External Email - Use Caution Hello,
It isn't an error with recon-all, at least I don't think it is. Recon-all ran without error and the file that Tracula is trying to access seems to be where it is supposed to be. It seems like Tracula is having an issue opening the lh.white file. I just included the recon-all log for that subject to show that recon-all hadn't had any issues. Do you still think it would have to do with recon-all? It seems to have to do with the way Tracula is trying to read the file? Best, *Daniel Callow* *PhD Student, Neuroscience and Cognitive Science* Exercise for Brain Health Lab University of Maryland, College Park *ddcc2...@gmail.com <ddcc2...@gmail.com>* 443-254-6298 On Thu, Oct 10, 2019 at 9:14 AM Yendiki, Anastasia <ayend...@mgh.harvard.edu> wrote: > Hi Daniel - is this an error in recon-all? Then I wouldn't put "tracula > error" in the subject line if you want the developers of the structural > stream to look into it. > > a.y > ------------------------------ > *From:* freesurfer-boun...@nmr.mgh.harvard.edu < > freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Daniel Callow < > ddcc2...@gmail.com> > *Sent:* Thursday, October 10, 2019 9:01:25 AM > *To:* Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > *Subject:* [Freesurfer] TRACULA error - MRISread could not open file > > > External Email - Use Caution > > Hello, > > I am running tracula on some of my DTI data and have had no issues for > most of my subjects. However, for one of them I get the following error > after mri_segreg > > MRISread(/Volumes/DANIEL/freesurfer_pin/APOE.269/surf/lh.white): could not > open file > > Loading mov > > Extracting frame 0 > > Projecting LH Surfs > > Loading lh.white surf > > No such file or directory > > > It doesn't make sense that I am getting this error because when looking in > that exact folder I see the following > > > [255a-280:freesurfer_pin/APOE.269/surf] amos% ls > > lh.area lh.smoothwm.FI.crv rh.area > rh.smoothwm.FI.crv > > lh.curv lh.smoothwm.H.crv rh.curv > rh.smoothwm.H.crv > > lh.defect_borders lh.smoothwm.K.crv rh.defect_borders > rh.smoothwm.K.crv > > lh.defect_chull lh.smoothwm.K1.crv rh.defect_chull > rh.smoothwm.K1.crv > > lh.defect_labels lh.smoothwm.K2.crv rh.defect_labels > rh.smoothwm.K2.crv > > lh.inflated lh.smoothwm.S.crv rh.inflated > rh.smoothwm.S.crv > > lh.inflated.H lh.smoothwm.nofix rh.inflated.H > rh.smoothwm.nofix > > lh.inflated.K lh.sphere rh.inflated.K rh.sphere > > lh.inflated.nofix lh.sphere.reg rh.inflated.nofix rh.sulc > > lh.orig lh.sulc rh.orig rh.white.H > > lh.orig.nofix lh.white.H rh.orig.nofix rh.white.K > > lh.qsphere.nofix lh.white.K rh.qsphere.nofix > rh.white.preaparc > > lh.smoothwm lh.white.preaparc rh.smoothwm > rh.white.preaparc.H > > lh.smoothwm.BE.crv lh.white.preaparc.H rh.smoothwm.BE.crv > rh.white.preaparc.K > > lh.smoothwm.C.crv lh.white.preaparc.K rh.smoothwm.C.crv > > > It looks like the file it can't open is there? I have attached the log > file for recon-all and trac-all the subject in case it might help. > > > Thank you, > *Daniel Callow* > *PhD Student, Neuroscience and Cognitive Science* > Exercise for Brain Health Lab > University of Maryland, College Park > *ddcc2...@gmail.com <ddcc2...@gmail.com>* > 443-254-6298 > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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