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

: 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

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

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

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? WARNUNG: Diese E-Mail kam von außerhalb der

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

External Email - Use Caution How to determine the PSF? From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of WONG Wan Wa Sent: Friday, April 5, 2024 12:14 PM To: Freesurfer support list Subject: Re: [Freesurfer] PetSurfer: Can kinetic

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

External Email - Use Caution Any idea about the PSF? From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of WONG Wan Wa Sent: Tuesday, April 2, 2024 12:36 PM To: Freesurfer support list Subject: Re: [Freesurfer] PetSurfer: Can kinetic

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

2.0mm Thanks, Angel From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Douglas N. Greve Sent: Saturday, March 30, 2024 5:23 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] PetSurfer: Can kinetic modeling be applied to PET data with single frame? That

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

- *From:* freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Douglas N. Greve *Sent:* Thursday, March 21, 2024 9:44 PM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] PetSurfer: Can kinetic modeling be applied to PET data with single frame? Yes, though that will n

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

n I use "2" for psf in the command? Thanks, Angel From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Douglas N. Greve Sent: Thursday, March 21, 2024 9:44 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] PetSurfer: Can kinetic mode

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

urfer-boun...@nmr.mgh.harvard.edu on behalf of Douglas N. Greve *Sent:* Wednesday, March 20, 2024 11:27 PM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] PetSurfer: Can kinetic modeling be applied to PET data with single frame? you cannot apply kinetic modeling to one frame. W

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

, 2024 11:27 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] PetSurfer: Can kinetic modeling be applied to PET data with single frame? you cannot apply kinetic modeling to one frame. What is you ligand? For a one frame acquisition, you usually use an SUV analysis. On 3/20/2024 12:03

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

you cannot apply kinetic modeling to one frame. What is you ligand? For a one frame acquisition, you usually use an SUV analysis. On 3/20/2024 12:03 AM, WONG Wan Wa wrote: External Email - Use Caution Hi experts, As stated in the subject, can kinetic modeling be applied to PET data

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

External Email - Use Caution Hi experts, As stated in the subject, can kinetic modeling be applied to PET data with only one frame? Or we just stop at ROI analysis without kinetic modeling? Best, Angel ___ Freesurfer mailing list

Re: [Freesurfer] PETSurfer

Hi, sorry for the many months to get back to you. I have just updated the documentation on https://surfer.nmr.mgh.harvard.edu/fswiki/PetSurfer to indicate how to use your own segmentations. I'm assuming that you have a volume with choroid plexus labeled that you want  to merge into the stream.

Re: [Freesurfer] PETsurfer kinetic modeling

There is not an easy way to do this yet. If you have your segmentations in the conformed anatomical space, you can merge them with gtmseg.mgz with something like mri_vol2vol --interp nearest --mov yoursegs.mgz --targ gtmseg.mgz --o yoursegs-in-gtmseg-space.mgz mergeseg --src gtmseg.mgz --merge

[Freesurfer] PETsurfer kinetic modeling

External Email - Use Caution Congratulations to the FreeSurfer team in the continued progress made in the FS tool set. I wondered if you could comment on whether it is feasible to create a custom reference region (other than specifying, for example, cerebellar cortex or

[Freesurfer] PETSurfer

External Email - Use Caution Hi I am reaching out to ask some questions about PetSurfer. I am working with an open access dataset

Re: [Freesurfer] PetSurfer, PET data format, mri_convert

, Zeyu Sent: Friday, July 28, 2023 10:14 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] PetSurfer, PET data format, mri_convert External Email - Use Caution Hi Freesurfer developers, I am new to PET and FreeSurfer. I am trying to go through the PetSurfer tutorial (MailScanner

[Freesurfer] PetSurfer, PET data format, mri_convert

External Email - Use Caution Hi Freesurfer developers, I am new to PET and FreeSurfer. I am trying to go through the PetSurfer tutorial

