Hi Jenni, Yes I have tried it. I guess I should have been clearer when I wrote "I have added the mgz extension", my mistake. Thanks, -Thang
-----Original Message----- From: Jenni Pacheco [mailto:jpacheco@nmr.mgh.harvard.edu] Sent: Wednesday, April 12, 2006 3:13 PM To: Nguyen, Thang Q Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FW: FW: Recon-all longitudinal script
Hi Thang,
I'm not sure if you've tried this, but try adding -mgz to the command line when running recon-all-nmr-long.
Jenni
On Wed, 12 Apr 2006, Nguyen, Thang Q wrote:
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Tuesday, April 11, 2006 5:42 PM To: Nguyen, Thang Q Subject: Re: FW: Recon-all longitudinal script
Hi Thang,
please post this to the list
Bruce On Tue, 11 Apr 2006, Nguyen, Thang Q wrote:
Hello Bruce Fischl, I was wondering if you could help me with this Freesurfer issue. I
am
trying to run the longituduinal script (recon-all-nmr-long) that Xiao sent me. We have installed the latest 2006 version of Freesurfer
which
works in mgz format. I have tried running recon-all on one subject
and
running the longitudinal script on the second subject.
Unfortunately,
it errors out saying that the script can't find the mgz format. I
have
added the mgz extension and it also gives me the same problem. I have tried recon-all on the second subject as well and then
running
the longitudinal script but it gives me this error:
Sphere rh Mon Apr 10 18:04:19 PDT 2006
/raid2/research/analysis/GE-SiemensCalibration/Freesurfer_longitudinal/S
zetoR2/scripts cp
/raid2/research/analysis/GE-SiemensCalibration/Freesurfer_longitudinal/S
zetoR/surf/rh.sphere
/raid2/research/analysis/GE-SiemensCalibration/Freesurfer_longitudinal/S
zetoR2/surf/rh.sphere
Surf Reg rh Mon Apr 10 18:04:19 PDT 2006
/raid2/research/analysis/GE-SiemensCalibration/Freesurfer_longitudinal/S
zetoR2/scripts Too many )'s.
Since Xiao left, I no longer have a contact for this problem. I have contacted Karl Helmer and he hasn't responded. I was wondering if
you
could help me. Thank you, Thang Nguyen
From: Doug Greve [mailto:greve@nmr.mgh.harvard.edu] Sent: Friday, April 07, 2006 3:36 PM To: Nguyen, Thang Q Subject: Re: Recon-all longitudinal script
I think you run recon-all on the first time point, then -long on the subsequent ones. But I've never actually run it myself :).
doug
Nguyen, Thang Q wrote: Hello Doug Greve, I am trying to run a longitudinal analysis using the
recon-all-nmr-long
binary from Xiao. I was wondering if you could answer some questions
I
have. Do I need to process each longitudinal scan using recon-all
first
and then apply the longitudinal analysis to the first scan or can I simply run the recon-all-nmr-long for the subsequent subjects without running recon-all on those datasets? Thank you for your time, -Thang
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