Re: [Freesurfer] recon-all -localGI with longitudinal pipeline output

Hi Mihaela,

probably you are trying to run the localGI on a longitudinal directory. As the help text output says, you need to make sure you tell that to recon-al by passing the original command again (including the -long ….) and instead of -all you specify -localGI.

Renaming hides from recon-all that this is a longitudinal run. It may work for this specific case (localGI) but not necessarily for other flags. So when touch a longitudinal directory always specify the full recon-al command with -long timepoint and base id.

Best, Martin

On 27 Jan 2017, at 21:01, Mihaela Stefan mikaelastephan@gmail.com wrote:

Hello FreeSurfers,

I am trying to run recon-all -s <subjID> -localGI on a longitudinal dataset but I get this error:

ERROR: Are you trying to run or re-run a longitudinal time point? If so, please specify the following parameters:

   \' -long <tpNid> <templateid> \'

   where <tpNid> is the time point id (SAME as cross sectional
   ID) and <templateid> is the ID created in the -base run.
   The directory <tpNid>.long.<templateid> will be created
   automatically or used for output, if it already exists.

Do I really need these if I want to run -localGI or for some reason recon-all thinks that I am trying to re-run the longitudinal pipeline? I renamed the folder replacing "long" (e.g. OAS2_0001_MR1.new.OAS2_0001 instead of OAS2_0001_MR1.long.OAS2_0001 ) and recon-all -localGI seems to work.

Is there a better way to do this?

Thanks! Mihaela _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer