External Email - Use Caution
Dear Freesurfer support team,
I noticed that the interpolation setting used within the first few steps of recon-all within the “mri_convert INPUT OUTPUT —conform” is reducing the data quality for data that has a rectangular field of view.
I need to use the `mri_convert` with another flag setting, and I was wondering if there’s a way to smoothly do this. This command is used twice within the recon-all. And I only need to change the second time it is used. The first time is to rename/convert the original file to “mri/orig/001.mgz”, and the second time, is when "/mri/rawavg.mgz “ will be converted to “mri/orig.mgz” using “—conform”. I only need to change the second time it is used, and I need to use the flag “--resample_type cubic “.
Any help is much appreciated
Kind regards, Jeiran
Jeiran Choupan, PhD, MSCS
Assistant Professor of Research Neurology Laboratory of Neuro Imaging USC Stevens Neuroimaging and Informatics Institute Keck School of Medicine University of Southern California
2025 Zonal Ave, Los Angeles, CA 90033, USA (323) 44-BRAIN
[image001.png] [image002.png]
External Email - Use Caution
Dear Freesurfer support team,
I noticed that the interpolation setting used within the first few steps of recon-all within the “mri_convert INPUT OUTPUT —conform” is reducing the data quality for data that has a rectangular field of view.
I need to use the `mri_convert` with another flag setting, and I was wondering if there’s a way to smoothly do this. This command is used twice within the recon-all. And I only need to change the second time it is used. The first time is to rename/convert the original file to “mri/orig/001.mgz”, and the second time, is when "/mri/rawavg.mgz “ will be converted to “mri/orig.mgz” using “—conform”. I only need to change the second time it is used, and I need to use the flag “--resample_type cubic “.
Any help is much appreciated
Kind regards, Jeiran
Jeiran Choupan, PhD, MSCS
Assistant Professor of Research Neurology Laboratory of Neuro Imaging USC Stevens Neuroimaging and Informatics Institute Keck School of Medicine University of Southern California
2025 Zonal Ave, Los Angeles, CA 90033, USA (323) 44-BRAIN
[image001.png] [image002.png]
On Aug 15, 2024, at 11:15 AM, Jeiran Choupan choupan@usc.edu wrote:
Dear Freesurfer support team,
I noticed that the interpolation setting used within the first few steps of recon-all within the “mri_convert INPUT OUTPUT —conform” is reducing the data quality for data that has a rectangular field of view.
I need to use the `mri_convert` with another flag setting, and I was wondering if there’s a way to smoothly do this. This command is used twice within the recon-all. And I only need to change the second time it is used. The first time is to rename/convert the original file to “mri/orig/001.mgz”, and the second time, is when "/mri/rawavg.mgz “ will be converted to “mri/orig.mgz” using “—conform”. I only need to change the second time it is used, and I need to use the flag “--resample_type cubic “.
Any help is much appreciated
Kind regards, Jeiran
Jeiran Choupan, PhD, MSCS
Assistant Professor of Research Neurology Laboratory of Neuro Imaging USC Stevens Neuroimaging and Informatics Institute Keck School of Medicine University of Southern California
2025 Zonal Ave, Los Angeles, CA 90033, USA (323) 44-BRAIN
<image001.png> <image002.png>
You can add -cubic to the recon-all command line (though you might get cubic at other times, but that probably won't hurt)
On 8/19/2024 1:40 PM, Jeiran Choupan wrote:
External Email - Use Caution
Dear Freesurfer support team,
I noticed that the interpolation setting used within the first few steps of recon-all within the “mri_convert INPUT OUTPUT —conform” is reducing the data quality for data that has a rectangular field of view.
I need to use the `mri_convert` with another flag setting, and I was wondering if there’s a way to smoothly do this. This command is used twice within the recon-all. And I only need to change the second time it is used. The first time is to rename/convert the original file to “mri/orig/001.mgz”, and the second time, is when "/mri/rawavg.mgz “ will be converted to “mri/orig.mgz” using “—conform”. I only need to change the second time it is used, and I need to use the flag “--resample_type cubic “.
Any help is much appreciated
Kind regards, Jeiran
Jeiran Choupan, PhD, MSCS
Assistant Professor of Research Neurology Laboratory of Neuro Imaging USC Stevens Neuroimaging and Informatics Institute Keck School of Medicine University of Southern California
2025 Zonal Ave, Los Angeles, CA 90033, USA (323) 44-BRAIN
image001.pngimage002.png
On Aug 15, 2024, at 11:15 AM, Jeiran Choupan choupan@usc.edu wrote:
Dear Freesurfer support team,
I noticed that the interpolation setting used within the first few steps of recon-all within the “mri_convert INPUT OUTPUT —conform” is reducing the data quality for data that has a rectangular field of view.
I need to use the `mri_convert` with another flag setting, and I was wondering if there’s a way to smoothly do this. This command is used twice within the recon-all. And I only need to change the second time it is used. The first time is to rename/convert the original file to “mri/orig/001.mgz”, and the second time, is when "/mri/rawavg.mgz “ will be converted to “mri/orig.mgz” using “—conform”. I only need to change the second time it is used, and I need to use the flag “--resample_type cubic “.
Any help is much appreciated
Kind regards, Jeiran
Jeiran Choupan, PhD, MSCS
Assistant Professor of Research Neurology Laboratory of Neuro Imaging USC Stevens Neuroimaging and Informatics Institute Keck School of Medicine University of Southern California
2025 Zonal Ave, Los Angeles, CA 90033, USA (323) 44-BRAIN
<image001.png><image002.png>
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