Okay, thanks! I'll give that a shot... but I have a couple of questions beforehand: 1) How would you recommend that I decide what scale factor to use? Trial and error to get a peak of ~116? 2) Should I run cp and mri_convert, then erase all other existing files and folders, and rerun recon-all from the very beginning (using the new 001.mgz as the input)? Or, can I run cp and mri_convert within the existing subject/mri/orig/ folder and then rerun recon-all (on the same existing file/folders)? I hope my question is clear...!
Thanks, - Jerry On Mon, Apr 28, 2008 at 1:52 PM, Bruce Fischl <[EMAIL PROTECTED]> wrote: > Hi Jerry, > > I think you can do something like: > > cp 001.mgz 001_orig.mgz > mri_convert --scale 3 001_orig.mgz 001.mgz > > then the same for the other runs and see how that works in recon-all. > Usually we detect and account for this, but I guess something is failing in > your case. > > cheers, > Bruce > > > > On Mon, 28 Apr 2008, Jerry Yeou-Wei Chen wrote: > > Hi Bruce, > > > > Looking at one of the successfully processed subjects in tkmedit, I > > would > > guesstimate the range in the brain to be ~20-65. The corresponding > > 001.mgz > > is equally dark. > > > > Regarding the scale option, would I run that initially ( with --scale > > <scale > > factor> ), and then run autorecon as normal? > > Do I find the scale factor as follows: 116 = old peak value * scale > > factor, > > where old peak value is the mri peak value attained from these dark > > images? > > > > Thanks, > > - Jerry > > > > On Sun, Apr 27, 2008 at 7:40 AM, Bruce Fischl < > > [EMAIL PROTECTED]> > > wrote: > > > > p.s. are the 001.mgz and 002.mgz dark? The orig.mgz? Sometimes > > > nu_correct > > > can create very dark images, and there are some switches you can loo > > > through > > > to correct them. Alternatively if it is the 001.mgz, mri_convert has a > > > scale > > > option you can use. > > > > > > cheers, > > > Bruce > > > > > > > > > > > > On Fri, 25 Apr 2008, Jerry Yeou-Wei Chen wrote: > > > > > > Okay, thanks for your help again Nick! > > > > > > > Regarding the scan data: I am actually working with data collected > > > > by a > > > > previous member of our lab, and there were indeed some problems... > > > > (related > > > > to the SCIC algorithm on our GE scanner). So, our technician created > > > > a > > > > program to "uncorrect" the intensity scaling. The images he saved > > > > appear > > > > dark when we load them freesurfer, but we expected autorecon's > > > > intensity > > > > normalization would handle this. In fact, autorecon did successfully > > > > process > > > > 34 out of 35 scans. (the cortical surface appears quite decent for > > > > them, > > > > and > > > > the thickness values on our average subject appears to be within > > > > normal > > > > range...) > > > > I wonder if I should be concerned about our results due to this > > > > intensity > > > > issue... > > > > > > > > On Tue, Apr 22, 2008 at 2:42 PM, Nick Schmansky < > > > > [EMAIL PROTECTED]> > > > > wrote: > > > > > > > > Jerry, > > > > > > > > > > > > > > At this point, I think Bruce will need to jump-in to answer (he is > > > > > out- > > > > > of-town today). I think he will ask about your scan parameters, > > > > > ie, > > > > > how > > > > > is your scanner setup? It sounds as if something is not quite > > > > > right > > > > > in > > > > > the data coming-off the scanner. > > > > > > > > > > Nick > > > > > > > > > > > > > > > On Tue, 2008-04-22 at 14:26 -0400, Jerry Yeou-Wei Chen wrote: > > > > > > > > > > Thanks for the reply, Nick. I think you correctly identified the > > > > > > problem. > > > > > > nu.mgz is oriented correctly, but looks very dark... However, it > > > > > > looks > > > > > > decent if I adjust the brightness/contrast.... > > > > > > I have other scans that were processed without error, and the > > > > > > orig.mgz, and nu.mgz also appear quite dark (and the mri peaks > > > > > > are > > > > > > very low, too: 29, 46, 52, ...) Also, for those successfully > > > > > > processed, the brainmask.mgz looks decent as well. > > > > > > Perhaps this scan that exited with error was too dark to be > > > > > > corrected > > > > > > by the intensity normalization algorithm? > > > > > > > > > > > > - Jerry > > > > > > > > > > > > On Tue, Apr 22, 2008 at 1:22 PM, Nick Schmansky > > > > > > <[EMAIL PROTECTED]> wrote: > > > > > > Jerry, > > > > > > > > > > > > I'm not sure why it exited without giving a better > > > > > > message, > > > > > > but this is > > > > > > a clue why it exited: > > > > > > > > > > > > > > > > > > before smoothing, mri peak at 0 > > > > > > after smoothing, mri peak at 0, scaling input intensities > > > > > > by > > > > > > inf > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > the mri peak is at zero, which is wrong (it should be > > > > > > around > > > > > > 116/117 or > > > > > > so). > > > > > > > > > > > > if you view nu.mgz (tkmedit -f nu.mgz), does it look ok? > > > > > > is > > > > > > it oriented > > > > > > correctly? > > > > > > > > > > > > Nick > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > On Tue, 2008-04-22 at 12:28 -0400, Jerry Yeou-Wei Chen > > > > > > wrote: > > > > > > > Hello, > > > > > > > > > > > > > > I am having trouble deciphering why I got the error > > > > > > attached > > > > > > below. > > > > > > > Any suggestions would be greatly appreciated! > > > > > > > > > > > > > > Thanks, > > > > > > > - Jerry > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > Tue Apr 22 10:15:22 EDT 2008 > > > > > > > talairach_avi done > > > > > > > > > > > > > > cp transforms/talairach.auto.xfm transforms/talairach.xfm > > > > > > > > > > > > > > #-------------------------------------------- > > > > > > > [EMAIL PROTECTED] Talairach Failure Detection Tue Apr 22 > > > > > > 10:15:23 EDT > > > > > > 2008 > > > > > > > /scratch/freesurfer/subjects/17/s017/mri > > > > > > > > > > > > > > talairach_afd -T 0.005 -xfm transforms/talairach.xfm > > > > > > > > > > > > > > talairach_afd: Talairach Transform: > > > > > > transforms/talairach.xfm > > > > > > OK > > > > > > > (p=0.7072, pval=0.4932 >= threshold=0.0050) > > > > > > > > > > > > > > awk - > > > > > > > > > > > > > f /scratch/freesurfer/bin/extract_talairach_avi_QA.awk > > > > > > > > > > > > /scratch/freesurfer/subjects/17/s017/mri/transforms/talairach_avi.log > > > > > > > > > > > > > > > > > > TalAviQA: 0.96840 > > > > > > > z-score: -2 > > > > > > > #-------------------------------------------- > > > > > > > [EMAIL PROTECTED] Intensity Normalization Tue Apr 22 10:15:23 > > > > > > EDT 2008 > > > > > > > /scratch/freesurfer/subjects/17/s017/mri > > > > > > > > > > > > > > mri_normalize -g 1 nu.mgz T1.mgz > > > > > > > > > > > > > > using max gradient = 1.000 > > > > > > > reading from nu.mgz... > > > > > > > normalizing image... > > > > > > > talairach transform > > > > > > > 0.976 0.083 0.030 -136.866; > > > > > > > -0.072 1.053 0.164 -153.262; > > > > > > > -0.020 -0.109 1.085 -122.101; > > > > > > > 0.000 0.000 0.000 1.000; > > > > > > > INFO: Modifying talairach volume c_(r,a,s) based on > > > > > > average_305 > > > > > > > building Voronoi diagram... > > > > > > > performing soap bubble smoothing... > > > > > > > 3d normalization pass 1 of 2 > > > > > > > building Voronoi diagram... > > > > > > > performing soap bubble smoothing... > > > > > > > 3d normalization pass 2 of 2 > > > > > > > building Voronoi diagram... > > > > > > > performing soap bubble smoothing... > > > > > > > writing output to T1.mgz > > > > > > > 3D bias adjustment took 19 minutes and 44 seconds. > > > > > > > white matter peak found at 111 > > > > > > > gm peak at 88 (88), valley at 80 (80) > > > > > > > csf peak at 57, setting threshold to 77 > > > > > > > white matter peak found at 111 > > > > > > > gm peak at 88 (88), valley at 80 (80) > > > > > > > csf peak at 55, setting threshold to 77 > > > > > > > #-------------------------------------------- > > > > > > > [EMAIL PROTECTED] Skull Stripping Tue Apr 22 10:35:16 EDT 2008 > > > > > > > /scratch/freesurfer/subjects/17/s017/mri > > > > > > > > > > > > > > mri_em_register -skull > > > > > > > > > > > > > nu.mgz > > > > > > > > > > > > /scratch/freesurfer/average/RB_all_withskull_2008-03-26.gca > > > > > > > > > > > transforms/talairach_with_skull.lta > > > > > > > > > > > > > > aligning to atlas containing skull, setting > > > > > > unknown_nbr_spacing = 5 > > > > > > > reading 1 input volumes... > > > > > > > logging results to talairach_with_skull.log > > > > > > > reading > > > > > > > > > > > > > > > > > > > > > > > > > '/scratch/freesurfer/average/RB_all_withskull_2008-03-26.gca'... > > > > > > > average std = 23.1 using min determinant for > > > > > > regularization = 53.4 > > > > > > > 0 singular and 5702 ill-conditioned covariance matrices > > > > > > regularized > > > > > > > reading 'nu.mgz'... > > > > > > > freeing gibbs priors...done. > > > > > > > bounding unknown intensity as < 20.2 or > 943.7 > > > > > > > total sample mean = 92.0 (1443 zeros) > > > > > > > ************************************************ > > > > > > > spacing=8, using 3481 sample points, tol=1.00e-05... > > > > > > > ************************************************ > > > > > > > register_mri: find_optimal_transform > > > > > > > find_optimal_transform: nsamples 3481, passno 0, spacing 8 > > > > > > > GCAhistoScaleImageIntensities: could not find wm peak > > > > > > > resetting wm mean[0]: 117 --> 126 > > > > > > > resetting gm mean[0]: 74 --> 74 > > > > > > > input volume #1 is the most T1-like > > > > > > > using real data threshold=9.0 > > > > > > > using (102, 110, 122) as brain centroid... > > > > > > > mean wm in atlas = 126, using box (80,83,98) --> (123, > > > > > > 136,146) to > > > > > > > find MRI wm > > > > > > > before smoothing, mri peak at 0 > > > > > > > after smoothing, mri peak at 0, scaling input intensities > > > > > > by > > > > > > inf > > > > > > > Linux kdavis8-efef.uhnres.utoronto.ca 2.6.23.1-21.fc7 #1 > > > > > > SMP > > > > > > Thu Nov 1 > > > > > > > 21:09:24 EDT 2007 i686 i686 i386 GNU/Linux > > > > > > > > > > > > > > recon-all exited with ERRORS at Tue Apr 22 10:41:40 EDT > > > > > > 2008 > > > > > > > > > > > > > _______________________________________________ > > > > > > > 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 > > > > > > > > > > > > _______________________________________________ > > > > > > Freesurfer mailing list > > > > > > Freesurfer@nmr.mgh.harvard.edu > > > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > >
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