Hi Ping,
This is an issue with the mac build, that we are currently working on fixing. Anastasia, (cc'd) is working on a patch that you can download to resolve this issue.
As far as the nb0 value is concerned you're correct, it assumes that the first 7 volumes are b0, but it uses that to compute an average b0 mask, so you should be fine using nb0 = 1. It will then use only the first volume (b0) to create the mask.
Please refer to this thread for details on nb0 value in the configuration file:
https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-June/018768.html
-Priti
HI Priti,
I've attached the trac-all.log. The "prior" had not finished, complaining about memory allocation.
*** error: can't allocate region *** set a breakpoint in malloc_error_break to debug MRIalloc(218, 182, 182): could not allocate 158704 bytes for 14th slice
Cannot allocate memory
The systems I tested were MAC OS X 10.5.8. with 2 x 2.66 Ghz Quad-Core
processors and 16 GB memory, and MAC OS X 10.6 with 20 GB memory. Both of them failed with the same errors.
In addition, I need to set nb0 = 1 in the configure file in order to run
the "prior", although there are 7 b0 sparked in every 7 volumes. I think "nb0=7" means the first 7 volumes will be assumed to
non-diffusion weighted. Correct me if I am wrong. Thanks.
Ping
On Fri, Jul 29, 2011 at 11:26 AM, Priti Srinivasan rspriti@nmr.mgh.harvard.edu wrote:
Hi Ping, The text files get created in the trac-all -prior stage. Maybe
something
went wrong in that step. Is this the case for all the tracts or just
for
this tract? If you can send us the trac-all.log file under the scripts
directory it'll be easier to troubleshoot as to what went wrong. -Priti
Hi, I got the error running "trac-all -path -c configure.txt" ERROR: Could not open ${SUBJECTS_DIR}/$Subject/dlabel/diff/lh.cst_AS_avg33_mni_flt_cpts_5.txt
I can only find only image files in the "dlabel/diff" directory, but not text files.
Which step(s) create the lh.cst_AS_avg33_mni_flt_cpts_5.txt file? Thanks, Ping _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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