Hi Martin,
Thank you for the tip. Indeed there is some issue with the character spacing in my qdec file.
I usually generate subject text files like this in excel and save them as csv .txt files. Do you have any suggestions for easily writing the qdec file without going line by line, space by space?
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
From: Martin Reuter <mreuter@nmr.mgh.harvard.edumailto:mreuter@nmr.mgh.harvard.edu> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Mon, 11 Jul 2016 13:59:53 +0200 To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] longitudinal qdec tables
Hi Derek, For debugging try a simple file with two lines (header and first row). Separate columns only with a space. Once that works add more rows.
Best Martin
On Jul 11, 2016 12:58 PM, "Andrews, Derek" <derek.andrews@kcl.ac.ukmailto:derek.andrews@kcl.ac.uk> wrote: 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.ukmailto:Derek.Andrews@kcl.ac.uk
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