Hi Ken, I cannot reproduce this error, and I can't find anything wrong with the file you sent. If you remove this subject, does the process complete?
doug
On 08/09/2013 10:58 AM, Rando, Kenneth wrote:
Hi Doug,
Thanks for having a look at these files. The first attached file, from Subject_Dir tb0294, is the file previous to the file with the error, tb0314, attached second.
Ken
Kenneth Rando Research Assistant 2 203-974-7731
Yale OCD Research Clinic Yale University School of Medicine Connecticut Mental Health Center 34 Park Street, Room W309 New Haven, CT 06519
From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: Thursday, August 08, 2013 5:23 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] QDEC error in asegstats2table
Ken, can you send the offending file and the file from the 6th subject? doug
On 08/08/2013 03:09 PM, Rando, Kenneth wrote:
Hello Experts,
This QDEC error is one that appears in the archives, but I did not see a solution that solves my problem. The error (after some information about initialization of the program) is as follows:
SUBJECTS_DIR : /home/freesurfer_ocd Parsing the .stats files ERROR: The stats file /home/freesurfer_ocd/tb0314 /stats/aseg.stats is not found or is too small to be a valid statsfile Use --skip flag to automatically skip bad stats files ERROR: In /usr/pubsw/packages/KWWidgets/CVS-vtk560/KWWidgets/vtkKWTkUtilities.cxx, line 230 vtkKWQdecApp (0x27a1f070): Script: vtkTemp2 GenerateStatsDataTables Returned Error on line 1: Uncaught exception: command failed: asegstats2table --common-segs --meas volume --tablefile /home/freesurfer_ocd/qdec/stats_tables/aseg.volume.stats.dat --statsfile=aseg.stats --subjects ta0743 ta0860 tb0168 tb0183 tb0195 tb0294 tb0314 tb0341 tb0529 tb0628 tb0728 tb0791 tb0817 tb0850 tb0861 tb0892 tb0901 tb1012 tb1043 tb1086 tb1450 tb1464 tb1646 tb1751 tb2002 tb2073 tr7582 tr7733 tr7825 tr7901 tr7932 tr7987 tr8167 tr8222 tr8240 tr8285 tr8345 tr8511 tr8529 tr8688 tr8740 tr8791 tr8860 tr9043 tr9124 tr9222 tr9332 tr9459 tr9515 tr9561 tr9707 tr9746 tr9765 tr9824
Stack trace: Uncaught exception: command failed: asegstats2table --common-segs --meas volume --tablefile /home/freesurfer_ocd/qdec/stats_tables/aseg.volume.stats.dat --statsfile=aseg.stats --subjects ta0743 ta0860 tb0168 tb0183 tb0195 tb0294 tb0314 tb0341 tb0529 tb0628 tb0728 tb0791 tb0817 tb0850 tb0861 tb0892 tb0901 tb1012 tb1043 tb1086 tb1450 tb1464 tb1646 tb1751 tb2002 tb2073 tr7582 tr7733 tr7825 tr7901 tr7932 tr7987 tr8167 tr8222 tr8240 tr8285 tr8345 tr8511 tr8529 tr8688 tr8740 tr8791 tr8860 tr9043 tr9124 tr9222 tr9332 tr9459 tr9515 tr9561 tr9707 tr9746 tr9765 tr9824
while executing"vtkTemp2 GenerateStatsDataTables"
The error occurs at the seventh subject in the dataset, so it appears to be subject-specific. As recommended in previous posts, I have verified that the aseg.stats file exists for that subject. I am new to Freesurfer, but a comparison of this aseg.stats file to the previous subject's file and a few others reveals no obvious differences (e.g., missing lines, extreme or corrupt data values).
One response to an earlier post asked the user to run asegstats2table -i aseg.stats -t test.dat in the stats directory of the file with the error. I followed that advice and it produces a file for this subject. There was, however, no follow-up posting, so I don't know what that indicates, and how I should follow-up.
Thanks for your help.
Ken
Kenneth Rando Research Assistant 2 203-974-7731
Yale OCD Research Clinic Yale University School of Medicine Connecticut Mental Health Center 34 Park Street, Room W309 New Haven, CT 06519
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