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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
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
 

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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
443-254-6298
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