Hello When I run the mri_preproc command I am getting the message ERROR: cannot find fsaverage in /space/barlab_002/users/cibu/dep_LGI But the fsaverage folder is in the path and subjects_dir is set correctly. So I am not sure what's wrong with the command Here's the command I am trying to run
mris_preproc --fsgd lgi_N32_Dep_Ctrl_Age_BDI.fsgd --target fsaverage -- hemi lh --meas lgi --out N32_lgi_dep_ctrl_Age_BDI_lh.mgh
Any help would be greatly appreciated
Thankyou Cibu Thomas
Hi Cibu,
can you provide more informations using bugr command? also log file?
Hello When I run the mri_preproc command I am getting the message ERROR: cannot find fsaverage in /space/barlab_002/users/cibu/dep_LGI But the fsaverage folder is in the path and subjects_dir is set correctly. So I am not sure what's wrong with the command Here's the command I am trying to run
mris_preproc --fsgd lgi_N32_Dep_Ctrl_Age_BDI.fsgd --target fsaverage -- hemi lh --meas lgi --out N32_lgi_dep_ctrl_Age_BDI_lh.mgh
Any help would be greatly appreciated
Thankyou Cibu Thomas
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Pratap See below for bugr info and I have attached the log file. I assumed you were asking for surfer.log. Let me know if it some other log file.
Thank you Cibu ---------------------------------------------------------------------
FREESURFER_HOME: /usr/local/freesurfer/stable4
Build stamp: freesurfer-Linux-centos4_x86_64-stable-v4.0.5-20080918
RedHat release: CentOS release 4.2 (Final)
Kernel info: Linux 2.6.9-22.0.2.106.unsupported x86_64
NMR Center info (/space/freesurfer exists):
machine: snapjudge
SUBJECTS_DIR: /space/barlab/5/users/mark/subjects_depMOCS_V4/
PWD: /autofs/space/barlab_002/users/cibu/dep_LGI
--------------------------------------------------------------------- Please include the following additional information in your report:
1) subject name 2) the entire command-line executed 3) the error message generated 4) optionally include the subject's /script/recon-all.log
See also: http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
On Thu, 2008-09-18 at 10:46 -0400, Pratap Kunwar wrote:
Hi Cibu,
can you provide more informations using bugr command? also log file?
Hello When I run the mri_preproc command I am getting the message ERROR: cannot find fsaverage in /space/barlab_002/users/cibu/dep_LGI But the fsaverage folder is in the path and subjects_dir is set correctly. So I am not sure what's wrong with the command Here's the command I am trying to run
mris_preproc --fsgd lgi_N32_Dep_Ctrl_Age_BDI.fsgd --target fsaverage -- hemi lh --meas lgi --out N32_lgi_dep_ctrl_Age_BDI_lh.mgh
Any help would be greatly appreciated
Thankyou Cibu Thomas
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
/space/barlab_002/users/cibu/dep_LGI does not exist
Cibu Thomas wrote:
Hello When I run the mri_preproc command I am getting the message ERROR: cannot find fsaverage in /space/barlab_002/users/cibu/dep_LGI But the fsaverage folder is in the path and subjects_dir is set correctly. So I am not sure what's wrong with the command Here's the command I am trying to run
mris_preproc --fsgd lgi_N32_Dep_Ctrl_Age_BDI.fsgd --target fsaverage -- hemi lh --meas lgi --out N32_lgi_dep_ctrl_Age_BDI_lh.mgh
Any help would be greatly appreciated
Thankyou Cibu Thomas
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
That's strange. The directory does exist. If I check pwd that's what I get. barlab_002 refers to a volume. So I changed the path to /space/barlab/2/users/cibu/dep_LGI and now it doesn't seem to have problems with the fsaverage
Thanks Doug
- Cibu
-----Original Message----- From: Doug Greve [mailto:greve@nmr.mgh.harvard.edu] Sent: Thursday, September 18, 2008 11:22 AM To: Cibu Thomas Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_preproc
/space/barlab_002/users/cibu/dep_LGI does not exist
Cibu Thomas wrote:
Hello When I run the mri_preproc command I am getting the message ERROR: cannot find fsaverage in /space/barlab_002/users/cibu/dep_LGI But the fsaverage folder is in the path and subjects_dir is set correctly. So I am not sure what's wrong with the command Here's the command I am trying to run
mris_preproc --fsgd lgi_N32_Dep_Ctrl_Age_BDI.fsgd --target fsaverage -- hemi lh --meas lgi --out N32_lgi_dep_ctrl_Age_BDI_lh.mgh
Any help would be greatly appreciated
Thankyou Cibu Thomas
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
I do get /autofs see below [snapjudge:dep_LGI] (nmr-std-env) pwd /autofs/space/barlab_002/users/cibu/dep_LGI
But I changed source directory to /autofs/space/barlab/2/users/cibu/dep_LGI
and as pratap pointed out ?h.lgi does not exist I changed it to ?h.pial_lgi and things are working fine I am a newbie to FS. Many thanks for helping with this Doug, Pratap
- Cibu
On Thu, 2008-09-18 at 11:22 -0400, Doug Greve wrote:
/space/barlab_002/users/cibu/dep_LGI does not exist
Cibu Thomas wrote:
Hello When I run the mri_preproc command I am getting the message ERROR: cannot find fsaverage in /space/barlab_002/users/cibu/dep_LGI But the fsaverage folder is in the path and subjects_dir is set correctly. So I am not sure what's wrong with the command Here's the command I am trying to run
mris_preproc --fsgd lgi_N32_Dep_Ctrl_Age_BDI.fsgd --target fsaverage -- hemi lh --meas lgi --out N32_lgi_dep_ctrl_Age_BDI_lh.mgh
Any help would be greatly appreciated
Thankyou Cibu Thomas
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu