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
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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Maksimovskiy, Arkadiy AMAKSIMOVSKIY@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
*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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Makaretz, Sara Johanna SMAKARETZ@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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Maksimovskiy, Arkadiy AMAKSIMOVSKIY@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
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 (smakaretz@mgh.harvard.edumailto:smakaretz@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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Makaretz, Sara Johanna SMAKARETZ@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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Maksimovskiy, Arkadiy AMAKSIMOVSKIY@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
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 (smakaretz@mgh.harvard.edumailto:smakaretz@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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Makaretz, Sara Johanna SMAKARETZ@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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Maksimovskiy, Arkadiy AMAKSIMOVSKIY@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
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 (smakaretz@mgh.harvard.edumailto:smakaretz@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 (smakaretz@mgh.harvard.edumailto:smakaretz@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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Makaretz, Sara Johanna SMAKARETZ@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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Maksimovskiy, Arkadiy AMAKSIMOVSKIY@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
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 (smakaretz@mgh.harvard.edumailto:smakaretz@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 (smakaretz@mgh.harvard.edumailto:smakaretz@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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Makaretz, Sara Johanna SMAKARETZ@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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Maksimovskiy, Arkadiy AMAKSIMOVSKIY@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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Hoopes, Andrew -
Makaretz, Sara Johanna -
Maksimovskiy, Arkadiy