You can use --meltzer BinThresh MaskThresh NDil BinThresh is the threshold used to binarize the GM+WM PVF image before any smoothing NDil is the number of times this mask is dialted MaskThresh excludes voxels based on GM+WM PVF after smoothing
There is also --rbv (region-based voxel-wise). There is a hidden option called --lgtm which does a "local" GTM by just doing a correction at a voxel based on the surrounding voxels.
On 4/27/2020 12:36 PM, Ferraro, Pilar wrote:
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Hi Freesurfer experts,
I’m trying to test different PVC methods using PetSurfer, and I would much appreciate your advice on the following topic.
Running the command:
mri_gtmpvc --i pet.nii.gz --reg template.reg.lta --psf FWHM --seg gtmseg.mgz
--default-seg-merge --auto-mask PSF .01 --mgx .01 --o gtmpvc.output
The --mgx option should run the Muller-Gartner analysis, with 01 being the GM threshold.
What if we would like to run the Meltzer method instead? With which option should we replace the —mgx one?
Many thanks for any help,
Pilar
Il giorno 27 apr 2020, alle ore 6:00 PM, freesurfer-request@nmr.mgh.harvard.edu mailto:freesurfer-request@nmr.mgh.harvard.edu ha scritto:
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Today's Topics:
1. Re: Intensity inhomogeneity messing with the wm.mgz (Bruce Fischl) 2. Re: exporting segmented mgz file (Bruce Fischl) 3. Re: Infant freesurfer (COLLEEN PLETCHER) 4. Threshold values changed/modified before display. (Devavrat Vartak PhD) 5. Re: Threshold values changed/modified before display. (Bruce Fischl) 6. Re: [External] Re: Intensity inhomogeneity messing with the wm.mgz (Zeng, Victor (BIDMC - Keshavan - Psychiatry)) 7. Re: [External] Re: Intensity inhomogeneity messing with the wm.mgz (Bruce Fischl) 8. correcting fsaverage surface area by eICV (Paul) 9. Re: Tracula error: ERROR: Must specify input table of gradient vectors (Figueiro Longo, Maria Gabriela) 10. Re: Overlapping Treatments and fsgd files (Douglas N. Greve) 11. Dear professor (???) 12. Re: Contrast file to be used in mri_glimfit (Douglas N. Greve) 13. Re: Mri_segstats for PET data: Reviewer question (Douglas N. Greve) 14. Re: Freeview surface loading error : MRISread failed (Douglas N. Greve) 15. Re: How is Total cortical gray matter volume calculated (Douglas N. Greve) 16. Re: correcting fsaverage surface area by eICV (Douglas N. Greve) 17. Re: Dear professor (Douglas N. Greve) 18. ???????? (???) 19. Re: Tracula error: ERROR: Must specify input table of gradient vectors (Yendiki, Anastasia)
Message: 1 Date: Sun, 26 Apr 2020 12:03:06 -0400 (EDT) From: Bruce Fischl fischl@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Intensity inhomogeneity messing with the wm.mgz To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Message-ID: alpine.LRH.2.20.2004261157500.6647@gate.nmr.mgh.harvard.edu Content-Type: text/plain; charset="utf-8"
Hi Victor
the best way to remove intensity inhomogeneities is with control points usually. The wm.mgz gives us an initial estimate of the surface locations, but we then deform it based on the intensities in the brain.mgz volume. So if it looks like wm extends that far out in the brain your wm.mgz edits are unliekly to fix things
cheers Bruce
On Sun, 26 Apr 2020, Zeng, Victor (BIDMC - Keshavan - Psychiatry) wrote:
Hi Freesurfer developers,
I have a subsample of a FS dataset that have scanner-originated hyperintensities in the bilateral supramarginal/temporal lobes. I've manually removed these hyperintensities by editing the wm.mgz, yet FS seems to be unable to recognize these edits when looking at the ?h.white and aparc+aseg.mgz. Is there a possible way to rectify these errors??
I am using FS6 for linux
Here are some pictures:?
[IMAGE]?[IMAGE]
Victor Zeng Beth Israel Deaconess Medical Center Keshavan Lab --
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Message: 2 Date: Sun, 26 Apr 2020 12:04:36 -0400 (EDT) From: Bruce Fischl fischl@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] exporting segmented mgz file To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Message-ID: alpine.LRH.2.20.2004261203210.6647@gate.nmr.mgh.harvard.edu Content-Type: text/plain; charset="utf-8"
Hi Atira
what was your mri_convert command line? Make sure to specify no scaling of the intensity volume. Can you try adding:
-ns 1
to the mri_convert command line, and if that doesn't work send us the full command line and full screen output from it? This is always a good thing to do as it gives us enough information to help
cheers Bruce
On Sun, 26 Apr 2020, atira gan-zvi bick wrote:
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Hi I'm new to freesurfer.
I used freesurfer to preform Thalamus segmentation, and can see the segmented?volume in freeview. I would like to export?the segmented volume to nii to continue analysis in MRvista. I was able to do this using?mri_convert - however the values in the nifti are not those on the label list (as seen in ?freeview). The number of different values is similar but not the same, and the values themselves? are totally different?(8103-8233 in freeview, 16384 - 32767). It is possible to compare regions based on visual inspection - however that is tedious?and might lead to mistakes. How can I export the labels of each region in the segmented mgz?
Any suggestions? I'd appreciate?to learn fro your experience
Thanks Atira
-- ?"? ????? ??-??? ??? ????? ?????? ???????? ???? ???-??? ??????????? ??????
Atira Bick (Phd) fMRI unit Hadassah medical center, Hebrew University Jerusalem
Message: 3 Date: Sun, 26 Apr 2020 15:57:57 +0000 From: COLLEEN PLETCHER ccpletcher@medicine.wisc.edu Subject: Re: [Freesurfer] Infant freesurfer To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Message-ID: 6E02A4C7-7B9E-4929-9CD4-DEDB93A40E64@medicine.wisc.edu Content-Type: text/plain; charset="utf-8"
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That would be great, thank you!
Colleen Pletcher colleen@tpck.net
On Apr 24, 2020, at 3:58 PM, Lilla Zollei lzollei@nmr.mgh.harvard.edu wrote:
? No, but I can definitely keep you in the loop. Lilla
On Wed, 22 Apr 2020, COLLEEN PLETCHER wrote:
Great, thank you! Do you have any idea around when that feature will be added? Thanks again _________________________________________________________________________________________________________________________________________________________________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Lilla Zollei lzollei@nmr.mgh.harvard.edu Sent: Wednesday, April 22, 2020 3:02 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Infant freesurfer Yes, I would like to add it. Lilla On Wed, 22 Apr 2020, COLLEEN PLETCHER wrote:
Ok, thank you! Do you think this option will eventually be added?
_
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Lilla Zollei lzollei@nmr.mgh.harvard.edu Sent: Wednesday, April 22, 2020 2:26 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Infant freesurfer
Hi Colleen, The manual editing option has not yet been added to the pipeline. Best, Lilla
On Wed, 22 Apr 2020, COLLEEN PLETCHER wrote:
Hello. I am working with the infant Freesurfer pipeline. I have noticed that some of our subjects may need to be manually edited, and then run through the pipeline again. However, when I
try
to
do an infant_recon_all command combined with something like autorecon2-wm, I am getting an error that says the command cannot be found. Are there any commands specific to infant Freesurfer
that
can be used in combination with manual edits? Thanks!
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Message: 4 Date: Sun, 26 Apr 2020 15:32:25 -0700 From: Devavrat Vartak PhD dvartak@berkeley.edu Subject: [Freesurfer] Threshold values changed/modified before display. To: freesurfer@nmr.mgh.harvard.edu Message-ID: CANfw89fO7JtmzL8TJ4cT1UW6seh3OPKBqJasNq0uuBz1sPj3Sg@mail.gmail.com Content-Type: text/plain; charset="utf-8"
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Hi freesurfer developers!,
I am using Freesurfer 6.0 and the latest (freeview -beta) to display overlays on my flat surfaces.
I am a novice user of freesurfer and I am a bit confused with how the overlays are displayed / thresholds calculated.
My overlay of rsquare values ranges from 0.2 to 1.0 (i.e all are positive values.). When the overlay is loaded, the threshold histogram depicts values that are negative and positive (centered around zero).
- Does freeview recaluate/modify the values before they are displayed?
- Is it possible to display the values of the overlay as they are?
Thank you. Stay healthy and safe!
Best, Devavrat