[Freesurfer] convert mgh to nii problems - cannot get output file to reshape properly
Hi. I am having a problem similar to that previously described on the freesurfer message boards from May 2011 (Subject: mgh conversion). Unfortunately, that thread ends with Doug asking the person to send him the files in question, so there does not appear to be any sort of publicly published solution. I was sent two .mgh files with the resulting activation maps from an fMRI analysis (both left and right hemispheres) and told that the maps were in fsaverage space. I was not sent any other accompanying files. I am trying to convert them to nii format. I have tried both: 1. mri_convert filename.mgh filename.nii.gz and mri_surf2surf (as was suggested in the previous thread) 2. mri_surf2surf —sval filename.mgh —tval filename.nii —reshape —reshape-factor 6 —s fsaverage —hemi lh (I realize that the command options should be preceded by double dashes, but my email program is quite insistent about automatically formatting these to long dashes.) In both cases the when checking the output file using mri_info, the dimensions are still: 163842 x 1 x 1. Are there any suggestions as to how best to proceed? Thanks in advance, Suzanne Witt ___ 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 Partners Compliance HelpLine at http://www.partners.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.
[Freesurfer] Help resolving ERROR: Invalid FreeSurfer license key found in license file
Hej. I recently tried to create a license file for a Unix-based installation of FreeSurfer that previously had no license file associated with it. With the help of our IT people, I have tried copying the lines I received via email into a file named ‘license.txt’ and then following responses I found on the message board to similar problems, into a file named ‘.license’. In both cases, I get the same error: ERROR: Invalid FreeSurfer license key found in license file /usr/local/freesurfer/license.txt or ERROR: Invalid FreeSurfer license key found in license file /usr/local/freesurfer/.license I have since tried performing a completely new installation of freesurfer, recreating the .license file using a text editor (per a previous message found about this error on the message boards). I am still receiving the same invalid FreeSurfer license error message. To the best that I can figure out, there do not appear to be any sort of ‘end of line’ characters in any of the iterations of our attempts to create this license file. I have noticed many messages about this error in the archives, but none of the suggested fixes seem to be working for me. Any help at this point would be much appreciated. Thanks in advance, suzanne ___ 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 Partners Compliance HelpLine at http://www.partners.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.
