Hello Edgar,
We think we were able to isolate the problem. Version 5.1 is failing to
apply the talairach transform to the nu.mgz. It gets computed and
applied to the orig.mgz but then not transferred during the next step.
When mri_normalize tries to run without this information, it fails, and
then this leads to watershed failing as well. mri_normalize usually
tries to fallback on other options if the talairach transform isn't
present, and this can work most of the time, but in some cases it fails
(which can explain why this subject in particular fails but other
subjects go through just fine).
try:
set mdir=$SUBJECTS_DIR/$subject/mri
mri_add_xform_to_header $mdir/transforms/talairach.xfm $mdir/nu.mgz
$mir/nu.mgz
to add the transform to your nu.mgz header. Then if you run recon-all
from this step onwards (you could even use recon-all -make all), it
should work.
Let me know if you try this, and if you have some success.
Thank you,
Ani Varjabedian
On 04/02/2015 04:26 PM, Ani Varjabedian wrote:
Hello Edgar,
I am going to be looking at your case and seeing if I can replicate
the error. I have your .nii file and will run it through our
processing stream here, but could you send me your subject folder so
that I can look through your files/logs to give me some more information?
You can upload the subject folder through filedrop2.0 which is a bit
easier to use, as long as your folder is under 2GB!
https://gate.nmr.mgh.harvard.edu/filedrop2/
Thank you,
Ani Varjabedian
On 04/02/2015 11:23 AM, Edgar Busovaca wrote:
Hello Bruce,
I just wanted to touch base regarding the "Indices_oob.nii" subject I
had sent to MGH. Were you by any chance able to detect the issue
with running recon-all on this subject. Thanks in advance for taking
a look at this.
Best regards,
Edgar Busovaca
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