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-boun...@nmr.mgh.harvard.edu> on behalf of Jennifer Bramen
<jbra...@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-boun...@nmr.mgh.harvard.edu> on behalf of "Douglas N. Greve"
<dgr...@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.edu<mailto: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_-n253xmwVW2zqRYpuZux-DzbDnp7lXnvb-V3ahiKI26oNpYiBzsIeyzBQswHtxidcQlUR5c0JW20ZquO7r03bCF0lrBZGH5I177ukC5El7g1xmElI6Qt-ER4UHfFhRip9mavSeyePh4a0Zri7S7Gt54fQ3CGzDmjWVj-L7mYjLeO0_t-mz01JOLLjAcHR5eqSS--Vsn5OamziXDBUW0EjnFoFXaSw-cNKER7wxd8y4Qi2tyNAkZlLFApp6OMqsTQFFUZyaMR5yvZ95zfEah9miGrp2BAh/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer<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>
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
