I think my last email didn't get through. Bruce, I've uploaded the 001.mgz. It should arrive in your mailbox. I can upload it again if there was any problem.
Thanks, Anil. On 2/20/07, Anil Roy <[EMAIL PROTECTED]> wrote:
> > Its uploaded > > On 2/20/07, Bruce Fischl < [EMAIL PROTECTED]> wrote: > > > > I need the 001.mgz > > On Tue, 20 Feb 2007, Anil Roy wrote: > > > > > Bruce, I had uploaded the orig.mgz for Nick. I think you should find > > the > > > link below. I can also upload the 001.mgz for you. > > > There are no dicoms because the scan is from a GE scanner (120 > > slices, > > > details are below)and all the files are named as I.??? > > > I could also upload these files for you. > > > > > > Anil. > > > > > > On 2/20/07, Bruce Fischl < [EMAIL PROTECTED] > wrote: > > >> > > >> I think it's something afni is doing, but I'm not sure. Did you > > give us > > >> the data before conversion (either the dicoms or the 001.mgz) > > >> > > >> On Tue, 20 Feb 2007, > > >> Anil Roy wrote: > > >> > > >> > Hey Freesurfers, > > >> > > > >> > I fed freesurfer the brainmask.mgz generated by AFNI. autorecon2 > > and > > >> > autorecon3 ran fine with no errors but the resulting surfaces are > > not > > >> very > > >> > accurate. > > >> > > > >> > Bruce, you mentioned that my background values were too high. Is > > there a > > >> way > > >> > to reduce them so that freesurfer can do the watershed without > > any > > >> glitches. > > >> > > > >> > Thanks, > > >> > > > >> > Anil. > > >> > > > >> > On 2/15/07, Bruce Fischl <[EMAIL PROTECTED]> wrote: > > >> >> > > >> >> I think it's because your background values are so high. > > >> >> On Thu, 15 Feb > > >> >> 2007, Anil Roy wrote: > > >> >> > > >> >> > Thanks a lot Nick. > > >> >> > > > >> >> > I'll try to convert the AFNI skull strip into brainmask and nu > > and > > >> see > > >> >> if I > > >> >> > can resume the pipeline. > > >> >> > > > >> >> > I put in the new values for the xfm and ran recon-all again > > with the > > >> >> > notalairach flag. > > >> >> > > > >> >> > recon-all -s Nl-TAl-001 -notalairach -all > > >> >> > > > >> >> > However, it still quits at the watershed step. I ran another > > brain > > >> where > > >> >> the > > >> >> > raw images were dcm and it ran fine so the problem is > > definitely > > >> >> something > > >> >> > specific to this brain. > > >> >> > > > >> >> > Nick, I know that autorecon1 ran fine for you so I really have > > no > > >> clue > > >> >> why > > >> >> > my machine quits at the watershed step even with the transform > > you > > >> gave > > >> >> me. > > >> >> > > > >> >> > Any clues, suggestions? > > >> >> > > > >> >> > Thanks a lot, > > >> >> > > > >> >> > Anil. > > >> >> > > > >> >> > On 2/14/07, Nick Schmansky < [EMAIL PROTECTED] > > > wrote: > > >> >> >> > > >> >> >> Anil, > > >> >> >> > > >> >> >> Here is the transform (the contents of the talairach.xfmfile) that > > >> I > > >> >> >> generated: > > >> >> >> > > >> >> >> Transform_Type = Linear; > > >> >> >> Linear_Transform = > > >> >> >> 9.265516e-01 5.678305e-04 2.317888e-03 3.736965e-01 > > >> >> >> -8.173273e-04 8.513330e-01 8.824052e-02 -1.653205e+01 > > >> >> >> - 2.688466e-03 -1.064786e-01 9.460568e-01 1.780552e+01 ; > > >> >> >> > > >> >> >> Remember to use the -notalairach flag with recon-all when you > > create > > >> > > >> >> the > > >> >> >> new talairach.xfm file, so that it doesnt get overwritten. > > >> >> >> > > >> >> >> 4GB is plenty to run Freesurfer, so it is strange that > > mri_watershed > > >> is > > >> >> >> encountering out-of-memory errors. > > >> >> >> > > >> >> >> Nick > > >> >> >> > > >> >> >> > > >> >> >> On Wed, 2007-02-14 at 17:20 -0600, Anil Roy wrote: > > >> >> >> > Also, I ran it on a Red Hat system and I'm still getting > > the error > > >> so > > >> >> >> > I don't think it is a machine specific problem. Any > > suggestions. > > >> >> >> > > > >> >> >> > Thanks. > > >> >> >> > Anil. > > >> >> >> > > > >> >> >> > On 2/14/07, Anil Roy < [EMAIL PROTECTED]> wrote: > > >> >> >> > Here are the details of the acquisitions: > > >> >> >> > > > >> >> >> > Images acquired on a 3T Signa scanner with a > > standard GE > > >> head > > >> >> >> > coil. 3D T1-weighted spiral volume scan (120 > > slices, > > >> >> 1.4875-mm > > >> >> >> > thick, TR = 20 msec, TE = 6 msec, 40 degrees flip > > angle, > > >> 256 > > >> >> * > > >> >> >> > 192 matrix) > > >> >> >> > > > >> >> >> > The machine has 4 gigs of RAM. Also, AFNI is able > > to > > >> >> talairach > > >> >> >> > and skull strip. Is there a way I can input the > > files from > > >> > > >> >> >> > AFNI to Freesurfer to resume the recon-all > > pipeline. > > >> >> >> > > > >> >> >> > Nick, is there a way for me to see your reg so that > > I can > > >> be > > >> >> >> > sure that its not my created xfm that is causing > > this > > >> >> >> > problem. > > >> >> >> > > > >> >> >> > Thanks, > > >> >> >> > > > >> >> >> > Anil. > > >> >> >> > > > >> >> >> > > > >> >> >> > On 2/14/07, Bruce Fischl <[EMAIL PROTECTED]> > > > > >> wrote: > > >> >> >> > why is the background so high? Also, what > > field > > >> >> >> > strength was this at? There > > >> >> >> > looks to be dielectric-like center > > brightening. > > >> The > > >> >> >> > contrast isn't terrible > > >> >> >> > though. > > >> >> >> > > > >> >> >> > On Wed, 14 Feb 2007, Nick > > >> >> >> > Schmansky wrote: > > >> >> >> > > > >> >> >> > > Bruce, > > >> >> >> > > > > >> >> >> > > the orig.mgz can be downloaded via the > > filedrop, > > >> >> see > > >> >> >> > link in email > > >> >> >> > > below. > > >> >> >> > > > > >> >> >> > > or i have copied it to: > > >> >> >> > > > > >> >> >> > > > >> >> >> > /autofs/space/minerva_001/users/nicks/subjects/anil/mri > > >> >> >> > > > > >> >> >> > > N. > > >> >> >> > > > > >> >> >> > > > > >> >> >> > > On Wed, 2007-02-14 at 17:02 -0500, Bruce > > Fischl > > >> >> >> > wrote: > > >> >> >> > >> put the .mgz somewhere and I'll take a > > look. > > >> And > > >> >> >> > make sure it's the > > >> >> >> > >> orig.mgz, which is un-normalized > > >> >> >> > >> > > >> >> >> > >> > > >> >> >> > >> On Wed, 14 Feb 2007, Nick Schmansky > > wrote: > > >> >> >> > >> > > >> >> >> > >>> Anil, > > >> >> >> > >>> > > >> >> >> > >>> The image has almost no contrast. I've > > > > >> attached > > >> >> a > > >> >> >> > TIFF of one slice. > > >> >> >> > >>> How was this acquired? Bruce, any idea > > why it > > >> > > >> >> >> > would be so white? > > >> >> >> > >>> > > >> >> >> > >>> Nick > > >> >> >> > >>> > > >> >> >> > >>> > > >> >> >> > >>> On Wed, 2007-02-14 at 16:10 -0500, > > >> >> >> > [EMAIL PROTECTED] wrote: > > >> >> >> > >>>> The following files have been uploaded > > to the > > >> >> >> > Martinos Center FileDrop site > > >> >> >> > >>>> by Anil Roy for you to download: > > >> >> >> > >>>> > > >> >> >> > >>>> (1) orig.mgz > > >> >> >> > >>>> > > >> >> >> > >>>> > > >> >> >> > >>>> > > >> >> >> > >>>> These files will expire in 30 days. > > >> >> >> > >>>> > > >> >> >> > >>>> To view or download these files, go in > > your > > >> web > > >> >> >> > browser to: > > >> >> >> > >>>> > > >> >> >> > >>>> > > >> >> >> > > > >> >> >> > > >> >> > > >> https://www.nmr.mgh.harvard.edu/facility/filedrop/showgroup/5010/426/7389dc72a7ad03d19b7736c8a7adff69 > > > > >> > > >> >> >> > >>>> > > >> >> >> > >>>> DO NOT SHARE this web address with > > anyone > > >> >> >> > else. It is your personal access key to > > the > > >> files. > > >> >> >> > >>>> > > >> >> >> > >>>> Overall Comment about files from Anil > > Roy: > > >> >> >> > >>>> > > >> >> >> > >>>> Hi, > > >> >> >> > >>>> > > >> >> >> > >>>> Attached is the orig.mgz file for the > > subject > > >> > > >> >> >> > that quits at the watershed step. > > >> >> >> > >>>> > > >> >> >> > >>>> Thanks, > > >> >> >> > >>>> > > >> >> >> > >>>> Anil. > > >> >> >> > >>>> > > >> >> >> > >>>> > > >> >> >> > >>> > > >> >> >> > >> > > >> >> >> > >> > > >> >> >> > > > > >> >> >> > > > > >> >> >> > > > > >> >> >> > > > >> >> >> > > > >> >> >> > > > >> >> >> > _______________________________________________ > > >> >> >> > Freesurfer mailing list > > >> >> >> > Freesurfer@nmr.mgh.harvard.edu > > >> >> >> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > >> >> >> > > >> >> >> > > >> >> > > > >> >> > > >> > > > >> > > > > > > >
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