Re: [Freesurfer] Longitudinal processing in v6.0 using manual edits from v5.3.0 - recon-all.log

2018-07-04 Thread Martin Reuter 
Hi Kaley, 

if you scroll down the log file you should find something like
new invocation of recon-all with the correct time stamp and v6 text. The old 
log is kept and the new one is appended. 

I am also not sure it is OK to re-run the base with 6.0. It could be that this 
looks OK in single cases and fails in others. The reason is that in 6.0 the 
position of the base image could be (slightly?) different than 5.3. So your 
edits, e.g. control points, would not be at the right anatomical spot. This is 
not a problem when re-running cross runs. 

You should check if the norm.mgz is at the same location in 5.3 base and the 
6.0 base. 
Also I would re-run the long from scratch. (probably there are no edits in long 
anyway)?
Optimally re-run bases also from scratch, could be you don’t need any edits 
because 6.0 is awesome (maybe). 

Best, Martin


> On 25. Jun 2018, at 18:41, KALEY E ELLIS  wrote:
> 
> Hello FreeSurfer experts,
> 
> I previously emailed regarding processing longitudinal data in v6.0 using 
> bases with manual edits that had been completed in v5.3. I went ahead and ran 
> recon-all -all on the base of a subject (originally generated in v5.3) in 
> v6.0, but it looks like the header of the recon-all.log still indicates v5.3. 
> Looking at the /stats output, all files indicate v6.0. Below is the head of 
> the log from running recon-all -all on this subject. Is this what you would 
> expect if you ran recon-all -all on a subject_base in v6.0 that was generated 
> in v5.3? If so, is this okay?
> 
> Recon-all log:
> setenv SUBJECTS_DIR /study1/nccam3/data/mri/freesurfer_v6/subjects
> FREESURFER_HOME /apps/x86_64_sci7/freesurfer-latest
> Actual FREESURFER_HOME /apps/freesurfer-5.3.0/x86_64_sci6
> build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
> Linux c139.keck.waisman.wisc.edu  
> 3.10.0-514.6.1.el7.x86_64 #1 SMP Tue Jan 17 11:12:41 CST 2017 x86_64 x86_64 
> x86_64 GNU/Linux
> 
> Thank you!
> Kaley Ellis
> 
> Associate Research Specialist
> Center for Healthy Minds
> Waisman Center for Brain Imaging and Behavior
> University of Wisconsin-Madison
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> Freesurfer mailing list
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> 
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[Freesurfer] Longitudinal processing in v6.0 using manual edits from v5.3.0 - recon-all.log

2018-06-25 Thread KALEY E ELLIS 
External Email - Use Caution

Hello FreeSurfer experts,


I previously emailed regarding processing longitudinal data in v6.0 using bases 
with manual edits that had been completed in v5.3. I went ahead and ran 
recon-all -all on the base of a subject (originally generated in v5.3) in v6.0, 
but it looks like the header of the recon-all.log still indicates v5.3. Looking 
at the /stats output, all files indicate v6.0. Below is the head of the log 
from running recon-all -all on this subject. Is this what you would expect if 
you ran recon-all -all on a subject_base in v6.0 that was generated in v5.3? If 
so, is this okay?

Recon-all log:

setenv SUBJECTS_DIR /study1/nccam3/data/mri/freesurfer_v6/subjects
FREESURFER_HOME /apps/x86_64_sci7/freesurfer-latest
Actual FREESURFER_HOME /apps/freesurfer-5.3.0/x86_64_sci6
build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
Linux c139.keck.waisman.wisc.edu 3.10.0-514.6.1.el7.x86_64 #1 SMP Tue Jan 17 
11:12:41 CST 2017 x86_64 x86_64 x86_64 GNU/Linux


Thank you!

Kaley Ellis


Associate Research Specialist
Center for Healthy Minds
Waisman Center for Brain Imaging and Behavior
University of Wisconsin-Madison
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addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.