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Dear FreeSurfer experts,
I have a raw nifti file created from a stack of DICOM scanner images, let's say it has dimension (162, 172, 188) along the 3 axes. I have also pre-processed this subject in FreeSurfer and have the resulting volume files (e.g., orig.mgz) available.
My question is: For a given voxel in the raw nifti file, how could I find the voxel (or coordinate) in the fsaverage subject that corresponds to this voxel?
I guess this should be a 2 step process: - first get and apply the affine matrix that leads from the raw file to the Freesurfer pre-processed version (which is resampled to dimension (256, 256, 256) among other changes) - then get and apply the matrix that leads from the pre-processed subject to fsaverage
But where exactly can I get these matrices from? I guess the talairach.xfm file and some volume like orig.mgz (using mri_info)?
Best,
Tim
-- Dr. Tim Schäfer Postdoc Computational Neuroimaging Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany
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Freesurfer Wizards, Any thoughts on this? Thanks in advance
## *I renamed:* /usr/local/cuda-8.0/lib64$ sudo cp libcudart.so.8.0 libcudart.so.5.0
*in the next step:* recon-all -i $sub_dir/$i/"$i".nii -all -sd $output_dir $i -use-gpu . . Testing for CUDA device: nvcc: NVIDIA (R) Cuda compiler driver Copyright (c) 2005-2012 NVIDIA Corporation Built on Fri_Sep_21_17:28:58_PDT_2012 Cuda compilation tools, release 5.0, V0.2.1221
Driver : 9.20 Runtime : 8.0
Acquiring CUDA device Using default device CUDA device: TITAN Xp *Segmentation fault * Linux Dond-12 1.25.0-13-generic #36~16.04.1-Ubuntu SMP Wed Aug 15 17:21:05 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s 2 exited with ERRORS at Mi 6. Feb 18:14:50 CET 2019
For more details, see the log file To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
have you seen this description of coordinate systems? https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems
On 2/5/19 11:47 AM, ts+ml@rcmd.org wrote:
External Email - Use CautionDear FreeSurfer experts,
I have a raw nifti file created from a stack of DICOM scanner images, let's say it has dimension (162, 172, 188) along the 3 axes. I have also pre-processed this subject in FreeSurfer and have the resulting volume files (e.g., orig.mgz) available.
My question is: For a given voxel in the raw nifti file, how could I find the voxel (or coordinate) in the fsaverage subject that corresponds to this voxel?
I guess this should be a 2 step process:
- first get and apply the affine matrix that leads from the raw file to the Freesurfer pre-processed version (which is resampled to dimension (256, 256, 256) among other changes)
- then get and apply the matrix that leads from the pre-processed subject to fsaverage
But where exactly can I get these matrices from? I guess the talairach.xfm file and some volume like orig.mgz (using mri_info)?
Best,
Tim
-- Dr. Tim Schäfer Postdoc Computational Neuroimaging Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Dear Douglas,
yes, I'm aware of that page. However conversion from the raw scanner coordinates ("unconformed") in the nifti to the freesurfer subject space ("conformed") does not seem to be mentioned, unless I misunderstand the page.
I guess the first step I want is similar to what the website calls "Scanner RAS", but I do not want it in conformed/orig.mgz space, but unconformed/rawavg.mgz space.
Tim
On February 7, 2019 at 10:14 PM "Greve, Douglas N.,Ph.D." DGREVE@mgh.harvard.edu wrote:
have you seen this description of coordinate systems? https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems
On 2/5/19 11:47 AM, ts+ml@rcmd.org wrote:
External Email - Use CautionDear FreeSurfer experts,
I have a raw nifti file created from a stack of DICOM scanner images, let's say it has dimension (162, 172, 188) along the 3 axes. I have also pre-processed this subject in FreeSurfer and have the resulting volume files (e.g., orig.mgz) available.
My question is: For a given voxel in the raw nifti file, how could I find the voxel (or coordinate) in the fsaverage subject that corresponds to this voxel?
I guess this should be a 2 step process:
- first get and apply the affine matrix that leads from the raw file to the Freesurfer pre-processed version (which is resampled to dimension (256, 256, 256) among other changes)
- then get and apply the matrix that leads from the pre-processed subject to fsaverage
But where exactly can I get these matrices from? I guess the talairach.xfm file and some volume like orig.mgz (using mri_info)?
Best,
Tim
-- Dr. Tim Schäfer Postdoc Computational Neuroimaging Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Greve, Douglas N.,Ph.D. -
Tim Schäfer -
ts+ml＠rcmd.org
-
vin rasa