yes, although why -make all didn't fix things is a mystery to me.
On Fri,
24 Jan 2014, Mihaela Stefan wrote:
Yes, -make all ran for about 7 hours and it exited without errors. How
should I fix this?
What about -qcache after recon-all -autorecon2-cp -autorecon3 -subjid
<subject>? Can I use that if it exited without errors? Can I assume that the
subject has all the correct files and continue my analysis?
Thanks!
Mihaela
On Fri, Jan 24, 2014 at 8:01 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu>
wrote:
it's possible that the timestamps on your system are wrong I
guess. Did -make all run anything?
On Fri, 24 Jan 2014, Mihaela Stefan wrote:
Hi Bruce,
I used that command and I got the same errors when I
ran -qcache again. I
also found that my colleague, who did the edits,
used the same command after
she manually edited the recons.
I re-ran the subject with the following command
recon-all -autorecon2-cp
-autorecon3 -subjid <subject> and, when it was done,
I ran -qcache again. It
finished without errors.
I am not sure what is going on.
Best,
Mihaela
On Thu, Jan 23, 2014 at 6:00 PM, Bruce Fischl
<fis...@nmr.mgh.harvard.edu>
wrote:
Hi Mihaela
usually that means the subject was partially
but not completely
rerun. You can try using recon-all -s
<subject> -make all
and see if it fixes it
cheers
Bruce
On Thu, 23 Jan 2014, Mihaela Stefan wrote:
Hello FreeSurfers,
I am trying to run a group analysis with
Qdec
followingthistutorial:
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/
QdecGroup
Anal
ysis_freeview
I got a series of errors when I
ran: recon-all -s
<subjid> -qcache
....
ERROR: number of vertices in
/home/subiculum/Desktop/local_recons/OCD_analysis/3662/surf/lh.volume
does
not match surface (126049,126592)
ERROR: reading curvature file
...
mri_concat
./tmp.mris_preproc.6022/3662.1.mgh --o
lh.volume.fsaverage.mgh
mghRead(./tmp.mris_preproc.6022/3662.1.mgh, -1):
could not open file
ninputs = 1
Checking inputs
ERROR: reading
./tmp.mris_preproc.6022/3662.1.mgh
...
Reading
sourcesurfacereg/home/subiculum/Desktop/local_recons/OCD_analysis/fsaverage/surf/
lh.sphe
re.
reg
Loading source data
ERROR: could not read
lh.volume.fsaverage.mgh as
type 3
Linux subiculum-Precision-T1650
3.5.0-45-generic
#68~precise1-Ubuntu SMP Wed
Dec 4 16:18:46 UTC 2013 x86_64 x86_64
x86_64
GNU/Linux
recon-all -s 3662 exited with ERRORS at
Thu Jan 23
15:22:21 EST 2014
One of the errors says "number of
vertices in...
does not match surface." I
found an older post where someone else
was
complaining about the same error
and Doug suggested running "recon-all
-surfvolume
..."
https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2012-September/025737
.html
I did that and then I ran -qcache again
but I got
the same errors. It also
seems to be a problem with fsaverage. I
do have a
copy of fsaverage in the
subject's directory of this study.
I am attaching the log file with details
about the
errors.
Can someone help me sort this out?
Thank you,
Mihaela
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