Re: [Freesurfer] long_qdec_table
Hey Martin, Thanks for your quick response and all the great work you've done on the longitudinal pipeline. Replacing the LongQdecTable.py did the trick. Thanks again, Chris On Thu, Mar 14, 2013 at 12:38 PM, Martin Reuter mreu...@nmr.mgh.harvard.edu wrote: Hi Chris, try to rename the LongQdecTable.* files in your FS install and place a new LongQdecTable.py file there from here: http://martinos.org/~mreuter/LongQdecTable.py the new one uses universal newline support. Not sure if the Python on your system supports this. Let me know (also what system you are using and what OS version, also the version of Python) Thanks, Martin On 03/13/2013 08:20 AM, Christopher McCarthy wrote: Hey All, I am trying to turn my long.qdec.table.dat into a cross.qdec.table.dat using the following command: long_qdec_table --qdec ./qdec/long.qdec.table.dat --cross --out ./qdec/cross.qdec.table.dat However, when I try and load it into QDEC afterwards I get the following error: Loading data table /data/freesurfer/qdec/cross.qdec.table.dat... Number of columns: 103 fsid column:1 Number of factors: 102 Number of subjects: 0 ERROR: QdecDataTable::Load: number of subjects = 0 Error loading the data table. I attached both the long.qdec and the cross.qdec tables, if someone knows what I am doing wrong, I would love some help! Chris ___ Freesurfer mailing listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Dr. Martin Reuter Assistant in Neuroscience - Massachusetts General Hospital Instructor in Neurology - Harvard Medical School MGH / HMS / MIT A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129 Phone: +1-617-724-5652 Email: mreu...@nmr.mgh.harvard.edu reu...@mit.edu Web : http://reuter.mit.edu 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] long_qdec_table
Hi Chris, the cross qdec table is messed up ( a single line without line breaks). long_qdec_table has problems reading your long-table because it contains 'tabs', several spaces instead of a single one between other columns and also not the line breaks it expects (the windows format). I will look into this, to see if I can make the program more flexible with respect to the input. In the meantime, you can - replace tabs with spaces - replace multiple spaces with single space - replace line breaks with linux style line breaks open it in linux with nedit and you'll see. Best, Martin On 03/13/2013 08:20 AM, Christopher McCarthy wrote: Hey All, I am trying to turn my long.qdec.table.dat into a cross.qdec.table.dat using the following command: long_qdec_table --qdec ./qdec/long.qdec.table.dat --cross --out ./qdec/cross.qdec.table.dat However, when I try and load it into QDEC afterwards I get the following error: Loading data table /data/freesurfer/qdec/cross.qdec.table.dat... Number of columns: 103 fsid column:1 Number of factors: 102 Number of subjects: 0 ERROR: QdecDataTable::Load: number of subjects = 0 Error loading the data table. I attached both the long.qdec and the cross.qdec tables, if someone knows what I am doing wrong, I would love some help! Chris ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Dr. Martin Reuter Assistant in Neuroscience - Massachusetts General Hospital Instructor in Neurology - Harvard Medical School MGH / HMS / MIT A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129 Phone: +1-617-724-5652 Email: mreu...@nmr.mgh.harvard.edu reu...@mit.edu Web : http://reuter.mit.edu ___ 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] long_qdec_table
Hi Chris, try to rename the LongQdecTable.