External Email - Use Caution
Hey!
I have recently started using FreeSurfer. I have encountered multiple errors over the past few days, and I would like to mention them all.
1. While testing the installation, the code ran for roughly 4-6 hours and generated the T1 and wm output images. The brainmask image failed to load even after multiple attempts. 2. We have patient data from a Seimens 1.5 T MRI machine. They are DICOM images (about 120-145 images). Running dcmunpack on the directory to locate the suitable T1 weighted image (to pass as the input image to freesurfer) returns an error message 'Element not found'. It fails to generate a list of usable input images. The log file also only mentions the error message. Basically, I am having trouble working with DICOM images using Freesurfer. Please advise me on how to go about it. 3. I tried using the dcm2nii tool on the DICOM images. The software gave out three (nearly identical) nii.gz files as output, each about 7 MB in size. I tried running reconstruction on all three one by one. Only the 'compressed' version output underwent reconstruction for a long time without giving any errors. However, the reconstruction process went on for 150 hours without completion. There were no errors during this time, and the mris_fix_topo process went on for about 74 hours until tonight. It was working on 'correcting defect 48' for most of this time, and then the PC suddenly stopped responding. The process had been utilizing 100% of the CPU and 87% of the RAM for a long time, but the computer was always responding. However it suddenly stopped responding after about 74 hours of mris_fix_topology process. My machine has 8 GB RAM and more than 3.4 GHz processing speed (Acer Veriton). 4. Previously, I tried running reconstruction on a different subject's data after converting it to nifti using dcm2niix. After 70 hours of execution, it terminated with an error which showed that the fsaverage folder was inaccessible. Further digging revealed that the folder was somehow pointing to itself. The original error said failed to read from the label file. I had to eventually reinstall FreeSurfer. 5. I tried running iElvis pipeline. After some time I got an error which said that the sphere.reg file couldn't be opened. I tried fixing this but nothing worked. I kept getting the error that lh.sphere.reg file could not be opened and so on.
Please help. I have been trying to run it for weeks now. I hope you will be able to address each of these problems soon.
Thank You
Sparsh