Hi all,
We are trying to run exactly the same analysis, particularly the recon-all command, from two different directories. We've found that both directories have '/fsaverage' but that they are sourcing two different links/paths. Why is this and is there a difference in how analysis will be run/processed? The two directories in question are :
/autofs/cluster/ablood/1/miriam/SD_recons AND /autofs/cluster/ablood/1/R01_Botox/R01BTX_recons
We have been running everything in /R01BTX_recons, so we want this to be the model.
I found out that: /autofs/cluster/ablood/1/miriam/SD_recons
already has an fsaverage directory
The difference between the fsaverage directories in /autofs/cluster/ablood/1/miriam/SD_recons AND /autofs/cluster/ablood/1/R01_Botox/R01BTX_recons
Are the following: fsaverage in /autofs/cluster/ablood/1/miriam/SD_recons points to: fsaverage -> /usr/local/freesurfer/stable5_1_0/subjects/fsaverage
and more specifically when I cd fsaverage from /autofs/cluster/ablood/1/miriam/SD_recons the pwd is: /autofs/cluster/freesurfer/centos4.0_x86_64/stable5_1_0/subjects/fsaverage
Whereas: fsaverage in /autofs/cluster/ablood/1/R01_Botox/R01BTX_recons points to: fsaverage -> /usr/local/freesurfer/stable5/subjects/fsaverage
and more specifically when I cd fsaverage from /autofs/cluster/ablood/1/R01_Botox/R01BTX_recons the pwd is: /autofs/cluster/freesurfer/centos4.0_x86_64/stable5/subjects/fsaverage
Not sure if: 1. there is a significant difference between these fsaverages and if we need to be using exactly the same fsaverage in /autofs/cluster/ablood/1/miriam/SD_recons as in /autofs/cluster/ablood/1/R01_Botox/R01BTX_recons?
Thank you!
Sandra
sandra,
the two fsaverage's that you are using are the same. you can change one of the links to point at the other if you prefer, or continue to use it as-is. it will not affect the results.
n.
On Tue, 2012-01-10 at 15:10 -0500, swoodman@nmr.mgh.harvard.edu wrote:
Hi all,
We are trying to run exactly the same analysis, particularly the recon-all command, from two different directories. We've found that both directories have '/fsaverage' but that they are sourcing two different links/paths. Why is this and is there a difference in how analysis will be run/processed? The two directories in question are :
/autofs/cluster/ablood/1/miriam/SD_recons AND /autofs/cluster/ablood/1/R01_Botox/R01BTX_recons
We have been running everything in /R01BTX_recons, so we want this to be the model.
I found out that: /autofs/cluster/ablood/1/miriam/SD_recons
already has an fsaverage directory
The difference between the fsaverage directories in /autofs/cluster/ablood/1/miriam/SD_recons AND /autofs/cluster/ablood/1/R01_Botox/R01BTX_recons
Are the following: fsaverage in /autofs/cluster/ablood/1/miriam/SD_recons points to: fsaverage -> /usr/local/freesurfer/stable5_1_0/subjects/fsaverage
and more specifically when I cd fsaverage from /autofs/cluster/ablood/1/miriam/SD_recons the pwd is: /autofs/cluster/freesurfer/centos4.0_x86_64/stable5_1_0/subjects/fsaverage
Whereas: fsaverage in /autofs/cluster/ablood/1/R01_Botox/R01BTX_recons points to: fsaverage -> /usr/local/freesurfer/stable5/subjects/fsaverage
and more specifically when I cd fsaverage from /autofs/cluster/ablood/1/R01_Botox/R01BTX_recons the pwd is: /autofs/cluster/freesurfer/centos4.0_x86_64/stable5/subjects/fsaverage
Not sure if:
- there is a significant difference between these fsaverages and if we
need to be using exactly the same fsaverage in /autofs/cluster/ablood/1/miriam/SD_recons as in /autofs/cluster/ablood/1/R01_Botox/R01BTX_recons?
Thank you!
Sandra
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Thank you!
sandra,
the two fsaverage's that you are using are the same. you can change one of the links to point at the other if you prefer, or continue to use it as-is. it will not affect the results.
n.
On Tue, 2012-01-10 at 15:10 -0500, swoodman@nmr.mgh.harvard.edu wrote:
Hi all,
We are trying to run exactly the same analysis, particularly the recon-all command, from two different directories. We've found that both directories have '/fsaverage' but that they are sourcing two different links/paths. Why is this and is there a difference in how analysis will be run/processed? The two directories in question are :
/autofs/cluster/ablood/1/miriam/SD_recons AND /autofs/cluster/ablood/1/R01_Botox/R01BTX_recons
We have been running everything in /R01BTX_recons, so we want this to be the model.
I found out that: /autofs/cluster/ablood/1/miriam/SD_recons
already has an fsaverage directory
The difference between the fsaverage directories in /autofs/cluster/ablood/1/miriam/SD_recons AND /autofs/cluster/ablood/1/R01_Botox/R01BTX_recons
Are the following: fsaverage in /autofs/cluster/ablood/1/miriam/SD_recons points to: fsaverage -> /usr/local/freesurfer/stable5_1_0/subjects/fsaverage
and more specifically when I cd fsaverage from /autofs/cluster/ablood/1/miriam/SD_recons the pwd is: /autofs/cluster/freesurfer/centos4.0_x86_64/stable5_1_0/subjects/fsaverage
Whereas: fsaverage in /autofs/cluster/ablood/1/R01_Botox/R01BTX_recons points to: fsaverage -> /usr/local/freesurfer/stable5/subjects/fsaverage
and more specifically when I cd fsaverage from /autofs/cluster/ablood/1/R01_Botox/R01BTX_recons the pwd is: /autofs/cluster/freesurfer/centos4.0_x86_64/stable5/subjects/fsaverage
Not sure if:
- there is a significant difference between these fsaverages and if we
need to be using exactly the same fsaverage in /autofs/cluster/ablood/1/miriam/SD_recons as in /autofs/cluster/ablood/1/R01_Botox/R01BTX_recons?
Thank you!
Sandra
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Nick Schmansky -
swoodman＠nmr.mgh.harvard.edu