull-strip worked properly: > > http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/SkullStripFix > > That is, make sure there are not bits of skull in brainmask.mgz > volume. > > Nick > > > > On Thu, 2007-01-25 at 14:45 -0500, Tanji, Kazuyo (NIH/NIMH) [F] wrote: > > Nick, > > > > Thanks for offering to take a look. I am attaching the log file. > > > > Best, > > Kazu > > > > > > -----Original Message----- > > From: Nick Schmansky [mailto:[EMAIL PROTECTED] > > Sent: Thu 1/25/2007 2:04 PM > > To: Tanji, Kazuyo (NIH/NIMH) [F] > > Subject: RE: [Freesurfer] -noaseg > > > > > > > > > > -----Original Message----- > > From: Nick Schmansky [mailto:[EMAIL PROTECTED] > > Sent: Thu 1/25/2007 2:04 PM > > To: Tanji, Kazuyo (NIH/NIMH) [F] > > Subject: RE: [Freesurfer] -noaseg > > > > Kazu, > > > > No it should not take so long...it usually takes no more than 10 hours. > > So this indicates something is unusual about the surface. Can you send me > > the recon-all.log file (in the subjects scripts dir)? I can check for > > problems in that. > > > > Nick > > > > > > > Hi Nick, > > > > > > Thanks so much for the suggestion. I specified the volume index and ran > > > recon-autorecon2-wm -noaseg. I started 5pm on Januray 22 (Monday) and it > > > has not finished processing. It is still at 'mris_fix_topology' (left > > > hemisphere). Could you suggest whether it is unusual for this step to take > > > this long or it is understandable given the non-standard method I am > > > trying? My CPU is quite new (Pentium D) and RAM is 2G. > > > > > > Thanks, > > > Kazu > > > > > > ________________________________ > > > > > > From: Nick Schmansky [mailto:[EMAIL PROTECTED] > > > Sent: Mon 1/22/2007 2:03 PM > > > To: Tanji, Kazuyo (NIH/NIMH) [F] > > > Cc: Freesurfer Mailing List > > > Subject: RE: [Freesurfer] -noaseg > > > > > > > > > > > > Kazu, > > > > > > This is for a non-human primate, right? If so, you will need to > > > manually define seed points for the corpus callosum and pons. To do so, > > > open the white matter volume in tkmedit: > > > > > > tkmedit <subjid> wm.mgz > > > > > > and using the cursor, identify the 'volume index' of the point where you > > > think the corpus callosum is located and make a note of it (for > > > instance, in an example subject 'bert', its around 128 117 123). Also > > > make a note of where the pons is located. > > > > > > Then, restart recon-all from mri_fill, passing those coordinates, for > > > example: > > > > > > recon-all -s bert -autorecon2-wm -noaseg \ > > > -cc-crs 128 117 123 \ > > > -pons-crs 128 154 108 > > > > > > Nick > > > > > > ps, i've posted this to the list as others may have a better suggestion. > > > > > > On Mon, 2007-01-22 at 12:55 -0500, Tanji, Kazuyo (NIH/NIMH) [F] wrote: > > >> Hi Nick, > > >> > > >> Thank you so much. It worked. > > >> Now I got an error message at 'mri_fill'. > > >> > > >> The message says: > > >> mri_fill: could not find corpus callosum > > >> INFO: Modifying dst c_(r,a,s), using the transform dst > > >> find_cutting_plane:seed point not in structure! Searching > > >> neighborhood... > > >> recon-all exited with ERRORS at Mon Jan 22 10:57:43 EST 2007 > > >> > > >> Is this error due to -noaseg flag? What should I do next? > > >> > > >> Kazu > > >> -----Original Message----- > > >> From: Nick Schmansky [mailto:[EMAIL PROTECTED] > > >> Sent: Sun 1/21/2007 6:38 PM > > >> To: Tanji, Kazuyo (NIH/NIMH) [F] > > >> Cc: Freesurfer Mailing List > > >> Subject: Re: [Freesurfer] -noaseg > > >> > > >> Kazu, > > >> > > >> It looks like the -noaseg option does make use of norm.mgz (a change > > >> that seems to have occurred since the option was created and tested). > > >> > > >> As a work-around, you should be able to do this: > > >> > > >> ln -s brainmask.mgz norm.mgz > > >> > > >> and then run the -autorecon2 -noaseg flags. brainmask.mgz is a close > > >> enough stand-in for norm.mgz. > > >> > > >> Nick > > >> > > >> > > >> On Sun, 2007-01-21 at 17:45 -0500, Tanji, Kazuyo (NIH/NIMH) [F] wrote: > > >> > Hi, > > >> > > > >> > I have a question on how to use -noaseg option. > > >> > > > >> > I tried a script: recon-all -autorecon2 -noaseg -subjid xxx. > > >> > > > >> > This seems to skip several steps of autorecon2 and start from > > >> 'mri_normalize' . This results in an error because norm.mgz is not > > >> existing. > > >> > > > >> > Could you suggest better ways to use -noaseg? > > >> > > > >> > Thanks, > > >> > Kazu > > >> > > > >> > > > >> > > > >> > > > >> > _______________________________________________ > > >> > Freesurfer mailing list > > >> > Freesurfer@nmr.mgh.harvard.edu > > >> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > >> > > > >> > > > >> > > >> > > >> > > > > > > > > > > > > > > > > > > > > >
<<attachment: filled_138_Jan27.jpg>>
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