14 Feb
2007
14 Feb
'07
4:04 p.m.
Anil,
Can you send me the orig.mgz file? You can upload it to my email address via:
https://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Nick
On Wed, 2007-02-14 at 14:54 -0600, Anil Roy wrote:
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, 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 > > > _______________________________________________ > 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