Hi Elijah,
On 01/15/2014 04:10 PM, Elijah Mak wrote:
Hi Martin,
Thank you for your help.
By re-processing, do you mean running recon-alls all over again?
Yes. 5.0 is old and it is better to run everything with 5.3 from
beginning to end. If you have a lot of data or a lot of edits, you can
try running -base and -long in 5.3 and keep the independent (cross
sectional) stuff in 5.0, but I don't recommend mixing versions.
Could you elaborate on the advantage of creating a new subjectsdir and
copying over the orig dirs for each subject?
This way you keep a backup copy of your old 5.0 processed data (to
lookup edits etc). If you have a script that calls recon-all with the -i
flag for inputs, you don't need to copy the mri/orig dirs (it will grab
the data from the dicoms again). Copying the orig dirs and dropping -i
will skip that step.
On a related note, would it be better to run the full recon-all
pipeline for each subject? I have been running batches of subjects at
each stage (i.e. autorecon1, autorecon2, and finally autorecon3).
Yes, full pipeline (-all) on all subjects is what I usually do. You can
run individual steps and check intermediate results if you like, but I
usually run everything and check everything at the end.
Best, Martin
Thank you again.
Best Wishes,
Elijah
On Wed, Jan 15, 2014 at 9:02 PM, Martin Reuter
<mreu...@nmr.mgh.harvard.edu <mailto:mreu...@nmr.mgh.harvard.edu>> wrote:
Hi Elijah,
if you have minimal edits, I'd recommend to reprocess the data
from scratch with 5.3 (that is supposed to be the same as using
the -clean flag when rerunning 5.3 on top of the old 5.0 data).
But I'd recommend to create a new subjectsdir, copy over the
subjedid/mri/orig dirs for each subject and rerun from scratch
with 5.3 the independent, base and long runs.
Best, Martin
On 01/13/2014 06:18 PM, Elijah Mak wrote:
Greetings Freesurfer Community,
I am running a longitudinal study using Freesurfer v.5.3 to
compare rate of cortical thinning between 2 groups of subjects. I
hope I can seek some expert advice on the following situation:
All data (both the baseline and follow-up) has been processed
independently using recon-all. This has been done on Freesurfer 5.0.
Since then, I have upgraded to Freesurfer v5.3 to utilize the
linear mixed effect capability.
For the construction of base and longs, I understand that it is
important to add -clean flag to my recon-all strings to overwrite
brainmask.mgz etc. When must this be done?
I am still new to Freesurer, and I'd greatly appreciate any
advice regarding workflow.
Many Thanks,
Elijah
--
Elijah Mak, B.A.
Doctoral Candidate *|* Psychiatry
University of Cambridge *| *Department of Psychiatry
Trinity College, Cambridge, CB2 1TQ
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--
Martin Reuter, Ph.D.
Assistant in Neuroscience - Massachusetts General Hospital
Instructor in Neurology - Harvard Medical School
MGH / HMS / MIT
A.A.Martinos Center for Biomedical Imaging
149 Thirteenth Street, Suite 2301
Charlestown, MA 02129
Phone:+1-617-724-5652 <tel:%2B1-617-724-5652>
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--
Elijah Mak, B.A.
Doctoral Candidate *|* Psychiatry
University of Cambridge *| *Department of Psychiatry
Trinity College, Cambridge, CB2 1TQ
--
Martin Reuter, Ph.D.
Assistant in Neuroscience - Massachusetts General Hospital
Instructor in Neurology - Harvard Medical School
MGH / HMS / MIT
A.A.Martinos Center for Biomedical Imaging
149 Thirteenth Street, Suite 2301
Charlestown, MA 02129
Phone: +1-617-724-5652
Email:
mreu...@nmr.mgh.harvard.edu
reu...@mit.edu
Web : http://reuter.mit.edu
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The information in this e-mail is intended only for the person to whom it is
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
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