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
>> > > >
>> > >
>> >
>> >
>>
>