[Freesurfer] PetSurfer analisis whit another atlas

External Email - Use Caution Good morning. I try to use surfer analysis with another atas instead of the built-in one. I have an atlas in nifti or mgz format. I tried using it in gtmseg's --head option and it doesn't work, maybe due to normalization issues but I'm not sure. I

Re: [Freesurfer] PETsurfer: PVC without psf of the scanner

External Email - Use Caution what is the justification for using half that? 7.3 is not high in general. what scanner are you using? On 5/8/2023 4:27 AM, Federica Di Antonio wrote: External Email - Use Caution Dear experts, I am here again because I'd like to  ask a

Re: [Freesurfer] PETsurfer: PVC without psf of the scanner

External Email - Use Caution Dear experts, I am here again because I'd like to ask a specification about the fwhm that the alghoritm evaluates: the main value that I obtained was 7.3 mm; It is an high value for a pv correction. May I put in half the value? Because I wonder if the

[Freesurfer] PETsurfer registration

On the PETsurfer wiki, https://surfer.nmr.mgh.harvard.edu/fswiki/PetSurfer, I had recommended using mri_coreg to register your PET to the FS anatomical using the following command line: mri_coreg --s subject --mov template.nii.gz --reg template.reg.lta This works well for PET scans that do

Re: [Freesurfer] PETsurfer: PVC without psf of the scanner

External Email - Use Caution Thank you so much! Il giorno gio 15 dic 2022 alle ore 16:24 Douglas N. Greve < dgr...@mgh.harvard.edu> ha scritto: > I have something called the adaptive GTM that is currently a "hidden" > feature in mri_gtmpvc as it has not been published yet. You

Re: [Freesurfer] PetSurfer - MG coregister

When you load it into freeview, use the aux/bbpet2anat.lta , eg, freeview orig.mgz aseg.mgz mgx.ctxgm.nii.gz:reg=aux/bbpet2anat.lta On 1/17/2023 12:46 PM, Marina Fernández wrote: External Email - Use Caution Dear experts, I am trying to do PVC on FBB-PET images using the following

Re: [Freesurfer] PetSurfer - MG coregister

External Email - Use Caution Thank you so much. Now I at least get a direction from where to start. Regards: Rahul Sharma Research Scholar NIT Silchar Assam 9827834360 *"Manners Maketh Man"* On Wed, Jan 18, 2023 at 5:36 PM Marina Fernández < marina.fdez.alva...@gmail.com>

Re: [Freesurfer] PetSurfer - MG coregister

External Email - Use Caution Dear Rahul, I just used the wiki of the Freesurfer functions, the information is very complete. If you want to use Freesurfer, you can start by doing the cortical reconstruction process for each subject (

Re: [Freesurfer] PetSurfer - MG coregister

External Email - Use Caution Hello Mam, I am not replying to your mail, instead I need to know the source where you learn Freesurfer and pre processing of MRI and PET. Please do reply. On Tue, 17 Jan 2023, 11:16 pm Marina Fernández, < marina.fdez.alva...@gmail.com> wrote: >

[Freesurfer] PetSurfer - MG coregister

External Email - Use Caution Dear experts, I am trying to do PVC on FBB-PET images using the following commands: " mri_coreg --s s_001 --mov s_001_pet_fbb.nii.gz --reg s_001_pet_fbb.reg.lta mri_gtmpvc --i s_001_pet_fbb.nii.gz --reg s_001_pet_fbb.reg.lta --psf 6 --seg gtmseg.mgz

Re: [Freesurfer] PETsurfer: PVC without psf of the scanner

I have something called the adaptive GTM that is currently a "hidden" feature in mri_gtmpvc as it has not been published yet. You can try it by adding the following flags --opt 1 --opt-tol 4 10e-6 .02 --opt-seg-merge When this is done, there will be a file called gtmdir/aux/opt.params.dat The

[Freesurfer] PETsurfer: PVC without psf of the scanner

External Email - Use Caution Dear experts, Few weeks ago i wrote to this mailing list but I didn't receive any answer, so I'll try again: mri_gtmpvc --i pet.nii.gz --reg template.reg.lta --psf FWHM --seg gtmseg.mgz --default-seg-merge --auto-mask 1 .01 --mgx .01 --o

[Freesurfer] PETsurfer: PVC without psf of the scanner

External Email - Use CautionDear experts,  mri_gtmpvc --i pet.nii.gz --reg template.reg.lta --psf FWHM --seg gtmseg.mgz --default-seg-merge  --auto-mask 1 .01 --mgx .01 --o gtmpvc.output About this command, is there the possibility for PETsurfer to compute the fwhm of the psf of

Re: [Freesurfer] PETSurfer tutorial images?

