My command line was "tksurfer mean.lh.thick_age.thickness.10.mgh lh inflate" d- which is when I got the error.
I have now tried loading fsaverage first with "tksurfer fsaverage lh inflated" and it seems to be working fine. The problem now is changing the colour scale to display only positive values. I have played around with the Min, Max and Slope and can't seem to remove values below zero. What I'm after is a scale showing thickness in mm ranging from something like 1mm-3.5mm (or if it's easier whatever the min and max thickness' are for the group) 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: 16 January 2015 19:52 To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Viewing QDEC results in tksurfer 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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
