Hi Yigu, I'm trying to understand how you obtained the label file with R package functions. What is your R command to generate the label file, and how did you view it in freeview?
Here is some information about the label file - https://surfer.nmr.mgh.harvard.edu/fswiki/LabelsClutsAnnotationFiles Besides the first two lines in the file, it needs 5 columns on each row. The error message suggested your label file doesn't follow the format on that line. Best, Yujing From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> On Behalf Of Yigu Zhou Sent: Tuesday, March 7, 2023 1:22 PM To: Freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] freesurfer could not parse freeview-loadable surface label External Email - Use Caution Hello Freesurfer community I am trying to transform a label file obtained in subject native surface space to subject native volume space. This label file was obtained through binarizing the subject lh.sulc morphological data through the function write.fs.label from R package freesurferformats, in the left hemisphere, resulting in a binary label for all sulci in the subject. Visual quality control of the label file through Freeview was adequate: I can load the surface label file with any surface of the subject. Now, I would like to map the corresponding voxels that belong to sulci in the left hemisphere of this subject. I tried to convert the label to volume using mri_label2vol first, but got the following error message could not parse 48510th line '1e+05 -37.5524826049805 -5.55967617034912 18.56817436218261' in label file I then tried to first convert the file to annot format using mris_label2annot and then convert to volume using mri_aseg2aparc. Similarly, mris_label2annot threw the error could not parse 48510th line '1e+05 -37.5524826049805 -5.55967617034912 18.56817436218261' in label file The list described similar errors but no obvious solution that I can access right now e.g. having a developer inspect the label file. I would love to get any pointer as to why the label file may have been unparse-able to Freesurfer tools. Sincerely Yigu
_______________________________________________ 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.
