This appears to be broken in 5.3. You can do 2 things: (1) specify the subjects in a different way, or (2) use the aparcstats2table below. I'm not 100% sure it will work in the 5.3 env, so make a backup of your aparcstats2table file.
https://gate.nmr.mgh.harvard.edu/safelinks/greve/aparcstats2table For your other questions a) average across what? Subject? You can use mri_glmfit --table ..., or you can load it into matlab with fast_ldtable and do your averages there b) Are what in fsaverage space? When you run aparcstats2table you get averages in the parcellations of the individual, fsaverage does not come into it c) We don't have anything that will do this easily (a harder problem than you might think). I would do it in matlab, loading the annotation using read_annotation.m, create a vector of values (one item per vertex), then assign all the vertices in a given parcellation the value for that parcellation from your average, then write it out as an mgh file using MRIwrite.m On 11/09/2016 08:27 PM, Martin Juneja wrote: > 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 <mailto: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> > <mailto: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> > >> <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 <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: 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 > 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
