Hi Dr. Greve, Please find the attached qdec file, along with diagnosis file which I used in QDEC, and this is the same qdec file I trying to use for the aparcstats2table command.
Thanks. PS: I was also wondering (a) how can I average thickness stats (b) are these in fsaverage (standard) space and (c) how can I display it on standard fsaverage for publications purpose? On Wed, Nov 9, 2016 at 10:52 AM, Douglas N Greve <gr...@nmr.mgh.harvard.edu> wrote: > can you send the qdec file with variables? > > > On 11/09/2016 11:51 AM, Martin Juneja wrote: > > Hi Dr. Greve, > > > > Somehow even after adding variables, it's not working, although same > > qdec file works fine when I perform GLM in qdec. > > So I replaced the flag with subjectsfile and provided subject list.txt > > file. So in that way, it's working fine now. > > > > I was also wondering (a) how can I average these thickness stats (b) > > are these in fsaverage (standard) space and (c) how can I display it > > on standard fsaverage for publications purpose? > > > > Thanks a lot. > > > > On Wed, Nov 9, 2016 at 7:39 AM, Douglas Greve > > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote: > > > > Appears to be having problems reading the qdec table. It might be > > expecting the qdec table to actually variables in it. Can you try > > adding variables? Also, try it without the --qdec flag instead > > specifying the subjects with --subjects HC003_1 HC004_1 ... > > > > > > On 11/8/16 8:09 PM, Martin Juneja wrote: > >> Hi everyone, > >> > >> I am trying to use following command to save stats from a set of > >> subjects in a table format: > >> > >> aparcstats2table --qdec qdec.dat --hemi lh --meas thickness -t > >> zzz.txt > >> > >> But after I run this, I get following error: > >> > >> Traceback (most recent call last): > >> > >> File "/usr/local/freesurfer/bin/aparcstats2table", line 353, in > >> <module> > >> > >> subj_listoftuples = assemble_inputs(options) > >> > >> File "/usr/local/freesurfer/bin/aparcstats2table", line 228, in > >> assemble_inputs > >> > >> fsid=row['fsid'].strip() > >> > >> KeyError: 'fsid' > >> > >> My qdec.dat file looks like below: > >> > >> fsidHC003_1 > >> HC004_1 > >> HC006_1 > >> HC015_1 > >> > >> This command works fine if I use subject IDs individually here e.g. > >> aparcstats2table --subjects HC_Example HC003_1 HC004_1 HC006_1 > >> HC015_1 --hemi lh --meas thickness -t zzz.txt > >> > >> Another question I have here is: How can I average these > >> thickness stats and display it on standard fsaverage? > >> > >> Any help would be really appreciated. > >> > >> > >> > >> > >> _______________________________________________ > >> 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> 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> . 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 > -- > 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 >
Diagnosis_HC_PRE
Description: Binary data
qdec.HC.dat
Description: Binary data
_______________________________________________ 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.
