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