Hi Doug,

I am also getting the error "IndexError: list index out of range" - I got the 
same error using FS6.0/FS5.3/dev. This is what I'm running for asegstats2table:


asegstats2table --common-segs -t aparc.a2009s+aseg.max.table -i 
aparc.a2009s+aseg.lst -m max

Parsing the .stats files
Traceback (most recent call last):
  File "/usr/local/freesurfer/stable6/bin/asegstats2table", line 548, in 
<module>
    id_name_map, measurelist = parsed.parse(options.meas)
  File "/autofs/cluster/freesurfer/centos7_x86_64/stable6/bin/fsutils.py", line 
115, in parse
    seg = strlst[1] # segmentation id is in the 2nd field
IndexError: list index out of range

This is what I ran to make my stats files, which look fine:
mri_label2vol --seg aparc.a2009s+aseg.nii --temp pet.nii --o 
ns_aparc.a2009s+aseg.nii --reg anat2pet.lta
mri_segstats --seg ns_aparc.a2009s+aseg.nii --i pet.nii --sum 
aparc.a2009s+aseg.stats


Do you have any tips on getting this working?


Thanks in advance for any help!

Sara

________________________________
From: freesurfer-boun...@nmr.mgh.harvard.edu 
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Maksimovskiy, Arkadiy 
<amaksimovs...@mclean.harvard.edu>
Sent: Monday, January 8, 2018 11:50:42 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] IndexError: list index out of range


Hi Doug,



I sent you the tar files, but just wanted to update you that I tried running 
this with just one subjects and am still getting an error but a different one. 
The two inputs and output errors in the terminal are pasted below:



[arkadiysimac:Freesurfer/Freesurfer_Files_with_Freesurfer_Masks/Post_Manual_Edits]
 amaksimovskiy% asegstats2table --subjects SILVA030  --meas volume --stats 
aseg.stats --tablefile Subcortical_GM_Volume1.Dec17.txt

SUBJECTS_DIR : 
/Volumes/silverilab/Arkadiy/Freesurfer/Freesurfer_Files_with_Freesurfer_Masks/Post_Manual_Edits

Parsing the .stats files

Traceback (most recent call last):

  File "/Applications/freesurfer/bin/asegstats2table", line 548, in <module>

    id_name_map, measurelist = parsed.parse(options.meas)

  File "/Applications/freesurfer/bin/fsutils.py", line 115, in parse

    seg = strlst[1] # segmentation id is in the 2nd field

IndexError: list index out of range

[arkadiysimac:Freesurfer/Freesurfer_Files_with_Freesurfer_Masks/Post_Manual_Edits]
 amaksimovskiy% asegstats2table --subjects SILVA040  --meas volume --stats 
aseg.stats --tablefile Subcortical_GM_Volume1.Dec17.txt

SUBJECTS_DIR : 
/Volumes/silverilab/Arkadiy/Freesurfer/Freesurfer_Files_with_Freesurfer_Masks/Post_Manual_Edits

Parsing the .stats files

Traceback (most recent call last):

  File "/Applications/freesurfer/bin/asegstats2table", line 548, in <module>

    id_name_map, measurelist = parsed.parse(options.meas)

  File "/Applications/freesurfer/bin/fsutils.py", line 122, in parse

    self.measurelist.append( float(strlst[self.measure_column_map[measure]] ))

ValueError: could not convert string to float: Left-Cerebellum-Cortex





Let me know if any further info is needed to troubleshoot. Thank you for 
helping with this.

-arkadiy



--

Arkadiy L. Maksimovskiy, Ph.D.

Postdoctoral Research Fellow
McLean Imaging Center, McLean Hospital
Department of Psychiatry, Harvard Medical School
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