Hi Koushik,
there seems to be a bug. There's a safety check (that usually makes
sense) but when adding a tp, of course it is not yet contained in the base.
Fix it by:
For Version 5.3 change the line 6148 in recon-all from
if ( ! $found_tpNid ) then
to
if ( ! $found_tpNid && ! $DoAddTp ) then
for 5.1 change line 5407 from
if ($status) then
to
if ( $status && ! $DoAddTp ) then
Good luck, Martin
On 03/19/2014 12:56 PM, Govindarajan, Koushik Athreya wrote:
Hi Martin,
I use version 5.1. I did try this with version 5.3 also but I end
up with the same error:
recon-all --long 23061_ip cr096_base --addtp --all
ERROR: 23061_ip is not in
/home/koushikg/data/longitudinal/cr096_base/base-tps
Thanks
Koushik
*From:*freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] *On Behalf Of *Martin
Reuter
*Sent:* Wednesday, March 19, 2014 11:21 AM
*To:* Govindarajan, Koushik Athreya; freesurfer@nmr.mgh.harvard.edu
*Subject:* Re: [Freesurfer] adding time points to longitudinal base
template {Disarmed}
Hi Koushik,
What version are you using? Not sure when we added this, maybe in 5.2.
So you would need 5.3 for it.
If you use 5.3 already, can you send me the exact command and output.
Thanks, Martin
On 03/19/2014 11:50 AM, Govindarajan, Koushik Athreya wrote:
Hi Martin,
I tried this method of --addtp to add a new time point but
recon-all failed with the message saying my new timepoint was not
in the 'base-tps' file of the base template. Should I be doing
something else before I run this step?
Thanks
Koushik
*From:*Martin Reuter [mailto:mreu...@nmr.mgh.harvard.edu]
*Sent:* Friday, March 14, 2014 9:31 AM
*To:* Govindarajan, Koushik Athreya;
freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>
*Subject:* Re: [Freesurfer] adding time points to longitudinal
base template
Hi Koushik,
there is a way to add time points without recreating the base:
recon-all -long <tpNsubjid> <longbasesubjid> -addtp -all
This is what the recon-all help says about that:
"If a new timepoint needs to be added to a longitudinal run where
a base subject
has already been created (from prior timepoints), then the -addtp
command
can be added to the -long command in order to 'fix-up' the
longitudinal
stream to accept the new timepoint. Note that the base subject is
*not*
recomputed using the new timepoint. This potentially introduces a
bias, and it
is recommended to NOT add a time point this way! Instead recreate
the base
from all time points and run all longitudinals again."
So it's up to you. But given you already have 5 time points in
your base and add only 1, you may be fine. The base should be
pretty stable with 5 and if the 6th is not too different, it
should not matter much. I don't think anyone has ever done a
thorough analysis about adding time points.
Best, Martin
On 03/11/2014 10:08 AM, Govindarajan, Koushik Athreya wrote:
Dear FS experts,
I have a serial study in which I have run
cross-sectional and longitudinal analysis on 5 time points.
Now, I want to add a 6^th time point to my dataset. Do I have
to rerun my base template creation step from scratch or is
there a way to just add further time points to an existing
template?
Thanks
Koushik
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Instructor in 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
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