no, you need to run autorecon2 first
On Fri, 22 Feb 2019, Weber, Wade A
wrote:
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I can, but how will autorecon3 run without finishing autorecon2?
-----Original Message-----
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> On Behalf Of Bruce Fischl
Sent: Friday, February 22, 2019 11:58 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] ?h.white does not exist
Hi Wade
I don't think you can just skip autorecon3. Can you try running it first and
see if that fixes your problems?
cheers
Bruce
On Fri, 22 Feb 2019, Weber, Wade A
wrote:
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Hi Bruce,
I'm using MPRAGEs that aren't as FreeSurfer friendly as they could be, so I
have to do some Pial edits. So I just skip autorecon3 to save time. After I
finish the edits, I re-run from -autorecon-pial and check again. Then I run
autorecon3.
Wade
-----Original Message-----
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> On Behalf Of Bruce Fischl
Sent: Friday, February 22, 2019 11:38 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] ?h.white does not exist
Hi Wade
from the recon-all.log it looks like you never ran autorecon3. Is
there a reason for this? Usually we run all the way through autorecon3
before running the T2pial stuff
cheers
Bruce
On Fri, 22 Feb 2019, Weber, Wade A wrote:
External Email - Use Caution
Hi all,
I’m trying to run –autorecon2 on 3 subjects (I already ran
–autorecon1 on them with no errors.) and I’m getting an error after
the –final_surfs part saying that lh.white does not exits (and it
doesn’t, I checked for it). I have run about 10 other subjects, and they all
ran fine and contain ?h.white files. I saw 2 other strings in the archive with
this same issue, but there was no resolution to them.
This error just started happening, and I didn’t change anything. Here’s the
command I’ve been using:
recon-all –subjid <my subject #> -T2 <name of t2.nii file> -T2pial
-autorecon2
Here’s the error output:
MRISread(/home/waw758/Desktop/secure/Mbemba/Mbemba_freesurfer_stuff/a
n
alysis_files/ANG_1034/surf/lh.wh
ite): could not open file
I’m running freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
on a virtual machine running Red Hat Enterprise Linux Workstation 7.6
I’ve attached the recon-all.log file
Thanks!
----
Wade A. Weber, MS
Psychiatry Research Program Coordinator
Dell Medical School | The University of Texas at Austin
o: 512-495-5217 | f: 512-495-5482 | dellmedschool.utexas.edu
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