Can you send all the terminal output? Also, you only have 4 time points in time.dat. Is this accurate? It's going to be hard to do KM with 4 time points.

On 1/31/2022 5:00 PM, Jennifer Bramen wrote:

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Hello FreeSurfer Developers,

I'm attempting to analyze amyloid PET data using PETSurfer. I am trying to do kinetic modeling and I am on the MRTM1 step. I have tried this two ways (one using the wiki instructions and the other using the tutorial ROI-based approach)

mri_glmfit --y $PET_DIR/PREV_019/gtmpvc.output/km.hb.tac.nii.gz --mrtm1 $PET_DIR/PREV_019/gtmpvc.output/km.ref.tac.dat $PET_DIR/time.dat --o mrtm1 --no-est-fwhm --nii.gz; done

mri_glmfit --y $PET_DIR/PREV_019/gtmpvc.output/gtm.nii.gz --mrtm1 $PET_DIR/PREV_019/gtmpvc.output/km.ref.tac.dat $PET_DIR/time.dat --o $PET_DIR/PREV_019/mrtm1.roi --nii.gz;done

Both times I get this error:

error: MatrixReadTxT: could not scan value [1][1]

I have opened all of the .dat files using my text editor (nano) and they seem ok. I have tried this in other subjects and I get the same error.

I searched the list and I cannot find any discussion regarding this error using mri_glmfit and PET data. Anything you can do to help me troubleshoot this error would be greatly appreciated!!! Attached is my time.dat file (I think this is the most likely culprit).

Warm regards,

Jennifer Bramen, PhD
(she/her/hers)
Senior Research Scientist, Neuroimaging
Assistant Professor
Pacific Brain Health Center | Pacific Neuroscience Institute & Foundation | Providence Saint John's Health Center
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