* files in your FS install and place a new LongQdecTable.py file there from here: http://martinos.org/~mreuter/LongQdecTable.py the new one uses universal newline support. Not sure if the Python on your system supports this. Let me know (also what system you are using and what OS version, also the version of Python) Thanks, Martin On 03/13/2013 08:20 AM, Christopher McCarthy wrote: Hey All, I am trying to turn my long.qdec.table.dat into a cross.qdec.table.dat using the following command: long_qdec_table --qdec ./qdec/long.qdec.table.dat --cross --out ./qdec/cross.qdec.table.dat However, when I try and load it into QDEC afterwards I get the following error: Loading data table /data/freesurfer/qdec/cross.qdec.table.dat... Number of columns: 103 fsid column:1 Number of factors: 102 Number of subjects: 0 ERROR: QdecDataTable::Load: number of subjects = 0 Error loading the data table. I attached both the long.qdec and the cross.qdec tables, if someone knows what I am doing wrong, I would love some help! Chris ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Dr. Martin Reuter Assistant in Neuroscience - Massachusetts General Hospital Instructor in Neurology - Harvard Medical School MGH / HMS / MIT A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129 Phone: +1-617-724-5652 Email: mreu...@nmr.mgh.harvard.edu reu...@mit.edu Web : http://reuter.mit.edu ___ 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] long_qdec_table and LongQdecTable.py errors
Hi Jiyang, Must have missed Derin's mail. Can you send the table And command? I can then try to see if this bug is still in our dev version or if it got fixed in the meantime. Best Martin On May 30, 2012, at 22:06, Jiyang Jiang jiyang.jiang.email.li...@gmail.com wrote: Hi Martin, I came across a problem when shrinking longitudinal qdec tables with 345 subject in two time points, into cross sectional form. The error states as follows: -- [jiyang@abc qdec]$ long_qdec_table --qdec ./long.qdec.table.dat --cross --out ./cross.qdec.table.test.dat Parsing the qdec table: ./long.qdec.table.dat Traceback (most recent call last): File /usr/local/software/freesurfer/freesurfer-5.1.0/bin/long_qdec_table, line 142, in module longqdec = LongQdecTable(options.qdec) File /usr/local/software/freesurfer/freesurfer-5.1.0/bin/LongQdecTable.py, line 30, in __init__ self.parse(stpmap) File /usr/local/software/freesurfer/freesurfer-5.1.0/bin/LongQdecTable.py, line 58, in parse if strlst[0].upper() == 'SUBJECTS_DIR': IndexError: list index out of range -- I found Derin posted the same question on 20 Apr 2012, but it seems no following answers after. This error disappeared after deconstructing longitudinal qdec table. Any suggestion or clue will be appreciated. Thanks! Jiyang ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ 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] long_qdec_table and LongQdecTable.py errors
Great. Thanks for letting me know. I post this to the list, so that other know. Best Martin On May 31, 2012, at 21:11, Jiyagn jiyang.jiang.email.li...@gmail.com wrote: Thanks for your reply Martin! I think I just found out where the problem was - a blank line at the end of the longitudinal table. The program works fine after deleting it. Probably the error is due to the different line break formats in Windows and Linux. Cheers, Jiyang On 05/31/2012 10:39 PM, Martin Reuter wrote: Hi Jiyang, Must have missed Derin's mail. Can you send the table And command? I can then try to see if this bug is still in our dev version or if it got fixed in the meantime. Best Martin On May 30, 2012, at 22:06, Jiyang Jiangjiyang.jiang.email.li...@gmail.com wrote: Hi Martin, I came across a problem when shrinking longitudinal qdec tables with 345 subject in two time points, into cross sectional form. The error states as follows: -- [jiyang@abc qdec]$ long_qdec_table --qdec ./long.qdec.table.dat --cross --out ./cross.qdec.table.test.dat Parsing the qdec table: ./long.qdec.table.dat Traceback (most recent call last): File /usr/local/software/freesurfer/freesurfer-5.1.0/bin/long_qdec_table, line 142, inmodule longqdec = LongQdecTable(options.qdec) File /usr/local/software/freesurfer/freesurfer-5.1.0/bin/LongQdecTable.py, line 30, in __init__ self.parse(stpmap) File /usr/local/software/freesurfer/freesurfer-5.1.0/bin/LongQdecTable.py, line 58, in parse if strlst[0].upper() == 'SUBJECTS_DIR': IndexError: list index out of range -- I found Derin posted the same question on 20 Apr 2012, but it seems no following answers after. This error disappeared after deconstructing longitudinal qdec table. Any suggestion or clue will be appreciated. Thanks! Jiyang ___ 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
