Hi Angela,

this does not seem to be related to longitudinal processing, your commands are OK. For some reason the nu_correct crashes (I changed the subject line). I don't know what causes that, maybe someone else has an idea. You have enough disk space?

I copy the part from the log here:

Iteration 1 Thu Feb 18 14:07:56 CET 2016
nu_correct -clobber ./tmp.mri_nu_correct.mni.56783/nu0.mnc ./tmp.mri_nu_correct.mni.56783/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.56783/0/
Can't locate MNI/Startup.pm in @INC (@INC contains: /Applications/freesurfer/mni /Library/Perl/5.12/darwin-thread-multi-2level /Library/Perl/5.12 /Network/Library/Perl/5.12/darwin-thread-multi-2level /Network/Library/Perl/5.12 /Library/Perl/Updates/5.12.3 /System/Library/Perl/5.12/darwin-thread-multi-2level /System/Library/Perl/5.12 /System/Library/Perl/Extras/5.12/darwin-thread-multi-2level /System/Library/Perl/Extras/5.12 .) at /Applications/freesurfer/mni/bin/nu_correct line 37.
BEGIN failed--compilation aborted at /Applications/freesurfer/mni/bin/nu_correct line 37.
ERROR: nu_correct
Darwin iMac-di-Angela.local 11.4.2 Darwin Kernel Version 11.4.2: Thu Aug 23 16:25:48 PDT 2012; root:xnu-1699.32.7~1/RELEASE_X86_64 x86_64
recon-all -s subj025.long.template100 exited with ERRORS at Thu Feb 18 14:07:56 CET 2016

Best, Martin


On 02/18/2016 08:11 AM, angela.favaro@unipd.it wrote:
Hi all,
I would be very grateful of any advice for the problem below with e-TIV.

I have another problem with the longitudinal streaming (it is the first
time I use it). I am running the .base and .long procedure in subjects
with only one measure to include them in a mixed liner model analysis (as
suggested in the wiki).
I run the following commands:

recon-all -base template100 -tp subj025 -all

recon-all -long subj025 template100 -all

However at the second command line an error occur (attached is the log):

BEGIN failed--compilation aborted at
/Applications/freesurfer/mni/bin/nu_correct line 37.
ERROR: nu_correct
Darwin iMac-di-Angela.local 11.4.2 Darwin Kernel Version 11.4.2: Thu Aug
23 16:25:48 PDT 2012; root:xnu-1699.32.7~1/RELEASE_X86_64 x86_64

recon-all -s subj025.long.template100 exited with ERRORS

Which is my mistake? I looked for a solution in the mailing list, but I
did not find an answer.
Thank you for any help!

Angela




Dear Freesurfer experts,
I have a question about eTIV (FS 5.3) which I use as a covariate where
appropriate. Is it in some way influenced by the presence of brain
atrophy?
I have a new sample of subjects in a longitudinal study: at time 1 they
have some atrophy (due to low body weight) that improves in time 2 (4
months). I observed that eTIV-time1 is slightly correlated with weight
(r=0.3) whereas no correlation is present at time 2. The correlation
between eTIV-time1 and eTIV-time2 is somewhat lower than expected (r=0.53)
and is lower than correlation between SegBrain_Vol_1 and SegBrain_Vol_2
(0.65).

Do you suggest in these cases to perform manual segmentation to obtain
TIV? or is there any other method (in freesurfer) to obtain an estimate of
TIV not influenced by brain atrophy? What about using BrainMask_to_TIV?

Thank you for any suggestion

Angela


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-- 
Martin Reuter, PhD
Assistant Professor of Radiology, Harvard Medical School
Assistant Professor of Neurology, Harvard Medical School
A.A.Martinos Center for Biomedical Imaging
Massachusetts General Hospital
Research Affiliate, CSAIL, MIT
Phone: +1-617-724-5652
Web  : http://reuter.mit.edu