Re: [Freesurfer] ERROR: aparcstats2table
Catherine, I've created new scripts (attached)that will allow you to do this. Put them into $FREESURFER_HOME/bin (but make backups of the ones there:). doug On 01/30/2013 05:43 PM, Nucleos P wrote: The options for these 3: GausCurv FoldInd CurvInd do not exist when I use the -h Thanks, Catherine On 1/29/13, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: yes, use the -m or --meas flags. If you run it with -h, you will get help and examples doug On 01/29/2013 04:12 PM, Nucleos P wrote: Hello again! Thank you for all your help so far. Just one more question now... is there a way to specify these values to be pulled using a script: GausCurv FoldInd CurvInd ...?? Thanks, Catherine On 1/23/13, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: They must be in a single folder and the $SUBJECTS_DIR env variable must be set to that folder. If you know a little unix, you can set up folders with symbolic links to subjects' true directories. doug On 01/23/2013 02:58 PM, Nucleos P wrote: Thank you for your help Doug! I was trying to specify the path to get to the subjects. Do I have to have all the subjects in a folder called 'subjects'? I know the naming conventions are important. Thanks again, Catherine On Fri, Jan 18, 2013 at 6:31 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: actually, looking at your cmd line more I see that you have slashes (/) in the subject names. The argument to --subjects should just be a list of name. See the help (aparcstats2table -h) for examples. doug On 01/18/2013 04:58 PM, Nucleos P wrote: Hello experts: Can someone please help me understand what I am doing wrong? This is the first time I am trying this command and it will not work... COMMAND: aparcstats2table --subjects /RGS4_31p/rgs0868_raw /RGS4_31p/rgs0871_raw /RGS4_31p/rgs0883_raw/ /RGS4_31p/rgs1194_raw144/ /RGS4_31p/rgs1311a/ /RGS4_31p/rgs1370a/ /RGS4_31p/rgs1383a/ -t RGS4_31p/aparc.volume.rh -m volume --hemi=rh PATH: [/usr/local/freesurfer/subjects/RGS4_31p/rgs0868_raw/stats]:pwd /usr/local/freesurfer/subjects/RGS4_31p/rgs0868_raw/stats ERROR: SUBJECTS_DIR : /usr/local/freesurfer/subjects Parsing the .stats files ERROR: The stats file /RGS4_31p/rgs0868_raw/stats/rh.aparc.stats is not found or is too small to be a valid statsfile Use --skip flag to automatically skip bad stats files Thank you, Catherine ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 tel:617-724-2358 Fax: 617-726-7422 tel:617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ 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. -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing:
Re: [Freesurfer] ERROR: aparcstats2table
The options for these 3: GausCurv FoldInd CurvInd do not exist when I use the -h Thanks, Catherine On 1/29/13, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: yes, use the -m or --meas flags. If you run it with -h, you will get help and examples doug On 01/29/2013 04:12 PM, Nucleos P wrote: Hello again! Thank you for all your help so far. Just one more question now... is there a way to specify these values to be pulled using a script: GausCurv FoldInd CurvInd ...?? Thanks, Catherine On 1/23/13, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: They must be in a single folder and the $SUBJECTS_DIR env variable must be set to that folder. If you know a little unix, you can set up folders with symbolic links to subjects' true directories. doug On 01/23/2013 02:58 PM, Nucleos P wrote: Thank you for your help Doug! I was trying to specify the path to get to the subjects. Do I have to have all the subjects in a folder called 'subjects'? I know the naming conventions are important. Thanks again, Catherine On Fri, Jan 18, 2013 at 6:31 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: actually, looking at your cmd line more I see that you have slashes (/) in the subject names. The argument to --subjects should just be a list of name. See the help (aparcstats2table -h) for examples. doug On 01/18/2013 04:58 PM, Nucleos P wrote: Hello experts: Can someone please help me understand what I am doing wrong? This is the first time I am trying this command and it will not work... COMMAND: aparcstats2table --subjects /RGS4_31p/rgs0868_raw /RGS4_31p/rgs0871_raw /RGS4_31p/rgs0883_raw/ /RGS4_31p/rgs1194_raw144/ /RGS4_31p/rgs1311a/ /RGS4_31p/rgs1370a/ /RGS4_31p/rgs1383a/ -t RGS4_31p/aparc.volume.rh -m volume --hemi=rh PATH: [/usr/local/freesurfer/subjects/RGS4_31p/rgs0868_raw/stats]:pwd /usr/local/freesurfer/subjects/RGS4_31p/rgs0868_raw/stats ERROR: SUBJECTS_DIR : /usr/local/freesurfer/subjects Parsing the .stats files ERROR: The stats file /RGS4_31p/rgs0868_raw/stats/rh.aparc.stats is not found or is too small to be a valid statsfile Use --skip flag to automatically skip bad stats files Thank you, Catherine ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 tel:617-724-2358 Fax: 617-726-7422 tel:617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ 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. -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] ERROR: aparcstats2table
