Re: [Freesurfer] Question on using thalseg_1.1.h5

[Georgios Argyropoulos]

External Email - Use Caution

Many thanks and apologies, Henry - I figured it out... I stupidly replaced
your improved segmentation script in both the scripts and the bin directory
instead of only replacing the former.

many thanks for your time, much appreciated

g
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Re: [Freesurfer] Recon-all stuck at topology fix

[Fischl, Bruce R.,PHD]

Hi Salil

This looks like a T2-weighted volume. Recon-all by default assumes T1 
weighting. Do you have a T1 you can use (like an MPRAGE or FLASH scan)?

Cheers
Bruce

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Bhole, Salil
Sent: Thursday, April 11, 2024 12:36 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Recon-all stuck at topology fix


External Email - Use Caution
Here are some images from the patient. I also have the recon-all log posted 
here is well. This is the same patient but taken from a file where I tried to 
manually skull strip to fix the issue, however, the same issue persisted. Thank 
you for your help!

Best,
Salil

From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Fischl, Bruce R.,PHD 
mailto:bfis...@mgh.harvard.edu>>
Sent: Wednesday, April 10, 2024 10:01 PM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Recon-all stuck at topology fix


* External Email - Caution *
Can you post some pictures? The norm.mgz, the wm.mgz, the lh.orig.nofix, the 
aseg.mgz, that kind of thing? Something is badly wrong….
Bruce


On Apr 10, 2024, at 7:05 PM, Bhole, Salil 
mailto:bh...@wustl.edu>> wrote:


External Email - Use Caution
Hello,

I have tried to process this MRI a few times now and it always seems to get 
stuck on the step I have pasted below here. I have tried to fix the defect 
myself by editing the voxels manually, but that has also not seemed to help. 
I've looked through the MRI and there are no obvious deformities/defects. Any 
help with the next steps would be much appreciated.

Best,
Salil



49 defects to be corrected

0 vertices coincident

reading input surface 
/Applications/freesurfer/7.4.1/subjects/Ross_MRI_Neg_LITT/surf/lh.qsphere.nofix...

reading brain volume from brain...

reading wm segmentation from wm...

Reading original properties of orig.nofix

Reading vertex positions of inflated.nofix

Computing Initial Surface Statistics

  -face   loglikelihood: -8.8808  (-4.4404)

  -vertex loglikelihood: -7.5174  (-3.7587)

  -normal dot loglikelihood: -3.4734  (-3.4734)

  -quad curv  loglikelihood: -5.9156  (-2.9578)

  Total Loglikelihood : -25.7872

CORRECTING DEFECT 0 (vertices=116175, convex hull=11639, v0=288)


From: Bhole, Salil
Sent: Wednesday, April 10, 2024 5:59 PM
To: freesurfer@nmr.mgh.harvard.edu 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Recon-all stuck at topology fix

Hello,

I have tried to process this MRI a few times now and it always seems to get 
stuck on the step I have pasted below here. I have tried to fix the defect 
myself by editing the voxels manually, but that has also not seemed to help. 
I've looked through the MRI and there are no obvious deformities/defects. Any 
help with the next steps would be much appreciated.

Best,
Salil



49 defects to be corrected

0 vertices coincident

reading input surface 
/Applications/freesurfer/7.4.1/subjects/Ross_MRI_Neg_LITT/surf/lh.qsphere.nofix...

reading brain volume from brain...

reading wm segmentation from wm...

Reading original properties of orig.nofix

Reading vertex positions of inflated.nofix

Computing Initial Surface Statistics

  -face   loglikelihood: -8.8808  (-4.4404)

  -vertex loglikelihood: -7.5174  (-3.7587)

  -normal dot loglikelihood: -3.4734  (-3.4734)

  -quad curv  loglikelihood: -5.9156  (-2.9578)

  Total Loglikelihood : -25.7872

CORRECTING DEFECT 0 (vertices=116175, convex hull=11639, v0=288)















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Re: [Freesurfer] Surface vertex tkr-ras to native T1 RAS without volume files

[Huang, Yujing]

These three TAGs (TAG_SURF_DATASPACE, TAG_SURF_MATRIXDATA, 
TAG_SURF_TRANSFORMEDSPACE) are available in the surface files if they are 
output from Freesurfer dev version.

They are the same as the metadata DataSpace/MatrixData/TransformedSpace in 
GIFTI. You can use the information to convert [x, y, z] coordinates between 
TAG_SURF_DATASPACE and TAG_SURF_TRANSFORMEDSPACE.

See freesurfer/utils/mrisurf_io.cpp:: __MRISwriteTriangularSurfaceTags() for 
implementation details.

Best,

Yujing



From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Dipterix Wang
Sent: Thursday, April 11, 2024 10:50 AM
To: Freesurfer support list 
Subject: [Freesurfer] Surface vertex tkr-ras to native T1 RAS without volume 
files


External Email - Use Caution
Dear FreeSurfer devs,

I'm writing a program in JavaScript that converts FreeSurfer surface (mesh) 
files to other formats, which require the vertices to sit in scanner RAS 
coordinates.

Right now I'm relying on the FreeSurfer brain.finalsurf.mgz or T1.mgz file to 
obtain the Torig (vox to tkr-ras) and Norig (vox to scanner ras) matrices, and 
using these matrices to calculate the rigid transform. This approach requires 
the users to upload the mgz volume files (but I only need the transforms).

Today I found that each binary surface file (e.g. lh.pial) has a little footer 
that starts with uint32 sequence `2 0 20`, followed by the meta information 
such as xras, yras, zras, and cras. For example:

valid = 1  # volume info valid
filename = ../mri/filled-pretess127.mgz
volume = 256 256 256
voxelsize = 1.000e+00 1.000e+00 1.000e+00
xras   = -1.000e+00 0.000e+00 0.000e+00
yras   = 0.000e+00 0.000e+00 -1.000e+00
zras   = 0.000e+00 1.000e+00 0.000e+00
cras   = -1.000e+00 -1.700e+01 1.900e+01
\u\u\u\u0003\u\u\u\u\u\u\u0001


From what I understand, cras is the xyz of the volume center, which is the 
translation from mesh vertices xyz (in tkr-ras) to native scanner RAS.

I wonder if I can rely on this information to calculate the transform from 
tkr-ras to scan-ras, if so, where are the rotation matrices? (Affine/rigid 
transform is a 4x4 matrix, if cras is the translation, where are the first 3x3 
elements, are those always identity matrices?)

Best,
- Dipterix
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[Freesurfer] Surface vertex tkr-ras to native T1 RAS without volume files

[Dipterix Wang]

External Email - Use Caution

Dear FreeSurfer devs,

I'm writing a program in JavaScript that converts FreeSurfer surface (mesh)
files to other formats, which require the vertices to sit in scanner RAS
coordinates.

Right now I'm relying on the FreeSurfer *brain.finalsurf.mgz* or *T1.mgz*
file to obtain the Torig (vox to tkr-ras) and Norig (vox to scanner ras)
matrices, and using these matrices to calculate the rigid transform. This
approach requires the users to upload the mgz volume files (but I only need
the transforms).

Today I found that each binary surface file (e.g. lh.pial) has a little
footer that starts with uint32 sequence `2 0 20`, followed by the meta
information such as xras, yras, zras, and cras. For example:

valid = 1  # volume info valid
filename = ../mri/filled-pretess127.mgz
volume = 256 256 256
voxelsize = 1.000e+00 1.000e+00
1.000e+00
xras   = -1.000e+00 0.000e+00 0.000e+00
yras   = 0.000e+00 0.000e+00 -1.000e+00
zras   = 0.000e+00 1.000e+00 0.000e+00
cras   = -1.000e+00 -1.700e+01 1.900e+01
\u\u\u\u0003\u\u\u\u\u\u\u0001


From what I understand, cras is the xyz of the volume center, which is the
translation from mesh vertices xyz (in tkr-ras) to native scanner RAS.

I wonder if I can rely on this information to calculate the transform from
tkr-ras to scan-ras, if so, where are the rotation matrices? (Affine/rigid
transform is a 4x4 matrix, if cras is the translation, where are the first
3x3 elements, are those always identity matrices?)

Best,
- Dipterix
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 .
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Re: [Freesurfer] surface-based filtering

[Fischl, Bruce R.,PHD]

Hi Jiaen

I'm not sure what you mean by "stacked smoothing". I think the N in nsmooth is 
the number of iterations of nearest neighbor smoothing to apply, which  
converges to Gaussian as N gets bigger. Not sure about the units for fwhm - I 
defer to Doug on that
Bruce

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Jiaen Liu
Sent: Thursday, April 11, 2024 4:41 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] surface-based filtering


External Email - Use Caution
Hi Bruce

Thanks for your response. In the help, I found the following options. Is the 
fwhm based on voxel unit? Does nsmooth-in or-out control the number of stacked 
smoothing?

