Brian,
When you specify a subject name, it will create the folder for you. You command string below is failing because it includes the characters ... If you eliminate those, it will create a subject named Sub1 (although I would give it a name with the letters 'base' in it).
Nick
On Mon, 2009-09-28 at 16:35 -0400, Weisinger, Brian (NIH/OD) [E] wrote:
Do I create a folder where the subjects are and then put that name in place of baseid?
I created a folder named Sub1 in the subjects folder with all the other scans and tried it but it gave me this
brianweisinger$ recon-all -base Sub1 -tp 00308 -tp 01150 ... -allERROR: Flag ... unrecognized. -base Sub1 -tp 00308 -tp 01150 ... -all Darwin CHP-MP2.local 9.8.0 Darwin Kernel Version 9.8.0: Wed Jul 15 16:55:01 PDT 2009; root:xnu-1228.15.4~1/RELEASE_I386 i386
recon-all exited with ERRORS at Mon Sep 28 16:33:07 EDT 2009
Any ideas?
On 9/28/09 4:25 PM, "Nick Schmansky" nicks@nmr.mgh.harvard.edu wrote:
Brian,
You decide on the name. It is a new subject composed of data from tp1id and tp2id. Once that 'base' subject is created, then you run your longitudinal analysis against that base:
recon-all -long tp1id baseid -all recon-all -long tp2id baseid -all
then compare tp1id.long.baseid to tp2id.long.baseid.
See:
http://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalProcessing
Nick
On Mon, 2009-09-28 at 16:08 -0400, Weisinger, Brian (NIH/OD) [E] wrote:
I am trying to run a longitudinal stream and I have already run all the scans through recon all already. I am on the second step
- "-base" create the base template and process it cross sectionally:
recon-all -base <baseid> -tp <tp1id> -tp <tp2id> ... -all
Where do I find the baseid to put in the <baseid> spot?
Thanks in advance for any help with this.
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