Hi Bruce,

They have the same geometry, but didn't have the same center (128 128 128 vs 128 118 72). I guess freeview doesn't not show this difference, or handle it in a different way than mris_calc. Nevertheless, when both volumes have the same center (mri_convert -oc 0 0 0), the mris_calc -o out.mgz binF2.mgz mul binF1.mgz gives the correct and expected result. Should have checked this earlier, but I have been lured by the overlay in freeview.

@ Rudolph : "problem" solved. I didn't express myself correctly, sorry about that. The content of binF1 and binF2 were absolutely not modified, the input volume was "shifted" (see why below) so that the resulting volume was different from what we expected when seeing the overlay in freeview.

Best,

Christopher

On 12.10.2012 16:57, Bruce Fischl wrote:

Hi Christophe

what does mri_info tell you about them? Are they the same geometry? Bruce On Fri, 12 Oct 2012, Christopher Coello wrote:

...

Dear Freesurfer community,

Using freeview, I can visualize that two binary volumes are overlaying in some parts. freeview -v binF1.mgz -v binF2.mgz

When using the command mris_calc -o out.mgz binF1.mgz mul binF2.mgz to create the intersection of these two volumes, I obtain a file with only zeros. To debug, I added the two volumes mris_calc -o out.mgz binF1.mgz add binF2.mgz I was surprise to see that one of the volumes (binF1) is shifted of tens of voxels along an axis. When doing mris_calc -o out.mgz binF2.mgz add binF1.mgz, the binF2 is shifted.

Is that a bug ?

mris_calc : v.1.37.2.4 2011/04/04 freeview : v1.0 2011/05/22

Best,

Christopher

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Hi Jeff, use -run 9 instead of -run 009 doug

On 10/12/2012 10:58 AM, jwaugh@nmr.mgh.harvard.edu wrote:

Dear Freesurfer community,

I am using the unpacksdcmdir command as part of a DTI analysis in stable51:

unpacksdcmdir -src /space/archive/60/siemens/Allegra-20401-20051011-143458-528000 -targ ./ -run 009 dti NII CD_cerv_ctrl2_sess2_dti.nii -unpackerr

and am getting the following error:

ERROR: nthRun=1 has an invalid run number (009) Input does not exist or is not in a supported format

I have gone back to the original unpacking steps and confirmed that 009 is the correct run number, and that the path to -src is correct. Running identically structured commands on other subjects in the group has completed without errors.

Have you encountered this error, and do you know how I can correct it?

Thank you!

Jeff


Jeff Waugh, MD/PhD
Fellow in Pediatric Movement Disorders, PGY-6
Massachusetts General Hospital / Boston Children's Hospital / Harvard

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