[Freesurfer] kvlQuantify naming problem [possible fix]
Hello all, My site has recently upgraded to the newest version of Freesurfer, and I've run a set of subjects on recon-all using the hippocampal subfield segmentation flag. Everything went well. Then in running kvlQuantifyHippocampalSubfieldSegmentations.sh, I received error messages indicating that certain expected files didn't exist. In particular, among output files labeled with the scheme $subj/mri/posterior_$side_$struct.mgz, the script expected ...CA2-3.mgz and ...CA4-DG.mgz, and existing files were named ...CA2_3.mgz and ...CA4_DG.mgz -- in other words, the script expected a hyphen but instead the filenames contained an underscroe. After renaming the files appropriately, kvlQuantify... successfully generated the nonPartialVolumeStats files and everything worked fine. I didn't see any threads with this solution, and only one or two that mentioned the problem (http://bit.ly/1vHbV5K), so I thought I'd offer it up in case it could be addressed in a future release. Cheers, C.P. Frost ___ 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.
Re: [Freesurfer] kvlQuantify naming problem [possible fix]
Follow-up: I then run into indexing problems when calling freeview with subfield volumes (similar to http://bit.ly/1pdEWRZ), which leads me to believe kvlQuantify is the only script that relies on the old convention. Changing the names back to CA2_3.mgz, etc., fixes THAT problem. Rather than changing the filenames to the old convention, it's probably better to fix the script and leave the filenames alone. On Wed, May 21, 2014 at 1:06 PM, C.P. Frost car...@gmail.com wrote: Hello all, My site has recently upgraded to the newest version of Freesurfer, and I've run a set of subjects on recon-all using the hippocampal subfield segmentation flag. Everything went well. Then in running kvlQuantifyHippocampalSubfieldSegmentations.sh, I received error messages indicating that certain expected files didn't exist. In particular, among output files labeled with the scheme $subj/mri/posterior_$side_$struct.mgz, the script expected ...CA2-3.mgz and ...CA4-DG.mgz, and existing files were named ...CA2_3.mgz and ...CA4_DG.mgz -- in other words, the script expected a hyphen but instead the filenames contained an underscroe. After renaming the files appropriately, kvlQuantify... successfully generated the nonPartialVolumeStats files and everything worked fine. I didn't see any threads with this solution, and only one or two that mentioned the problem (http://bit.ly/1vHbV5K), so I thought I'd offer it up in case it could be addressed in a future release. Cheers, C.P. Frost ___ 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.
Re: [Freesurfer] kvlQuantify naming problem [possible fix]
Thank you very much! We'll certainly fix this in the next release Cheers, /Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer - Original Message - From: C.P. Frost cpfr...@wisc.edu To: freesurfer@nmr.mgh.harvard.edu Sent: Wednesday, May 21, 2014 9:58:32 PM Subject: Re: [Freesurfer] kvlQuantify naming problem [possible fix] Follow-up: I then run into indexing problems when calling freeview with subfield volumes (similar to http://bit.ly/1pdEWRZ ), which leads me to believe kvlQuantify is the only script that relies on the old convention. Changing the names back to CA2_3.mgz, etc., fixes THAT problem. Rather than changing the filenames to the old convention, it's probably better to fix the script and leave the filenames alone. On Wed, May 21, 2014 at 1:06 PM, C.P. Frost car...@gmail.com wrote: Hello all, My site has recently upgraded to the newest version of Freesurfer, and I've run a set of subjects on recon-all using the hippocampal subfield segmentation flag. Everything went well. Then in running kvlQuantifyHippocampalSubfieldSegmentations.sh, I received error messages indicating that certain expected files didn't exist. In particular, among output files labeled with the scheme $subj/mri/posterior_$side_$struct.mgz, the script expected ...CA2-3.mgz and ...CA4-DG.mgz, and existing files were named ...CA2_3.mgz and ...CA4_DG.mgz -- in other words, the script expected a hyphen but instead the filenames contained an underscroe. After renaming the files appropriately, kvlQuantify... successfully generated the nonPartialVolumeStats files and everything worked fine. I didn't see any threads with this solution, and only one or two that mentioned the problem ( http://bit.ly/1vHbV5K ), so I thought I'd offer it up in case it could be addressed in a future release. Cheers, C.P. Frost ___ 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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
