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Hello Freesurfer experts,
I am trying to run recon-all to assess cortical thickness on a 3D FSPGR+C scan. The run keeps timing out during the fix topology lh step. I have looked at the resulting images and I am not sure whether I need to fix the white matter, add control points, or do something else entirely to fix the problem. The lh.inflated.nofix does not seem to have anything unwanted still attached and the lh.defect_label will not load. The lh.inflated.nofix does show some areas that have strands/spikes, which I think might be due to the gadolinium contrast. I wanted to ask for opinions on how to proceed. I have attached the recon-all.log.
This is also a link to the output folder: https://drive.google.com/drive/folders/14fj1JAGAvuB-DpgLCxQwOXQ08u6-Vfvj?usp...
Thank you! Ricky
Hi Ricky
how did you try to load the defect_labels? The end of the recon-all.log file lists a defect with 26K vertices, which is probably too big to fix (it's about 1/5 of a normal surface). You should be able to visualize it by loading the lh.defect_labels file as an overlay on the lh.inflated.nofix and lh.orig.nofix surfaces. Make sure to change the threshold for the overlay to 0, then finde defect #116, which is the one it is stuck on. I think we actually add 1 to the index in the labels file so that non-defective vertices show as 0, so it may be 117. It should be clear though as it will be a lot bigger than others
cheers Bruce
On Sat, 14 Mar 2020, Hoang, Ricky wrote:
External Email - Use Caution
Hello Freesurfer experts, I am trying to run recon-all to assess cortical thickness on a 3D FSPGR+C scan. The run keeps timing out during the fix topology lh step. I have looked at the resulting images and I am not sure whether I need to fix the white matter, add control points, or do something else entirely to fix the problem. The lh.inflated.nofix does not seem to have anything unwanted still attached and the lh.defect_label will not load. The lh.inflated.nofix does show some areas that have strands/spikes, which I think might be due to the gadolinium contrast. I wanted to ask for opinions on how to proceed. I have attached the recon-all.log.
This is also a link to the output folder: https://drive.google.com/drive/folders/14fj1JAGAvuB-DpgLCxQwOXQ08u6-Vfvj?us p=sharing
Thank you! Ricky
also, if you run defect-seg, it will create a segmentation of the defects which you can visualize in the volume. Run defect-seg with --help for more info
On 3/13/2020 8:45 PM, Bruce Fischl wrote:
Hi Ricky
how did you try to load the defect_labels? The end of the recon-all.log file lists a defect with 26K vertices, which is probably too big to fix (it's about 1/5 of a normal surface). You should be able to visualize it by loading the lh.defect_labels file as an overlay on the lh.inflated.nofix and lh.orig.nofix surfaces. Make sure to change the threshold for the overlay to 0, then finde defect #116, which is the one it is stuck on. I think we actually add 1 to the index in the labels file so that non-defective vertices show as 0, so it may be 117. It should be clear though as it will be a lot bigger than others
cheers Bruce
On Sat, 14 Mar 2020, Hoang, Ricky wrote:
External Email - Use Caution
Hello Freesurfer experts, I am trying to run recon-all to assess cortical thickness on a 3D FSPGR+C scan. The run keeps timing out during the fix topology lh step. I have looked at the resulting images and I am not sure whether I need to fix the white matter, add control points, or do something else entirely to fix the problem. The lh.inflated.nofix does not seem to have anything unwanted still attached and the lh.defect_label will not load. The lh.inflated.nofix does show some areas that have strands/spikes, which I think might be due to the gadolinium contrast. I wanted to ask for opinions on how to proceed. I have attached the recon-all.log.
This is also a link to the output folder: https://drive.google.com/drive/folders/14fj1JAGAvuB-DpgLCxQwOXQ08u6-Vfvj?us
p=sharing
Thank you! Ricky
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Hoang, Ricky