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 mailto: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 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 mailto: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 mailto: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 mailto: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 mailto: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 http://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 http://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 mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto: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 mailto: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 http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer