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.nolan@mail.mcgill.ca wrote:
External Email - Use CautionHello 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 https://secure-web.cisco.com/1jYW48mj_BY16q-EMax4fRk_hOnEV9Yg01sUZWrNAoPumiJ... https://secure-web.cisco.com/1jYW48mj_BY16q-EMax4fRk_hOnEV9Yg01sUZWrNAoPumiJQRF4jcS46_TjkdFfwJh0F1Sv24W8tn1UHAgsvDOfh2en7DB48GXPV4GDx33muLJDg7iLADhmrihvrvDgfOUZucbDFqt8mevsI6lll2lbgUrrPh8jA2f13a1vp2UlLuYdmAyywwbuPdvP230ixNpFBwoBg6WirphL4yeGkbm6pm2yPalIAf-Yn2S_MuTHZL2pPzO3wIrVYLmMq0Om2wd6vzOGUvoax2D9TgUt7tug/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer