[Freesurfer] Ubuntu + Freesurfer VM passcode

[Sarah Dziura]

External Email - Use Caution

 Hi,

Could I please get the passcode for unzipping the virtual image
FS_7_2_0_Ubuntu_18_04_06.ova.7z

?

Thank you,
Sarah


-- 
Sarah L. Dziura, Ph.D.
Postdoctoral Research Associate
Developmental Social Cognitive Neuroscience Lab
University of Maryland, College Park
Pronouns: she/her
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[Freesurfer] Deface DICOM

[Victor Montal Blancafort]

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Dear FS experts,

I am using mri_deface to annon our data. Nevertheless, for a recent
project, we were requested to share our DICOM original files, instad of
.nii or .mgz.
Thus, I was wondering if you know a simple way to deface T1 data inputing a
DICOM and obtaining a series of DICOM as output?

I have tried to
   1) deface using mri_deface,
   2) convert the .nii to dicom using the nifti2dicom utility and
   3) correct DICOM info thats incorrecly parsed at step 2).

However,  such approach does not work correctly for all our data (it fails
for several reasons, such as correctly storing acq direction, or dimensions
when sampling from nifti 2 dicom).

I have seen that @Doug has been working on a new deface utility (mideface)
but it seems to work also only for .nii

Any insight?
Victor Montal
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[Freesurfer] Tissue fraction effects correction

[Marina Fernández]

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Dear FS experts,

We are planning to correct for tissue fraction effects on T1w/T2w ratio
images using PETsurfer, setting the point spread function estimate to
zero. My questions are:

1. Does it make sense to correct for tissue fraction effects on T1w/T2w
ratio images even when T1w and T2w images were acquired using the same
matrix size with identical voxel resolution (i.e., 1mm3)?

2. If that makes sense, which PVC method would work best for correcting
tissue fraction effects (i.e., SGTM, MG, RBV) on structural MRI scans?

Many thanks in advance.

Best,
Marina
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Re: [Freesurfer] Tissue fraction effects correction

[Glasser, Matt]

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This is not something we have typically done with T1w/T2w myelin mapping.  Is 
there a reason you are especially concerned about these issues?  We tend to 
find that issues with surface placement, which are more prevalent at 1mm 
isotropic than at higher resolutions, are a far bigger issue and I don’t know 
that PETsurfer will help with this because it is based on the surfaces 
themselves.  I would recommend just sticking with the default HCP Pipelines 
approach for T1w/T2w myelin mapping.

Matt.

From:  on behalf of Marina Fernández 

Reply-To: Freesurfer support list 
Date: Tuesday, May 24, 2022 at 10:54 AM
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: [Freesurfer] Tissue fraction effects correction



External Email - Use Caution
Dear FS experts,

We are planning to correct for tissue fraction effects on T1w/T2w ratio
images using PETsurfer, setting the point spread function estimate to
zero. My questions are:

1. Does it make sense to correct for tissue fraction effects on T1w/T2w
ratio images even when T1w and T2w images were acquired using the same
matrix size with identical voxel resolution (i.e., 1mm3)?

2. If that makes sense, which PVC method would work best for correcting
tissue fraction effects (i.e., SGTM, MG, RBV) on structural MRI scans?

Many thanks in advance.

Best,
Marina


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Re: [Freesurfer] Deface DICOM

[Wighton, Paul]

Hi Victor,

If you have the original DICOMs you could try something like pydicom to 
overwrite the voxel values.  The process would go something like:

1) Convert DICOM to nifti using your favorite tool
2) Deface niftii data using your favorite tool
3) Load the defaced data into python using nibabel,
4) Load the original dicom data into python using pydicom
5) Overwrite voxel values in the dicom with defaced nifti data
6) Use pydicom to save a new defaced DICOM series

Good luck!

-Paul


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Victor Montal Blancafort 

Sent: Tuesday, May 24, 2022 10:39 AM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: [Freesurfer] Deface DICOM


External Email - Use Caution

Dear FS experts,

I am using mri_deface to annon our data. Nevertheless, for a recent project, we 
were requested to share our DICOM original files, instad of .nii or .mgz.
Thus, I was wondering if you know a simple way to deface T1 data inputing a 
DICOM and obtaining a series of DICOM as output?

I have tried to
   1) deface using mri_deface,
   2) convert the .nii to dicom using the nifti2dicom utility and
   3) correct DICOM info thats incorrecly parsed at step 2).

However,  such approach does not work correctly for all our data (it fails for 
several reasons, such as correctly storing acq direction, or dimensions when 
sampling from nifti 2 dicom).

I have seen that @Doug has been working on a new deface utility (mideface) but 
it seems to work also only for .nii

Any insight?
Victor Montal
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contains patient information, please contact the Mass General Brigham 
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Please note that this e-mail is not secure (encrypted).  If you do not wish to 
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