I'll keep an eye one it. As an aside, I tried to run freesurfer on an image acquired at 3T (I converted it to 8 bit first), and got an error during stage1 of recon-all. I've included the relevant bits below. Any ideas?
Transforming slices:...............................................................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Transforming slices:..........................................................................................................................................................................................................................................................................................................................................Done mri_convert nu/nu4.mnc nu mri_convert nu/nu4.mnc nu reading from nu/nu4.mnc... DimSizes: 3, 330, 330, 330, 1 DataType: 1 MINC Linear Transform -1.0000 0.0000 0.0000 165.0000 0.0000 0.0000 1.0000 -165.0000 0.0000 -1.0000 0.0000 165.0000 0.0000 0.0000 0.0000 1.0000 Done reading minc TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) Original Data has (1, 1, 1) mm size and (330, 330, 330) voxels. Data is conformed to 1 mm size and 330 voxels for all directions writing to nu... non-standard value for imnr1 (330, usually 256) in volume structure non-standard value for width (330, usually 256) in volume structure non-standard value for height (330, usually 256) in volume structure ... #it then seems to proceed as normal until I get this: --------------------------------------------- Tessellate rh Tue Jun 14 18:34:47 EST 2005 mri_tessellate /data/flanders/work/alex/freesurfer/subjects/mw_3T/mri/filled 127 /data/flanders/work/alex/freesurfer/subjects/mw_3T/surf/rh.orig /data/flanders/work/alex/freesurfer/subjects/mw_3T/scripts warning: non-standard value for imnr1 (330, usually 256) in file /data/flanders/work/alex/freesurfer/subjects/mw_3T/mri/filled/COR-.info warning: non-standard value for x (330, usually 256) in file /data/flanders/work/alex/freesurfer/subjects/mw_3T/mri/filled/COR-.info warning: non-standard value for y (330, usually 256) in file /data/flanders/work/alex/freesurfer/subjects/mw_3T/mri/filled/COR-.info slice 80: 25 vertices, 35 faces slice 90: 2235 vertices, 2414 faces slice 100: 7950 vertices, 8225 faces slice 110: 14980 vertices, 15343 faces slice 120: 24760 vertices, 25210 faces slice 130: 35948 vertices, 36485 faces slice 140: 47251 vertices, 47791 faces slice 150: 59398 vertices, 59994 faces slice 160: 69840 vertices, 70396 faces slice 170: 79968 vertices, 80513 faces slice 180: 89126 vertices, 89647 faces slice 190: 97517 vertices, 98045 faces slice 200: 104180 vertices, 104653 faces slice 210: 110417 vertices, 110849 faces slice 220: 115639 vertices, 116067 faces slice 230: 120291 vertices, 120699 faces slice 240: 123600 vertices, 123982 faces slice 250: 125319 vertices, 125574 faces slice 260: 125319 vertices, 125574 faces slice 270: 125319 vertices, 125574 faces slice 280: 125319 vertices, 125574 faces slice 290: 125319 vertices, 125574 faces slice 300: 125319 vertices, 125574 faces slice 310: 125319 vertices, 125574 faces slice 320: 125319 vertices, 125574 faces slice 330: 125319 vertices, 125574 faces using the conformed surface RAS to save vertex points... writing /data/flanders/work/alex/freesurfer/subjects/mw_3T/surf/rh.orig --------------------------------------------- Smooth1 rh Tue Jun 14 18:35:32 EST 2005 mris_smooth /data/flanders/work/alex/freesurfer/subjects/mw_3T/surf/rh.orig /data/flanders/work/alex/freesurfer/subjects/mw_3T/surf/rh.smoothwm /data/flanders/work/alex/freesurfer/subjects/mw_3T/scripts Segmentation fault ------------------------------------------ Filesystem 1k-blocks Used Available Use% Mounted on /dev/hda9 130282400 12524220 111140208 11% /data/flanders ------------------------------------------ recon-all exited with errors at Tue Jun 14 18:35:33 EST 2005 -----Original Message----- From: Bruce Fischl [mailto:[EMAIL PROTECTED] Sent: Wed 6/15/2005 12:33 PM To: Fornito, Alexander Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] recon-all stage3 then you should just run the rest of the analysis I guess and see if it works. In general all the surfaces of a hemisphere should have the same # of edges/faces/vertices *except* the ?h.qsphere surface. They should have all have an euler number of 2. cheers, Bruce On Wed, 15 Jun 2005, Fornito, Alexander wrote: > > Hi Bruce, > I ran the topology fixer again and it seemed to work. Unfortunately, silly me > just wrote over the original files, so all I have is the euler number from > the orig surface that is output in the recon-all log. > > > Euler Number lh Sat Jun 11 04:20:04 EST 2005 > /data/flanders/work/alex/freesurfer/subjects/1000192 > mris_euler_number > /data/flanders/work/alex/freesurfer/subjects/1000192/surf/lh.orig > euler # = v-e+f = 2g-2: 179761 - 539277 + 359518 = 2 --> 0 holes > F =2V-4: 359518 = 359522-4 (0) > 2E=3F: 1078554 = 1078554 (0) > > total defect index = 0 > Euler: NHoles = 0 > > > > -----Original Message----- > From: Bruce Fischl [mailto:[EMAIL PROTECTED] > Sent: Tue 6/14/2005 10:12 PM > To: Fornito, Alexander > Cc: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] recon-all stage3 > Hi Alex, > > that's a starnge one. Did the partition run out of space? Can you do an ls > -l in the surf dir and send it along? Also, run mris_euler_number on > lh.orig, lh.smoothwm, lh.inflated and lh.qsphere. > > > > On Tue, 14 Jun 2005, Fornito, > Alexander wrote: > >> Hi, >> I got an error when running recon-all -stage3.I've included the relevant >> part of the log below. Any ideas as to what went wrong? >> Thanks, >> alex >> >> writing spherical brain to >> /data/flanders/work/alex/freesurfer/subjects/1000192/surf/lh.qsphere >> spherical transformation took 0.91 hours >> navgs=32 and tol=1.000e-01 >> integrating with navgs=32 and tol=1.000e-01 >> integrating with navgs=8 and tol=1.000e-01 >> taking momentum steps... >> integrating with navgs=8 and tol=1.000e-01 >> integrating with navgs=8 and tol=1.000e-01 >> integrating with navgs=2 and tol=1.000e-01 >> taking momentum steps... >> integrating with navgs=2 and tol=1.000e-01 >> integrating with navgs=2 and tol=1.000e-01 >> integrating with navgs=0 and tol=1.000e-01 >> pass 1 complete, delta sse/iter = 0.16/60 = 0.00 >> final distance error %31.34 >> optimization complete. >> unfolding took 0.81 hours >> --------------------------------------------- >> Fix Topology lh Sat Jun 11 04:24:54 EST 2005 >> /data/flanders/work/alex/freesurfer/subjects/1000192/scripts >> mris_fix_topology 1000192 lh >> reading input surface >> /data/flanders/work/alex/freesurfer/subjects/1000192/surf/lh.qsphere... >> before topology correction, eno=-301 (nv=188932, nf=378516, ne=567749, g=151) >> mrisReadTriangleFile(/data/flanders/work/alex/freesurfer/subjects/1000192/surf/lh.orig): >> surface doesn't match >> /data/flanders/work/alex/freesurfer/subjects/1000192/surf/lh.qsphere >> >> No such file or directory >> mrisReadTriangleFile failed. >> >> No such file or directory >> MRISreadOriginalProperties: could not read surface file orig >> No such file or directory >> mris_fix_topology: could not read original surface orig >> No such file or directory >> reading T1 volume from T1... >> reading wm segmentation from wm... >> >> recon-all exited with errors at Sat Jun 11 04:24:58 EST 2005 >> >> _______________________________________________ >> 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
