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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 (<AYENDIKI@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.ggastiasoro@deusto.es> wrote:

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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


Avda. de las Universidades 24, 
48007, Bilbao (Spain)
Phone: +34 944139000 (ext. 3268)

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--
Ainara Gómez Gastiasoro

Dpt of Methods and Experimental Psychology
Neuropsychology of Severe Medical Conditions research team
Faculty of Psychology and Education 
University of Deusto


Avda. de las Universidades 24, 
48007, Bilbao (Spain)
Phone: +34 944139000 (ext. 3268)