Hi Scott - Sending to the list is always good so that others can find it in the archives when they have similar problems.
Do you specify the .dcm or .mgz file in your dmrirc? Does dwi.nii.gz have the right dimensions/frames?
a.y
On Mon, 12 Dec 2011, Scott Hayes wrote:
Thanks for the prompt response Anastasia--I ran it over the weekend and it worked.
I've subsequently encountered a new issue (copied below from the trac-all.log). The file (dwi.nii.gz) exists in the correct location (it was written there by tracula). I use unpacksdcmdir for unpacking the dicoms, and then point the config file to the appropriate .mgz file, so I'm not doing anything particularly unusual in terms of unpacking or messing w/ the headers (We scan on a Siemens 3T tim trio.) I can send this to the listserv if you prefer. Best, Scott
fslstats -t /Volumes/RAID_4TB/futhink/nc331_recon/dmri/dwi.nii.gz -k /Volumes/RAID_4TB/futhink/nc331_recon/dlabel/diff/White-Matter++.bbr.nii.gz -m -s | awk '{print $1/$2}' > /Volumes/RAID_4TB/futhink/nc331_recon/dmri/dwi_snr.txt ** ERROR (nifti_image_read): failed to find header file for '-t' ** ERROR: nifti_image_open(-t): bad header info Error: failed to open file -t ERROR: Could not open image -t Image Exception : #22 :: Failed to read volume -t terminate called after throwing an instance of 'RBD_COMMON::BaseException'
On Fri, Dec 9, 2011 at 12:44 PM, Anastasia Yendiki ayendiki@nmr.mgh.harvard.edu wrote:
Hi Scott - Here are the tracula executables for snow leopard that we posted in response to that thread:
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/macos-snow-leopard-intel/dmri_5.1_snow_leopard.tar.gz
Let me know if this solves the memory errors.
a.y
On Fri, 9 Dec 2011, Scott Hayes wrote:
Hi Anastasia, I've encountered an error using tracula w/ snow leopard OS that was previously reported on the FS listserv:
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg18829.html
I'm wondering if there is a documented solution available? Recompiling from source code would be beyond my expertise.
David: I'm cc'ing you just as a heads up--all of the workstations in the imaging center run snow leopard OS.
Best, Scott
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