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?
And
mris_preproc --qdec-long long.qdec.table.dat --target fsaverage --hemi -lh --meas thickness --out lh.thickness.mgh
ERROR: no subjects specified
I imagine something silly with the qdec file must be going on. Any advice would be very appreciated.
Best, Derek
________________________________
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