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]> 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]> wrote:
>>
>> I'll install the CentOS build and run the brain again.
>>
>> Anil.
>>
>> On 2/8/07, Anil Roy <[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]> 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
>> > > 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
>> > > >
>> > >
>> >
>> >
>>
>
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