--fwhm-src fwhmsrc: smooth the source to fwhmsrc
   --fwhm-trg fwhmtrg: smooth the target to fwhmtrg
   --nsmooth-in N  : smooth the input
   --nsmooth-out N : smooth the output

Best
Jiaen

From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Fischl, Bruce R.,PHD
Sent: Thursday, April 11, 2024 14:24
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] surface-based filtering

EXTERNAL MAIL
Yes, we support surface-based smoothing. Check out the help for mri_surf2surf


Cheers
Bruce

From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Jiaen Liu
Sent: Thursday, April 11, 2024 2:14 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] surface-based filtering


External Email - Use Caution
I'm wondering if freesurfer provides functions to filter the surface data 
within certain neighborhood exclusively on the surface. It's essentially 
similar to regular smoothing in 3D space. But the filtering kernel only runs on 
the surface.
I can think of a solution to filter adjacent vertex in the surface file. But 
I'm not sure if the adjacent vertex is also close in space.
Thanks!

Best regards,
Jiaen Liu Ph.D.
Assistant Professor
Advanced Imaging Research Center & Radiology
UT Southwestern Medical Center
2201 Inwood Ln
Dallas, TX, USA, 75390
Office: 214.645.2750
Website: Liu (Jiaen) Lab | UT Southwestern, Dallas, 
Texas




UT Southwestern

Medical Center

The future of medicine, today.

CAUTION: This email originated from outside UTSW. Please be cautious of links 
or attachments, and validate the sender's email address before replying.
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addressed.  If you believe this e-mail was sent to you in error and the e-mail 
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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Re: [Freesurfer] surface-based filtering

[Jiaen Liu]

External Email - Use Caution

Hi Bruce

Thanks for your response. In the help, I found the following options. Is the 
fwhm based on voxel unit? Does nsmooth-in or-out control the number of stacked 
smoothing?

--fwhm-src fwhmsrc: smooth the source to fwhmsrc
   --fwhm-trg fwhmtrg: smooth the target to fwhmtrg
   --nsmooth-in N  : smooth the input
   --nsmooth-out N : smooth the output

Best
Jiaen

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Fischl, Bruce R.,PHD
Sent: Thursday, April 11, 2024 14:24
To: Freesurfer support list 
Subject: Re: [Freesurfer] surface-based filtering

EXTERNAL MAIL
Yes, we support surface-based smoothing. Check out the help for mri_surf2surf


Cheers
Bruce

From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Jiaen Liu
Sent: Thursday, April 11, 2024 2:14 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] surface-based filtering


External Email - Use Caution
I'm wondering if freesurfer provides functions to filter the surface data 
within certain neighborhood exclusively on the surface. It's essentially 
similar to regular smoothing in 3D space. But the filtering kernel only runs on 
the surface.
I can think of a solution to filter adjacent vertex in the surface file. But 
I'm not sure if the adjacent vertex is also close in space.
Thanks!

Best regards,
Jiaen Liu Ph.D.
Assistant Professor
Advanced Imaging Research Center & Radiology
UT Southwestern Medical Center
2201 Inwood Ln
Dallas, TX, USA, 75390
Office: 214.645.2750
Website: Liu (Jiaen) Lab | UT Southwestern, Dallas, 
Texas




UT Southwestern

Medical Center

The future of medicine, today.

CAUTION: This email originated from outside UTSW. Please be cautious of links 
or attachments, and validate the sender's email address before replying.
___
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addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
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[Freesurfer] surface-based filtering

[Jiaen Liu]

External Email - Use Caution

I'm wondering if freesurfer provides functions to filter the surface data 
within certain neighborhood exclusively on the surface. It's essentially 
similar to regular smoothing in 3D space. But the filtering kernel only runs on 
the surface.
I can think of a solution to filter adjacent vertex in the surface file. But 
I'm not sure if the adjacent vertex is also close in space.
Thanks!

