it seems that it is failing on a particular subject....when I exclude this
subject from the list then the command works and when I try to give the
command on that particular subject I get the error:
SUBJECTS_DIR : /usr/local/freesurfer/subjects
Parsing the .stats files
Traceback (most recent call last):
File "/usr/local/freesurfer/bin/aparcstats2table", line 321, in <module>
parc_measure_map = parsed.parse(options.meas)
File "/usr/local/freesurfer/bin/fsutils.py", line 194, in parse
parcid = strlist[0]
IndexError: list index out of range
I visually inspected the subject...there are some processing defects (i.e.
the superior temporal girus is not well segmented despite editing).
Could that be the problem?
Thanks
2013/9/2 pietro de rossi <deross...@gmail.com>
> Hi Doug,
>
> my command line is
>
> aparcstats2table --subjects subject1 subject2 subject3 --hemi rh --meas
> thickness --tablefile aparc_stats.txt
>
> I tried it on single subjects randomly chosen from the complete list and
> it works....anyway it's still not working on the complete list while it
> works fine for the left hemisphere (same list of subjects).
>
> Sorry for bothering and thanks again for your help,
>
> Pietro
>
>
> 2013/8/29 Douglas N Greve <gr...@nmr.mgh.harvard.edu>
>
>>
>> What is your command line? Try it on a single subject to see if it fails
>> doug
>>
>>
>>
>>
>> On 08/29/2013 02:00 PM, Pietro De Rossi wrote:
>>
>>> Hi Doug,
>>>
>>> It doesn't seem it is failing on a particular subject...or I am not able
>>> to get it from the error. Futhermore, nothing changes if I use the --skip
>>> flag.
>>> What does it mean when it says:
>>>
>>> "List index out of range"?
>>>
>>> Inviato da iPhone
>>>
>>> Il giorno 29/ago/2013, alle ore 19:38, Douglas N Greve <
>>> gr...@nmr.mgh.harvard.edu> ha scritto:
>>>
>>> Is it failing on one particular subject?
>>>>
>>>>
>>>> On 08/29/2013 09:38 AM, pietro de rossi wrote:
>>>>
>>>>> Dear FreeSurfers,
>>>>>
>>>>> I am extracting thickness values through the aparcstats2table command
>>>>> line.
>>>>>
>>>>> Everything works just fine for --hemi lh using the --skip flag.
>>>>>
>>>>> However, when it comes to the right hemisphere I get
>>>>>
>>>>> SUBJECTS_DIR : /usr/local/freesurfer/subjects
>>>>> Parsing the .stats files
>>>>> Traceback (most recent call last):
>>>>> File "/usr/local/freesurfer/bin/**aparcstats2table", line 321, in
>>>>> <module>
>>>>> parc_measure_map = parsed.parse(options.meas)
>>>>> File "/usr/local/freesurfer/bin/**fsutils.py", line 194, in parse
>>>>> parcid = strlist[0]
>>>>> IndexError: list index out of range
>>>>>
>>>>> I find it weird given that I am extracting thickness values for the
>>>>> same subjects.
>>>>>
>>>>> Can anybody help me find out what the problem is?
>>>>>
>>>>> Thank you in advance,
>>>>>
>>>>> Pietro
>>>>>
>>>>> --
>>>>> Pietro De Rossi, MD
>>>>> ------------------------------**-------
>>>>> Sapienza Università di Roma, Facoltà di Medicina e Psicologia,
>>>>> Dipartimento NESMOS (Neuroscienze, Salute Mentale, Organi di Senso),
>>>>> Ospedale Sant'Andrea, Via di Grottarossa 1035-1039, 00189 Roma
>>>>>
>>>>> NESMOS Department (Neurosciences, Mental Health and Sensory
>>>>> Functions), School of Medicine and Psychology, Sapienza University,
>>>>> Sant’Andrea Hospital, Via di Grottarossa 1035-1039, 00189 Rome, Italy
>>>>>
>>>>> Neurobehavioral Clinical Research Section, Social and Behavioral
>>>>> Research Branch, National Human Genome Research Institute (NHGRI),
>>>>> National Institutes of Health (NIH), Bethesda, Maryland 20892, USA
>>>>>
>>>>>
>>>>> ______________________________**_________________
>>>>> Freesurfer mailing list
>>>>> Freesurfer@nmr.mgh.harvard.edu
>>>>> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
>>>>>
>>>> --
>>>> Douglas N. Greve, Ph.D.
>>>> MGH-NMR Center
>>>> gr...@nmr.mgh.harvard.edu
>>>> Phone Number: 617-724-2358
>>>> Fax: 617-726-7422
>>>>
>>>> Bugs:
>>>> surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
>>>> FileDrop:
>>>> https://gate.nmr.mgh.harvard.**edu/filedrop2<https://gate.nmr.mgh.harvard.edu/filedrop2>
>>>> www.nmr.mgh.harvard.edu/**facility/filedrop/index.html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
>>>> Outgoing: ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/**
>>>> greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/>
>>>>
>>>> ______________________________**_________________
>>>> Freesurfer mailing list
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>>>> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer<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<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
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>>>
>> --
>> Douglas N. Greve, Ph.D.
>> MGH-NMR Center
>> gr...@nmr.mgh.harvard.edu
>> Phone Number: 617-724-2358
>> Fax: 617-726-7422
>>
>> Bugs:
>> surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
>> FileDrop:
>> https://gate.nmr.mgh.harvard.**edu/filedrop2<https://gate.nmr.mgh.harvard.edu/filedrop2>
>> www.nmr.mgh.harvard.edu/**facility/filedrop/index.html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
>> Outgoing: ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/**
>> greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/>
>>
>>
>
>
> --
> Pietro De Rossi, MD
> -------------------------------------
> Sapienza Università di Roma, Facoltà di Medicina e Psicologia,
> Dipartimento NESMOS (Neuroscienze, Salute Mentale, Organi di Senso),
> Ospedale Sant'Andrea, Via di Grottarossa 1035-1039, 00189 Roma
>
> NESMOS Department (Neurosciences, Mental Health and Sensory Functions),
> School of Medicine and Psychology, Sapienza University, Sant’Andrea
> Hospital, Via di Grottarossa 1035-1039, 00189 Rome, Italy
>
> Neurobehavioral Clinical Research Section, Social and Behavioral Research
> Branch, National Human Genome Research Institute (NHGRI), National
> Institutes of Health (NIH), Bethesda, Maryland 20892, USA
>
--
Pietro De Rossi, MD
-------------------------------------
Sapienza Università di Roma, Facoltà di Medicina e Psicologia, Dipartimento
NESMOS (Neuroscienze, Salute Mentale, Organi di Senso), Ospedale
Sant'Andrea, Via di Grottarossa 1035-1039, 00189 Roma
NESMOS Department (Neurosciences, Mental Health and Sensory Functions),
School of Medicine and Psychology, Sapienza University, Sant’Andrea
Hospital, Via di Grottarossa 1035-1039, 00189 Rome, Italy
Neurobehavioral Clinical Research Section, Social and Behavioral Research
Branch, National Human Genome Research Institute (NHGRI), National
Institutes of Health (NIH), Bethesda, Maryland 20892, USA
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