you shouldn't be running the initial recon with a flair volume though,
are you? That would utterly fail I would think
Bruce
On Tue, 16 Apr 2013, Watson,
Christopher wrote:
> Hi Veronica,
> Did you try initially doing "recon-all -i $FLAIR -s $SUBJECT"?
> And then, when you do the remaining recon-
Hi Veronica
what recon-all command lines did you run? You did run it with a T1 first,
right?
Bruce
On Tue, 16 Apr 2013, Popescu, Veronica wrote:
> Hi, Christopher!
> Best of luck to you all in these difficult times!
> Thank you very much for your advice. I'll try this as well.
> Best wishes,
>
Dear Bruce,
I ran the follwing:
autorecon-all -cw256 -bigventricles -i $FILENAME -subjid $SUBJ_ID -all.
And my file was indeed a 3D T1 scan.
Thank you very much!
Best wishes,
Veronica
-Original Message-
From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu]
Sent: Tuesday, 16 April, 20
ok, then I don't see what's going wrong. Nick: any thoughts?
On Tue, 16 Apr
2013, Popescu, Veronica wrote:
>
> Dear Bruce,
> I ran the follwing:
> autorecon-all -cw256 -bigventricles -i $FILENAME -subjid $SUBJ_ID -all.
> And my file was indeed a 3D T1 scan.
> Thank you very much!
> Best wishes,
Yes, if I just type bet2 I still get: libmeshclass.so: cannot open shared
object file: No such file or directory.
On Fri, Apr 12, 2013 at 4:07 PM, Douglas N Greve
wrote:
> Hi Corinna, if you just run bet2 at the command line, do you get the
> same error?
> doug
>
> On 04/12/2013 03:56 PM, Corin
Thanks so much for the improvement!
I ran the new mris_make_surfaces and the pial surfaces look much better in
FS 5.2!
Here is the comparison slice if you're interested.
https://yalesurvey.qualtrics.com/SE/?SID=SV_ddwW7I9yMQuCtPn
Best,
Daniel
--
Yung-Jui "Daniel" Yang, PhD
Postdoctoral Resea
glad to hear it
Bruce
On Tue, 16 Apr 2013, Yang, Daniel wrote:
> Thanks so much for the improvement!
>
> I ran the new mris_make_surfaces and the pial surfaces look much better in
> FS 5.2!
>
> Here is the comparison slice if you're interested.
>
> https://yalesurvey.qualtrics.com/SE/?SID=SV_ddwW7
Dear Bruce,
Thanks so much again for improving it.
When looking at the pial surfaces, I noticed that sometimes the pial
surfaces and the main surfaces are entangled in 5.2 (but it seems less so
in 5.1).
Here are two slides
(https://dl.dropboxusercontent.com/u/65918007/FS%205.2.pptx) with this
ve
Hi Corinna, I hate to pass the buck, but I think you'll have to contact
the FSL people to get it sorted out.
doug
On 4/16/13 9:31 AM, Corinna Bauer wrote:
Yes, if I just type bet2 I still get: libmeshclass.so: cannot open
shared object file: No such file or directory.
On Fri, Apr 12, 2013
For #2, it is hard to say without seeing the design. I would not say
that covariates should not change the results (otherwise one would not
add them), especially age. If you have a balanced design, then one would
hope that adding age would reduce the residual noise and show more of an
effect.
Hi Yufeng, it cannot handle only a single run. You must have both polar
and eccen. You can "fool" it by copying your polar run into another run
and calling it eccen.
doug
ps. Please remember to send email to the list and not to me personally.
Thanks!
On 4/16/13 11:02 AM, yuf...@mail.ustc.edu.
Hi,
I have recently installed Freesurfer on a new computer, and downloaded the
latest version of Freesurfer (centos 64 bit) and when ran:
recon-all -subject test001 -autorecon2
I got the following error message:
$Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $
cwd
cmdline mri_segs
Hi Miklos, did you run all the steps that go before autorecon2?
doug
On 04/16/2013 12:23 PM, Miklos Argyelan wrote:
> Hi,
>
> I have recently installed Freesurfer on a new computer, and downloaded
> the latest version of Freesurfer (centos 64 bit) and when ran:
>
> recon-all -subject test001 -
Hi Doug, You mean autorecon1? Yes I did, ran without problem, and it seems
I have all the output files from autorecon2 as well. Miklos
--
argyelan, miklos
On Tue, Apr 16, 2013 at 1:06 PM, Douglas N Greve
wrote:
> Hi Miklos, did you run all the steps that go before autorecon2?
> doug
>
>
>
>
> On
Thanks Nick, (and thanks Doug too for the answer to question 2.)
It must indeed have been a disk-space issue, as running the -qcache again,
after clearing up some space, produced all the expected .mgh files
If I can follow up on two of my previous questions:
3) Not sure I understand your answer.
That's alright. I had to add these lines to my .bashrc file
# get FSL config loaded
if [ -f /usr/share/fsl/5.0/etc/fslconf/fsl.sh ]; then
. /usr/share/fsl/5.0/etc/fslconf/fsl.sh;
fi
but now, I get this error when running preproc-sess -per-run -fwhm 3 -force
-so up -surface self lhrh -s . -d . -f
Veronica,
Can you send me the recon-all.log? The one where it is getting hung
when you run this:
recon-all -autorecon3 -subjid ${SUBJ_ID} -FLAIR $FLAIRFILE -FLAIRpial
this should work, by importing the flair and then re-running the surface
creation code, but perhaps there is a dependency bug th
actually, on closer look, adding those lines to the FSL config did not fix
the problem. However, if I call bet2 by typing fsl5.0-bet2, then it works.
I am not sure why, but to call anything from fsl I have to first put
fsl5.0- first.
On Tue, Apr 16, 2013 at 2:40 PM, Corinna Bauer wrote:
> Tha
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