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.xfm file) > 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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