I looked at the nifti files in freeview. The orientation in freeview is correct, but it appears all of the T1s that resulted in an error are washed out in freeview. I can vaguely see the outline of the head, but there's a gray box covering the image. When I click on regions of bone or brain in the washed out images, the intensities are comparable with those of non-washed out images.
I created the nifti files using spm. When I display the nifti files in afni or spm they look great. Is there something about the spm-generated nifti files that freesurfer doesn't like? Should I use a different program to convert the dicoms into niftis? I also went back to the original dicoms. If I generate the 001.mgz file from the dicoms, recon-all works appropriately and the image is not washed out. I could always go back and work with the dicoms directly, but moving forward I would prefer working with the nifti files for protected health information reasons. Thanks, Jared On Dec 12, 2013, at 4:56 PM, Jared Nielsen <jared.niel...@hsc.utah.edu> wrote: > Hi Bruce, > > Thanks for your response. It's a bit of a pain to access the dicoms, but it's > possible. The bigger problem now is that I can't get freeview to work. I type > in freeview into the command line and receive the following error: > > freeview.bin: error while loading shared libraries: libvtkverdict.so.5.6: > cannot open shared object file: No such file or directory > > Forgive my lack of linux knowledge, but is there some software I failed to > download? I searched for the error in the Mail Archive and the only entry is > from April 7, 2011. The response to the query says something about glxgear. > Is that something I should try to get freeview running? If so, how do I do > that? > > As a side note, tksurfer and tkmedit seem to work fine. > > Jared > > > On Dec 12, 2013, at 3:36 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu> wrote: > >> Hi Jared >> >> for the ones that run quickly and end, it's because you haven't told it to >> do anything. The first couple of lines of the recon-all.log file give the >> command line as: >> >> Thu Dec 5 14:00:18 MST 2013 >> /mnt/NAS3/freesurfer/freesurfer//bin/recon-all >> -i Time3_28908_s11038064-0005-00001-000001-01.nii -subject Time3_28908 >> >> this will just convert the nifti and create the subject dirs for >> Time3_28908. You need to add "-all" at the end of the line, as you did in >> the other ones. >> >> For the one that failed the talairach it's hard to say. You are starting >> with nifti - can you try it directly on the dicoms? Where did you get the >> nifti from? If you bring the nifti input volume up in freeview does it show >> in the correct orientation? That is, is what freeview thinks is anterior >> truly anterior, etc....? >> >> cheers >> Bruce >> >> >> >> >> On Thu, 12 Dec 2013, JARED NIELSEN wrote: >> >>> Hi, >>> >>> I'm new to FreeSurfer and have been going through the tutorials, YouTube >>> videos, and Mail Archive. I've run recon-all on a handful of scans with >>> variable success. Some of the scans are processed after five or six hours >>> without any problems, and the output looks good. Others are processed >>> "without any errors" after a matter of minutes, and logically I don't see >>> any output. Finally, others hit a hard error after a few minutes of >>> processing during the talairach transformation step. I looked at the >>> orig.mgz file (for the scan that failed at transformation step) through >>> tkmedit, and it is a blank white rectangle. I don't see anything that >>> resembles a head or brain. I've attached examples of each recon-all.log >>> (i.e., good, bad, and bad_talairach). Any help would be greatly appreciated. >>> >>> Thanks, >>> Jared >>> >> >> >> 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. >> > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