Hello again! Thank you for all your help so far. Just one more question now... is there a way to specify these values to be pulled using a script: GausCurv FoldInd CurvInd ...?? Thanks, Catherine On 1/23/13, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: They must be in a single folder and the $SUBJECTS_DIR env variable must be set to that folder. If you know a little unix, you can set up folders with symbolic links to subjects' true directories. doug On 01/23/2013 02:58 PM, Nucleos P wrote: Thank you for your help Doug! I was trying to specify the path to get to the subjects. Do I have to have all the subjects in a folder called 'subjects'? I know the naming conventions are important. Thanks again, Catherine On Fri, Jan 18, 2013 at 6:31 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: actually, looking at your cmd line more I see that you have slashes (/) in the subject names. The argument to --subjects should just be a list of name. See the help (aparcstats2table -h) for examples. doug On 01/18/2013 04:58 PM, Nucleos P wrote: Hello experts: Can someone please help me understand what I am doing wrong? This is the first time I am trying this command and it will not work... COMMAND: aparcstats2table --subjects /RGS4_31p/rgs0868_raw /RGS4_31p/rgs0871_raw /RGS4_31p/rgs0883_raw/ /RGS4_31p/rgs1194_raw144/ /RGS4_31p/rgs1311a/ /RGS4_31p/rgs1370a/ /RGS4_31p/rgs1383a/ -t RGS4_31p/aparc.volume.rh -m volume --hemi=rh PATH: [/usr/local/freesurfer/subjects/RGS4_31p/rgs0868_raw/stats]:pwd /usr/local/freesurfer/subjects/RGS4_31p/rgs0868_raw/stats ERROR: SUBJECTS_DIR : /usr/local/freesurfer/subjects Parsing the .stats files ERROR: The stats file /RGS4_31p/rgs0868_raw/stats/rh.aparc.stats is not found or is too small to be a valid statsfile Use --skip flag to automatically skip bad stats files Thank you, Catherine ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 tel:617-724-2358 Fax: 617-726-7422 tel:617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ 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. -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] ERROR: aparcstats2table
yes, use the -m or --meas flags. If you run it with -h, you will get help and examples doug On 01/29/2013 04:12 PM, Nucleos P wrote: Hello again! Thank you for all your help so far. Just one more question now... is there a way to specify these values to be pulled using a script: GausCurv FoldInd CurvInd ...?? Thanks, Catherine On 1/23/13, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: They must be in a single folder and the $SUBJECTS_DIR env variable must be set to that folder. If you know a little unix, you can set up folders with symbolic links to subjects' true directories. doug On 01/23/2013 02:58 PM, Nucleos P wrote: Thank you for your help Doug! I was trying to specify the path to get to the subjects. Do I have to have all the subjects in a folder called 'subjects'? I know the naming conventions are important. Thanks again, Catherine On Fri, Jan 18, 2013 at 6:31 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: actually, looking at your cmd line more I see that you have slashes (/) in the subject names. The argument to --subjects should just be a list of name. See the help (aparcstats2table -h) for examples. doug On 01/18/2013 04:58 PM, Nucleos P wrote: Hello experts: Can someone please help me understand what I am doing wrong? This is the first time I am trying this command and it will not work... COMMAND: aparcstats2table --subjects /RGS4_31p/rgs0868_raw /RGS4_31p/rgs0871_raw /RGS4_31p/rgs0883_raw/ /RGS4_31p/rgs1194_raw144/ /RGS4_31p/rgs1311a/ /RGS4_31p/rgs1370a/ /RGS4_31p/rgs1383a/ -t RGS4_31p/aparc.volume.rh -m volume --hemi=rh PATH: [/usr/local/freesurfer/subjects/RGS4_31p/rgs0868_raw/stats]:pwd /usr/local/freesurfer/subjects/RGS4_31p/rgs0868_raw/stats ERROR: SUBJECTS_DIR : /usr/local/freesurfer/subjects Parsing the .stats files ERROR: The stats file /RGS4_31p/rgs0868_raw/stats/rh.aparc.stats is not found or is too small to be a valid statsfile Use --skip flag to automatically skip bad stats files Thank you, Catherine ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 tel:617-724-2358 Fax: 617-726-7422 tel:617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ 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. -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] ERROR: aparcstats2table
