Thanks Martin, I tried that on version 5.1 and it worked.
Regards Koushik
From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Martin Reuter Sent: Tuesday, March 25, 2014 9:55 AM To: Govindarajan, Koushik Athreya; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] adding time points to longitudinal base template {Disarmed} {Disarmed}
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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@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.edumailto: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:mreuter@nmr.mgh.harvard.edu] Sent: Friday, March 14, 2014 9:31 AM To: Govindarajan, Koushik Athreya; freesurfer@nmr.mgh.harvard.edumailto: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 6th 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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