External Email - Use Caution Dear Douglas, Thank you so much. It's done. Regards Ramesh
On Tue, Sep 17, 2024, 7:34 PM Douglas N. Greve <dgr...@mgh.harvard.edu> wrote: > The argument to the --s flag should be the name of the subject as was > specified when you ran recon-all, eg > recon-all -i t1_SPGR.nii -s subjectname -all > Then use dt_rcon -s subjectname ... > > On 9/12/2024 7:45 AM, Ramesh Babu wrote: > > External Email - Use Caution > Dear All, > > I am new to dti analysis. I am trying analysis in a single subject. I set > the environment as mentioned below. > export DTI_DATA=export > DTI_DATA=/mnt/data_analysis/mchp_projects/sneha/dti_analysis/FS_DTI_analysis > export SUBJECTS_DIR=$DTI_DATA/subjects/t1_data/ > > In the last step, I received this error. > dt_recon --i dti_data.nii --b bvals.txt bvecs.txt --s > $SUBJECTS_DIR/t1_SPGR.nii --o dtioutput2 > error: > mghRead(/mnt/data_analysis/mchp_projects/sneha/dti_analysis/FS_DTI_analysis/subjects/t1_data//t1_SPGR.nii/mri/brainmask.mgz, > -1): could not open file > > How to get this brain mask? Should it be from subject T1 image or bo map? > I attached the full error report as a text file. > I kindly request you to provide me with a solution. > > Thanks in advance > Ramesh > > _______________________________________________ > Freesurfer mailing > listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > 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 > https://www.massgeneralbrigham.org/complianceline < > https://www.massgeneralbrigham.org/complianceline> . >
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu 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 https://www.massgeneralbrigham.org/complianceline <https://www.massgeneralbrigham.org/complianceline> . 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.
