Hello Edgar,
Could you upload the whole subject folder? I could try to run it through
recon all here and see if I can reproduce the error. It would also allow
me to look through your log files to see if I can spot anything that
could be causing this issue.
You can use FileDrop2.0 if the directory is under 2GB
https://gate.nmr.mgh.harvard.edu/filedrop2/
Thank you,
Ani Varjabedian
On 03/25/2015 11:06 AM, Edgar Busovaca wrote:
Hello Bruce,
I took a look at the file with freeview and I can't identify anything
peculiar about the data. The file is named Indices_oob.nii and has
been uploaded to /transfer/incoming on the FTP file exchange server.
Thank you for your swift reply and in advance for your time.
Best regards,
Edgar Busovaca
On Tue, Mar 24, 2015 at 5:34 PM, Bruce Fischl
<fis...@nmr.mgh.harvard.edu <mailto:fis...@nmr.mgh.harvard.edu>> wrote:
Hi Edgar
the LINE SEARCH thing is not a real problem. I've never seen
"indices out of bounds" before though. Is there anything strange
about your dataset? Does freeview display it properly (that is,
are what freeview thinks the RAS dirs the correct anatomical
ones)? If you upload the dataset we'll see if we can replicate and
fix the problem
cheers
Bruce
On Tue, 24 Mar 2015, Edgar Busovaca wrote:
Dear Freesurfer users,
I have attempted to process a subject (.nii type input)
through recon-all
-all, but for some reason the processing gambit is terminated
early ( during
the skullstrip).
During skullstripping the following warning appears twice:
IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE
MCSRCH ERROR
RETURN OF LINE SEARCH: INFO=3 POSSIBLE CAUSES FUNCTION OR
GRADIENT ARE
INCORRECT OR INCORRECT TOLERANCESoutof WuasiNewtonEMA: 007:
-log(p) =
10341.8 tol 0.000010
following the skullstrip step in ***********WATERSHED********
the following
appears:
mri_watershed Error: indices out of bounds
Oddly, this particular subject failed where the rest of the
data set
successfully completed recon-all -all.
As a reference I am running freesurfer 5.1
Build stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0
RedHat release: CentOS release 6.5 (Final)
Kernel info: Linux 2.6.32-431.11.2.e16.x86_64 x86_64
Is there a flag to push this subject through recon-all?
Thanks in advance for your time.
Best,
Edgar Busovaca
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