Best regards,
Jiaen Liu Ph.D.
Assistant Professor
Advanced Imaging Research Center & Radiology
UT Southwestern Medical Center
2201 Inwood Ln
Dallas, TX, USA, 75390
Office: 214.645.2750
Website: Liu (Jiaen) Lab | UT Southwestern, Dallas, 
Texas




UT Southwestern

Medical Center

The future of medicine, today.
___
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The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

Re: [Freesurfer] surface-based filtering

[Fischl, Bruce R.,PHD]

Yes, we support surface-based smoothing. Check out the help for mri_surf2surf


Cheers
Bruce

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Jiaen Liu
Sent: Thursday, April 11, 2024 2:14 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] surface-based filtering


External Email - Use Caution
I'm wondering if freesurfer provides functions to filter the surface data 
within certain neighborhood exclusively on the surface. It's essentially 
similar to regular smoothing in 3D space. But the filtering kernel only runs on 
the surface.
I can think of a solution to filter adjacent vertex in the surface file. But 
I'm not sure if the adjacent vertex is also close in space.
Thanks!

Best regards,
Jiaen Liu Ph.D.
Assistant Professor
Advanced Imaging Research Center & Radiology
UT Southwestern Medical Center
2201 Inwood Ln
Dallas, TX, USA, 75390
Office: 214.645.2750
Website: Liu (Jiaen) Lab | UT Southwestern, Dallas, 
Texas




UT Southwestern

Medical Center

The future of medicine, today.

___
Freesurfer mailing list
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https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

Re: [Freesurfer] surface-based filtering

[Jiaen Liu]

External Email - Use Caution

I thought N controls the number of smoothing iterations and the smoothing in 
each iteration is defined by fwhm which is some measurement of the smoothing 
kernel width.
Can I ask how to achieve smoothing effect similar to gaussian smoothing with 
certain sigma, where sigma is defined by voxel unit?
Thanks!

Best
Jiaen

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Fischl, Bruce R.,PHD
Sent: Thursday, April 11, 2024 15:50
To: Freesurfer support list 
Subject: Re: [Freesurfer] surface-based filtering

Hi Jiaen

I'm not sure what you mean by "stacked smoothing". I think the N in nsmooth is 
the number of iterations of nearest neighbor smoothing to apply, which  
converges to Gaussian as N gets bigger. Not sure about the units for fwhm - I 
defer to Doug on that
Bruce

From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Jiaen Liu
Sent: Thursday, April 11, 2024 4:41 PM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] surface-based filtering


External Email - Use Caution
Hi Bruce

Thanks for your response. In the help, I found the following options. Is the 
fwhm based on voxel unit? Does nsmooth-in or-out control the number of stacked 
smoothing?

--fwhm-src fwhmsrc: smooth the source to fwhmsrc
   --fwhm-trg fwhmtrg: smooth the target to fwhmtrg
   --nsmooth-in N  : smooth the input
   --nsmooth-out N : smooth the output

Best
Jiaen

From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Fischl, Bruce R.,PHD
Sent: Thursday, April 11, 2024 14:24
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] surface-based filtering

EXTERNAL MAIL
Yes, we support surface-based smoothing. Check out the help for mri_surf2surf


Cheers
Bruce

From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Jiaen Liu
Sent: Thursday, April 11, 2024 2:14 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] surface-based filtering


External Email - Use Caution
I'm wondering if freesurfer provides functions to filter the surface data 
within certain neighborhood exclusively on the surface. It's essentially 
similar to regular smoothing in 3D space. But the filtering kernel only runs on 
the surface.
I can think of a solution to filter adjacent vertex in the surface file. But 
I'm not sure if the adjacent vertex is also close in space.
Thanks!

Best regards,
Jiaen Liu Ph.D.
Assistant Professor
Advanced Imaging Research Center & Radiology
UT Southwestern Medical Center
2201 Inwood Ln
Dallas, TX, USA, 75390
Office: 214.645.2750
Website: Liu (Jiaen) Lab | UT Southwestern, Dallas, 
Texas




UT Southwestern

Medical Center

The future of medicine, today.

CAUTION: This email originated from outside UTSW. Please be cautious of links 
or attachments, and validate the sender's email address before replying.
___
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The information in this e-mail is 

Re: [Freesurfer] mri_synthmorph

[Hoffmann, Malte,PhD]

Hi Antoine,

I would guess this is a memory issue. You could try allocating more and/or look 
at the exit code. I believe 137 would indicate that Python ran out of memory.

Malte


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Antoine Royer 

Sent: Thursday, April 11, 2024 16:21
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] mri_synthmorph

External Email - Use Caution

Hi,

I am developping a Nextflow DSL2 module through nf-core for registration using 
mri_synthmorph, through the dockerised version:
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" 
claiming to be 
https://hub.docker.com/r/freesurfer/synthmorph

Here is a couple of screenshots showing the ressource consumption of my 
computer and through Docker.

I don't have any issue running it locally, but there seems to be an issue 
through my container which is set at 16 core at 24 GB. Does anyone have any 
insight on how to troubleshoot this?

Thank you!


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addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
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[Freesurfer] BBRegistration with FSL topup

[Gianluca Guglietti]

External Email - Use Caution

Hi,

I had a question as to how to integrate fsl's topup command for correcting B0 
distortion with freesurfer's boundary-based registration. I am working with 
high-resolution epi data (0.8mm isotropic) with a reduced FOV and am trying to 
register it to an MP2RAGE structural scan that I've already run through free 
surfer's recon-all. When I use the BBR command it works perfectly fine but when 
I try to add the topup field map it fails, returning this error 
"MRIvol2surfVSM: vsm dimension mismatch 1".

the field map was generated using two reverse phase encoded SE-EPI volumes with 
the same resolution and field of view as the GE-EPI BOLD data I am trying to 
register.

Any advice would be greatly appreciated!

Best,

Gianluca
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Re: [Freesurfer] WMH-SynthSeg - Torch module not found

[fsbuild]

External Email - Use Caution

The current nightly build dated April 12th available from 
under,https://secure-web.cisco.com/1eprQplECVjQEgFy-DNvfPnzwSjew2U260XYR6pjQfShhM9gtsn58XZ4YRUlHYleeawzdPreispMAkZ2MQM7djCWtpvLAsdUowgmUhDSJuQv8O_5fefPPEs1LslaJbLvtLiYSihrPpDMqQl8XI-wfA6fvBLvdZGEorSSHkE8HZc964yhAJAU0LYSYOy9cD9hlCMe5NUexf5FlsSHnL5tt8VUWpdEbJ4kGOxPh5yeIs8vl4_Cv8UwrnmG7lIrS6lOu9oUQLQnNBK5VKpADCMYEek0svgu1wUv1NH8cYOpg4jfy9cfhhXCpznkSR99lHGKlu4Wnj2ZdK-iefKmAPd91yQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2Fdev%2F-
 should have all the modules as well.
- R.

