Resolved - thank you Andrew!
Solution: operator error, needed to cat file w/ input list for --inputs instead of just specifying file w/ input list ________________________________ From: Hoopes, Andrew Sent: Thursday, February 15, 2018 4:43:18 PM To: Makaretz, Sara Johanna; Freesurfer support list Subject: Re: [Freesurfer] IndexError: list index out of range Thanks Sarah, I haven’t been able to replicate this - do you mind sending the stats file that you’re using as input? Andrew On February 15, 2018 at 3:58:17 PM, Makaretz, Sara Johanna (smakar...@mgh.harvard.edu<mailto:smakar...@mgh.harvard.edu>) wrote: Hi Andrew, python --version = Python 2.7.3 -- EPD 7.3-1 (64-bit) Sara ________________________________ From: Hoopes, Andrew Sent: Thursday, February 15, 2018 3:56:22 PM To: Makaretz, Sara Johanna; Freesurfer support list Subject: Re: [Freesurfer] IndexError: list index out of range Hi Sara and Arkadiy, What version of python2 are you using? python --version thanks Andrew On February 13, 2018 at 10:16:34 AM, Makaretz, Sara Johanna (smakar...@mgh.harvard.edu<mailto:smakar...@mgh.harvard.edu>) wrote: *I also got this error when I ran w/ python 2: python2 $FREESURFER_HOME/bin/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 ________________________________ From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Makaretz, Sara Johanna <smakar...@mgh.harvard.edu> Sent: Tuesday, February 13, 2018 10:12:07 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] IndexError: list index out of range 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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
