Try running "recon-all -surfvolume ..." doug
On 09/20/2012 02:03 PM, Darren Gitelman wrote:
Dear List
I am adding to the post on this error from yesterday regarding problems with running qcache.
I know this has been posted to the list before, but the suggested fixes and checks don't fix the problem.
See the error below (ERROR: number of vertices in /projects/d20277/dek/done/analyzed/3300/surf/lh.volume does not match surface (145332,147148) ERROR: reading curvature file)
- Running recon-all -s <subjid> -vno-check does not find any
problems. It says everything is verified and checks out ok.
- Running recon-all -s <subjid> -make all returns the message: make:
Nothing to be done for `all'.
But when I try recon-all -s <subjid> -qcache I get the error on this and several other subjects, but not all subjects.
Checking the modification times on some files it looks like the thickness file came after the curv file.
[drg@quser03 surf]$ ll *.thickness -rwxrwxrwx 1 dek322 d20277 588607 Sep 11 21:54 lh.thickness -rwxrwxrwx 1 dek322 d20277 593959 Sep 11 22:10 rh.thickness [drg@quser03 surf]$ ll *.curv -rwxrwxrwx 1 dek322 d20277 588607 Sep 11 21:45 lh.curv -rwxrwxrwx 1 dek322 d20277 593959 Sep 11 22:01 rh.curv
Any suggestions for fixing the qcache error would be appreciated.
Darren
#@# 1/1 3300 Wed Sep 19 13:52:44 CDT 2012 --------------
mri_surf2surf --srcsubject 3300 --srchemi lh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi lh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.6938/3300.1.mgh --sval /projects/d20277/dek/done/analyzed/3300/surf/lh.volume --sfmt curv --noreshape --no-cortex
Source registration surface changed to sphere.reg
Target registration surface changed to sphere.reg
srcsubject = 3300
srcval = /projects/d20277/dek/done/analyzed/3300/surf/lh.volume
srctype = curv
trgsubject = fsaverage
trgval = ./tmp.mris_preproc.6938/3300.1.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 /projects/d20277/dek/done/analyzed/3300/surf/lh.sphere.reg
Loading source data
Reading curvature file /projects/d20277/dek/done/analyzed/3300/surf/lh.volume
ERROR: number of vertices in /projects/d20277/dek/done/analyzed/3300/surf/lh.volume does not match surface (145332,147148)
ERROR: reading curvature file
Linux quser01 2.6.18-128.el5 #1 SMP Wed Dec 17 11:41:38 EST 2008 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s 3300 exited with ERRORS at Wed Sep 19 13:52:46 CDT 2012
-- Darren Gitelman, MD Northwestern University 710 N. Lake Shore Dr. Abbott 11th Floor Chicago, IL 60611 Ph: (312) 908-8614 Fax: (312) 908-5073
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