Re: [Freesurfer] longitudinal qdec tables
So you exported CSV from excel on Mac with space separation and it does not work? Try to export only a few lines to make sure it is not a weird character somewhere else. Best Martin On Jul 11, 2016 5:44 PM, "Andrews, Derek" <derek.andr...@kcl.ac.uk> wrote: 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.edu> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Date: Mon, 11 Jul 2016 13:59:53 +0200 To: Freesurfer support list <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.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 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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] longitudinal qdec tables
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.andr...@kcl.ac.uk From: Martin Reuter <mreu...@nmr.mgh.harvard.edu<mailto:mreu...@nmr.mgh.harvard.edu>> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Date: Mon, 11 Jul 2016 13:59:53 +0200 To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu<mailto: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.andr...@kcl.ac.uk<mailto:derek.andr...@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 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<mailto:derek.andr...@kcl.ac.uk> ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
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"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 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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] longitudinal qdec tables
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 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 fsidfsid-base years 0008Y1 00080 0011Y1 00110 0011Y2 00110.490410959 0012Y1 00120 0012Y2 00120.490410959 0033Y1 00330 0033Y2 00330 0093Y1 00930 0095Y1 00950 0095Y2 00950.95890411 0097Y2 00970 0098Y1 00980 0101Y1 01010 0101Y2 01010.989041096 0101Y3 01011.980821918 0104Y1 01040 0105Y3 01050 0106Y1 01060 0106Y2 01061.208219178 0107Y3 01070 0108Y2 01080 0110Y1 01100 0110Y3 01102.169863014 0112Y1 01120 0112Y2 01121.054794521 0114Y1 01140 0114Y2 01141.315068493 0116Y1 01160 0116Y2 01160.989041096 0117Y1 01170 0120Y1 01200 0127Y1 01270 0128Y1 01280 0134Y1 01340 0135Y1 01350 0135Y2 01350 0136Y1 01360 0136Y2 01361.002739726 0136Y3 01362 0137Y3 01370 0138Y1 01380 0139Y1 01390 0139Y3 01390.978082192 0146Y3 01460 0153Y1 01530 0153Y2 01530.95890411 0153Y3 01531.994520548 0158Y1 01580 0158Y2 01581.169863014 0160Y2 01600 0160Y3 01601.035616438 0175Y1 01750 0175Y2 01750 0180Y1 01800 1004Y2 10040 1005Y1 10050 1005Y2 10051.178082192 1005Y3 10052.301369863 1006Y2 10060 1006Y3 10060.997260274 1007Y1 10070 1009Y1 10090 1016Y2 10160 1017Y1 10170 1017Y2 10171.054794521 1017Y3 10172.123287671 1022Y1 10220 1023Y1 10230 1023Y2 10231.476712329 1027Y1 10270 1027Y2 10270.961643836 1032Y2 10320 1032Y3 10321.054794521 1034Y1 10340 1034Y2 10341.112328767 1034Y3 10342.109589041 1041Y1 10410 1041Y3 10412.293150685 1042Y2 10420 1042Y3 10420.997260274 1044Y1 10440 1045Y2 10450 1046Y1 10460 1046Y2 10461.109589041 1046Y3 10462.068493151 1052Y1 10520 1052Y2 10521.156164384 1052Y3 10522.271232877 1054Y2 10540 1054Y3 10541.073972603 1057Y2 10570 1057Y3 10570.912328767 1071Y2 10710 1071Y3 10710 1073Y3 10730 1075Y2 10750 1075Y3 10750.978082192 1077Y1 10770 1091Y1 10910 1091Y2 10910 1091Y3 10911.994520548 1096Y2 10960 Y1 0 Y3 2.473972603 1121Y1 11210 1121Y2 11211.22739726 1141Y1 11410 1144Y3 11440 1151Y1 11510 1159Y1 11590 1159Y2 11590.989041096 1159Y3 11592.024657534 1161Y1 11610 1161Y2 1161-0.115068493 1164Y1 11640 1164Y2 11641.035616438___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you