External Email - Use Caution Hi Yujing, thanks for your response
Yes my subject directory is /tmp/HCP. But I cannot modify it, so I’d like to reference and use the fsaverage_sym template which is located outside of the subjects directory. Is this possible? If not then I’ll have to find a way to transfer the data from the unmodifiable subjects folder to one that I can play around with directly. Thanks again and hoping this can be clarified! Sent from Mail<https://secure-web.cisco.com/1ArIGscYU5_PUjb3savkEUe_K4wTDUsbi4XbTMcn_2BhYhHKy0EPRo3ocwRmHA2HVGAbr2GFM_wIuKEPm8G_tpM6T7pcpu1IIo_h_wvFqEkPMIIxeD7ZYNhS8YYhQcdZYBSGTyaMCY9wAcMrDkJUZ-L5ffgRiMMyZPNtejrdOAT8jEoIg2t-qtBGl6lUF6tTwWSBR8-EH1oRMh6hGWW_6PaEBkmjdQqg1yL8xsCaeWQINvDuzoqGiGAsSuLgldkZ0KfLcUDULZbv1A0HW3jrmoyExDGk3YTTjY8iMtsb2aFCoxs9KfVwR6qrhhJE99g-_/https%3A%2F%2Fgo.microsoft.com%2Ffwlink%2F%3FLinkId%3D550986> for Windows From: Huang, Yujing<mailto:yhuan...@mgh.harvard.edu> Sent: February 8, 2023 11:41 AM To: Freesurfer support list<mailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Directory I think you can try to use mris_register directly. https://secure-web.cisco.com/1d4xXv390RSqRD_opGj0-XuXab7ok3SfI4G7JYCqiQ_BTgRbJa22wO7qB0VYDI5vOq9BDDQYvPTVSZvSxvA6fdTsEPJ_vH0iaem9TT12V9NrZuEX_yKJzfLMAvi0aFFgzxzyIdEpTs3oALMc4FRKk8ngsE7Lh4BwJA95H8lwBcXvKPFnm4RPPV_cSQH6qnvQHppg68HalKd-l3GEFD6FLQWfJf2vHBggR5YN_tCiPGz_PrC9fnh0hinobQpAZNs58J6DNWvNVXcUOcFxyCCqwCHTuaTLkolG-pOqGYbROwm5rPYizK6GMb-bwNrz5n-go/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2Fmris_register<https://secure-web.cisco.com/1MdCNqUPqWLHQbkTotxi7Hau8g_nLeeaziXtd6RXGnmHcZTkaDE5zv7Hfp4Cig4FrMtVT-gWNEZN8-yyaKKzXAo3li5AlyLogt7rFRWsy4n3GbYgK6UMupPo-3s5j-fTQufHU8Fm57npeVLBnjLfNyXtTJZauLdWQ557xmDKq21QUIrGvtXXGz4g_ud7XZtB9VSzng9AbynrAyX7GT4VI93PoDvl4V2nMJRGP6oduYo7T2jPIlMtLsz0lnmqlRFshpbBdRPzKXeFJ7S_a6OJzyCaQr67itnko99CrJ5MScm1dXzUtyvgScJTp3y4VRA-_/https%3A%2F%2Fcan01.safelinks.protection.outlook.com%2F%3Furl%3Dhttps%253A%252F%252Fsurfer.nmr.mgh.harvard.edu%252Ffswiki%252Fmris_register%26data%3D05%257C01%257Casa.borzabadifarahani%2540mail.mcgill.ca%257C476621fe73084f57fb2f08db09f356df%257Ccd31967152e74a68afa9fcf8f89f09ea%257C0%257C0%257C638114712966005043%257CUnknown%257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%253D%257C3000%257C%257C%257C%26sdata%3DQd4eZf3z51E3%252Bp1D%252Bz%252B7ggsoFBeAWpFhYCj95y08Zg4%253D%26reserved%3D0> From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> On Behalf Of Huang, Yujing Sent: Wednesday, February 8, 2023 11:05 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Directory Hi Asa, I’m wondering if your SUBJECTS_DIR is /tmp/HCP? It looks like surfreg checks if target is ‘fsaverage_sym’. Can you try passing just ‘fsaverage_sym’? Best, Yujing From: freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> <freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> On Behalf Of Asa Borzabadi Farahani Sent: Wednesday, February 8, 2023 10:38 AM To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> <Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>> Subject: [Freesurfer] Directory External Email - Use Caution Hi there experts! I’m hoping to use the surfreg function on some data in which I can’t make any modifications to the subject directory (I’m using a cluster and the data is for public use thus prohibits any changes to it). I want to use the fsaverage_sym as my target file, though the function seems to only be looking for this folder within the subjects directory. Thus when running the following command: surfreg --s 126426 --t /project/60019995/coopapap/data/HCP/fsaverage_sym --lh I get the following error: ERROR: cannot find /project/60019995/coopapap/data/HCP/fsaverage_sym in /tmp/HCP I’m wondering if there is a workaround to using this command even when I can’t make any modifications to the subjects directory. To summarize, I’d like all outputs to go to a personal folder, and I’d like to use a template file that is in my personal folder. Thank you kindly. Asa Farahani
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