what is your command line? On 01/16/2015 11:02 AM, Worker, Amanda wrote: > Hi Doug, > > I have set up and run the usual Group Analysis through the command line. I > have then run " mri_concat output-of-preproc.mgh --mean --o > mean.output-of-preproc.mgh" to obtain a mean thickness for all subjects > included in the preprocessing. > > I'm now having a problem with visualising this with tksurfer, getting ERROR: > could not read header info from T1 or orig in > /home/k1204763/images/BRCATLAS/FREESURFER.v5.3.0/GroupAnalysis/mri > > Presumably this is because all of the T1/orig are stored in each subjects > data file and I'm not trying to look at a specific subject. Is there a way to > get around this problem? > > Best wishes, > > Amanda > > ________________________________________ > From: freesurfer-boun...@nmr.mgh.harvard.edu > <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas N Greve > <gr...@nmr.mgh.harvard.edu> > Sent: 15 January 2015 16:56 > To: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] Viewing QDEC results in tksurfer > > QDEC will not produce mean maps for each group. If this is something you > want to do, you will need to do it in the command-line group analysis > stream. See > http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis > > > > > On 01/15/2015 05:25 AM, Worker, Amanda wrote: >> Hi, >> >> I am currently only able to open a thickness map for a single subject using >> "tksurfer SUBJECT lh inflated". I can use the analysis figures from qdec, >> but I'd really like to plot the mean thickness for a particular group to >> compare to others visually. Is this possible? >> >> Thanks, >> >> Amanda >> >> ________________________________________ >> From: freesurfer-boun...@nmr.mgh.harvard.edu >> <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas N Greve >> <gr...@nmr.mgh.harvard.edu> >> Sent: 14 January 2015 23:46 >> To: freesurfer@nmr.mgh.harvard.edu >> Subject: Re: [Freesurfer] Viewing QDEC results in tksurfer >> >> what is your tksurfer command line? >> >> On 01/13/2015 07:12 AM, Worker, Amanda wrote: >>> Hi, >>> >>> >>> Is it possible to view the results of a qdec analysis (correlation >>> with a single continuous group) in tksurfer? I am currently unable to >>> open it and I'm getting an error saying "could not open >>> file */mri/transforms/talairach.xfm ..no such file or directory" . Is >>> this a file that is not created with qdec? >>> >>> >>> I'm also trying to visualise group mean thickness' in different >>> colours to allow difference between groups, that are not significant >>> in the analysis to be visualised. I cannot find any advice on how to >>> do this, is this something it's possible to do using either freeview >>> of tksurfer? >>> >>> >>> Thanks, >>> >>> >>> Amanda >>> >>> >>> >>> _______________________________________________ >>> 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 >> >> >> 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 >> >> > -- > 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 > _______________________________________________ > 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
