12 Feb
2007
12 Feb
'07
6:15 p.m.
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, which checks the > > talairach.xfm against a known set of proper alignments, indicates that > > this alignment is bad. You probably will need to manually align. > > > > Nick > > > > On Thu, 2007-02-08 at 20:46 -0500, Bruce Fischl wrote: > > > > > you need to visualize it in tkmedit. Use file -> load transform for main > > > volume and see if it looks reasonable (should be slightly looking down, > > > and pretty vertical so for example the interhemispheric 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 flag in 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 Freesurfer still quits at the same place. > > > > > > > > > > > I've > > > > > > > > > > > attached the recon-all.log file to this email. 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 the brain again. > > > > > > > > > > > > > > Anil. > > > > > > > > > > > > > > On 2/8/07, Anil Roy > > > > > > > > > > > > > > <aroy85@gmail.com> wrote: > > > > > > > > > > > > > > > Yes. When I convert to BRIK and open with AFNI, the images show up > > > > > > > > > > > > > fine > > > > > > > > > > > > > in all three planes. > > > > > > > > > > > > > > > > There is some noise towards the very end but it only shows up after > > > > > > > > > > > > > the > > > > > > > > > > > > > slices with no brain tissue (or any that I can see). > > > > > > > > > > > > > > > > Anil. > > > > > > > > > > > > > > > > On 2/8/07, Bruce Fischl < > > > > > > > > > > > > > > > > fischl@nmr.mgh.harvard.edu> wrote: > > > > > > > > > > > > > > > > > if you convert it to BRIK and visualize it does it look correct? > > > > > > > > > On Thu, 8 > > > > > > > > > Feb 2007, Anil Roy wrote: > > > > > > > > > > > > > > > > > > > > > > > > > > > > Hello all, > > > > > > > > > > > > > > > > > > > > I have some raw data and I'm not sure of the format. Its > > > > > > > > > > > > > > > definitely > > > > > > > > > > > > > > not > > > > > > > > > > > > > > > > > > > dicom. I ran recon-all on these files but I get an error saying > > > > > > > > > > > > > > > it > > > > > > > > > > > > > > can't > > > > > > > > > > > > > > > > > > > read the files. I have posted the output below. I tried to > > > > > > > > > > > > > > > convert > > > > > > > > > > > > > > the files > > > > > > > > > > > > > > > > > > > to afni format (BRIK + HEAD), and tried recon-all again. It ran > > > > > > > > > > > > > > > for > > > > > > > > > > > > > > a while > > > > > > > > > > > > > > > > > > > but gave an error that I've attached to a text file. > > > > > > > > > > > > > > > > > > > > Can someone please tell me how I can get Freesurfer to read these > > > > > > > > > > > > > > > > > > > files. I > > > > > > > > > > > > > > > > > > > can also upload the raw files if you'd like to take a look at > > > > > > > > > > > > > > > them. > > > > > > > > > > > > > > > Thanks a lot - Anil. > > > > > > > > > > > > > > > > > > > > [root@dhcp-129-105-146-127 freesurfer]# 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 8 13:25 > > > > > > > > > > /root/Freesurfer/Tone_Acquisition/Nl-TA1-001/scripts/recon- > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > all.log > > > > > > > > > > > > > > > Linux dhcp-129-105-146-127.speech.northwestern.edu > > > > > > > > > > > > > > > > > > > 2.6.17-1.2157_FC5smp #1 > > > > > > > > > > > > > > > > > > > SMP Tue Jul 11 23:24:16 EDT 2006 i686 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 file name 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 2006 i686 i686 i386 GNU/Linux > > > > > > > > > > > > > > > > > > > > recon-all exited with ERRORS at Thu Feb 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 steps in: > 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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