LCModel GABA Difference Analysis

Analysis / Modeling
1

Hi everyone!

I am trying to use LCModel to analyze GABA difference spectra. To specify simulation parameters and soft constraints on concentration ratios, I have been attempting to add the following LCModel manual suggested lines to my shell script:

echo " nsimul= 1" >> $controlfile
echo " chsimu(1)= ’MM09 @ .91 ± .02 FWHM= .14 < .17 ± .015 AMP= 3.’" >> $controlfile
echo " nratio= 1" >> $controlfile
echo " chrato(1)= ’NAAG/NAA = .15 ± .15’" >> $controlfile

However, I have been continuously getting the following error when running my script in Linux:
“FATAL ERROR MYCONT 2
This error occurred before the plot could be produced.”

When the above four lines are commented out, the script runs without any errors. I was wondering if anyone might have any insight into this issue or advice on how to fix it?

Thank you in advance!

2

Are you actually using the plus/minus sign? That almost certainly won’t fly (it’ll have to be +-).

Once you get it to work, I’d further suggest that you add a MM30 component (check osprey/fit/code/osp_fitInitialise.m at develop · schorschinho/osprey · GitHub lines 548f for inspiration; see also Comparison of seven modelling algorithms for γ-aminobutyric acid-edited proton magnetic resonance spectroscopy - PubMed and Comparison of linear combination modeling strategies for edited magnetic resonance spectroscopy at 3 T - PubMed for more on the importance of this)

3

I am using + - in my shell script file, not the actual sign. The forum is formatting the + - to the actual sign, but in the shell I have the proper formatting!

4

IIRC we’ve also previously struggled with the formatting of the ` vs. ’ - you may want to give the respective other a try.

5

Could you share the rest of your control file as well as the full one that doesn’t run?

6

Yes, below is the control file that doesn’t work:

 $LCMODL
 OWNER='Jamie Near, Douglas CIC, McGill University'
 KEY=210387309
 TITLE= ' megapress diff_lcm'
 degppm= 0
 degzer= 0
 attmet= 1
 atth2o= 1
 DELTAT= 4.1700e-04
 doecc= T
 dows= T
 FILBAS= '/Users/amyc/.lcmodel/basis-sets/jn_MEGA_PRESS_diff.basis'
 FILPRI = 'detailed_noGSH'
 FILCOO='/Volumes/NearLab_4TB/POND/PND03_HBK/PND03_HBK_0016/PND03_HBK_0016_01_SE01_MR/mp1/megapress/lcm-out/diff_lcm.coord'
 FILTAB= '/Volumes/NearLab_4TB/POND/PND03_HBK/PND03_HBK_0016/PND03_HBK_0016_01_SE01_MR/mp1/megapress/lcm-out/diff_lcm.table'
 FILPS= '/Volumes/NearLab_4TB/POND/PND03_HBK/PND03_HBK_0016/PND03_HBK_0016_01_SE01_MR/mp1/megapress/lcm-out/diff_lcm.ps'
 FILH2O= '/Volumes/NearLab_4TB/POND/PND03_HBK/PND03_HBK_0016/PND03_HBK_0016_01_SE01_MR/mp1/megapress_w/w_lcm'
 FILRAW= '/Volumes/NearLab_4TB/POND/PND03_HBK/PND03_HBK_0016/PND03_HBK_0016_01_SE01_MR/mp1/megapress/diff_lcm'
 HZPPPM= 123.255827
 ipage2= 2
 LCOORD= 9
 lps= 8
 ltable= 7
 LPRINT= 6
 nbckmn= 4
 dkntmn= 0.2
 neach = 999
 nsubtk= 5
 NUNFIL= 2080
 ppmend= 0
 ppmst= 4
 sddegz= 0
 sddegp= 0
 SUBBAS = F
 ietcou= 6
 xstep= 1
 wsppm= 2.01
 wsmet= 'NAA'
 ratipm= 10
 nrefpk(2)= 1
 nobase= .false.
 nsimul= 1
 chsimu(1)= ’MM09 @ .91 +- .02 FWHM= .14 < .17 +- .015 AMP= 3.’
 nratio= 1
 chrato(1)= ’NAAG/NAA = .15 +- .15’
 namrel= 'Cr'
 $END

This control file runs without error:

 $LCMODL
 OWNER='Jamie Near, Douglas CIC, McGill University'
 KEY=210387309
 TITLE= ' megapress diff_lcm'
 degppm= 0
 degzer= 0
 attmet= 1
 atth2o= 1
 DELTAT= 4.1700e-04
 doecc= T
 dows= T
 FILBAS= '/Users/amyc/.lcmodel/basis-sets/jn_MEGA_PRESS_diff.basis'
 FILPRI = 'detailed_noGSH'
 FILCOO='/Volumes/NearLab_4TB/POND/PND03_HBK/PND03_HBK_0016/PND03_HBK_0016_01_SE01_MR/mp1/megapress/lcm-out/diff_lcm.coord'
 FILTAB= '/Volumes/NearLab_4TB/POND/PND03_HBK/PND03_HBK_0016/PND03_HBK_0016_01_SE01_MR/mp1/megapress/lcm-out/diff_lcm.table'
 FILPS= '/Volumes/NearLab_4TB/POND/PND03_HBK/PND03_HBK_0016/PND03_HBK_0016_01_SE01_MR/mp1/megapress/lcm-out/diff_lcm.ps'
 FILH2O= '/Volumes/NearLab_4TB/POND/PND03_HBK/PND03_HBK_0016/PND03_HBK_0016_01_SE01_MR/mp1/megapress_w/w_lcm'
 FILRAW= '/Volumes/NearLab_4TB/POND/PND03_HBK/PND03_HBK_0016/PND03_HBK_0016_01_SE01_MR/mp1/megapress/diff_lcm'
 HZPPPM= 123.255827
 ipage2= 2
 LCOORD= 9
 lps= 8
 ltable= 7
 LPRINT= 6
 nbckmn= 4
 dkntmn= 0.2
 neach = 999
 nsubtk= 5
 NUNFIL= 2080
 ppmend= 0
 ppmst= 4
 sddegz= 0
 sddegp= 0
 SUBBAS = F
 ietcou= 6
 xstep= 1
 wsppm= 2.01
 wsmet= 'NAA'
 ratipm= 10
 nrefpk(2)= 1
 nobase= .false.
 namrel= 'Cr'
 $END
7

Can you try

 nsimul= 1
 chsimu(1)= 'MM09 @ .91 +- .02 FWHM= .14 < .17 +- .015 AMP= 3.'
 nratio= 1
 chrato(1)= 'NAAG/NAA = .15 +- .15'

instead of

See the difference between ' and ’.

8

That fixed the issue, thank you for your help!

1 Like