Yes, this is a bug. I have fixed it in our development version. For
now, you can use your workaround.
On 12/7/2024 1:28 AM, Shen, Qian wrote:
External Email - Use Caution
Hi Dr. Greve and Experts,
I encountered an issue while running the following command to resample
meltzer.nii.gz
Hi Zeno,
We recommend using the output of gtmseg for the segmentaion.
See: https://surfer.nmr.mgh.harvard.edu/fswiki/PetSurfer
To change the reference region, change the `--km-ref` values when running
mri_gtmpvc. You can use freeview to open gtmseg.mgz to find the values
visually, or use the
External Email - Use Caution
Thank you Doug.
Regards,
Sneha
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Douglas N. Greve
Sent: Monday, September 30, 2024 10:42 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [EXTERNAL] Re: [Freesurfer] petsurfer using brainstem
:* freesurfer@nmr.mgh.harvard.edu
*Subject:* [EXTERNAL] Re: [Freesurfer] petsurfer using brainstem subfields
It is tricky but possible, but not might be worth it. You need to have
a whole brain segmentation, so you could superimpose the subfields
onto the aparc+aseg. You will need to create a co
ect: [EXTERNAL] Re: [Freesurfer] petsurfer using brainstem subfields
It is tricky but possible, but not might be worth it. You need to have a whole
brain segmentation, so you could superimpose the subfields onto the aparc+aseg.
You will need to create a color table for it (see gtmseg. ctab af
It is tricky but possible, but not might be worth it. You need to have a
whole brain segmentation, so you could superimpose the subfields onto
the aparc+aseg. You will need to create a color table for it (see
gtmseg.ctab after running gtmseg). You can then specify the new seg with
--seg to mri_
External Email - Use Caution
Dear team,
I wanted to follow up on the following question. Thank you.
Regards,
Sneha
From: Sneha Pandya
Sent: Tuesday, August 27, 2024 12:22 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: petsurfer using brainstem subfields
Dear team,
We need to u
--o
CerebellumGrayMatterMaskEroded_gtmseg.mgz --match 8 47 --erode 2
Thank you,
Sneha
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Douglas N. Greve
Sent: Friday, August 23, 2024 6:25 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [EXTERNAL] Re: [Freesurfer] petsurfer questions - No PVC stats file in
the simi
looks like it is only different in the first or second decimal place, is
that right? If so, then it is acceptable.
On 8/22/2024 4:11 PM, Sneha Pandya wrote:
External Email - Use Caution
Dear team,
A] I am running mri_gtmpvc on our data and need to extract stats data
that is in the s
On 8/13/2024 12:38 AM, WONG Wan Wa wrote:
External Email - Use Caution
Hi FS experts,
I want to do PET SUVR analysis using PetSurfer. When determining the
FWHM of the PSF of the scanner, is it the same value for Siemens
(Biograph40_mCT vs. Biograph128_mCT) or (Biograph64_Vision 600
You can run something like
mri_convert nopvc.nii.gz --ascii nopvc.dat
This will give you a text file
To put a bunch together across subject, you can run something like
mri_concat */nopvc.nii.gz --o all.nopvc.nii.gz
Then do the same trick as above.
On 8/20/2024 12:01 AM, WONG Wan Wa wrote:
External Email - Use Caution
Any idea?
Angel Wong, PhD
Scientific Officer
Hong Kong Center for Neurodegenerative Diseases (HKCeND)
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of WONG Wan Wa
Sent: Thursday, August 15, 2024 12:13 PM
T
External Email - Use Caution
Dear Doug,
Thank you for the response.
Regards,
Sneha
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Douglas N. Greve
Sent: Wednesday, June 12, 2024 9:11 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [EXTERNAL] Re: [Freesurfer
It is not PVC corrected. To do that, you'd have to use the --mgx or --rbv
Note that doing voxel-wise PVC is tricky because you have multiple
tissue types in each voxel. So you can keep the same resolution but
then you have to represent only one tissue type (mgx) or you have to
create a higher
: 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
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
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
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
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
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 2mm
-
*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
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 modeling be ap
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
, 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
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
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.
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 y
External Email - Use Caution
Hi Zeyu,
It looks like your files are in 'interfile' format.
If you have access to pmod, you might be able to use that to convert your files
to nifti.
https://secure-web.cisco.com/1zqVVdVIc7totHjAN-r1V2oHpo0YeUbAKoFLyEzf5hGF_2QpNKUkYjapa61k7l3PSjeARv
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 spe
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
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
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 co
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> wro
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 (
https://secure-web.cisco.com/1Lj_XzmtE_iAYreTtm
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:
>
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 va
that's from a tutorial that I never finished. You can get the data from here
https://gate.nmr.mgh.harvard.edu/safelinks/greve/sb01.tar.gz
https://gate.nmr.mgh.harvard.edu/safelinks/greve/uw.fsf01anat.tar.gz
username guest
pwd collab
On 9/26/2022 12:13 PM, daedalu...@aol.com wrote:
Exte
rom: * 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 v
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-wise analysis? If an ROI analysis,
then use mri_gtmpvc (with or withou
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 mask?
