Dear all,
I am trying to perform a longitudinal lme analysis using freesurfer 5.3.0. For qdec tables with many columns the asegstats2table (and similarly aparcstats2table) commands fail with error message:
asegstats2table --qdec-long ./qdec/long.qdec.table.dat --delimiter space --meas volume --stats aseg.stats --tablefile ./measures/lme.aseg.table.txt SUBJECTS_DIR : /sw/global/applications/freesurfer/5.3.0/x86_64/subjects Traceback (most recent call last): File "/sw/global/applications/freesurfer/5.3.0/x86_64/bin/asegstats2table", line 514, in <module> subj_listoftuples = assemble_inputs(options) File "/sw/global/applications/freesurfer/5.3.0/x86_64/bin/asegstats2table", line 316, in assemble_inputs dialect = csv.Sniffer().sniff(f.read(1024)) File "/home/dgeisler/env/lib/python2.7/csv.py", line 184, in sniff raise Error, "Could not determine delimiter" _csv.Error: Could not determine delimiter
A solution in my case is to change the line: dialect = csv.Sniffer().sniff(f.read(1024)) to: dialect = csv.Sniffer().sniff(f.read(2048))
Namely the snifffer needs a larger chunk of file to be able to determine the delimiter, in my case. However I think it would be good if one could give the delimiter of the infile as an option from command line. If I have correctly understood the --delimiter option available so far is for the output file, which I called ./measures/lme.aseg.table.txt .
Cheers, Fabio
Dr. Fabio Bernardoni wiss. Mitarbeiter Klinik und Poliklinik für Kinder- und Jugendpsychiatrie und -psychotherapie
Tel. +49 (0)351 458-5245 Fax +49 (0)351 458-7206
Universitätsklinikum Carl Gustav Carus an der Technischen Universität Dresden Anstalt des öffentlichen Rechts des Freistaates Sachsen Fetscherstraße 74, 01307 Dresden http://www.uniklinikum-dresden.de
Vorstand: Prof. Dr. med. D. M. Albrecht (Sprecher), Wilfried E. B. Winzer Vorsitzender des Aufsichtsrates: Prof. Dr. med. Peter C. Scriba USt.-IDNr.: DE 140 135 217, St.-Nr.: 203 145 03113