External Email - Use Caution Hi Anastasia,
In the past days, we have obtained the original T1s from the original study and we are running Freesurfer in all of the subjects in order to run TRACULA correctly so we can avoid all the problems you mention. TRACULA is running in some of the subjects and the outputs look okay after having run Freesurfer. Thank you very much again, Ainara El vie., 11 ene. 2019 a las 15:48, Yendiki, Anastasia (< ayend...@mgh.harvard.edu>) escribió: > Have you checked the registration between the structural and diffusion? > The concern here would be that some of your subjects' brains could look > more like bert's brain than others, and the registration could be better > for the former than the latter. You would have to ensure that this doesn't > introduce biases between groups (or age/gender biases) in your specific > study, and therefore does not induce false group differences or accentuate > any real differences. > > On Jan 11, 2019 9:35 AM, Ainara Gomez <ainara.ggastias...@deusto.es> > wrote: > > External Email - Use Caution > > Hi Anastasia, > > thank you for your rapid response. Since I do not have the T1 of my > subjects, I have not run the recon-all. Instead of that, I have copy-pasted > the "mri" folder (including the aparc+aseg.mgz file) located in > $FREESURFER_HOME/freesurfer/subjects/bert/mri into each subject's folder ($ > SUBJECTS_DIR/$subjectid/) so TRACULA can find all the files from > Freesurfer that are needed in trac-all prep step. > > Thanks a lot again, > > Ainara > > El vie., 11 ene. 2019 a las 14:49, Yendiki, Anastasia (< > ayend...@mgh.harvard.edu>) escribió: > > Hi Ainara - What do you mean by default freesurfer files? Can you describe > how you created each subject's recon-all style directory under > SUBJECTS_DIR? TRACULA looks for $SUBJECTS_DIR/$subjectid/mri/aparc+aseg.mgz > for each subject ID. > > a.y > > > On Jan 11, 2019 8:30 AM, Ainara Gomez <ainara.ggastias...@deusto.es> > wrote: > > External Email - Use Caution > > Dear Freesurfer experts, > > I am trying to run TRACULA as a complementary analysis on a patients and > healthy controls sample. I have read in the tutorial that it is assumed > that FreeSurfer has already been run on all the subjects' T1-weighted data > because TRACULA will use the aparc+aseg.mgz from each subject's FreeSurfer > reconstruction. However, T1s of my subjects are not available for this > study and I only have the diffusion images. > > I have run the three steps of the trac-all separately (using the default > freesurfer files: aseg+aparc.mgz...) and all the processes have ended > without errors. > > Is this correct? Is it possible to use the default freesurfer files > instead of each subject's recon-all files in order to run trac-all? > > Thank you very much in advance, > > Ainara > > -- > Ainara Gómez Gastiasoro > > Dpt of Methods and Experimental Psychology > Neuropsychology of Severe Medical Conditions research team > Faculty of Psychology and Education > University of Deusto > > neurolab.deusto.es > https://twitter.com/deustoneurolab > > Avda. de las Universidades 24, > 48007, Bilbao (Spain) > Phone: +34 944139000 (ext. 3268) > <%2B34%20944139000> > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > -- > Ainara Gómez Gastiasoro > > Dpt of Methods and Experimental Psychology > Neuropsychology of Severe Medical Conditions research team > Faculty of Psychology and Education > University of Deusto > > neurolab.deusto.es > https://twitter.com/deustoneurolab > > Avda. de las Universidades 24, > 48007, Bilbao (Spain) > Phone: +34 944139000 (ext. 3268) > <%2B34%20944139000> > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Ainara Gómez Gastiasoro Dpt of Methods and Experimental Psychology Neuropsychology of Severe Medical Conditions research team Faculty of Psychology and Education University of Deusto neurolab.deusto.es https://twitter.com/deustoneurolab Avda. de las Universidades 24, 48007, Bilbao (Spain) Phone: +34 944139000 (ext. 3268) <%2B34%20944139000>
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
