Hi Derek - Good to know things worked out! a.y
On Tue, 19 Jul 2016, Derek Pisner wrote: > Hi Anastasia, > > I thought I should let you know that this issue has now been resolved. We > specified the base ID's/ subject ID's incorrectly in the config file! Sorry > for the confusion. Now our group output looks correct. > > Thanks for your help, > Derek > ________________________________________ > From: freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Derek Pisner > [dpis...@psychiatry.arizona.edu] > Sent: Tuesday, July 12, 2016 5:06 PM > To: Freesurfer support list > Subject: Re: [Freesurfer] TRACULA group stats visualization > > Hi Anastasia, > > All subjects had both time-points (for DWI and T1-weighted recons). The > recons were run following the standard longitudinal pipeline for FS. > > Would it matter that I ran the pipeline piecemeal (i.e. separate > configuration files for each subject--see attached example)? In case you are > wondering, I did it this way in order to run the pipeline in parallel (i.e. > by subject) on our cluster... > > Another consideration is that we did preprocessing outside of TRACULA (i.e. > using FSL's tools directly so that we could apply a fieldmap, use new EDDY > with TOPUP, as well as apply a denoising algorithm). We then setup the folder > structure and filenames to begin TRACULA at the trac-all -intra stage, which > we have done successfully in the past when not using the longitudinal > pipeline (i.e. single-subject analyses) > > Still, I have a feeling that none of these customizations should have made > any difference as our merged outputs look excellent for both timepoints, for > all subjects... Any other thoughts about what might be causing this? > > Kind regards, > -Derek > ________________________________________ > From: freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Anastasia Yendiki > [ayend...@nmr.mgh.harvard.edu] > Sent: Tuesday, July 12, 2016 1:45 PM > To: Freesurfer support list > Subject: Re: [Freesurfer] TRACULA group stats visualization > > Hi Derek - Indeed this looks not to be in MNI coordinates, and I haven't > been able to replicate the problem in our own longitudinal data. Did you > by any chance have any subjects that had only a single time point? > > a.y > > On Thu, 7 Jul 2016, Derek Pisner wrote: > >> Sure thing. fmajor mean.txt file is attached. >> >> >> Thanks a bunch, >> -Derek >> ________________________________________ >> From: freesurfer-boun...@nmr.mgh.harvard.edu >> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Anastasia Yendiki >> [ayend...@nmr.mgh.harvard.edu] >> Sent: Thursday, July 07, 2016 4:48 AM >> To: Freesurfer support list >> Subject: Re: [Freesurfer] TRACULA group stats visualization >> >> Hi Derek - this is strange. The dev and 5.3 version of freeview should >> display them differently. Can you send me one of those mean.txt files? >> >> a.y >> >> On Wed, 6 Jul 2016, Derek Pisner wrote: >> >>> Hi Anastasia, >>> >>> This occurs for me on both stable and dev versions of freview and trac-all >>> -stat >>> >>> -Derek >>> ________________________________________ >>> From: freesurfer-boun...@nmr.mgh.harvard.edu >>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Anastasia Yendiki >>> [ayend...@nmr.mgh.harvard.edu] >>> Sent: Monday, July 04, 2016 12:47 AM >>> To: Freesurfer support list >>> Subject: Re: [Freesurfer] TRACULA group stats visualization >>> >>> Hi Derek - Are you by any chance using the dev version of freeview? >>> >>> a.y >>> >>> On Fri, 1 Jul 2016, Derek Pisner wrote: >>> >>>> Dear Anastasia, >>>> I am running into an issue with the trac-all -stat option on our >>>> longitudinal TRACULA data. >>>> >>>> Everything runs smoothly through all earlier stages, and I checked >>>> individual subjects' merged outputs in freeview with -tv mode. Everything >>>> looks fine. >>>> >>>> Also, then when I run trac-all -c dmric_config -stat, everything finishes >>>> without error. >>>> >>>> But then when I open the results with the command: >>>> freeview -v $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz -w >>>> /data/blt/TRACULA/tractography_output/stats.long/*.path.mean.txt >>>> >>>> I get the image seen in the attached .png file. Any idea what might be >>>> causing this? >>>> >>>> Many thanks in advance for you help. >>>> >>>> Best, >>>> Derek >>>> >>>> >>>> >>>> >>> >>> _______________________________________________ >>> 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 >> >> >> 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 > > _______________________________________________ > 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
