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Alternative ways to calculate the brain mask for ASL
Summary of what happened: I noticed very high CBF values when exploring BASIL GM CBF. After exploration, the maps seem to be good and accurate, but the issue seems to be with the masks. When I explore the within-subject anatomical outputs, the brain masks look great (/anat/*_desc-brain_mask.nii.gz OR anat/*_space-MNI152NLin2009aSym_desc-brain_mask.nii.gz), but when exploring the perfusion outputs, the masks include non-brain tissue (/perf/*_space-T1w_desc-brain_mask.nii.gz OR /perf/*_space-MNI152NLin2009aSym_desc-brain_mask.nii.gz) The problem is that masks that include non-brain tissue also i
Casino culture meets the predictive brain
Max Read has a recent sharp piece in the New York Times Magazine, "Gambling Is the Culture," that I want to pass on, along with some thoughts it set off in me. His argument is that gambling money no longer just pays for our culture. It has become the culture. Sportsbooks, offshore casinos, crypto, options-trading apps and prediction markets like Kalshi and Polymarket are merging into one speculative sector. That sector now underwrites sports broadcasting, podcasts, the streamer-influencer economy and increasingly the news itself, through data partnerships with CNN, Fox and Dow Jones. The more
QSIPrep on HCP-development data
Hi i’m just want to make sure i’m doing this right, because eddy_cpu has been running for 2 days on 40 CPUs and it doesnt seem like it will complete anytime soon. I’m running qsiprep 26.0.0 using singularity: singularity run --cleanenv \ -B $fs_license,$bids_dir,$output_dir,$work_dir \ $HOME/QSIprep \ $bids_dir \ $output_dir \ participant \ -w $work_dir/"$d" \ --participant-label $d \ --nthreads 40 \ --omp-nthreads 40 \ --skip-bids-validation \ --output-resolution 2 \ --fs-license-file $fs_license this is the fil
ASLPrep - CSF shows elevated CBF in BASIL output (multi-PLD UK Biobank data)
Summary of what happened: I’m running ASLPrep on multi-PLD pCASL UK Biobank data (using fMRIPrep derivatives for structural processing). In the “BASIL CBF by Tissue Type” panel of the visual report (the uncorrected BASIL output, sampled through the GM/WM/CSF tissue masks), I see little separation between the 3 tissue types. Per documentation, I’d expect CSF to show ~0 CBF, but instead the distribution is very close to GM and WM (median ~37 vs. GM ~42, WM ~38). Can anybody advise what might be causing this? Command used (and if a helper script was used, a link to the helper script or the comman
Sex information missing in HBN RBC
For some subjects sex is marked as “Other” but in the CMI phenotype data from LORIS it is always Male or Female, and I was able to find the sex for most subjects but there are a few subjects from my filtered sample (there could be more missing) that I cannot find it the LORIS system. This would matter for some phenotypic scoring which adjusts for age and sex, and I suspect it may be why some of those “harmonized” symptom measures are missing. Is there an explaination for this? https://github.com/ReproBrainChart/HBN_BIDS/blob/main/study-HBN_desc-participants.tsv Subject 1 post - 1 participant R
Trouble running nibabies on third-party segmentation
Summary of what happened: Hi neurostars, I’m new to this list, and I’m trying to run nibabies on a segmentation for a six-month old baby that was generated by a third-party organization (probably before nibabies/bibsnet existed). The GM/WM boundary looks surprising good, despite the age. I am trying to fool nibabies into believing it is bibsnet-generated, so I relabeled the ROI’s to match FreeSurferColorLUT.txt ( freesurfer/distribution/FreeSurferColorLUT.txt at dev · freesurfer/freesurfer · GitHub ). There were a few ROI’s missing, including Left/Right-Accumbens-area. You can see my errors
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