: External Email - Use Caution Dear FreeSurfer/PETSurfer experts, I am beginning to explore the functionality of PETSurfer, and in the Wiki there is reference to a set of 18 folders (" called s01, s02, etc"), and I am wondering if that dataset is publicly available (and if so, whe

[Freesurfer] PETSurfer tutorial images?

External Email - Use Caution Dear FreeSurfer/PETSurfer experts, I am beginning to explore the functionality of PETSurfer, and in the Wiki there is reference to a set of 18 folders ("  called s01, s02, etc"), and I am wondering if that dataset is publicly  available

Re: [Freesurfer] PetSurfer: subcortical volume-based analysis

From: * on behalf of "Douglas N. Greve" *Reply-To: *Freesurfer support list *Date: *Friday, February 25, 2022 at 10:25 AM *To: *"freesurfer@nmr.mgh.harvard.edu" *Subject: *Re: [Freesurfer] PetSurfer: subcortical volume-based analysis Are you doing an ROI analysis or a voxel-

Re: [Freesurfer] PetSurfer: subcortical volume-based analysis

surfer support list Date: Friday, February 25, 2022 at 10:25 AM To: "freesurfer@nmr.mgh.harvard.edu" Subject: Re: [Freesurfer] PetSurfer: subcortical volume-based analysis Are you doing an ROI analysis or a voxel-wise analysis? If an ROI analysis, then use mri_gtmpvc (with or without PVC

Re: [Freesurfer] PetSurfer: subcortical volume-based analysis

half of "Douglas N. Greve" *Reply-To: *Freesurfer support list *Date: *Tuesday, February 22, 2022 at 3:00 PM *To: *"freesurfer@nmr.mgh.harvard.edu" *Subject: *Re: [Freesurfer] PetSurfer: subcortical volume-based analysis I don't understand. What mask? On 2/22/2022 8:55 A

Re: [Freesurfer] PetSurfer: subcortical volume-based analysis

310-315-4069 From: on behalf of "Douglas N. Greve" Reply-To: Freesurfer support list Date: Tuesday, February 22, 2022 at 3:00 PM To: "freesurfer@nmr.mgh.harvard.edu" Subject: Re: [Freesurfer] PetSurfer: subcortical volume-based analysis I don't understand. What ma

Re: [Freesurfer] PetSurfer: subcortical volume-based analysis

rd.edu *Subject:* Re: [Freesurfer] PetSurfer: subcortical volume-based analysis The GTM gives you values for each ROI regardless of whether it is GM, WM, or CSF. They will probably give you similar answers, but the GTM will be more robust. On 2/21/2022 8:48 PM, Jennifer Bramen wrote: Ex

Re: [Freesurfer] PetSurfer: subcortical volume-based analysis

kef> From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Douglas N. Greve Sent: Monday, February 21, 2022 7:13:39 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] PetSurfer: subcortical volume-based analysis The GTM gives you values for each ROI rega

Re: [Freesurfer] PetSurfer: subcortical volume-based analysis

half of "Douglas N. Greve" *Reply-To: *Freesurfer support list *Date: *Monday, February 21, 2022 at 2:02 PM *To: *"freesurfer@nmr.mgh.harvard.edu" *Subject: *Re: [Freesurfer] PetSurfer: subcortical volume-based analysis You need to first map your pet to the anatomical

