try looking here to submit a bug report with information that we can use
to help you
https://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
On 11/5/17 8:17 AM, Danny Deng wrote:
Dear Freesurfer developers,
when I tried to perform example 3: perform a full recon-all on a
preexisting subject
Dear Freesurfer developers,
when I tried to perform example 3: perform a full recon-all on a preexisting
subject folder
The error occurs as follow:
syntax error near unexpected token `newline’
I don’t know how to proceed further.
please help.
Thanks.
Best Regards,
Danny Deng
> Begin forwar
Hi Chris, this problem was created because of a change in the way
tcshell works. When fname2stem fails, it should not go on to set fsvol =
tmp because status should be set to 1. This is the way tcshell used to
work. With newer version of CentOS, it sets status=0 because the set tmp
was success
Thank you Chris for pointing this potential bug and the possible culprit
in the source code. We will take a closer look it and determine the best
way to proceed.
-Zeke
On 06/02/2013 10:16 PM, Chris Adamson wrote:
> During the reg-feat2anat script fslregister produces errors. I tracked
> it to
During the reg-feat2anat script fslregister produces errors. I tracked
it to the argument parsing code
419 case "--fsvol":
420 if ( $#argv < 1) goto arg1err;
421 set fsvol = $argv[1]; shift;
422 set tmp = `fname2stem $fsvol`;
423 if(! $status) set fsvol = $tmp;
424 breaksw
The reg-feat2anat scri
Yes, I am sure.
For instance, with FDR at 0.95, I see the following in the terminal:
MRISfdr2vwth(): np = 163842, nv = 163842, fdr = 0.95, vwth=1.63965
Found 3954 of 163842 vertices above FDR threshold (of 1.63965)
I then change FDR to 0.05, and the terminal brings out two more lines which
are i
Are you sure it is actually changing the threshold? Oftentimes changing
the FDR will not change the threhsold because it is already at its
maximum. If you look in the terminal window you should see something
like this:
MRISfdr2vwth(): np = 163842, nv = 163842, fdr = 0.2, vwth=4.60487
Found 0
Just reporting a GUI bug in QDEC: after setting a different FDR threshold
and pressing the "Set Using FDR" button, more often than not the results
image doesn’t change accordingly. I noticed that the button only has an
effect after moving around the QDEC window and/or waiting a minute or so.
Hope
Thanks to Mike's determination, I have found a bug in the way that the
Supratentoral volume in aseg.stats is computed.
A fixed linux version can be obtained from
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_segstats.linux
. Copy this into $FREESURFER_HOME/bin/mri_segstats,
Hello,
I am using a DELL precision T3500 on Mandriva 2008
my SUBJECTS_DIR is :
/neurospin/grip/protocols/MRI/childrenNS5_7y_Monzalvo_2012/Subject/
(from the "neurospin/grip" network in my lab).
I am using the 5.1 version of freesurfer.
An the command line I ran was
recon-all -s ab080228 -a
Hi Knut - What are the permissions of this file? One thing you could try
is to run bedpostx on /media/Elements/freesurfer/dti/1/dtsave/1/dmri
directly from the command line instead of through trac-all and see if that
works (monitor is a script that bedpostx launches that prints to the
screen t
Hi
I have started to run tracula on my own data. However when I run the
second stage I get this erros bedpostx_seychelles: line 260:
/media/Elements/freesurfer/dti/1/dtsave/1/dmri.bedpostX/monitor:
Permission denied. I have tried running is as root as well but it did
not help. Is there anythin
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