On 25 Aug 2017, at 11:11 pm, Boyd, Emma <EBOYD2@mgh.harvard.edu> wrote:

Hi Bronwyn,

Doug is out of the office today. What is the command you ran after deleting everything in the surf folder? Can you send us the recon-all.log?

Best,

Emma 

---------

Emma Boyd

Research Technician II

Laboratory for Computational Neuroimaging

Martinos Center for Biomedical Imaging

---

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Bronwyn Overs <b.overs@neura.edu.au>
Sent: Thursday, August 24, 2017 9:14 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Recon-all error

 

Hi Douglas,

Do you have any thoughts about the new missing directory error I am getting detailed below? 

Kind regards,

Bronwyn Overs
Research Assistant

Neuroscience Research Australia
Margarete Ainsworth Building
Barker Street Randwick Sydney NSW 2031 Australia
M 0411 308 769 T +61 2 9399 1883 F +61 2 9399 1265

neura.edu.au 

On 17 Aug 2017, at 1:16 pm, Bronwyn Overs <b.overs@neura.edu.au> wrote:

Hi Douglas,

Thanks for your reply. I followed your suggestion and deleted everything in the surf folder for each subject. I am not getting the following error:

Reading source surface reg /workingdata/ID_001/surf/lh.sphere.reg

No such file or directory

mri_surf2surf: could not read surface /workingdata/ID_001/surf/lh.sphere.reg

No such file or directory

Linux katana.neura.edu.au 2.6.32-504.3.3.el6.x86_64 #1 SMP Wed Dec 17 01:55:02 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s ID_001 exited with ERRORS at Thu Aug 17 11:14:08 AEST 2017

To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

Should I try running the recon-all -all for each subject?

Kind regards,

Bronwyn Overs
Research Assistant

Neuroscience Research Australia
Margarete Ainsworth Building
Barker Street Randwick Sydney NSW 2031 Australia
M 0411 308 769 T +61 2 9399 1883 F +61 2 9399 1265

neura.edu.au 

On 17 Aug 2017, at 8:27 am, Douglas N Greve <greve@nmr.mgh.harvard.edu> wrote:

That means that the surfaces are out of sync. the -make-all only works 
in certain circumstances. You can delete everything in the surf folder 
(it should all be recreated anyway with -autorecon2-cp)


On 08/15/2017 10:04 PM, Bronwyn Overs wrote:

Dear mailing list,

I am trying to batch a series of 30 MRI images using the following 
command:
recon-all -autorecon2-cp -subjid ID001 -qcache

But for each image the process exits with the following errors:
---------------------------------------------------
#@# 1/1 ID_001 Wed Aug 16 11:39:12 AEST 2017 --------------
-----------------------
mri_surf2surf --srcsubject ID_001 --srchemi lh --srcsurfreg sphere.reg 
--trgsubject fsaverage --trghemi lh --trgsurfreg sphere.reg --tval 
./tmp.mris_preproc.18138/ID_001.1.mgh --sval 
/mridata/workingdata/CHD/BAR/PROCESSING/baseline_5.3.fix/ID_001/surf/lh.volume 
--jac --sfmt curv --noreshape --no-cortex
Source registration surface changed to sphere.reg
Target registration surface changed to sphere.reg
srcsubject = ID_001
srcval     = 
/mridata/workingdata/CHD/BAR/PROCESSING/baseline_5.3.fix/ID_001/surf/lh.volume
srctype    = curv
trgsubject = fsaverage
trgval     = ./tmp.mris_preproc.18138/ID_001.1.mgh
trgtype    =
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
srchemi    = lh
trghemi    = lh
frame      = 0
fwhm-in    = 0
fwhm-out   = 0
label-src  = (null)
label-trg  = (null)
OKToRevFaceOrder  = 1
Reading source surface reg 
/mridata/workingdata/CHD/BAR/PROCESSING/baseline_5.3.fix/ID_001/surf/lh.sphere.reg
Loading source data
Reading curvature file 
/mridata/workingdata/CHD/BAR/PROCESSING/baseline_5.3.fix/ID_001/surf/lh.volume
ERROR: number of vertices in 
/mridata/workingdata/CHD/BAR/PROCESSING/baseline_5.3.fix/ID_001/surf/lh.volume 
does not match surface (109952,110385)
ERROR: reading curvature file
Linux katana.neura.edu.au <http://katana.neura.edu.au> 
2.6.32-504.3.3.el6.x86_64 #1 SMP Wed Dec 17 01:55:02 UTC 2014 x86_64 
x86_64 x86_64 GNU/Linux

recon-all -s ID_001 exited with ERRORS at Wed Aug 16 11:39:13 AEST 2017

To report a problem, see 
http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

I came across an earlier post in relation to a similar error 
(https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2009-February/009807.html) where 
it was recommended that you run “recon-all -s subjid -make all” to 
rebuild all files where the dependency chain is wrong. I ran this for 
each of the subjects and then tried to rerun my original recon-all 
command again but got the same error. Do you have any alternate 
suggestions for fixing this problem?

Kind regards,

Bronwyn Overs
Research Assistant

Neuroscience Research Australia

Neuroscience Research Australia
Margarete Ainsworth Building
Barker Street Randwick Sydney NSW 2031 Australia
*M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265

neura.edu.au <http://neura.edu.au>

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-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.