On Apr 11, 2024, at 10:03, Iglesias Gonzalez, Juan E. 
jiglesiasgonza...@mgh.harvard.edu wrote:The idea would be to 
source 7.4.1 and then run:fspython 
[location_of_FS_dev]/python/packages/WMHSynthSeg/inference.py 
[arguments]Cheers,/Eugenio--Juan Eugenio 
Iglesiashttp://http://secure-web.cisco.com/1Bz_4nONhypuVg0at2yxM7j3iTzJ-6aeFlVMFOtu6kJDKPxwTMe7ZJnmmIkRXMNWFEGYYGq8NlCAbNhKFyGulewwR4fTOUBHQBiQDI0dEdGr0ZJP2jrcZbc10tC1447QVz6_ZVvrhVUx5n-lgiJJVXzeCOZ-6vl-bx6VFTc10EYES77izWOBFVPPlHLBqzSdlysIuI93NkD8E_G4I-HwZg0EpyNtwvLbO4TvKg0137MivLsXAZkuJTY-am7YdxPIonKE3oUFJDeblwytpcKdrOrio7MJX3S3xjSQOA-7Oo4DIYbpVrrldmcLJNWe8x_Syu0HnwnbLJlaS_76DMzUyCQ/http%3A%2F%2Fwww.jeiglesias.com%C2%A0From%3A%C2%A0freesurfer-bounces%40nmr.mgh.harvard.edu
 freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Corinne Alison 
Donnay corinne.don...@linacre.ox.ac.ukDate:Wednesday, April 10, 
2024 at 8:39 AMTo:Freesurfer support list 
freesurfer@nmr.mgh.harvard.eduSubject:Re: [Freesurfer] 
WMH-SynthSeg - Torch module not 
foundExternal Email - Use 
CautionHi 
Eugenio,Thanks for getting back to me – I had the newest version 
installed and still get the same error (pasted below).mri_WMHsynthseg --i 
flair_ax.nii.gz --o flair_ax_WML.nii.gz --threads -1Arguments seem 
correct; loading Python packages...Traceback (most recent call last): 
File 
"/usr/local/apps/freesurfer/dev-2024-04-19/python/packages/WMHSynthSeg/inference.py",
 line 284, in module  main() File 
"/usr/local/apps/freesurfer/dev-2024-04-19/python/packages/WMHSynthSeg/inference.py",
 line 76, in main  import torchModuleNotFoundError: No module named 
'torch'I also installed FreeSurfer 7.4.1. Would you be able to expand on 
what you mean by “a way around this is installing FreeSurfer 7.4.1, and 
using its fspython to run the WMh-SynthSeg code”?I loaded FreeSurfer 
7.4.1, and then changed the location of the model in inference.py and tried 
using FreeSurfer 7.4.1 fspython but now its missing the'unet3d' 
module:[donnayca@cn4270 anat]$ module load freesurfer[-] Unloading 
freesurfer 7.4.1 on cn4270[+] Loading freesurfer 7.4.1 
on cn4270[donnayca@cn4270 anat]$ fspython ../inference_cd.py --i 
flair_ax.nii.gz --o flair_ax_WML.nii.gzArguments seem correct; loading Python 
packages...Traceback (most recent call last): File "../inference_cd.py", 
line 285, in module  main() File 
"../inference_cd.py", line 79, in main  from unet3d.model import 
UNet3DModuleNotFoundError: No module named 'unet3d'[donnayca@cn4270 anat]$ 
fspythonPython 3.8.13 (default, Apr 21 2022, 14:55:37)[GCC 8.3.1 20190311 
(Red Hat 8.3.1-3)] on linuxType "help", "copyright", "credits" or "license" for 
more information. exit()Thank 
you!CorinneFrom:freesurfer-boun...@nmr.mgh.harvard.edu on behalf 
of "Iglesias Gonzalez, Juan E." 
jiglesiasgonza...@mgh.harvard.eduReply-To:Freesurfer support list 
freesurfer@nmr.mgh.harvard.eduDate:Saturday, April 6, 2024 at 
1:04 PMTo:Freesurfer support list 
freesurfer@nmr.mgh.harvard.eduSubject:Re: [Freesurfer] 
WMH-SynthSeg - Torch module not foundWrong answer: apparently this has 
been fixed in the latest dev; maybe try that?Cheers,/Eugenio--Juan 
Eugenio 
Iglesiashttp://http://secure-web.cisco.com/1Bz_4nONhypuVg0at2yxM7j3iTzJ-6aeFlVMFOtu6kJDKPxwTMe7ZJnmmIkRXMNWFEGYYGq8NlCAbNhKFyGulewwR4fTOUBHQBiQDI0dEdGr0ZJP2jrcZbc10tC1447QVz6_ZVvrhVUx5n-lgiJJVXzeCOZ-6vl-bx6VFTc10EYES77izWOBFVPPlHLBqzSdlysIuI93NkD8E_G4I-HwZg0EpyNtwvLbO4TvKg0137MivLsXAZkuJTY-am7YdxPIonKE3oUFJDeblwytpcKdrOrio7MJX3S3xjSQOA-7Oo4DIYbpVrrldmcLJNWe8x_Syu0HnwnbLJlaS_76DMzUyCQ/http%3A%2F%2Fwww.jeiglesias.com%C2%A0From%3A%C2%A0freesurfer-bounces%40nmr.mgh.harvard.edu
 freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Iglesias Gonzalez, 
Juan E. jiglesiasgonza...@mgh.harvard.eduDate:Friday, April 5, 
2024 at 3:58 PMTo:Freesurfer support list 
freesurfer@nmr.mgh.harvard.eduSubject:Re: [Freesurfer] 
WMH-SynthSeg - Torch module not foundDear Corinne,A bunch of libraries are 
currently broken in the development version; apologies for this. A way around 
this is installing FreeSurfer 7.4.1, and using its fspython to run the 
WMh-SynthSeg code. Apologies for the inconvenience!Cheers,/EPS: I just updated 
the wiki to include this information.--Juan Eugenio 

Re: [Freesurfer] PetSurfer: Can kinetic modeling be applied to PET data with single frame?

