Hi everyone,
Just a quick question: I noticed that the -legacy option of recon-all was
removed in version 5.1. Is there any way to keep the manual edits and all the
processing from previous versions while reprocessing with 5.1?
Thank you very much,
Marie
__
-Original Message-
From: Nick Schmansky [mailto:ni...@nmr.mgh.harvard.edu]
Sent: Wednesday, September 22, 2010 6:51 PM
To: Juranek, Jenifer
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] -legacy
yes, the -legacy flag was only necessary for the v3.0 to v4.0
transition. v4.0 data
yes, the -legacy flag was only necessary for the v3.0 to v4.0
transition. v4.0 data should be fully compatible with reprocessing in
v5.
n.
On Wed, 2010-09-22 at 17:31 -0500, Juranek, Jenifer wrote:
> I'm hoping to push my legacy datasets (processed and edited in FSv4.0.5)
> through FSv5.0.0. Af
I'm hoping to push my legacy datasets (processed and edited in FSv4.0.5)
through FSv5.0.0. After installing FSv5.0.0, I received an error that it didn't
look like a legacy analysis (see below).
[jjura...@localhost subjects]$ recon-all -legacy -s SB_057_H21001
ERROR: you have specified -legacy,
Just wanted to keep as much of the older analysis as possible to save time,
because there are many subjects. Where can I start to save some time?
On Wed, Oct 8, 2008 at 10:04 AM, Bruce Fischl <[EMAIL PROTECTED]>wrote:
> you need to run it from earlier in the analysis. Is there any reason you
> do
you need to run it from earlier in the analysis. Is there any reason you
don't want to just rerun them from the start? I guess you could just run
the aseg stages individually
On Wed, 8 Oct 2008, R D wrote:
Thanks, this works and it recognizes it as a legacy analysis. Some subjects
work
fine th
Thanks, this works and it recognizes it as a legacy analysis. Some subjects
work
fine this way. But for some other subjects, it exits with
an error saying aseg.mgz not found.
mris_make_surfaces: could not read segmentation volume
/usr/home/rhdesai/From_old_apu_home3/freesurfer.subjects/335/mri/ase
hmm, Doug or Nick would be better at this, but try:
touch $SUBJECTS_DIR/$subjects/scripts/recon-all.status
then rerun the subject. Hopefully it will then recognize that it is a
legacy analysis.
cheers,
Bruce
On Mon, 6 Oct 2008, R D
wrote:
Hello,
I have some surfaces created by freesuf
Hello,
I have some surfaces created by freesufer in 2006. Spherical registration
was not done at that time, which needs to be done. I ran recon-all with
-legacy, but it crashed due to disk space problems. Now it doesn't run
either with or without -legacy option. When -legacy is specified, it says
You can get brain.mgz by converting the COR files in
/space/ventzl/1/users/SUBJECTS_DIR/mano001/mri/brain to mgz using
mri_convert --in_type cor --out_type mgz
Robert Levy wrote:
Hi Doug,
I just got around to looking at this problem again and trying what you
had suggested (link brain.mgz to
Hi Doug,
I just got around to looking at this problem again and trying what you
had suggested (link brain.mgz to brainmask.mgz), and the problem is,
there is no brain.mgz either. I would expect to see it in
$SUBJECTS_DIR/$subject/mri/brain.mgz, but instead what I see, both in
individual subj
Try coping or linking the brain.mgz to brainmask.mgz
Robert Levy wrote:
Hi,
Yes, I set the rate to various values to test it, and all resulted in
the same threshold. I didn't mask to brain, because that causes an
error message (it cites the lack of a brainmap.mgz as the reason, so
that
Hi,
Yes, I set the rate to various values to test it, and all resulted in
the same threshold. I didn't mask to brain, because that causes an
error message (it cites the lack of a brainmap.mgz as the reason, so
that at least I know is due to it being processed in an older stream).
So I wonde
what do you mean by "staring p value"? Do you mean the FDR itself?
Robert Levy wrote:
Hi,
Is it possible to use FDR in stable3 for data that was processed prior
to the introduction of brainmask.mgz? It seems like I can view the
data just fine in stable3, or stable2 for that matter (though
Hi,
Is it possible to use FDR in stable3 for data that was processed prior
to the introduction of brainmask.mgz? It seems like I can view the
data just fine in stable3, or stable2 for that matter (though not stable
4), but FDR gives results that seem wrong. FDR sets the threshold to
-log10
--Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Fornito,
Alexander
Sent: Sunday, February 11, 2007 10:45 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Legacy flag
Hi,
I was just seeking some clarification re: the legacy flag in recon-all.
Can I
Hi,
I was just seeking some clarification re: the legacy flag in recon-all.
Can I use it on subjects procssed with older versions of Freesurfer to
reconstruct surfaces that will be consistent with those generated with older
versions (i.e., I can collapse data from the two versions), or is the leg
Hi Vasanth,
The command-line below does not have -legacy
[biggs:mri] (nmr-dev-env) recon-all -subjid CARG29_recon
-autorecon1 -autorecon2
Also, please remember to follow the bug reporting guidlines in:
surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
doug
Vasanth Pappu wrote:
Hi,
Hi,
I started to run an old subject through autorecon1 and 2. I used the
-legacy flag. However, I still got the error below, saying that I need
some *mgz files in the orig/ directory. I thought -legacy would do this
conversion.
The orig/ had a COR volume, but the error said to have a 001.mgz
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