Re: [Freesurfer] PetSurfer: subcortical volume-based analysis

#150 Santa Monica, CA 90404 Phone: 310-525-0865 | Fax: 310-315-4069 From: on behalf of "Douglas N. Greve" Reply-To: Freesurfer support list Date: Monday, February 21, 2022 at 2:02 PM To: "freesurfer@nmr.mgh.harvard.edu" Subject: Re: [Freesurfer] PetSurfer: subcortical vo

Re: [Freesurfer] PetSurfer: subcortical volume-based analysis

#150 Santa Monica, CA 90404 *Phone:* 310-525-0865  | *Fax: *310-315-4069 *From: * on behalf of "Douglas N. Greve" *Reply-To: *Freesurfer support list *Date: *Wednesday, February 16, 2022 at 7:30 AM *To: *"freesurfer@nmr.mgh.harvard.edu" *Subject: *Re: [Freesurfer] PetSurfer:

Re: [Freesurfer] PetSurfer: subcortical volume-based analysis

0865 | Fax: 310-315-4069 From: on behalf of "Douglas N. Greve" Reply-To: Freesurfer support list Date: Wednesday, February 16, 2022 at 7:30 AM To: "freesurfer@nmr.mgh.harvard.edu" Subject: Re: [Freesurfer] PetSurfer: subcortical volume-based analysis If you want to do an ROI

Re: [Freesurfer] PetSurfer: CORTICAL volume-based analysis

I just sent info on how to do this, but see step 5 in the wiki On 2/14/2022 6:27 PM, Jennifer Bramen wrote: External Email - Use Caution Dear Freesurfer Developers I am doing an ROI--based amyloid PET scan analysis. I am following the steps from the PetSurfer wiki. I see

Re: [Freesurfer] PetSurfer: subcortical volume-based analysis

If you want to do an ROI analysis using FS-based ROIs, you should do that at the individual level. Resample the PET to the anatoimical space, then run mri_segstats passing the PET with --i and using --seg to spec the segmentation. If you really want to do it in MNI305 space, then it is the

[Freesurfer] PetSurfer: CORTICAL volume-based analysis

External Email - Use Caution Dear Freesurfer Developers I am doing an ROI--based amyloid PET scan analysis. I am following the steps from the PetSurfer wiki. I see instructions for how to do a cortical surface-based group analysis. I also see how to do a subcortical ROI-based

[Freesurfer] PetSurfer: subcortical volume-based analysis

External Email - Use Caution Dear Freesurfer Developers I am doing an ROI--based amyloid PET scan analysis. I have completed all of the steps from the PetSurfer wiki. I now have the preprocessed, averaged, resampled, smoothed PET data in MNI305 space which is constrained to the

Re: [Freesurfer] PETSurfer: error: MatrixReadTxT: could not scan value [1][1]

eply-To: Freesurfer support list Date: Monday, February 7, 2022 at 9:50 AM To: Freesurfer support list 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 d

Re: [Freesurfer] PETSurfer: error: MatrixReadTxT: could not scan value [1][1]

" Reply-To: Freesurfer support list Date: Friday, February 4, 2022 at 5:09 AM To: "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

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

[Freesurfer] PETSurfer: error: MatrixReadTxT: could not scan value [1][1]

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

[Freesurfer] PETSurfer: Which is the right way to turn off PVC?

External Email - Use Caution Hello, I have a question regarding the following PETSurfer command: mri_gtmpvc --i pet.nii.gz --reg template.reg.lta --psf FWHM --seg gtmseg.mgz --default-seg-merge --auto-mask 1 .01 --mgx .01 --o gtmpvc.output I have been trying to run the

[Freesurfer] PETSurfer: Which is the right way to turn off PVC?

External Email - Use Caution Hello, I have a question regarding the following PETSurfer command: mri_gtmpvc --i pet.nii.gz --reg template.reg.lta --psf FWHM --seg gtmseg.mgz --default-seg-merge --auto-mask 1 .01 --mgx .01 --o gtmpvc.output I have been trying to run the

[Freesurfer] PETSurfer: Which is the right way to turn off PVC?

