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 < [EMAIL PROTECTED]
<mailto:[EMAIL PROTECTED]>> 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 <[EMAIL PROTECTED]> <mailto:[EMAIL PROTECTED]> 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 <[EMAIL PROTECTED]> <mailto:[EMAIL PROTECTED]> wrote:
I'll install the CentOS build and run the brain again.
Anil.
On 2/8/07, Anil Roy
<[EMAIL PROTECTED]> <mailto:[EMAIL PROTECTED]> 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 <
[EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]>> 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.
[EMAIL PROTECTED] 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
[EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]>
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
--
Douglas N. Greve, Ph.D.
MGH-NMR Center
[EMAIL PROTECTED]
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
