Hello,
I know that we can resume a recon-all command, if it's a cross-sectionnally process. In this case the command is:
recon-all -make all -s subject
But I had a power failure during a longitudinal study, when I try to execute : recon-all -sd . -base 'Test_base_22' -tp 'OAS2_0001_MR1' -tp 'OAS2_0001_MR2'
That's why I would like to resume this command, that's why I tried : recon-all -make all -sd . -s 'Test_base_22'
But I received this error :
ERROR: It appears that this subject ID is an existing base/template from longitudinal processing (-base). Please make sure you pass all necessary flags. For example, if you are trying to re-run a -base:
' -base <templateid> -tp <tpNid> ... '
So I tried this command:
recon-all -make all -sd . -base 'Test_base_22' -tp 'OAS2_0001_MR1' -tp 'OAS2_0001_MR2'
But I received the same error:
Subject Stamp: freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0 Current Stamp: freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0 Subject 'Test_base_22': make all recon-all -s /Users/****/tool_test/FreeSurfer/longi/restart/Test_base_22 -talairach -tal-check
ERROR: It appears that this subject ID is an existing base/template from longitudinal processing (-base). Please make sure you pass all necessary flags. For example, if you are trying to re-run a -base:
' -base <templateid> -tp <tpNid> ... ' make: *** [/Users/****/tool_test/FreeSurfer/longi/restart/Test_base_22/mri/transforms/talairach.auto.xfm] Error 1
Somebody can help me and tell me which command I need to execute.
Natacha
Hi Natacha,
make-all does not work for base and long. The easiest is to delete the base (unless you made edits of course), and rerun the base from scratch.
You can also look at scripts/recon-all.log and see where it stopped, then use flags like -autorecon2 -autorecon3 (or more fine steps) to start from where it left of. Then you also need to pass the -base .. -tp ... stuff.
Best, Martin
(sorry for the late reply, slipped through)
On Tue, 2012-07-03 at 20:06 +0000, Natacha Beck, Ms wrote:
Hello,
I know that we can resume a recon-all command, if it's a cross-sectionnally process. In this case the command is:
recon-all -make all -s subject
But I had a power failure during a longitudinal study, when I try to execute : recon-all -sd . -base 'Test_base_22' -tp 'OAS2_0001_MR1' -tp 'OAS2_0001_MR2'
That's why I would like to resume this command, that's why I tried : recon-all -make all -sd . -s 'Test_base_22'
But I received this error :
ERROR: It appears that this subject ID is an existing base/template from longitudinal processing (-base). Please make sure you pass all necessary flags. For example, if you are trying to re-run a -base:
\' -base <templateid> -tp <tpNid> ... \'So I tried this command:
recon-all -make all -sd . -base 'Test_base_22' -tp 'OAS2_0001_MR1' -tp 'OAS2_0001_MR2'
But I received the same error:
Subject Stamp: freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0 Current Stamp: freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0 Subject 'Test_base_22': make all recon-all -s /Users/****/tool_test/FreeSurfer/longi/restart/Test_base_22 -talairach -tal-check
ERROR: It appears that this subject ID is an existing base/template from longitudinal processing (-base). Please make sure you pass all necessary flags. For example, if you are trying to re-run a -base:
\' -base <templateid> -tp <tpNid> ... \'make: *** [/Users/****/tool_test/FreeSurfer/longi/restart/Test_base_22/mri/transforms/talairach.auto.xfm] Error 1
Somebody can help me and tell me which command I need to execute.
Natacha
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Natacha Beck, Ms