External Email - Use Caution        

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:

        External Email - Use Caution        

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!! 

_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be 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 Mass General Brigham Compliance HelpLine at MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://www.massgeneralbrigham.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.
Please note that this e-mail is not secure (encrypted).  If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately.  Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.