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Dear Freesurfers,
I am attempting to run the full reconstruction in Freesurfer on several hundred patient images with diseased areas of the brain.
Without skipping any steps of the analysis chain, I am able to complete the full reconstruction for about 50% of said patients. When the analysis is able to complete, the disease sites are generally not included in the white or gray segmentation labels, which is ideal for my use case. However, when the disease is far from the cortical surface, it generally results in a large topological defect. (In other cases, the Talairach check fails.) I would like to know, does it really make sense to try to analyze the images with a "real" topological defect, and if so, how to accomplish it?
I have tried to run the reconstruction with flags "-nofix" and "-notal-check" to accept an imperfect Talairach transform and avoid crashes trying to fix these unfixable topological defects. Unfortunately, the step "mris_autodet_gwstats" which comes after "mris_sphere", seems to look for a file "surf/lh.orig.premesh" which is not found, causing a crash. From what I can understand, that file is produced by the so-called old topology fix [1], so it would imply that a full analysis chain is not supported if you eschew topology-fixing. Is this a feature, or do you recommend modifying the logic of the script to work around it? This is as far as I got, but I suppose there may be steps later in the analysis chain that will also look for files only produced if the topology fix runs.
For your information, I am currently using the nightly build from February 12 for CentOS7, and I am amenable to switching to an older or newer build. Thank you for taking the time to help me.
Best regards,
Dylan Hsu, Ph.D
Memorial Sloan-Kettering Cancer Center
[1] https://github.com/freesurfer/freesurfer/tree/dev/scripts#L3128-L3139 https://github.com/freesurfer/freesurfer/blob/6044b3df08de93c15e4b44807349f2...
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Hi Dylan
I think you could probably do a recon without topology fixing although of course the spherical mapping will then be multi-valued. It will take a bit of hacking at recon-all to get it to work though as it is not a use-case that we explicitly support.
cheers Bruce On Thu, 27 Feb 2020, HsuD3@mskcc.org wrote:
External Email - Use Caution
Dear Freesurfers,
I am attempting to run the full reconstruction in Freesurfer on several hundred patient images with diseased areas of the brain.
Without skipping any steps of the analysis chain, I am able to complete the full reconstruction for about 50% of said patients. When the analysis is able to complete, the disease sites are generally not included in the white or gray segmentation labels, which is ideal for my use case. However, when the disease is far from the cortical surface, it generally results in a large topological defect. (In other cases, the Talairach check fails.) I would like to know, does it really make sense to try to analyze the images with a "real" topological defect, and if so, how to accomplish it?
I have tried to run the reconstruction with flags "-nofix" and "-notal-check" to accept an imperfect Talairach transform and avoid crashes trying to fix these unfixable topological defects. Unfortunately, the step "mris_autodet_gwstats" which comes after "mris_sphere", seems to look for a file "surf/lh.orig.premesh" which is not found, causing a crash. From what I can understand, that file is produced by the so-called old topology fix [1], so it would imply that a full analysis chain is not supported if you eschew topology-fixing. Is this a feature, or do you recommend modifying the logic of the script to work around it? This is as far as I got, but I suppose there may be steps later in the analysis chain that will also look for files only produced if the topology fix runs.
For your information, I am currently using the nightly build from February 12 for CentOS7, and I am amenable to switching to an older or newer build. Thank you for taking the time to help me.
Best regards,
Dylan Hsu, Ph.D
Memorial Sloan-Kettering Cancer Center
[1] https://github.com/freesurfer/freesurfer/blob/6044b3df08de93c15e4b44807 349f21d9e4bc794/scripts/recon-all#L3128-L3139
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Please note that this e-mail and any files transmitted from Memorial Sloan Kettering Cancer Center may be privileged, confidential, and protected from disclosure under applicable law. If the reader of this message is not the intended recipient, or an employee or agent responsible for delivering this message to the intended recipient, you are hereby notified that any reading, dissemination, distribution, copying, or other use of this communication or any of its attachments is strictly prohibited. If you have received this communication in error, please notify the sender immediately by replying to this message and deleting this message, any attachments, and all copies and backups from your computer.
freesurfer@nmr.mgh.harvard.edu
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Bruce Fischl -
HsuD3＠mskcc.org