External Email - Use Caution Hello, I have a question regarding the following PETSurfer command: mri_gtmpvc --i pet.nii.gz --reg template.reg.lta --psf FWHM --seg gtmseg.mgz --default-seg-merge --auto-mask 1 .01 --mgx .01 --o gtmpvc.output I have been trying to run the

Re: [Freesurfer] PETsurfer

Great! Thanks SO much. Kindly, Ludovica On Nov 3, 2021, at 20:43, Adam Martersteck wrote:  External Email - Use Caution PETsurfer wasn't released until the v6.0.0 stable build. You can see it in the release notes here: MailScanner has detected a possible fraud attempt from

Re: [Freesurfer] PETsurfer

External Email - Use Caution PETsurfer wasn't released until the v6.0.0 stable build. You can see it in the release notes here:

Re: [Freesurfer] PETsurfer

Hi! Thanks a lot. I have freesurfer 5.3.0 installed. If I type on the terminal commands such as tkregister it works , but if I try PETsurfer commands I have errors such as "mri_gtmpvc: Command not found”. Any idea? Thank you, Ludovica > On Nov 3, 2021, at 10:05, Douglas N. Greve wrote: > >

Re: [Freesurfer] PETsurfer

There is nothing special you have to do. What version of FS do you have? You still have to source the FS environment. If you can run recon-all, you should be able to run PETsurfer On 11/1/2021 12:26 PM, Brusaferri, Ludovica wrote: Hi! I have been using freesurfer regularly and I am now

[Freesurfer] PETsurfer

Hi! I have been using freesurfer regularly and I am now trying to implement a few commands from PETsurfer https://surfer.nmr.mgh.harvard.edu/fswiki/PetSurfer . It seems like I cannot use any of the commands listed in the wiki (such as gtmseg

Re: [Freesurfer] PETSurfer voxelwise statistic

Traditionally, MG analysis is only run on GM. In principle, it is possible to run it on WM, but we don't offer that as an option. On 11/25/2020 8:16 AM, Boris Rauchmann wrote: External Email - Use Caution Dear all, How can I run a voxelwise statistic using grey and white matter

Re: [Freesurfer] PETSurfer

One way you can do it is to specify all the GM ROIs with --rescale Id1 Id2 ... Otherwise, you can run fscalc, eg, fscalc mgx.ctxgm.nii.gz div `cat global.gm.dat ` -mul 100 -o mgx.ctxgm.rescaled.nii.gz On 11/20/2020 11:44 AM, Boris Rauchmann wrote: External Email - Use Caution Dear

[Freesurfer] PETSurfer voxelwise statistic

External Email - Use Caution Dear all, How can I run a voxelwise statistic using grey and white matter uptake? mgx.ctxgm.nii.gz and the other files in output all only include gm as I understand. My goal is to run whole brain volume-based analysis. Like in this example for

[Freesurfer] PETSurfer

External Email - Use Caution Dear all, How can I easily scale the mgx.ctxgm.nii.gz files with the whole brain mean intensity using PETSufer? Is there a command to use in mri_gtmpvc like --rescale X? I know that I can find the mean in global.gm.dat and I can use that value for

[Freesurfer] PETSURFER for AV1451

External Email - Use Caution Hi PETSURFERs,  A quick question to the group: Does any one have experience using PETSURFER on dynamic AV1451 scans? How can I know whether the MRTM1 or MRTM2 using midbrains (due to off target AV1451 binding) is suitable for my data?  Thank you!

Re: [Freesurfer] Petsurfer - negative values after RBV partial volume correction

Yes, this is not unusual. The GTM (which RBV is based on) is just a GLM where it uses a linear model to estimate the ROI intensities. There are no constraints on positivity. When the model is not exactly correct (which it never will be) it is possible to get negative values. Usually this only

Re: [Freesurfer] PETSurfer questions part III

6 >>> --seg Subj_gtmseg.mgz --default-seg-merge --Meltzer .1 .1 1 --o >>> gtm_MZ.output >>> >>> Then: >>> >>> mri_segstats --i gtm_MZ.output/meltzer.nii.gz --seg >>> gtm_MZ.output/aux/seg.nii.gz --ctab gtm_MZ.output/aux/seg.ctab --sum >

