External Email - Use Caution Goodmorning Dr. Greve,
Thank you for responding. The symbolic links should not be a problem if the .pial and .pialT1 files are essentially the same. If they were to come out as distinct files ( .pial not being a symbolic link for .pialT1), would both the .pial surface and the .pialT1 surface be the same, when opened in freeview? Thank you for your help, Erika Nolan Get Outlook for iOS<https://secure-web.cisco.com/1LZgtKzoZYVk6AZ0J6Yd4J4bbIBv4fpj_eJX61NxjSg8Uv23HletvmK4Hi6ZxrGo3EWABkTpiVb8mW-iuA9-xL98Y2Vv6djQ2YubBO6R1WGXTq0oMp39xutxMcOOH6uDHNWKMDLBQxuQVLiPuy_KWU1T9xeLeopO9eKK5DF8ubhxOVm7DL2NJkl6Tfd_zfF0vUZMkOLs4YvxCtP8eQi6_rNWGiVJuvPMHrO64KzbhUsIAQ0jkMWBHGjbmtulIVtTDhBPHUBBiIfMuOLdTkIYoFg/https%3A%2F%2Faka.ms%2Fo0ukef> ________________________________ From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas N. Greve <dgr...@mgh.harvard.edu> Sent: Monday, January 25, 2021 10:36:21 PM To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] lh.pial and rh.pial ALIAS, become lh.pialT1 and rh.pial T1 in Freeview Why are the symbolic links creating a problem? Is it a mac thing? On 1/24/2021 10:17 AM, Erika Nolan wrote: External Email - Use Caution Hi Horsng, Thank you for you response. I am confused as to why AFAIK is happening to me, while this is not the case in FreeSurfer 6.0, and also the subject Bert in 7.1.1. My colleagues have also run the same subject and it is also not happening to them: the only difference is that they are not using a Mac. Erika _____________________________ Erika Nolan Ph.D. Candidate Clinical Psychology, Department of Psychology Montreal Neurological Institute McGill University Montreal, Canada ________________________________ 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 Horsng Junn <hsj...@gmail.com><mailto:hsj...@gmail.com> Sent: January 23, 2021 7:31 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu><mailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] lh.pial and rh.pial ALIAS, become lh.pialT1 and rh.pial T1 in Freeview External Email - Use Caution Hi Erika, Disclaimer: I’m not one of the developers of FreeSurfer so this is not the definitive answer. AFAIK, it’s designed that way from the beginning and isn’t a problem in itself. For example I’m using FreeSurfer 7.1.1 and my recon-all script is like this: at lines 3895~3899: set pial = ../surf/$hemi.pial.T1 set cmd = (mris_place_surface --adgws-in $ads --seg $aseg --threads $OMP_NUM_THREADS\ --wm $wm --invol $bfs --$hemi --i $inputsurf --o $pial \ --pial --nsmooth 0 --rip-label $cortexha --pin-medial-wall $cortex \ --aparc $aparc --repulse-surf $white --white-surf $white) and at 3918: cd ../surf; ln -sf $hemi.pial.T1 $hemi.pial; cd ../mri So the script specifically creates {lh|rh}.pial.T1 as a regular file and then it symbolically links {lh|rh}.pial to that file. If you somehow always need {lh|rh}.pial to be a regular file, you can modify the line at 3918 like this for example: cd ../surf; cp -f $hemi.pial.T1 $hemi.pial; cd ../mri Best, Horsng Junn On Jan 24, 2021, at 12:22 AM, Erika Nolan <erika.no...@mail.mcgill.ca<mailto:erika.no...@mail.mcgill.ca>> wrote: External Email - Use Caution Hello everyone, I am new using FreeSurfer and would really appreciate your help with an issue I am encountering when running recon-all (using: recon-all -subject subjectname -i filename.nii -all and recon-all -s TEST2 -i 103515_t1_final.nii -3T -mprage -hires -all). I am using HCP data. Although my white surface reconstruction seems fine, I am having an issue with the gray matter reconstruction: the rh.pial and lh.pial come out as alias files (see attached screenshot) and when I open them in Freeview they open as rh.pialT1 and lh.pialT1 instead! How do I rectify this situation? Thank you for your help, Erika <Screen Shot 2021-01-23 at 10.06.37 AM.png>_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1NXQCD5rBWpN3IhD2sJASP1fpLD5zCynO2_iWGXyxjaX3RTx7Ecbx40oIZLEhIiH8hpATvoKeSQdT-qcyymJ1lKd6lSt0YqKLRiSHKMGTECerJA4bdcrU4DJfchzSGQ-zG-ZAoqklvFalrD9tLJvsXLRB1HhLvViNoH3McfbxSr1JCTDpO4pc8n-ALEYxxih4QnbS3deKAJl3E_3eITXNBJYeNp7bWkeeT6jlEAIu4QqwuMJWGSWnBZnEnyGDjyEMrs3golMv9uKUCibts2wLvA/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer<https://secure-web.cisco.com/1jYW48mj_BY16q-EMax4fRk_hOnEV9Yg01sUZWrNAoPumiJQRF4jcS46_TjkdFfwJh0F1Sv24W8tn1UHAgsvDOfh2en7DB48GXPV4GDx33muLJDg7iLADhmrihvrvDgfOUZucbDFqt8mevsI6lll2lbgUrrPh8jA2f13a1vp2UlLuYdmAyywwbuPdvP230ixNpFBwoBg6WirphL4yeGkbm6pm2yPalIAf-Yn2S_MuTHZL2pPzO3wIrVYLmMq0Om2wd6vzOGUvoax2D9TgUt7tug/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://secure-web.cisco.com/1NXQCD5rBWpN3IhD2sJASP1fpLD5zCynO2_iWGXyxjaX3RTx7Ecbx40oIZLEhIiH8hpATvoKeSQdT-qcyymJ1lKd6lSt0YqKLRiSHKMGTECerJA4bdcrU4DJfchzSGQ-zG-ZAoqklvFalrD9tLJvsXLRB1HhLvViNoH3McfbxSr1JCTDpO4pc8n-ALEYxxih4QnbS3deKAJl3E_3eITXNBJYeNp7bWkeeT6jlEAIu4QqwuMJWGSWnBZnEnyGDjyEMrs3golMv9uKUCibts2wLvA/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
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