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:
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.eshttp://neurolab.deusto.es/ https://twitter.com/deustoneurolab
Avda. de las Universidades 24, 48007, Bilbao (Spain) Phone: +34 944139000 (ext. 3268) tel:%2B34%20944139000
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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:
External Email - Use CautionDear 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
freesurfer@nmr.mgh.harvard.edu
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Ainara Gomez -
Yendiki, Anastasia