Hi Noam
it looks like the talairach alignment failed. You can usually find answers
on our wiki for what to do in this type of case. For example:
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach_tktools
cheers
Bruce
On Mon, 9 Feb 2015, Ben Eliezer, Noam wrote:
Hi Freesurfer support,
I am receiving an error from recon-all and would be happy to get your
opinion.
This dataset, I am processing, is generated by a 3D MPR (Sagittal
orientation) protocol.
It’s only one of many datasets I have and this is the only one giving me
problems…
The run seems to generate the typical directory listing:
total 0
drwxrwxr-x 12 noambe staff 408 Feb 8 19:24 .
drwxr-xr-x@ 20 noambe staff 680 Feb 9 07:49 ..
drwxrwxr-x 2 noambe staff 68 Feb 8 19:24 bem
drwxrwxr-x 2 noambe staff 68 Feb 8 19:24 label
drwxrwxr-x 10 noambe staff 340 Feb 8 19:28 mri
drwxrwxr-x 10 noambe staff 340 Feb 8 19:28 scripts
drwxrwxr-x 2 noambe staff 68 Feb 8 19:24 src
drwxrwxr-x 2 noambe staff 68 Feb 8 19:24 stats
drwxrwxr-x 2 noambe staff 68 Feb 8 19:24 surf
drwxrwxr-x 2 noambe staff 68 Feb 8 19:24 tmp
drwxrwxr-x 4 noambe staff 136 Feb 8 19:27 touch
drwxrwxr-x 2 noambe staff 68 Feb 8 19:24 trash
but the ‘mri’ folder, for example, is missing most of the data
noambe-mac:03_FSseg noambe$ cd mri
noambe-mac:mri noambe$ l
total 50112
drwxrwxr-x 10 noambe staff 340 Feb 8 19:28 .
drwxrwxr-x 12 noambe staff 408 Feb 8 19:24 ..
-rw-rw-r-- 1 noambe staff 21230 Feb 8 19:28 mri_nu_correct.mni.log
-rw-rw-r-- 1 noambe staff 21230 Feb 8 19:26
mri_nu_correct.mni.log.bak
drwxrwxr-x 3 noambe staff 102 Feb 8 19:25 orig
-rw-rw-r-- 1 noambe staff 6915766 Feb 8 19:25 orig.mgz
-rw-rw-r-- 1 noambe staff 21230 Feb 8 19:28 orig_nu.log
-rw-rw-r-- 1 noambe staff 6175023 Feb 8 19:28 orig_nu.mgz
-rw-rw-r-- 1 noambe staff 12484984 Feb 8 19:25 rawavg.mgz
drwxrwxr-x 8 noambe staff 272 Feb 8 19:28 transforms
noambe-mac:mri noambe$
The whole thing runs for a few minutes before it exists with errors.
I’m attaching the output of the recon-all run.
Thanks in advance,
— Noam
--
Noam Ben-Eliezer, PhD
Adjunct Assistant Professor of Radiology
Center for Biomedical-Imaging
New-York University Medical School
noam.ben-elie...@nyumc.org
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