BTW, you should be able to
setenv UNPACK_MGH_DTI 0
to force it to ignore the gradient tables.
doug
Steven Swinford wrote:
Hi Doug,
This unsetenv step only works with stable4. In stable5 it still throws the:
ERROR: cannot open /usr/local/freesurfer/stable5/diffusion/mgh-dti-seqpack/gradient_mgh_dti06.gdt
My mri_convert is called as a subscript of a larger process that I am trying to run, and I need to use a newer version of freesurfer to access commands like flip4fsl.
I think I need a more permanent solution. Is there a way to directly feed mri_convert the gradient_mgh_dti6.gdt? Or could you make a copy of the gradient_mgh_dti6.gdt file named gradient_mgh_dti06.gdt in the stable5 directory?
I'm up for any other ideas, too. Please let me know if you need more information.
Thanks,
Steven
On Mon, 27 Sep 2010, Douglas N Greve wrote:
I'm surprised that it is actually failing. Does it produce an output volume? Before running mri_convert, try running
unsetenv UNPACK_MGH_DTI
This won't copy the gradient table into the output, but now that you know where it is, you can copy it yourself:).
doug
Steven Swinford wrote:
The contents are identical, but the mri_convert appears to call for a file with a leading zero and fails to find the stable5 file.
Here is more of the output:
. . . 53 ep_b700#3 700.000000 3 54 ep_b700#4 700.000000 4 55 ep_b700#5 700.000000 5 bValue = 700 nB0 = 1 nDir = 6 GradFile /usr/local/freesurfer/stable5/diffusion/mgh-dti-seqpack/gradient_mgh_dti06.gdt
ERROR: cannot open /usr/local/freesurfer/stable5/diffusion/mgh-dti-seqpack/gradient_mgh_dti06.gdt
There was an error when tyring to load the gradient directions If you 'setenv UNPACK_MGH_DTI 0', it will not attempt to load the gradients
Here is the command that I ran:
mri_convert /space/solo/4/users/dcm//COBA63/cdrom/01151727/36435607 /cluster/cagn/1/users/SRT_fcMRI/COBA63//diffusion/006/diffusion_highres-vb17.6.mgz
--sdcmlist /cluster/cagn/1/users/SRT_fcMRI/COBA63//diffusion/006/flf -ot mgz --nspmzeropad 3 --in_type siemens_dicom
And here is the environment:
FREESURFER_HOME: /usr/local/freesurfer/stable5
Build stamp: freesurfer-Linux-centos4_x86_64-stable-v5.0.0-20100923
RedHat release: CentOS release 5.5 (Final)
Kernel info: Linux 2.6.18-194.8.1.el5 x86_64
NMR Center info (/space/freesurfer exists):
machine: yaddle
SUBJECTS_DIR: /cluster/cagn/1/users/SRT_fcMRI
PWD: /cluster/cagn/1/users/SRT_fcMRI
ssh yaddle setenv SUBJECTS_DIR /cluster/cagn/1/users/SRT_fcMRI cd /cluster/cagn/1/users/SRT_fcMRI
Thanks for your help,
Steven
On Mon, 27 Sep 2010, Douglas N Greve wrote:
You can check whether they are different by looking at them in a
text > viewer (emacs, vi, wordpad, less, more, cat) or by running the unix diff > command on them.
doug Steven Swinford wrote: Hi FreeSurfer gurus,
> I'm trying to run a diffusion analysis on some old scans
and am > > running
into this error during mri_convert:
> ERROR: cannot open
/usr/local/freesurfer/stable5/diffusion/mgh-dti-seqpack/gradient_mgh_dti06.gdt
> > > I noticed that stable4 has the GradFile with this
naming convention, > > but
stable5 only has a GradFile that omits the leading 0.
usr/local/freesurfer/stable5/diffusion/mgh-dti-seqpack/gradient_mgh_dti6.gdt
> > > Are these the same GradFiles? Is there a way run these
old scans > > through
stable5 without this error?
> Thanks for your help, > Steven
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