Hi Diane,
for -tp you need to pass the id of the processed time points from the
first step. So if you have two time points and called the subject ids
subPRE and subPOST then
recon-all -base subTemplate -tp subPRE -tp subPost -sd <subjects_dir>
Both the subPRE and the subPost need to be in the same subjects_dir, in
your case it looks like they are in separate directories with the same
name as the subject id. Either copy that into a single directory or
create a new one and use symbolic links (ln -s souce target).
Then re-run the base command. Your subjects directory should look like this:
subPRE
subPost
the -base command will add:
subTemplate
and after the longitudinal commands:
subPRE.long.subTemplate
subPost.long.subTemplate
with the final results.
Cheers, Martin
On 07/22/2015 06:53 PM, nswa66 wrote:
Hi,
I am running longitudinal processing with Freesurfer according to the
instructions on freesurfer website here:
https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalStatistics
So in step2, I ran
recon-all -base template -tp subPRE/subPRE/mri/norm.mgz -tp
subPOST/subPOST/mri/norm.mgz -sd /home/study/sub
then the screen output says "recon-all -s template finished without error"
[note, after this, a folder called "Template" was created in my
subject directory "/home/study/sub", but actually I do not see any MRI
data in there, the total size of this folder is only 336.8KB]
then I ran Step 3 as written in the instruction:
recon-all -long subPRE template -all -sd /home/study/sub
and it gave me an error: "file /home/study/sub/template/base-tps does
not exist!"
which is true since I indeed cannot find this file, but what was the
problem in this process? and what shall I do to solve this problem?
Thanks a lot!!!
-Diane
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--
Dr. Martin Reuter
Assistant Professor of Radiology
Assistant Professor of Neurology
Harvard Medical School
Assistant in Neuroscience
Dept. of Radiology, Massachusetts General Hospital
Dept. of Neurology, Massachusetts General Hospital
Research Affiliate
Computer Science and Artificial Intelligence Lab,
Dept. of Electrical Engineering and Computer Science,
Massachusetts Institute of Technology
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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