They must be in a single folder and the $SUBJECTS_DIR env variable must be set to that folder. If you know a little unix, you can set up folders with symbolic links to subjects' true directories. doug On 01/23/2013 02:58 PM, Nucleos P wrote: Thank you for your help Doug! I was trying to specify the path to get to the subjects. Do I have to have all the subjects in a folder called 'subjects'? I know the naming conventions are important. Thanks again, Catherine On Fri, Jan 18, 2013 at 6:31 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: actually, looking at your cmd line more I see that you have slashes (/) in the subject names. The argument to --subjects should just be a list of name. See the help (aparcstats2table -h) for examples. doug On 01/18/2013 04:58 PM, Nucleos P wrote: Hello experts: Can someone please help me understand what I am doing wrong? This is the first time I am trying this command and it will not work... COMMAND: aparcstats2table --subjects /RGS4_31p/rgs0868_raw /RGS4_31p/rgs0871_raw /RGS4_31p/rgs0883_raw/ /RGS4_31p/rgs1194_raw144/ /RGS4_31p/rgs1311a/ /RGS4_31p/rgs1370a/ /RGS4_31p/rgs1383a/ -t RGS4_31p/aparc.volume.rh -m volume --hemi=rh PATH: [/usr/local/freesurfer/subjects/RGS4_31p/rgs0868_raw/stats]:pwd /usr/local/freesurfer/subjects/RGS4_31p/rgs0868_raw/stats ERROR: SUBJECTS_DIR : /usr/local/freesurfer/subjects Parsing the .stats files ERROR: The stats file /RGS4_31p/rgs0868_raw/stats/rh.aparc.stats is not found or is too small to be a valid statsfile Use --skip flag to automatically skip bad stats files Thank you, Catherine ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 tel:617-724-2358 Fax: 617-726-7422 tel:617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ 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. -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] ERROR: aparcstats2table
does the file exist? If so, is it empty(maybe because the disk is full)? On 01/18/2013 04:58 PM, Nucleos P wrote: Hello experts: Can someone please help me understand what I am doing wrong? This is the first time I am trying this command and it will not work... COMMAND: aparcstats2table --subjects /RGS4_31p/rgs0868_raw /RGS4_31p/rgs0871_raw /RGS4_31p/rgs0883_raw/ /RGS4_31p/rgs1194_raw144/ /RGS4_31p/rgs1311a/ /RGS4_31p/rgs1370a/ /RGS4_31p/rgs1383a/ -t RGS4_31p/aparc.volume.rh -m volume --hemi=rh PATH: [/usr/local/freesurfer/subjects/RGS4_31p/rgs0868_raw/stats]:pwd /usr/local/freesurfer/subjects/RGS4_31p/rgs0868_raw/stats ERROR: SUBJECTS_DIR : /usr/local/freesurfer/subjects Parsing the .stats files ERROR: The stats file /RGS4_31p/rgs0868_raw/stats/rh.aparc.stats is not found or is too small to be a valid statsfile Use --skip flag to automatically skip bad stats files Thank you, Catherine ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ 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] ERROR: aparcstats2table
actually, looking at your cmd line more I see that you have slashes (/) in the subject names. The argument to --subjects should just be a list of name. See the help (aparcstats2table -h) for examples. doug On 01/18/2013 04:58 PM, Nucleos P wrote: Hello experts: Can someone please help me understand what I am doing wrong? This is the first time I am trying this command and it will not work... COMMAND: aparcstats2table --subjects /RGS4_31p/rgs0868_raw /RGS4_31p/rgs0871_raw /RGS4_31p/rgs0883_raw/ /RGS4_31p/rgs1194_raw144/ /RGS4_31p/rgs1311a/ /RGS4_31p/rgs1370a/ /RGS4_31p/rgs1383a/ -t RGS4_31p/aparc.volume.rh -m volume --hemi=rh PATH: [/usr/local/freesurfer/subjects/RGS4_31p/rgs0868_raw/stats]:pwd /usr/local/freesurfer/subjects/RGS4_31p/rgs0868_raw/stats ERROR: SUBJECTS_DIR : /usr/local/freesurfer/subjects Parsing the .stats files ERROR: The stats file /RGS4_31p/rgs0868_raw/stats/rh.aparc.stats is not found or is too small to be a valid statsfile Use --skip flag to automatically skip bad stats files Thank you, Catherine ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ 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.
