Hello all,
Having a slight issue with recon-all 5.2. For reference, we're using Freesurfer 5.0.0 and trying to use recon-all 5.2 to alleviate some issues with disappearing white matter. I'm wondering if it is necessary to have Freesurfer 5.2 in order for recon-all 5.2 to work properly?
When I say "crash" I mean it runs to completion after 30 seconds. Log files are not revelatory.
best, jon
Hi Jon
we'll need more info than that. Can you send us the recon-all.log?
cheers Bruce
On Mon, 7 Jan 2013, Jonathan Holt wrote:
Hello all,
Having a slight issue with recon-all 5.2. For reference, we're using Freesurfer 5.0.0 and trying to use recon-all 5.2 to alleviate some issues with disappearing white matter. I'm wondering if it is necessary to have Freesurfer 5.2 in order for recon-all 5.2 to work properly?
When I say "crash" I mean it runs to completion after 30 seconds. Log files are not revelatory.
best, jon _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
you can also run it with --debug as the first option. That should be more enlightening On 01/07/2013 01:39 PM, Bruce Fischl wrote:
Hi Jon
we'll need more info than that. Can you send us the recon-all.log?
cheers Bruce
On Mon, 7 Jan 2013, Jonathan Holt wrote:
Hello all,
Having a slight issue with recon-all 5.2. For reference, we're using Freesurfer 5.0.0 and trying to use recon-all 5.2 to alleviate some issues with disappearing white matter. I'm wondering if it is necessary to have Freesurfer 5.2 in order for recon-all 5.2 to work properly?
When I say "crash" I mean it runs to completion after 30 seconds. Log files are not revelatory.
best, jon _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Log file attached. Will try with debug ASAP.
On Jan 7, 2013, at 1:38 PM, Jonathan Holt wrote:
Hello all,
Having a slight issue with recon-all 5.2. For reference, we're using Freesurfer 5.0.0 and trying to use recon-all 5.2 to alleviate some issues with disappearing white matter. I'm wondering if it is necessary to have Freesurfer 5.2 in order for recon-all 5.2 to work properly?
When I say "crash" I mean it runs to completion after 30 seconds. Log files are not revelatory.
best, jon _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Hi Jonathan,
you'll need the full FreeSurfer 5.2 install in order to run the recon-all script from 5.2. Running the 5.2 recon-all script with 5.0 binaries will not work.
Best Martin
On Mon, 2013-01-07 at 13:38 -0500, Jonathan Holt wrote:
Hello all,
Having a slight issue with recon-all 5.2. For reference, we're using Freesurfer 5.0.0 and trying to use recon-all 5.2 to alleviate some issues with disappearing white matter. I'm wondering if it is necessary to have Freesurfer 5.2 in order for recon-all 5.2 to work properly?
When I say "crash" I mean it runs to completion after 30 seconds. Log files are not revelatory.
best, jon _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
This line hidden in the output I think is the reason:
mri_make_uchar: Command not found.
That command was introduced in 5.1, and is used by the talairach stage. As Martin suggests, a separate v5.2 install is necessary.
Nick
On Mon, 2013-01-07 at 15:40 -0500, Martin Reuter wrote:
Hi Jonathan,
you'll need the full FreeSurfer 5.2 install in order to run the recon-all script from 5.2. Running the 5.2 recon-all script with 5.0 binaries will not work.
Best Martin
On Mon, 2013-01-07 at 13:38 -0500, Jonathan Holt wrote:
Hello all,
Having a slight issue with recon-all 5.2. For reference, we're using Freesurfer 5.0.0 and trying to use recon-all 5.2 to alleviate some issues with disappearing white matter. I'm wondering if it is necessary to have Freesurfer 5.2 in order for recon-all 5.2 to work properly?
When I say "crash" I mean it runs to completion after 30 seconds. Log files are not revelatory.
best, jon _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
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Bruce Fischl -
Douglas N Greve -
Jonathan Holt -
Martin Reuter -
Nick Schmansky