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A Decade of NITRC-CE: What It Built, and What Comes Next
62,000+ downloads later, NITRC-CE is entering its sunset. Here's what's still available. A Decade of NITRC-CE — and What Comes Next In 2012, getting FSL, AFNI, FreeSurfer, and SPM running together on one machine was a week of your life. Then, after updating all the software versions, sometimes you would not even have enough compute power to run the study. We heard horror stories of labs chaining multiple computers together overnight in order to get a study done. As a result, we created the NITRC Computational Environment (NITRC-CE), making that headache all go away with a download and
Duplicate T1w image data across sub-NDAREF662XZT and sub-NDARVN370YL8 in the RBC HBN release
Posting here at the suggestion of @tientong, who asked me to move this over from ReproBrainChart/HBN_BIDS#2. Two subjects in the HBN release have identical T1w image data but conflicting demographics. sub-NDAREF662XZT sub-NDARVN370YL8 session ses-HBNsiteCBIC ses-HBNsiteCBIC acq acq-HCP acq-HCP age 18.59 8.91 race White Asian handedness Left Right The two volumes have identical voxel arrays (max absolute difference 0), identical NIfTI headers and identical affines. The .nii.gz files differ only in gzip framing. The json sidecars are byte identical, including fields recorded per
Future-Capable: Curiosity, Adaptability, and Kindness in the Age of AI
I want to pass on the following edited Claude 4.8 reduction of a Colin Lewis article which I recommend you read through in its full form: Curiosity, Adaptability, and Kindness No one is future-proof. The better ambition is to become future-capable. Curiosity is the refusal to let yesterday's competence become today's cage. Adaptability is the dignity to change your methods without losing your soul. Kindness is the choice to remain human when the system offers a thousand reasons to be a machine. The Wrong Job Description When OpenAI released ChatGPT in November 2022, office workers, students, l
It's a Bitter, Bitter Lesson
I can't resist passing this on, from Ethan Mollick's Substack "One Useful Thing': ...I thought that getting agents to work effectively as a group would take careful construction, akin to building a company, and that this would take time to figure out. Nope. I fell prey to The Bitter Lesson, the hard truth, learned over and over again, that things that we thought required elaborate human rules and thinking can be solved with the brute force of better machine learning systems and more AI. The Bitter Lesson is everywhere among AI startups and companies adopting AI. A huge amount of effort went i
`download failed: Forbidden` error on all files in ds008547
Summary of what happened: Trying to datalad get ds008547 resulted in download failed: Forbidden errors for all files in the dataset. The datalad get command proceeded normally without error on the ds008328 and ds008579 datasets in the same environment. Command used (and if a helper script was used, a link to the helper script or the command generated): datalad install https://github.com/OpenNeuroDatasets/ds008547.git # said it worked cd ds008547 datalad get -r -J 4 . Version: datalad 1.6.5 Environment (Docker, Singularity / Apptainer, custom installation): micromamba env with datalad installe
Question about using the nudge tool in FSLeyes
Summary of what happened: I’m doing a study where I injected a contrast agent into the brains of 8 rats and looked at changes in intensity over time in selected ROIs on T1 MRIs. When I’m doing rat brain registration, 5/8 of rats successfully register, while the other 3 fail. For those 3 animals, I ended up doing manually registration with the nudge tool. Before registration, I converted all DICOMs to NIFTIs, reoriented them to the correct orientation, made 4D stacks, motion corrected, and took the means of the 4Ds. For the registration, I’m using the T2s as well I’m having trouble with registr
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