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.andr...@kcl.ac.uk
1.long.qdec.table.dat
Description: 1.long.qdec.table.dat
2.long.qdec.table.dat
Description: 2.long.qdec.table.dat
fsid fsid-base years 0008Y1 0008 0 0011Y1 0011 0 0011Y2 0011 0.490410959 0012Y1 0012 0 0012Y2 0012 0.490410959 0033Y1 0033 0 0033Y2 0033 0 0093Y1 0093 0 0095Y1 0095 0 0095Y2 0095 0.95890411 0097Y2 0097 0 0098Y1 0098 0 0101Y1 0101 0 0101Y2 0101 0.989041096 0101Y3 0101 1.980821918 0104Y1 0104 0 0105Y3 0105 0 0106Y1 0106 0 0106Y2 0106 1.208219178 0107Y3 0107 0 0108Y2 0108 0 0110Y1 0110 0 0110Y3 0110 2.169863014 0112Y1 0112 0 0112Y2 0112 1.054794521 0114Y1 0114 0 0114Y2 0114 1.315068493 0116Y1 0116 0 0116Y2 0116 0.989041096 0117Y1 0117 0 0120Y1 0120 0 0127Y1 0127 0 0128Y1 0128 0 0134Y1 0134 0 0135Y1 0135 0 0135Y2 0135 0 0136Y1 0136 0 0136Y2 0136 1.002739726 0136Y3 0136 2 0137Y3 0137 0 0138Y1 0138 0 0139Y1 0139 0 0139Y3 0139 0.978082192 0146Y3 0146 0 0153Y1 0153 0 0153Y2 0153 0.95890411 0153Y3 0153 1.994520548 0158Y1 0158 0 0158Y2 0158 1.169863014 0160Y2 0160 0 0160Y3 0160 1.035616438 0175Y1 0175 0 0175Y2 0175 0 0180Y1 0180 0 1004Y2 1004 0 1005Y1 1005 0 1005Y2 1005 1.178082192 1005Y3 1005 2.301369863 1006Y2 1006 0 1006Y3 1006 0.997260274 1007Y1 1007 0 1009Y1 1009 0 1016Y2 1016 0 1017Y1 1017 0 1017Y2 1017 1.054794521 1017Y3 1017 2.123287671 1022Y1 1022 0 1023Y1 1023 0 1023Y2 1023 1.476712329 1027Y1 1027 0 1027Y2 1027 0.961643836 1032Y2 1032 0 1032Y3 1032 1.054794521 1034Y1 1034 0 1034Y2 1034 1.112328767 1034Y3 1034 2.109589041 1041Y1 1041 0 1041Y3 1041 2.293150685 1042Y2 1042 0 1042Y3 1042 0.997260274 1044Y1 1044 0 1045Y2 1045 0 1046Y1 1046 0 1046Y2 1046 1.109589041 1046Y3 1046 2.068493151 1052Y1 1052 0 1052Y2 1052 1.156164384 1052Y3 1052 2.271232877 1054Y2 1054 0 1054Y3 1054 1.073972603 1057Y2 1057 0 1057Y3 1057 0.912328767 1071Y2 1071 0 1071Y3 1071 0 1073Y3 1073 0 1075Y2 1075 0 1075Y3 1075 0.978082192 1077Y1 1077 0 1091Y1 1091 0 1091Y2 1091 0 1091Y3 1091 1.994520548 1096Y2 1096 0 1111Y1 1111 0 1111Y3 1111 2.473972603 1121Y1 1121 0 1121Y2 1121 1.22739726 1141Y1 1141 0 1144Y3 1144 0 1151Y1 1151 0 1159Y1 1159 0 1159Y2 1159 0.989041096 1159Y3 1159 2.024657534 1161Y1 1161 0 1161Y2 1161 -0.115068493 1164Y1 1164 0 1164Y2 1164 1.035616438
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