Hi All,
I followed the steps in the tutorial on tkregister2 to align the two volumes and saved the new reg. Following this I ran recon-all again but freesurfer still quits at the watershed step. I've attached a file with the output to this email. Do you know if something else could be causing the problem.
Thanks a lot,
Anil.
On 2/12/07, Nick Schmansky nicks@nmr.mgh.harvard.edu wrote:
Anil,
exclude the argument '--surf orig' from tkregister2 if the surfaces are not available.
Nick
On Mon, 2007-02-12 at 16:58 -0600, Anil Roy wrote:
Hi,
I loaded up the orig volumes and the xfm. The brainmask volume isn't there because freesurfer quit at the skull strip phase. I've attached the tiffs of the orig and xfm to this email. As you'll see, the xfm does look quite bad. Do you know how I could correct this.
The manual mentions using tkregister2, but when I run it I get an error(also attached) because the surfaces weren't generated. Is there a different way to use tkregister2 to correct the output.
Thanks,
Anil
On 2/9/07, Doug Greve greve@nmr.mgh.harvard.edu wrote: Hi Anil,
my suggestion was to first look at the volume in tkmedit without the xfm, then, if that is oriented correctly and looks ok, move on to the xfm doug Anil Roy wrote: > Thanks a lot for all your input. I will check out the xfm in > tkmedit and get back to you with the results. > > Anil. > > On 2/9/07, Doug Greve <greve@nmr.mgh.harvard.edu> wrote: > I think the first thing you should do is visualize > your input in tkmedit to make sure it is oriented > correctly. FreeSurfer and AFNI may be making > different assumptions about the data. > > doug > > > Nick Schmansky wrote: > > Anil, > > > > See this tutorial: > > > >https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach
> > > > > > > > Also, a tool to appear in the next release, whichchecks the
> > talairach.xfm against a known set of properalignments, indicates that
> > this alignment is bad. You probably will need tomanually align.
> > > > Nick > > > > On Thu, 2007-02-08 at 20:46 -0500, Bruce Fischlwrote:
> > > > > you need to visualize it in tkmedit. Use file ->load transform for main
> > > volume and see if it looks reasonable (should beslightly looking down,
> > > and pretty vertical so for example theinterhemispheric fissure goes
> > > > > > > > > straight up and down in a coronal view > > > On Thu, 8 Feb 2007, Anil Roy wrote: > > > > > > > > > > I've attached the talairach.xfm to this email.I'm a newbie to MRI analysis
> > > > so I don't know what exactly would be a red flagin this file. Please do
> > > > tell me if you see something odd. > > > > > > > > > > > > Anil. > > > > > > > > > > > > On 2/8/07, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:
> > > > > > > > > did you check the talairach.xfm? > > > > > On Thu, 8 Feb 2007, Anil Roy wrote: > > > > > > > > > > > > > > > > Hi All, > > > > > > > > > > > > I installed the new build and Freesurferstill quits at the same place.
> > > > > > > > > > > I've > > > > > > > > > > > attached the recon-all.log file to thisemail. Its still giving an error
> > > > > > > > > > > at > > > > > > > > > > > the watershed step. > > > > > > > > > > > > Anil. > > > > > > > > > > > > On 2/8/07, Anil Roy <aroy85@gmail.com>wrote:
> > > > > > > > > > > > > > > > > > > > > > > > > I'll install the CentOS build and run thebrain again.
> > > > > > > > > > > > > > Anil. > > > > > > > > > > > > > > On 2/8/07, Anil Roy > > > > > > > > > > > > > > <aroy85@gmail.com> wrote: > > > > > > > > > > > > > > > Yes. When I convert to BRIK and openwith AFNI, the images show up
> > > > > > > > > > > > > fine > > > > > > > > > > > > > in all three planes. > > > > > > > > > > > > > > > > There is some noise towards the very endbut it only shows up after
> > > > > > > > > > > > > the > > > > > > > > > > > > > slices with no brain tissue (or any thatI can see).
> > > > > > > > > > > > > > > > Anil. > > > > > > > > > > > > > > > > On 2/8/07, Bruce Fischl < > > > > > > > > > > > > > > > > fischl@nmr.mgh.harvard.edu> wrote: > > > > > > > > > > > > > > > > > if you convert it to BRIK andvisualize it does it look correct?
