External Email - Use Caution

This is the message I get when I use --debug as the first flag.

Mirsols-MacBook-Pro:~ mirsolchoi$ vol2subfield --debug --i fa.nii.gz --reg reg.lta --sf rh.hippoAmygLabels-T1.v22.HBT.mgz --outreg outreg.lta

set echo = 1 ;

breaksw

breaksw

end

end

while ( $#argv != 0 )

while ( 8 != 0 )

set flag = $argv[1] ; shift ;

set flag = --i

shift

switch ( $flag )

switch ( --i )

if ( $#argv < 1 ) goto arg1err ;

if ( 7 < 1 ) goto arg1err

set invol = $argv[1] ; shift ;

set invol = fa.nii.gz

shift

breaksw

breaksw

end

end

while ( $#argv != 0 )

while ( 6 != 0 )

set flag = $argv[1] ; shift ;

set flag = --reg

shift

switch ( $flag )

switch ( --reg )

if ( $#argv < 1 ) goto arg1err ;

if ( 5 < 1 ) goto arg1err

set reg = $argv[1] ; shift ;

set reg = reg.lta

shift

breaksw

breaksw

end

end

while ( $#argv != 0 )

while ( 4 != 0 )

set flag = $argv[1] ; shift ;

set flag = --sf

shift

switch ( $flag )

switch ( --sf )

if ( $#argv < 1 ) goto arg1err ;

if ( 3 < 1 ) goto arg1err

set subfieldvol = $argv[1] ; shift ;

set subfieldvol = rh.hippoAmygLabels-T1.v22.HBT.mgz

shift

breaksw

breaksw

end

end

while ( $#argv != 0 )

while ( 2 != 0 )

set flag = $argv[1] ; shift ;

set flag = --outreg

shift

switch ( $flag )

switch ( --outreg )

if ( $#argv < 1 ) goto arg1err ;

if ( 1 < 1 ) goto arg1err

set outreg = $argv[1] ; shift ;

set outreg = outreg.lta

shift

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 ( $#invol == 0 ) then

if ( 1 == 0 ) then

if ( $#subfieldvol == 0 ) then

if ( 1 == 0 ) then

if ( $#reg == 0 ) then

if ( 1 == 0 ) then

set subject = `reg2subject --r $reg`

set subject = `reg2subject --r $reg`

reg2subject --r reg.lta

set orig = $SUBJECTS_DIR/$subject/mri/orig.mgz

set orig = /Users/mirsolchoi/Desktop/subjects/ERROR: cannot find reg.lta/mri/orig.mgz

set: Variable name must contain alphanumeric characters.

Mirsols-MacBook-Pro:~ mirsolchoi$

On Thu, Nov 16, 2023 at 4:27 PM Mirsol Choi mirsol@ualberta.ca wrote:

Hi Douglas,

Thank you so much for your response. Attached is the message I receive when I input the --debug.

[image: Screenshot 2023-11-16 at 4.26.05 PM.png]

On Wed, Nov 15, 2023 at 7:50 PM Douglas N. Greve dgreve@mgh.harvard.edu wrote:

...

Can you run it with --debug as the first option and send the resulting terminal output?

On 11/9/2023 12:54 PM, Mirsol Choi wrote:

    External Email - Use Caution

Hello Freesurfers,

I am trying to segment the hippocampus into its subfields and take the FA values from each subfield area.

I am able to segment the hippocampus using the command (segmentHA_T1.sh) and I was also able to perform the dt-recon function on dwi data.

I am trying to map the fa.nii file from dt-recon into the hippocampus subfield volume rh.hippoAmygLabels-T1.v22.HBT.mgz, however when I run the code that is provided by vol2subfield -help:

vol2subfield --i fa.nii.gz --reg reg.lta --sf rh.hippoAmygLabels-T1.v21.HBT.mgz --outreg outreg.lta

or

vol2subfield --i fa.nii.gz --reg reg.lta --sf rh.hippoAmygLabels-T1.v21.HBT.mgz --o fa.rh.hbt.mgz

I am met with a message stating "set: Variable name must contain alphanumeric characters."

How can I fix this "variable name must contain alphanumeric characters" issue and run this command?

Thank you all for your time, help and expertise.

M

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