Dear FreeSurfer Developers and Community,

I have been trying to run some commands using the —qdec-long flag (I.e. asegstats2table & mris_preproc) but am encountering errors. In the past I have used .rtf files to read in my data using the —fsgd flag but am unsure of how to go about this with longitudinal data, therefore I am using the qdec.dat file structure.

I believe something must be wrong with the format of my qdec file. I’m working on MacOSx 10.9.3. I created the qdec in text editor and changed the suffix to .dat under get info (1). I also created one in gedit and saved it using a .dat suffix (2). See these qdec files attached. 

I receive the following errors:

asegstats2table --qdec-long long.qdec.table.dat -t ./outdir/aseg.long.table

SUBJECTS_DIR : /Users/dandrews/Data/MIAMRC/MIAMRC_SPGR_FS

Traceback (most recent call last):

  File "/Applications/freesurfer/bin/asegstats2table", line 514, in <module>

    subj_listoftuples = assemble_inputs(options)

  File "/Applications/freesurfer/bin/asegstats2table", line 320, in assemble_inputs

    for row in reader:

  File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/csv.py", line 103, in next

    self.fieldnames

  File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/csv.py", line 90, in fieldnames

    self._fieldnames = self.reader.next()

_csv.Error: new-line character seen in unquoted field - do you need to open the file in universal-newline mode?

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Derek Sayre Andrews, MSc
PhD Candidate

The Sackler Institute for Translational Neurodevelopment

Department of Forensic and Neurodevelopmental Sciences 

Institute of Psychiatry, Psychology & Neuroscience, King's College London

Telephone: +44 (0)20 7848 5701
Email: Derek.Andrews@kcl.ac.uk