External Email - Use Caution Hi Erika,
As I understand it, FreeSurfer 7.1.1 is like an entirely different pipeline from FreeSurfer 6.0. So discussing why one file is a regular file in one version and a symbolic link in another seems to be a moot point. I think it's advisable that you and your colleagues standardize on one version and platform if you're intending to work on each other's output files. (There are reports that discuss this, such as https://secure-web.cisco.com/1d30Vye54lPhEM27Kh7YX3tIWbncSFy3YkGylORXnaFi5c4dp1dYi_V9kSe56Csc4TNHYBRspE3SMy0A3ajaVXcQpGj0SG57N7nE1oKp9IZZSFz6XsmHoSimSzU0FVNlTZUnabdX7hJKrPytEoyV6HP-0ttYgpZ0P30YyibghmStY4khGmMiblYdMwh1Ft5eV2gKISO7pgPZ8-hUmkSBq03RsI4CovfnnwYRCCcso71iguAVOb0ab2lIjHGglTrHMrmHOPsouBvdO0tqsBXOP0A/https%3A%2F%2Fdoi.org%2F10.1371%2Fjournal.pone.0038234 <https://secure-web.cisco.com/1d30Vye54lPhEM27Kh7YX3tIWbncSFy3YkGylORXnaFi5c4dp1dYi_V9kSe56Csc4TNHYBRspE3SMy0A3ajaVXcQpGj0SG57N7nE1oKp9IZZSFz6XsmHoSimSzU0FVNlTZUnabdX7hJKrPytEoyV6HP-0ttYgpZ0P30YyibghmStY4khGmMiblYdMwh1Ft5eV2gKISO7pgPZ8-hUmkSBq03RsI4CovfnnwYRCCcso71iguAVOb0ab2lIjHGglTrHMrmHOPsouBvdO0tqsBXOP0A/https%3A%2F%2Fdoi.org%2F10.1371%2Fjournal.pone.0038234> .) (But from the look of it, I think it's possible that they did this to facilitate some T2/Flair-related analyses.) And about why that is happening to that one subject only, I think there could be misunderstandings. For example both lh.pial and rh.pial are symbolic links for my bert. Are you sure they aren't leftovers from old FreeSurfer 6 runs for example? One way to check whether the output is from FreeSurfer 7 is to see which directory the "fsaverage" symbolic link points to. At least in FreeSurfer 7, FreeSurfer creates that symbolic link next to the subject directory such as bert. Mine is like this: % ls -l fsaverage lrwxrwxr-x ... fsaverage@ -> /Applications/freesurfer/7.1.1/subjects/fsaverage And I don't have a Linux PC to test this on, but I guess it won't be different there. You can check that by running this command under Linux: $ ls -l lh.pial lrwxrwxr-x ... lh.pial@ -> lh.pial.T1 Best, Horsng Junn > On Jan 25, 2021, at 12:17 AM, Erika Nolan <[email protected] > <mailto:[email protected]>> 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: [email protected] > <mailto:[email protected]> > <[email protected] > <mailto:[email protected]>> on behalf of Horsng Junn > <[email protected] <mailto:[email protected]>> > Sent: January 23, 2021 7:31 PM > To: Freesurfer support list <[email protected] > <mailto:[email protected]>> > 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 <[email protected] >> <mailto:[email protected]>> 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 >> [email protected] <mailto:[email protected]> >> MailScanner has detected a possible fraud attempt from >> "secure-web.cisco.com" claiming to be >> https://secure-web.cisco.com/1Vz582LVAIDCxwOQmSgKbtDOZAZzRVV-nqyGF42XmvleNKiwvtoEOOkQsxxujIDWkEe2nzCnB-x6NE4399aa9_SLJ8ystpxMtkhxS5vqSkxvdSthsHhYpJzDGL4QavWWiIlSiiFG-6NirjTMwPy5EYWLnPDVr4g1qj6rpEEqfUzsyNEdp3lT19QSe5vs5KK9YK0VROsR7ARECNk7_1vgFVyJ3TD-Q4I7ZCRvjVhn-ehDicPsJ1VINhc6A8O1YF39TreoSPzUhxrQX_sSq2RAonQ/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 > [email protected] <mailto:[email protected]> > https://secure-web.cisco.com/1Vz582LVAIDCxwOQmSgKbtDOZAZzRVV-nqyGF42XmvleNKiwvtoEOOkQsxxujIDWkEe2nzCnB-x6NE4399aa9_SLJ8ystpxMtkhxS5vqSkxvdSthsHhYpJzDGL4QavWWiIlSiiFG-6NirjTMwPy5EYWLnPDVr4g1qj6rpEEqfUzsyNEdp3lT19QSe5vs5KK9YK0VROsR7ARECNk7_1vgFVyJ3TD-Q4I7ZCRvjVhn-ehDicPsJ1VINhc6A8O1YF39TreoSPzUhxrQX_sSq2RAonQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer > > <https://secure-web.cisco.com/1Vz582LVAIDCxwOQmSgKbtDOZAZzRVV-nqyGF42XmvleNKiwvtoEOOkQsxxujIDWkEe2nzCnB-x6NE4399aa9_SLJ8ystpxMtkhxS5vqSkxvdSthsHhYpJzDGL4QavWWiIlSiiFG-6NirjTMwPy5EYWLnPDVr4g1qj6rpEEqfUzsyNEdp3lT19QSe5vs5KK9YK0VROsR7ARECNk7_1vgFVyJ3TD-Q4I7ZCRvjVhn-ehDicPsJ1VINhc6A8O1YF39TreoSPzUhxrQX_sSq2RAonQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer>
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