[WONG Wan Wa]

External Email - Use Caution

Hi experts,

A follow-up question: how to verify if the results (gtm.stats.dat) generated by 
mri_gtmpvc make sense?

Thanks,
Angel


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of WONG Wan Wa 

Sent: Wednesday, April 10, 2024 5:16 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] PetSurfer: Can kinetic modeling be applied to PET 
data with single frame?


External Email - Use Caution

Thanks Michael!

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Rullmann, Michael 

Sent: Tuesday, April 9, 2024 7:27 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] PetSurfer: Can kinetic modeling be applied to PET 
data with single frame?


You can just google those values for each scanner.

For example:

MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" 
claiming to be 
https://secure-web.cisco.com/1QhqrvAvEoqm5LPwY4Zobyu2ikbwoP-wu6qcl0XecyA4TLwDHsnZn146qFvDNeQn3jb-qmiMMnVaOaSeKR-rSNIOmh1VWLJBCMPakN6yIeSE3Zmdq7aW17YgDcuMhin8DtSZypV8GYRGmKyISvwEiCDyzpmnjpLG2CC1KKGyvKiFgnxUdhc04exFYPgIdEz3xjPf-HxPNki64sl24TI9Jj3iu7DnCxTQsSoiMv3sMzSRuMSdNCNBBaQ88693Rcxm2twJRHQo-KKzOXray7lTKc-QQER8msZNOPOc_sP8hvb_snHS6esi2_TvUWikqokdrYD_NYXO6G_2M2G5qVjE_MQ/https%3A%2F%2Fwww.google.com%2Fsearch%3Fq%3Dnema%2Bfwhm%2Bsiemens%2BmMR



Second result links directly to the Siemens website:

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https://secure-web.cisco.com/1vR310-IMpTNOILEHO9JHWbD7YqwaQJjTYWwPbGET_p-STVR95RchffDUVIZklZFP4ZbwQnBzQOCX_wr1vFg9jRAGV2Ipc9y6Z2Mmekz6R4Nq1371Otbhww7zMaWR0VXGGFjYu8dxo3aI1m5ox5RNFvUXuPWvOnQkLAdes0Y4t8Jll0JSc2HUUN3a3RB0x7fc5KGPsHX8-k3A4k2QXQK91TVEW9myjDcKf54VLFGCAqpOgsiCWczDgRwUeO-zrGnvV1w4_LusAVhY1xWcbX8kLtkFbb258tceZ4R66FcgzrGXp_-m3YjPqR-a1AX6G-DcatxMgP3zGlqS6EqkyeD6oA/https%3A%2F%2Fwww.siemens-healthineers.com%2Fmagnetic-resonance-imaging%2Fmr-pet-scanner%2Fbiograph-mmr



There, it is stated:

Transverse spatial resolution (NEMA 2012)

FWHM @ 1 cm : 4.6 mm





You can also determine the parameters yourself by following the NEMA standards.



Best

Michael





Von: freesurfer-boun...@nmr.mgh.harvard.edu 
 Im Auftrag von WONG Wan Wa
Gesendet: Dienstag, 9. April 2024 12:03
An: Freesurfer support list 
Betreff: Re: [Freesurfer] PetSurfer: Can kinetic modeling be applied to PET 
data with single frame?



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How to determine the PSF?



From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of WONG Wan Wa mailto:angelw...@ust.hk>>
Sent: Friday, April 5, 2024 12:14 PM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] PetSurfer: Can kinetic modeling be applied to PET 
data with single frame?



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Any idea about the PSF?



From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of WONG Wan Wa mailto:angelw...@ust.hk>>
Sent: Tuesday, April 2, 2024 12:36 PM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] PetSurfer: Can kinetic modeling be applied to PET 
data with single frame?



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Hi Douglas,



Here is the information given by the technician from the PET center:



There are a total of 3 machines used for PIB PET/CT or PET/MR scans



  1.  PET/CT1 ( mCT)(contain "mCT" in the pet series)

Manufacturer: Siemens
ManufacturersModelName: Biograph128_mCT

recon method : TrueX + TOF (ultra HD-PET)

iteration: 5 subset:21 matrix: 400x400

zoom: 2.0  Gaussian filter FWHM: 2.0mm