Ahhhhhh.  That makes sense, now.  I will do that, then.  Thank you!

 

 

you can do -autorecon2 -autorecon3 and it should work. The T2pial is done in the middle of  autorecon3. If you don't spec autorecon3, then it will skip the initial part of autorecon3, and that is what is causing the error

no, you need to run autorecon2 first
On Fri, 22 Feb 2019, Weber, Wade A wrote:

       External Email - Use Caution

I can, but how will autorecon3 run without finishing autorecon2?

-----Original Message-----
From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@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-bounces@nmr.mgh.harvard.edu
<freesurfer-bounces@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:

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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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