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 <dgr...@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 > listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://secure-web.cisco.com/1DNwVxd-qsdBrqXyrK06wVTFL1NFHVIkX9g9qZ1tPXHe_bXhvRbgfYGwOswY7U-JfQcPIgzRWOXSlKQd_DzcdVsH0HEHccoM5KaxAjhN6o6WWZenjwHV0z284LJo8kSVvtX4H7hSb5tuTK4FhURTbvf_USv5Lr7agTE3DW45W76coXm5jzZmuFPpDrFfFCGNxmvwYibxvKMWv_jh8G_tnncibfMsUKpsYlkxeXqSLXU4w4HHSX44PQ-JRxvs8RbgDIwQr_oYp7H8RJyc6o6qOCA/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer > 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 > http://secure-web.cisco.com/1jTZoWxS_YLhTSE13gn9KJXUGwklxPXiEBh53eZWeDPbF_PTL2LhjF69arNoKNtEF5zCj5ts7kriR6j0KZqMarNCNvMPr6y-Jr1rFKkcwX_dNx9o5iKd1x3BT_xuZI_HOz5GMIhnsvkeViA2PYUGRpEx66JYdCnglDyh94CZIf1BAuEL8BZEP6w1fUXNpLhJgp8i2EpM60LGVyvP8xOZfSQTyTNprAAntZqdt_iVGIt-xvKD1jyamVDE_cwBxRf36zYC5kAMBVNJwOrE-yAfK3A/http%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline > . 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. >
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