[Freesurfer] mri_convert problem

Hi, I'm trying to run mri_convert to convert CT dicoms into nifti format but I keep getting the following error: [multnomah:CT] (nmr-std-env) mri_convert -i 1.2.840.10008.5.1.4.1.22342498128.100.dcm -o ct.nii mri_convert -i 1.2.840.10008.5.1.4.1.22342498128.100.dcm -o ct.nii file not found or

[Freesurfer] SPM coreg error

While trying to coregister a ct.nii and a orig.mgz file using the following command: spmregister --s SUBJECT --mov ct.nii --reg spm.reg.dat --fsvol orig I get the following error: >> >> >> ERROR: spm_coreg >> ??? Undefined function or variable 'x'. >> Finished after 0.023302 sec >> >> Parameter

[Freesurfer] SPM coreg error

Hi, I'm getting an error trying to coregister a ct.nii and a orig.mgz file. The subjects directory is: /autofs/space/multnomah_002/users/Cashlab/BW10 Working directory: /autofs/space/multnomah_002/users/Cashlab/BW10/BW10_Pre_Op_MRI "which spmregister" outputs this: /usr/local/freesurfer/sta

[Freesurfer] Recon error

Hi, I'm getting an error trying to run a reconstruction. I'm working on multnomah and my subjects directory is: /autofs/space/multnomah_002/users/Cashlab/ I'm using the following command: [multnomah:Cashlab] (nmr-std-env) recon-all -autorecon1 -autorecon2 -subject MG25_SurferOutput -i MG25/MR

Re: [Freesurfer] Recon error

able to handle that recon, I've run many recons there and never had this problem. Thank you! Rodrigo On Wed, Aug 26, 2009 at 1:34 PM, Douglas N Greve wrote: > Looks like that is a pretty weak computer. Can you run it on a stronger > computer? > > Rodrigo Zepeda wrote: > >&g

[Freesurfer] LGI error

Hello, I'm getting an error running a LGI compute. I'm working on multnomah on the directory: /autofs/space/multnomah_002/users/Cashlab/MG07 I'm using the following command line: [multnomah:MG07] (nmr-std-env) mris_compute_lgi --i lh.pial --close_sphere_size 30 --smooth_iters 60 I'm getting

[Freesurfer] Recon error: Talairach Failure Detection

s/inverse/subjects MNI_DIR /usr/local/freesurfer/stable4/mni FSL_DIR /usr/pubsw/packages/fsl/current Any help will be appreciated! Thanks, Rodrigo Zepeda ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.n

[Freesurfer] recon-all now taking too long

Hi, I have noticed that recently recon-all is taking a lot longer than usual to finish. It used to take around 30 to 48 hours, but the last couple that I have done are taking a whole week. It seems to get stuck in a repetitive step and it numbers each iteration like this: not handling expand