External Email - Use Caution
Hi again,
I did try to amend the VERSION line to what is listed in the original 7.1.0
file, yet I still received the "Command not found" error. I have attached
output with and without --debug flag when executing the original 7.1.0
reg-feat2anat vs. the updated file from the command line. The original lists
the reg-feat2anat usage/options as one would expect.
Any other suggestions you all might have regarding how to troubleshoot would be
greatly appreciated.
Thanks again for your time,
Erin
--
Erin Walsh, Ph.D.
Assistant Professor
University of North Carolina-Chapel Hill
Department of Psychiatry
Chapel Hill, NC 27599-3367
[email protected]
pronouns: she/her
________________________________
From: Walsh, Erin <[email protected]>
Sent: Monday, November 16, 2020 12:13 PM
To: Douglas N. Greve <[email protected]>; [email protected]
<[email protected]>
Subject: Re: tkregister issue with reg-feat2anat
Hi, following up on this. The difference I see in the file sent vs previous
file is the version line:
Old:
set VERSION = 'reg-feat2anat 7.1.0';
New:
set VERSION = 'reg-feat2anat @FS_VERSION@';
Could this be the issue? Hence the @FS_VERSION@ error in the debug output?
Thanks again,
Erin
________________________________
From: Walsh, Erin <[email protected]>
Sent: Friday, November 13, 2020 1:45 PM
To: Douglas N. Greve <[email protected]>; [email protected]
<[email protected]>
Subject: Re: tkregister issue with reg-feat2anat
Thanks. I have attached the error output when using the debug option when
attempting to run a subject. When I type from the command line (no --feat or
--subject options), it is an identical error:
[edub@longleaf-login1 Freesurfer]$ reg-feat2anat --debug
: Command not found.
: Command not found.
: Command not found.
: Command not found.
: Command not found.
: Command not found.
: Command not found.
: Command not found.
: Command not found.
: Command not found.
: Command not found.
: Command not found.
: Command not found.
: Command not found.
: Command not found.
: Command not found.
: Command not found.
: Command not found.
: Command not found.
: Command not found.
: Command not found.
: Command not found.
: Command not found.
: Command not found.
: Command not found.
: Command not found.
: Command not found.
: Command not found.
reg-feat2anat @FS_VERSION@
: Command not found.
--
Erin Walsh, Ph.D.
Assistant Professor
University of North Carolina-Chapel Hill
Department of Psychiatry
Chapel Hill, NC 27599-3367
[email protected]
pronouns: she/her
________________________________
From: Douglas N. Greve <[email protected]>
Sent: Friday, November 13, 2020 12:01 PM
To: Walsh, Erin <[email protected]>; [email protected]
<[email protected]>
Subject: Re: tkregister issue with reg-feat2anat
I'm sure they will. When you re-run it, add --debug as the first argument and
capture the entire terminal output to a file (don't try to take a snapshot)
On 11/13/2020 11:50 AM, Walsh, Erin wrote:
External Email - Use Caution
Not presently, as I would need to install on my personal computer. I can ask
HPC IT to replace the file again and retest to see if things replicate...
Erin
________________________________
From: Douglas N. Greve <[email protected]><mailto:[email protected]>
Sent: Friday, November 13, 2020 11:48 AM
To: Walsh, Erin <[email protected]><mailto:[email protected]>;
[email protected]<mailto:[email protected]>
<[email protected]><mailto:[email protected]>
Subject: Re: tkregister issue with reg-feat2anat
Can you run it outside of the HCP?
On 11/13/2020 11:27 AM, Walsh, Erin wrote:
{\rtf1\ansi\ansicpg1252\cocoartf1671\cocoasubrtf600
{\fonttbl\f0\fnil\fcharset0 Menlo-Regular;}
{\colortbl;\red255\green255\blue255;\red0\green0\blue0;}
{\*\expandedcolortbl;;\csgray\c0;}
\margl1440\margr1440\vieww17900\viewh11180\viewkind0
\pard\tx560\tx1120\tx1680\tx2240\tx2800\tx3360\tx3920\tx4480\tx5040\tx5600\tx6160\tx6720\pardirnatural\partightenfactor0
\f0\fs22 \cf2 \CocoaLigature0 [edub@longleaf-login1 /]$ reg-feat2anat.new1\
: Command not found.\
: Command not found.\
: Command not found.\
: Command not found.\
: Command not found.\
: Command not found.\
: Command not found.\
: Command not found.\
: Command not found.\
: Command not found.\
: Command not found.\
: Command not found.\
: Command not found.\
: Command not found.\
: Command not found.\
: Command not found.\
: Command not found.\
: Command not found.\
: Command not found.\
: Command not found.\
: Command not found.\
: Command not found.\
: Command not found.\
: Command not found.\
: Command not found.\
: Command not found.\
usage_exit: label not found.\
: Command not found.\
\
\
[edub@longleaf-login1 /]$ reg-feat2anat.new1 --debug\
: Command not found.\
: Command not found.\
: Command not found.\
: Command not found.\
: Command not found.\
: Command not found.\
: Command not found.\
: Command not found.\
: Command not found.\
: Command not found.\
: Command not found.\
: Command not found.\
: Command not found.\
: Command not found.\
: Command not found.\
: Command not found.\
: Command not found.\
: Command not found.\
: Command not found.\
: Command not found.\
: Command not found.\
: Command not found.\
: Command not found.\
: Command not found.\
: Command not found.\
: Command not found.\
: Command not found.\
: Command not found.\
reg-feat2anat 7.1.0\
: Command not found.}{\rtf1\ansi\ansicpg1252\cocoartf1671\cocoasubrtf600
{\fonttbl\f0\fnil\fcharset0 Menlo-Regular;}
{\colortbl;\red255\green255\blue255;\red0\green0\blue0;}
{\*\expandedcolortbl;;\csgray\c0;}
\margl1440\margr1440\vieww17900\viewh11180\viewkind0
\pard\tx560\tx1120\tx1680\tx2240\tx2800\tx3360\tx3920\tx4480\tx5040\tx5600\tx6160\tx6720\pardirnatural\partightenfactor0
\f0\fs22 \cf2 \CocoaLigature0 [edub@longleaf-login1 /]$ reg-feat2anat.orig \
\
USAGE: reg-feat2anat\
\
--feat dir : directory in which to find example_func\
--subject id : FreeSurfer subjectid\
\
Optional flags and arguments:\
\
--overwrite-exf2std : replace Feat-generated example_func2standard\
\
--manual : interactively view/edit registration\
--manxfm xfmtype : interactively view/edit registration for xfmtype\
xfmtype can be: func2anat, std2anat, or func2std\
--dof dof : FLIRT DOF (default is 6)\
--bins bins : FLIRT bins (default is 256)\
--cost cost : FLIRT cost (default is corratio)\
--maxangle angle : FLIRT max search angle (default is 90)\
--bet : run betfunc on example_func (not with FSL 4.0)\
\
--title : title for tkregister window\
--no-bbr : do not use boundary-based registration\
--spm : use SPM instead of flirt, 6 dof only\
--no-inorm : do not inorm when running tkregister2\
--fmov fmov : for tkregister2\
--version : print version and exit\
--help : print help and exit\
--debug : turn on debugging\
\
\
[edub@longleaf-login1 /]$ reg-feat2anat.orig --debug\
set echo = 1 ;\
set debug = 1 ;\
set debug = 1\
breaksw\
breaksw\
\
end\
end\
while ( $#argv != 0 )\
while ( 0 != 0 )\
\
goto parse_args_return ;\
goto parse_args_return\
\
\
goto check_params ;\
goto check_params\
\
if ( $DoBBR ) then\
if ( 1 ) then\
which bbregister > /dev/null\
which bbregister\
if ( $status ) then\
if ( 0 ) then\
endif\
endif\
\
if ( $#FeatDir == 0 ) then\
if ( 0 == 0 ) then\
echo "ERROR: must specify feat dir"\
echo ERROR: must specify feat dir\
ERROR: must specify feat dir\
exit 1 ;\
exit 1\
\
\
\
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