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Dear Dr. Douglas,

Thank you so much for your response. I just checked in the surf folder of this specific subject and yes, rh.white does exist. Not 100% sure how to check if it's readable for freesurfer - could you please explain? Thank you!

On Tue, Aug 17, 2021 at 5:45 PM Douglas N. Greve dgreve@mgh.harvard.edu wrote:

It says that it cannot find /Applications/freesurfer/subjects/DCNL-fBMI-001_Siemens_MPRAGE/surf/rh.white does that file exist and readable?

On 8/17/2021 5:12 PM, Lab of Autism and Developmental Neuroscience, Lab of Autism and Developmental Neuroscience wrote:

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Hello again FreeSurfer experts,

I am having some issues creating the output file with the LGI data for each subject. Could you please help me with this? See below the code (in bold) that I used and the outputs that I got. Please let me know if you need additional information!

*mri_segstats --annot DCNL-fBMI-001_Siemens_MPRAGE rh aparc --i $SUBJECTS_DIR/DCNL-fBMI-001_Siemens_MPRAGE/surf/rh.pial_lgi --sum rh.DCNL_001_aparc.pial_lgi.stats* 7.1.0 cwd cmdline mri_segstats --annot DCNL-fBMI-001_Siemens_MPRAGE rh aparc --i /Applications/freesurfer/subjects/DCNL-fBMI-001_Siemens_MPRAGE/surf/rh.pial_lgi --sum rh.DCNL_001_aparc.pial_lgi.stats sysname Darwin hostname CCAPSY-0GYM0XV machine x86_64 user ajobsaid whitesurfname white UseRobust 0 Constructing seg from annotation error: No such file or directory error: MRISread(/Applications/freesurfer/subjects/DCNL-fBMI-001_Siemens_MPRAGE/surf/rh.white): could not open file

The lh or rh.pial_lgi file is located in the surf folder in each subject. Should I transfer them to the stats folder and try something like *asegstats2table -s subjectID --statsfile=rh.pial_lgi --meas mean --tablefile SubjectID_rh_lgi_final.txt ? *

Thank you so much!!

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