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 *ddcc2442@gmail.com ddcc2442@gmail.com* 443-254-6298
On Thu, Oct 10, 2019 at 9:14 AM Yendiki, Anastasia AYENDIKI@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-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Daniel Callow < ddcc2442@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 CautionHello,
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 *ddcc2442@gmail.com ddcc2442@gmail.com* 443-254-6298 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer