Hi,
I tried to run longitudinal analysis, I started by reading the LongitudinalTutorial (http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/LongitudinalTutorial) In order to follow the tutorial, I downloaded the longitudinal tutorial dataset (long-tutorial.tar.gz) here http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Data. I uncompressed it in $FREESURFER_HOME/subjects. But I saw some symbolics links, for example:
Mon May 07 user1 /Applications/freesurfer/subjects/long-tutorial =>find . -name "00*.mgz" -type l -ls 16661742 8 lrwxrwxrwx 1 user1 admin 74 Jun 24 2011 ./OAS2_0001_MR1/mri/orig/001.mgz -> /autofs/cluster/freesurfer/test/oasis/origs/OAS2_0001_MR1/mri/orig/001.mgz 16661743 8 lrwxrwxrwx 1 user1 admin 74 Jun 24 2011 ./OAS2_0001_MR1/mri/orig/002.mgz -> /autofs/cluster/freesurfer/test/oasis/origs/OAS2_0001_MR1/mri/orig/002.mgz ... 16678379 8 lrwxrwxrwx 1 user1 admin 74 Jun 24 2011 ./OAS2_0185_MR2/mri/orig/001.mgz -> /autofs/cluster/freesurfer/test/oasis/origs/OAS2_0185_MR2/mri/orig/001.mgz 16678380 8 lrwxrwxrwx 1 user1 admin 74 Jun 24 2011 ./OAS2_0185_MR2/mri/orig/002.mgz -> /autofs/cluster/freesurfer/test/oasis/origs/OAS2_0185_MR2/mri/orig/002.mgz
My problem is that the target files do not exist. Is it a problem in the dataset ? or have I missed a step ?
Thanks. Natacha Beck
you can ignore those missing links. the tutorial should still work.
n.
On Tue, 2012-05-08 at 15:34 +0000, Natacha Beck, Ms wrote:
Hi,
I tried to run longitudinal analysis, I started by reading the LongitudinalTutorial (http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/LongitudinalTutorial) In order to follow the tutorial, I downloaded the longitudinal tutorial dataset (long-tutorial.tar.gz) here http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Data. I uncompressed it in $FREESURFER_HOME/subjects. But I saw some symbolics links, for example:
Mon May 07 user1 /Applications/freesurfer/subjects/long-tutorial =>find . -name "00*.mgz" -type l -ls 16661742 8 lrwxrwxrwx 1 user1 admin 74 Jun 24 2011 ./OAS2_0001_MR1/mri/orig/001.mgz -> /autofs/cluster/freesurfer/test/oasis/origs/OAS2_0001_MR1/mri/orig/001.mgz 16661743 8 lrwxrwxrwx 1 user1 admin 74 Jun 24 2011 ./OAS2_0001_MR1/mri/orig/002.mgz -> /autofs/cluster/freesurfer/test/oasis/origs/OAS2_0001_MR1/mri/orig/002.mgz ... 16678379 8 lrwxrwxrwx 1 user1 admin 74 Jun 24 2011 ./OAS2_0185_MR2/mri/orig/001.mgz -> /autofs/cluster/freesurfer/test/oasis/origs/OAS2_0185_MR2/mri/orig/001.mgz 16678380 8 lrwxrwxrwx 1 user1 admin 74 Jun 24 2011 ./OAS2_0185_MR2/mri/orig/002.mgz -> /autofs/cluster/freesurfer/test/oasis/origs/OAS2_0185_MR2/mri/orig/002.mgz
My problem is that the target files do not exist. Is it a problem in the dataset ? or have I missed a step ?
Thanks. Natacha Beck
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Thank you for your reply,
I try to run the first command
"recon-all -subjid OAS2_0001_MR1 -all"
and I receive the following trace:
Tue May 08 user1 /Applications/freesurfer/subjects/long-tutorial =>recon-all -subjid OAS2_0001_MR1 -all INFO: FreeSurfer build stamps do not match Subject Stamp: freesurfer-Linux-centos4_x86_64-stable-v5.1.0-20110517 Current Stamp: freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0 INFO: SUBJECTS_DIR is /Applications/freesurfer/subjects/long-tutorial Actual FREESURFER_HOME /Applications/freesurfer -rw-r--r-- 1 user1 admin 390840 Jun 24 2011 /Applications/freesurfer/subjects/long-tutorial/OAS2_0001_MR1/scripts/recon-all.log Darwin host.ca 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:33:36 PDT 2011; root:xnu-1504.15.3~1/RELEASE_I386 i386 INFO: current FREESURFER_HOME does not match that of previous processing. Current: /Applications/freesurfer/ Previous: /space/freesurfer/centos4.0_x86_64/stable5 #-------------------------------------------- #@# MotionCor Tue May 8 15:02:39 EDT 2012 Found 2 runs /Applications/freesurfer/subjects/long-tutorial/OAS2_0001_MR1/mri/orig/001.mgz /Applications/freesurfer/subjects/long-tutorial/OAS2_0001_MR1/mri/orig/002.mgz Checking for (invalid) multi-frame inputs... if: Expression Syntax.
Seems like FreeSurfer has a problem with the inputs 001.mgz and 002.mgz because it can't reach them.
Natacha
you do not need to run recon-all -all on the tutorial subjects, as is stated in the tutorial. its already been processed.
On Tue, 2012-05-08 at 19:16 +0000, Natacha Beck, Ms wrote:
Thank you for your reply,
I try to run the first command
"recon-all -subjid OAS2_0001_MR1 -all"
and I receive the following trace:
Tue May 08 user1 /Applications/freesurfer/subjects/long-tutorial =>recon-all -subjid OAS2_0001_MR1 -all INFO: FreeSurfer build stamps do not match Subject Stamp: freesurfer-Linux-centos4_x86_64-stable-v5.1.0-20110517 Current Stamp: freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0 INFO: SUBJECTS_DIR is /Applications/freesurfer/subjects/long-tutorial Actual FREESURFER_HOME /Applications/freesurfer -rw-r--r-- 1 user1 admin 390840 Jun 24 2011 /Applications/freesurfer/subjects/long-tutorial/OAS2_0001_MR1/scripts/recon-all.log Darwin host.ca 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:33:36 PDT 2011; root:xnu-1504.15.3~1/RELEASE_I386 i386 INFO: current FREESURFER_HOME does not match that of previous processing. Current: /Applications/freesurfer/ Previous: /space/freesurfer/centos4.0_x86_64/stable5 #-------------------------------------------- #@# MotionCor Tue May 8 15:02:39 EDT 2012 Found 2 runs /Applications/freesurfer/subjects/long-tutorial/OAS2_0001_MR1/mri/orig/001.mgz /Applications/freesurfer/subjects/long-tutorial/OAS2_0001_MR1/mri/orig/002.mgz Checking for (invalid) multi-frame inputs... if: Expression Syntax.
Seems like FreeSurfer has a problem with the inputs 001.mgz and 002.mgz because it can't reach them.
Natacha
freesurfer@nmr.mgh.harvard.edu
-
Natacha Beck, Ms -
Nick Schmansky