[Freesurfer] PETSurfer questions part III

tput >> >> Then: >> >> mri_segstats --i gtm_MZ.output/meltzer.nii.gz --seg >> gtm_MZ.output/aux/seg.nii.gz --ctab gtm_MZ.output/aux/seg.ctab --sum >> MZ_ROI.txt >> >> >> Do you recognize any errors in the commands? >> >>

Re: [Freesurfer] PETSurfer questions - Part II

t;> Subject: Re: [Freesurfer] PETSurfer analysis question To: <mailto:freesurfer@nmr.mgh.harvard.edu>> Message-ID: <mailto:d56acc7d-3273-4f40-ed17-570a893b2...@mgh.harvard.edu>> Content-Type: text/plain; charset="utf-8" The NoPVC and SGTM values are reasonable.

Re: [Freesurfer] PetSurfer Crashing

Did you really mean to pass subject/mri/gtmseg.lta ? The registration is supposed to be the registration of the input (PET.template.nii.gz) to the anatomical. subject/mri/gtmseg.lta is the registration of gtmseg.mgz to the anatomical. On 7/20/20 11:21 AM, Crawford, Anna wrote:

[Freesurfer] PetSurfer Crashing

External Email - Use Caution Hello, I am trying to run the PetSurfer process for the first time. I was able to run gtmseg and mri_coreg which seemed to go okay. When I tried running mri_gtmpvc, it is crashing, but I am not sure why. The command I am using and output are

[Freesurfer] PETSurfer questions - Part II

gtm_MZ.output/aux/seg.ctab --sum MZ_ROI.txt Do you recognize any errors in the commands? Many thanks, Pilar Message: 13 Date: Thu, 16 Jul 2020 10:19:32 -0400 From: "Douglas N. Greve" mailto:dgr...@mgh.harvard.edu>> Subject: Re: [Freesurfer] PETSurfer analysis question To: m

Re: [Freesurfer] PETSurfer analysis question

The NoPVC and SGTM values are reasonable. The MG value is pretty crazy. I don't put stock in MZ. Is the MG value much higher than SGTM in other ROIs? What is your mri_gtmpvc command? On 7/16/2020 4:38 AM, Ferraro, Pilar wrote: External Email - Use Caution Hi Freesurfer experts,

[Freesurfer] PETSurfer analysis question

External Email - Use Caution Hi Freesurfer experts, I’ve run a PETSurfer analysis in order to compare mean uptake values of ROIs obtained with different methods: No PVC, SGTM, MG and MZ. However, I’ve now extracted the mean values and they are extremely heterogeneous. As an

Re: [Freesurfer] PETsurfer: --usf in gtmseg

yes, that controls how finely the surface-based segmentations are resampled into the volume. The surface is semi-continuous so you can sample them into the volume as finely as you like. 0.5mm seems to work fine. On 5/26/2020 4:33 PM, Julie Ottoy wrote: External Email - Use Caution

[Freesurfer] PETsurfer: --usf in gtmseg

External Email - Use Caution Hi, In PETsurfer gtmseg, there is the --usf (upsampling factor) which is by default 2, corresponding to 0.5 mm voxelsize. I was wondering if the usf is recommended to be chosen depending on your mri voxelsize (eg, usf 1 for 1mm voxelsize of the mri),

Re: [Freesurfer] PETSurfer / Questions

On 4/14/2020 5:40 AM, Ferraro, Pilar wrote: External Email - Use Caution Dear Freesurfer experts, We are conducting a PETSurfer analysis, and have some questions on the best way to proceed.  Briefly, this is what we have done: After running the standard Freesurfer analysis an all

Re: [Freesurfer] PETSurfer / Questions

External Email - Use Caution Dear Freesurfer experts, We are conducting a PETSurfer analysis, and have some questions on the best way to proceed. Briefly, this is what we have done: After running the standard Freesurfer analysis an all the T1 images, we have generated the

Re: [Freesurfer] Petsurfer: Gtmstats < 1, voxel wise mean is fine

0.809017 From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Douglas N. Greve Sent: Wednesday, April 1, 2020 10:16 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Petsurfer: Gtmstats < 1, voxel wise mean is fine Can you include previous ema

Re: [Freesurfer] Petsurfer: Gtmstats < 1, voxel wise mean is fine

: [Freesurfer] Petsurfer: Gtmstats < 1, voxel wise mean is fine What is the value for cerebellum in those three scenarious (gtm, no pvc, and mgx)? On 3/10/2020 12:37 PM, Eckbo, Ryan wrote: Hello experts, I've recently run into a case the gtmstats uptake (reference region: cerebel

Re: [Freesurfer] Petsurfer: Gtmstats < 1, voxel wise mean is fine

...@nmr.mgh.harvard.edu on behalf of Douglas N. Greve Sent: Wednesday, March 11, 2020 10:01 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Petsurfer: Gtmstats < 1, voxel wise mean is fine What is the value for cerebellum in those three scenarious (gtm, no pvc, and mgx)? On 3/10/2020 12:37

Re: [Freesurfer] PetSurfer reference region

, Aylin ___ Message: 11 Date: Fri, 6 Mar 2020 16:59:53 -0500 From: "Douglas N. Greve" Subject: Re: [Freesurfer] PetSurfer reference region To: Message-ID: <8c262861-3272-151b-ae18-906898408...@mgh.harvard.edu> Content-Type: text/plain; charset="windows-125

Re: [Freesurfer] PetSurfer reference region

-0500 From: "Douglas N. Greve" Subject: Re: [Freesurfer] PetSurfer reference region To: Message-ID: <8c262861-3272-151b-ae18-906898408...@mgh.harvard.edu> Content-Type: text/plain; charset="windows-1252" I think the issue is that your input has multiple frames (6). It wil

Re: [Freesurfer] Petsurfer: Gtmstats < 1, voxel wise mean is fine

What is the value for cerebellum in those three scenarious (gtm, no pvc, and mgx)? On 3/10/2020 12:37 PM, Eckbo, Ryan wrote: Hello experts, I've recently run into a case the gtmstats uptake (reference region: cerebellum) for the pericarlcarine ROI's are as low as 0.40, however computing the

[Freesurfer] Petsurfer: Gtmstats < 1, voxel wise mean is fine

Hello experts, I've recently run into a case the gtmstats uptake (reference region: cerebellum) for the pericarlcarine ROI's are as low as 0.40, however computing the voxel wise mean using input.rescaled.nii.gz and mgx.ctxgm.nii.gx and aux/seg.nii.gz, the values are closer to 1, as expected: |

Re: [Freesurfer] PetSurfer reference region

wrote: External Email - Use Caution Thanks for the quick reply. I attached the terminal output to this email. We are running this on v6. Best, Aylin ___ Message: 9 Date: Fri, 6 Mar 2020 11:50:51 -0500 From: "Douglas N. Greve" Subject: Re: [Freesurfer]

Re: [Freesurfer] PetSurfer reference region

External Email - Use Caution Thanks for the quick reply. I attached the terminal output to this email. We are running this on v6. Best, Aylin ___ Message: 9 Date: Fri, 6 Mar 2020 11:50:51 -0500 From: "Douglas N. Greve" Subject: Re: [Freesurfer]

Re: [Freesurfer] PetSurfer reference region

I cannot replicate this in either v6 or v7beta. Can you send the terminal output? On 3/5/2020 1:32 PM, Dincer, Aylin wrote: External Email - Use Caution Hello PetSurfer experts, We are using the cerebellum cortex as our reference region, but noticed that the SUVR values for lh/rh

Re: [Freesurfer] petsurfer

I cannot replicate this, eg In matlab a = fast_vol2mat(MRIread('gtm.nii.gz')); a(1:10)   Columns 1 through 7     0.7957    1.0565    1.5711    1.7842    1.8625    1.9539 1.2499   Columns 8 through 10     1.3188    1.4063    1.2536 From gtm,.stats.dat   1    2 Left-Cerebral-White-Matter  wm  

[Freesurfer] PetSurfer reference region

External Email - Use Caution Hello PetSurfer experts, We are using the cerebellum cortex as our reference region, but noticed that the SUVR values for lh/rh cerebellum cortex do not have a value of 1 (which is what we were expecting). The actual SUVR values are 1.31 for the lh

[Freesurfer] petsurfer

External Email - Use Caution Dear Freesurfer experts, I have compared the PVC uptake values of gtm.stats with the values of gtm.nii.gz with the function load_nii in matlab. I noted that values in matlab are reversed, i. e., the first value in gtm.stats matches with the last value

Re: [Freesurfer] PetSurfer questions

External Email - Use Caution Thank you Dr.Greve. I applied to rbv.nii.gz volume to anatomical space. You said, bbpet2anat.lta. using mri_vol2vol but I tested. registration using bbpet2anat.lta was not correct on native T1 space. So I tested rbv2anat.lta for registration. that

Re: [Freesurfer] PetSurfer questions

External Email - Use Caution *Thank you Dr. Greve for your answer* I checked all about your comment. I have questions more. 1. I found that volumes or counts in gtm.stats.dat are for native PET space. If co-registered PET onto corresponding MRI(i.e. MRI space) is available

Re: [Freesurfer] PetSurfer questions

On 2/9/2020 10:19 PM, Soo-Jong Kim wrote: External Email - Use Caution Thank you, Dr. Greve I checked all about your comment. I have questions more. 1. I found that volumes or counts in gtm.stats.dat are for native PET space. If co-registered PET onto corresponding MRI(i.e. MRI

Re: [Freesurfer] PetSurfer questions

External Email - Use Caution Thank you, Dr. Greve I checked all about your comment. I have questions more. 1. I found that volumes or counts in gtm.stats.dat are for native PET space. If co-registered PET onto corresponding MRI(i.e. MRI space) is available using rbv.nii.gz from

Re: [Freesurfer] PetSurfer questions

External Email - Use Caution Thank you, Dr. Greve I checked all about your comment. I have questions more. 1. I found that volumes or counts in gtm.stats.dat are for native PET space. If co-registered PET onto corresponding MRI(i.e. MRI space) is available using rbv.nii.gz from

Re: [Freesurfer] PetSurfer questions

On 2/3/2020 11:56 PM, Soo-Jong Kim wrote: External Email - Use Caution Thank you, Dr. Greve I checked all about your comment. I have questions more. 1. I found that volumes or counts in gtm.stats.dat are for native PET space. If co-registered PET onto corresponding MRI(i.e. MRI

Re: [Freesurfer] PetSurfer questions

External Email - Use Caution Thank you, Dr. Greve I checked all about your comment. I have questions more. 1. I found that volumes or counts in gtm.stats.dat are for native PET space. If co-registered PET onto corresponding MRI(i.e. MRI space) is available using rbv.nii.gz from

Re: [Freesurfer] PetSurfer questions

On 1/30/2020 3:39 AM, Soo-Jong Kim wrote: External Email - Use Caution I ran gtmseg for my partial volume correction 1. but I have a question. What regions are for the detail?? in this option. mri_gtmpvc --default-seg-merge. I searched mri_gtmpvc --help but it is default schema

Re: [Freesurfer] PetSurfer questions

External Email - Use Caution I ran gtmseg for my partial volume correction 1. but I have a question. What regions are for the detail?? in this option. mri_gtmpvc --default-seg-merge. I searched mri_gtmpvc --help but it is default schema for merging ROIs. So I wanna know what

Re: [Freesurfer] PETSurfer individual atlas for subcortocal segmentation

External Email - Use Caution Dear Doug, thank you for your effort. Let me know if you have any updates on this. Best, Boris On Fri, Dec 6, 2019 at 5:45 PM Greve, Douglas N.,Ph.D. < dgr...@mgh.harvard.edu> wrote: > Hi Boris, I'll try to get to it today. Unfortunately, I think

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