> > > > > > > > > On Thu, 8 > > > > > > > > > Feb 2007, Anil Roy wrote: > > > > > > > > > > > > > > > > > > > > > > > > > > > > Hello all, > > > > > > > > > > > > > > > > > > > > I have some raw data and I'm notsure of the format. Its
> > > > > > > > > > > > > > > definitely > > > > > > > > > > > > > > not > > > > > > > > > > > > > > > > > > > dicom. I ran recon-all on thesefiles but I get an error saying
> > > > > > > > > > > > > > > it > > > > > > > > > > > > > > can't > > > > > > > > > > > > > > > > > > > read the files. I have posted theoutput below. I tried to
> > > > > > > > > > > > > > > convert > > > > > > > > > > > > > > the files > > > > > > > > > > > > > > > > > > > to afni format (BRIK + HEAD), andtried recon-all again. It ran
> > > > > > > > > > > > > > > for > > > > > > > > > > > > > > a while > > > > > > > > > > > > > > > > > > > but gave an error that I've attachedto a text file.
> > > > > > > > > > > > > > > > > > > > Can someone please tell me how I canget Freesurfer to read these
> > > > > > > > > > > > > > > > > > > files. I > > > > > > > > > > > > > > > > > > > can also upload the raw files ifyou'd like to take a look at
> > > > > > > > > > > > > > > them. > > > > > > > > > > > > > > > Thanks a lot - Anil. > > > > > > > > > > > > > > > > > > > > [root@dhcp-129-105-146-127freesurfer]# recon-all -force -i > > > > > > > > > >/root/U_Chicago/Tone_Acquisition/Nl-TA1-001/I.001 -subjid
> > > > > > > > > > > > > > > Nl-TA1-001 > > > > > > > > > > > > > > -sd > > > > > > > > > > > > > > > > > > > /root/Freesurfer/Tone_Acquisition-all
> > > > > > > > > > INFO: SUBJECTS_DIR is/root/Freesurfer/Tone_Acquisition
> > > > > > > > > > INFO:/root/Freesurfer/Tone_Acquisition/Nl-TA1-001 exists with
> > > > > > > > > > > > > > > -i, > > > > > > > > > > > > > > but > > > > > > > > > > > > > > > > > > > -force specified. > > > > > > > > > > Deleting any previous source volumes > > > > > > > > > > Actual FREESURFER_HOME/usr/local/freesurfer
> > > > > > > > > > -rw-rw-r-- 1 root root 76880 Feb 813:25
> > > > > > > > > >/root/Freesurfer/Tone_Acquisition/Nl-TA1-001/scripts/recon-
> > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > all.log > > > > > > > > > > > > > > > Linuxdhcp-129-105-146-127.speech.northwestern.edu
> > > > > > > > > > > > > > > > > > > 2.6.17-1.2157_FC5smp #1 > > > > > > > > > > > > > > > > > > > SMP Tue Jul 11 23:24:16 EDT 2006i686 i686 i386 GNU/Linux
> > > > > > > > > > strings: Command not found. > > > > > > > > > > WM removal version > > > > > > > > > >/root/Freesurfer/Tone_Acquisition/Nl-TA1-001
> > > > > > > > > > > > > > > > > > > > mri_convert/root/U_Chicago/Tone_Acquisition/Nl-TA1-001/I.001
> > > > > > > > > > > > > > > > > > > > > > > > > > > > > >/root/Freesurfer/Tone_Acquisition/Nl-TA1-001/mri/orig/001.mgz
> > > > > > > > > > > > > > > > > > > > mri_convert/root/U_Chicago/Tone_Acquisition/Nl-TA1-001/I.001
> > > > > > > > > >/root/Freesurfer/Tone_Acquisition/Nl-TA1-001/mri/orig/001.mgz
> > > > > > > > > > reading from/root/U_Chicago/Tone_Acquisition/Nl-TA1-001/I.001...
> > > > > > > > > > > > > > > > > > > > > > > > > > > > > > genesisRead(): can't determine filename format for
> > > > > > > > > >/root/U_Chicago/Tone_Acquisition/Nl-TA1-001/I.001
> > > > > > > > > > Linux > > > > > > > > > > > > > > > > > > > >dhcp-129-105-146-127.speech.northwestern.edu
> > > > > > > > > > > > > > > > > > > 2.6.17-1.2157_FC5smp #1 > > > > > > > > > > > > > > > > > > > SMP Tue Jul 11 23:24:16 EDT 2006i686 i686 i386 GNU/Linux
> > > > > > > > > > > > > > > > > > > > recon-all exited with ERRORS at ThuFeb 8 13:52:57 CST 200
> > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > _______________________________________________ > > > 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
> > > > > > > > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve@nmr.mgh.harvard.edu > > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > In order to help us help you, please follow the stepsin:
> surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > > > > > ____________________________________________________________ > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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