External Email - Use Caution

Hi Doug

I think I figured out my answer. ADNI does 4 volume Amyloid PET analyses by averaging the 4 volumes together. I do not need to do kinetic modeling. I hope this helps someone else in the same situation in the future.

Thanks! 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 1301 20th St. #150 Santa Monica, CA 90404

From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Jennifer Bramen jbramen@pacificneuro.org Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Monday, February 7, 2022 at 9:50 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] PETSurfer: error: MatrixReadTxT: could not scan value [1][1]

External Email - Use Caution Hi Doug

I think my first question should be “do I need to do KM?”. This is an amyloid scan and I want to estimate intensity within regions of interest. Do I need KM to estimate mean intensity?

This is what I know about the timing of the 4 amyloid PET volumes:

5 min (300 sec) – Amyloid Brain

* (5 minx 4 beds) * 40 min uptake * 10 mCi IV injection

Can I just create a mean volume from this image or some other simple metric instead of KM?

Thanks for your help.

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 1301 20th St. #150 Santa Monica, CA 90404

From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of "Douglas N. Greve" dgreve@mgh.harvard.edu Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Friday, February 4, 2022 at 5:09 AM To: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] PETSurfer: error: MatrixReadTxT: could not scan value [1][1]

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:

External Email - Use Caution 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

_______________________________________________

Freesurfer mailing list

Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu

MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1eZiIhtszMZEFIQLM5mSk606ezRs_5aImrw_-n253xmwVW2...https://secure-web.cisco.com/10nf2AL62v0JqktSPo3yVbHRsAsxYmB0RqQ4T1KsXIps_k68SFx68P2V_UOWQe-3fgp0LywsEJ_7mKCYxrZliNmu1BADVn8sM86A3NLuueKzBU-_ht-IkzuqZIXLTCrvzzHo4EzvdFGkZI7ao9LFF8ELRRJYgyMTCQzJ8_F-602282DJZWe6e_O6P8qADXfouJVk5CvD2cG5iEf-07ZaNDpvK9voS44YAvwpUbZwoHwxQnbT74BxIlYabrtrJsVULPnjGZgeYz00-98CEf07dh2m-dvKWciq5Z78go6UinOj8LapKpPBgrCbFHmQrbld4OeGXcEUySDxJrpiYUj0gYA/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer