if that file does not exist, then it will crash. That file should be created by recon-all. Is that file not there?
On 04/28/2017 05:22 AM, Duy Nguyen wrote: > Hello Douglas > > Thank you for your response. > I have just run the subjects from the data on OASIS through qdec and I > followed the steps on freesurfer. > > Everything is ok until the step of pressing 'Generate Stats Data > Tables' that I have asked you before somehow I keep getting the same > issue. > There is the following error log being attached to this email. > From the log, it was asking me for the wmparc.stats, but somehow my > subjects'stats directory does not have that file. How can I change to > lh.aparc.stats but I want to analyze the cortical thickness. > > Your help is appreciated. > > Thank you and best regards > > *--v-- Peace --v--* > *Duy Nguyễn * > *Biomedical Engineering Department- IU HCMC* > *Cell: (+84)909999056* > *Email: duy.nguyen...@gmail.com <mailto:duy.nguyen...@gmail.com>* > > On Fri, Mar 24, 2017 at 10:11 PM, Douglas Greve > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote: > > does that file exist? If it does, look at its contents and compare > it to > others in terms of size > > > On 3/24/17 9:11 AM, Duy Nguyen wrote: > > Dear Doughlas > > > > When I tried to run the aparcstats2table command, it shows the > following > > error in the terminal window: > > SUBJECTS_DIR : /home/toibigi2007/Desktop > > Parsing the .stats files > > ERROR: The stats file > > /home/toibigi2007/Desktop/004/stats/lh.aparc.stats is not found > or is > > too small to be a valid statsfile > > Use --skip flag to automatically skip bad stats files > > > > The group of subjects is from the tutorial data set. > > Please help me sort this out. > > > > Thank you and best regards, > > > > > > *--v-- Peace --v--* > > *Duy Nguyễn * > > *Biomedical Engineering Department- IU HCMC* > > *Cell: (+84)909999056* > > *Email: duy.nguyen...@gmail.com <mailto:duy.nguyen...@gmail.com> > <duy.nguyen...@gmail.com <mailto:duy.nguyen...@gmail.com>>* > > > > On Thu, Mar 23, 2017 at 10:23 PM, Douglas N Greve > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> > >> wrote: > >> need more info > >> > >> > >> On 03/22/2017 09:37 PM, Duy Nguyen wrote: > >>> Dear Douglas > >>> > >>> Thank you for your response. I cannot run asegstats2table and > >>> aparcstats2table command outside of qdec. > >>> > >>> Best regards, > >>> Duy Nguyen > >>> > >>> *--v-- Peace --v--* > >>> *Duy Nguyễn * > >>> *Biomedical Engineering Department- IU HCMC* > >>> *Cell: (+84)909999056* > >>> *Email: duy.nguyen...@gmail.com > <mailto:duy.nguyen...@gmail.com> <mailto:duy.nguyen...@gmail.com > <mailto:duy.nguyen...@gmail.com>>* > >>> > >>> On Thu, Mar 23, 2017 at 5:07 AM, Douglas Greve > >>> <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>>> wrote: > >>> > >>> don't know what is going on there. Can you run the > asegstats2table > >>> command outside of qdec? > >>> > >>> > >>> On 3/17/17 8:29 AM, Duy Nguyen wrote: > >>>> Dear FS Expert > >>>> > >>>> I am doing analysis from the group_analysis_tutorial data to > >>>> practice and learn. However, I come across the error > window like > >>>> it shows on the attached picture (please see the > attachment) when > >>>> I press the button "Generate Stats Data Table." Please > help me > >>>> how can I can find the file aseg.volume.stats.dat. If > the file > >>>> does not exist, how can I create one? > >>>> > >>>> Thank you for your response. Any help would be > appreciated!!! > >>>> *--v-- Peace --v--* > >>>> *Duy Nguyễn * > >>>> *Biomedical Engineering Department- IU HCMC* > >>>> *Cell: (+84)909999056* > >>>> *Email: duy.nguyen...@gmail.com > <mailto:duy.nguyen...@gmail.com> <mailto:duy.nguyen...@gmail.com > <mailto:duy.nguyen...@gmail.com>>* > >>>> > >>>> > >>>> _______________________________________________ > >>>> Freesurfer mailing list > >>>> Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > >>>> <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > >>>> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > >>> _______________________________________________ > Freesurfer mailing > >>> list Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > >>> <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > >>> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <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 > <http://www.partners.org/complianceline> > >>> <http://www.partners.org/complianceline > <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 > <mailto:Freesurfer@nmr.mgh.harvard.edu> > >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <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 > >> Fax: 617-726-7422 > >> > >> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > >> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > <https://gate.nmr.mgh.harvard.edu/filedrop2> > >> 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/ > <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 > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > >> > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <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 -- 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: https://gate.nmr.mgh.harvard.edu/filedrop2 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
