Hi Anna,
that was not my suggestion, I suggested to pass both the cross sectional time point ID and the base id (together with the long flag) and additionally the -localGI flag.
So if you time point 1 is XXX_1 and time point 2 is XXX_2 and your base is XXX_base then
recon-all -long XXX_1 XXX_base -localGI
and for the second time point
recon-all -long XXX_2 XXX_base -localGI
The base is not one of your time points, it gets created in the -base step and you give it a name (here XXX_base). In order for the above to work you need 5 directories per subject:
the 2 cross XXX_1 and XXX_2 the base XXX_base the results of the -long runs: XXX_1.long.XXX_base XXX_2.long.XXX_base
the last two are the ones where the GI will be created.
Best, Martin
On Jul 23, 2014, at 9:02 AM, Anna Jonsson ajonsson09@gmail.com wrote:
hi Martin, I just tried this and it resulted in errors/ Do I not have to specify a flag for the baseid or for each subject, eg -s?
What I did (according to your suggestion)
recon-all -long XXX_1.long XXX_2.long -localGI
This did not work? Do you know why potentially?
On Wed, Mar 26, 2014 at 3:28 PM, Martin Reuter mreuter@nmr.mgh.harvard.edu wrote: Hi Anna,
no, you would still do:
recon-all -long tpid baseid -localGI
just not use the '-all'.
Best, Martin
On 03/26/2014 11:12 AM, Anna Jonsson wrote:
thank you. But if the lnog process has already been done and these induviduals already have long directories so to speak, I would just put the lgi flag on as normal but just replace the subject name with the long subject name eg ? recon-all -s XXXX_long -localGI
Thank you
On Sat, Mar 15, 2014 at 2:07 PM, Martin Reuter mreuter@nmr.mgh.harvard.edu wrote: Hi Anna,
for the image processing, you just add the lgi flag to the regular longitudinal recon-all command recon-all -long …… -lgi
for the analysis after that you use the long directories.
Best, Martin
On Mar 15, 2014, at 10:04 AM, Anna Jonsson ajonsson09@gmail.com wrote:
Dear group,
If I want conduct gyrification analyses on the long runs that have been through the longitudinal stream, do I just perform the "normal" baseline command on the .long data?
thank you,
kind wishes
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Dr. Martin Reuter Assistant in Neuroscience - Massachusetts General Hospital Instructor in Neurology - Harvard Medical School MGH / HMS / MIT
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A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129
Phone: +1-617-724-5652
Email: mreuter@nmr.mgh.harvard.edu reuter@mit.edu Web : http://reuter.mit.edu
--------------------------------- Dr. Martin Reuter 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: mreuter@nmr.mgh.harvard.edu reuter@mit.edu Web : http://reuter.mit.edu