Please try: segmentHA_T1.sh subject1_preOp_T1MRI_axial-anon /Users/lou.blanpain/Desktop/freesurfer_output/
Cheers, /Eugenio Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.com From: <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of "Blanpain, Lou" <lou.blanp...@emory.edu> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Date: Wednesday, August 26, 2020 at 22:01 To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] [External] Re: Error using segmentHA_T1.sh External Email - Use Caution Sure thing: segmentHA_T1.sh '' /Users/lou.blanpain/Desktop/freesurfer_output/subject1_preOp_T1MRI_axial-anon Note: the folder “subject1_preOp_T1MRI_axial-anon” contains the recon-all output, i.e. folders label, mri, scripts etc. Thank you for the quick reply! Lou Lou Blanpain MD-PhD candidate 2024 Willie Lab, Dpt. of Neurosurgery, Emory Singer Lab, Dpt. of Biomedical Engineering, GATech lou.blanp...@emory.edu<mailto:lou.blanp...@emory.edu> 443 676 9804 From: <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of "Iglesias Gonzalez, Juan E." <jiglesiasgonza...@mgh.harvard.edu> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Date: Wednesday, August 26, 2020 at 9:48 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Subject: [External] Re: [Freesurfer] Error using segmentHA_T1.sh Hi Lou, Can you please send us your exact command line? Cheers, /Eugenio Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.com From: <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of "Blanpain, Lou" <lou.blanp...@emory.edu> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Date: Wednesday, August 26, 2020 at 20:56 To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] Error using segmentHA_T1.sh External Email - Use Caution Hello, I attempted using segmentHA_T1.sh after running recon-all on a subject, but got the following error: “ Error using segmentSubjectT1_autoEstimateAlveusML (line 72) Side must be 'left' or 'right' “ I am using the following specs: _ platform: MacOS Catalina version 10.15.5 _ freesurfer version: 7.1.0 Could you help me with this matter? Thank you so much in advance for any input you may be able to provide regarding this! ________________________________ This e-mail message (including any attachments) is for the sole use of the intended recipient(s) and may contain confidential and privileged information. If the reader of this message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this message (including any attachments) is strictly prohibited. If you have received this message in error, please contact the sender by reply e-mail message and destroy all copies of the original message (including attachments).
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
