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