On 2/22/2
Fax: 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 understan
harvard.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:
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 regardl
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 volume-based analysis
You need to first map your pet to the anatomical spa
St. #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: subcortic
St. #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] PetSur
-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: subcortical volume-based analysis
If you want to do a
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 instructions
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 same
n
Reply-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 do K
ve"
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
tim
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
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
"secur
External Email - Use Caution
PETsurfer wasn't released until the v6.0.0 stable build. You can see it in
the release notes here:
https://secure-web.cisco.com/1n9uot8CDL1X4zb4xQXVdkvdqbv2ngmmjy0xI-YpaJo1tCft8AUJ0fOq2tnIi9H-neObzRYbNnzQ_f-6Te5NpdO_gdoIcUF7wBpGrIgl62EZEaig2VymVFjCNARkn
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:
>
> T
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 trying
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 uptake?
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 al
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 h
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
>
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. The
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:
Extern
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,
I
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
Hi
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
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 segm
0.47 |
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
:* 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:
cerebe
-boun...@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
much,
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-1
-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
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 v
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]
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]
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 ce
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
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 w
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
usin
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 spa
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 m
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 m
On 2/3/2020 11:56 PM, Soo-Jong Kim wrote:
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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 spa
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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 m
On 1/30/2020 3:39 AM, Soo-Jong Kim wrote:
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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
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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 reg
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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 th
Hi Boris, I'll try to get to it today. Unfortunately, I think this is going to
require a fair amount of effort on my part. When I wrote this part of
PETsurfer, I just did not make it super flexible.
doug
On 12/5/2019 10:17 PM, Boris Rauchmann wrote:
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Did yo
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Did you already have the time to look at the logfile? Do you have any
suggestions how to proceed?
Thank you!
> Am 02.12.2019 um 19:18 schrieb Boris Rauchmann :
>
>
> In this example tried it with only the subcortical segmentations from my
> atlas
what ligand are you using? Do you expect it to be higher in GM and in WM? What
are the values in the gtm.stats file relative to when you run it without PVC?
How did you choose 5 as the --psf?
On 11/26/2019 2:53 AM, Soo-Jong Kim wrote:
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Dear FreeSurfer expert
The MGX method is only valid in voxels that have some gray matter in
them (defined as 1% in the command line below), so any WM is set to 0
(probably accounts for the big hole that you see). The mgx output is
divided into cortical GM and subcortical GM, so you are probably looking
at the cortica
I'm not sure I understand. It seems like the picture is misoriented but then
you say that bbpet2anat.lta is correct because you applied it to the
mgx.gm.nii.gz and it is aligned with the orig.
On 7/10/2019 2:32 PM, Eckbo, Ryan wrote:
Hi Doug and experts,
We're interested in running a voxel wis
Did yyou check the tal registration of the subjects as created by
recon-all?
tkregister2 --mgz --s subject --fstal --surf orig
On 7/10/19 2:32 PM, Eckbo, Ryan wrote:
>
> Hi Doug and experts,
>
> We're interested in running a voxel wise test-retest reliability
> analysis on a set of PBR28 PET i
Yes, look in the gtm.stats.dat file. See this page for whichi column you need
to look at
https://surfer.nmr.mgh.harvard.edu/fswiki/PetSurfer
On 5/17/2019 12:42 PM, Boris Rauchmann wrote:
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Hi all,
is there a way to easily get the volume stats for all regions
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Thanks, Doug. I think the command is MCFLIRT.
https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/MCFLIRT
Best Wishes,Shane
On Friday, May 3, 2019, 6:18:54 PM GMT+1, Shane Schofield
wrote:
Hi Freesurfer Team,
How may I align 5 volumes of my PET data ( 5
If you have them in nifti format, you can use afni or fsl (we don't have our
own motion correction)
On 5/3/2019 1:18 PM, Shane Schofield wrote:
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Hi Freesurfer Team,
How may I align 5 volumes of my PET data ( 5 min acquisitions each) to a mean
image for moti
What is fICL161363_06_1_MRI_9746_series_2_MPRAGE_ADNI_P2.nii ? In general,
you should not give mri_coreg a reference when using --s unless it is the same
geometry as the orig.mgz
On 3/29/19 11:55 AM, ?? wrote:
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Hi developers,
I am using the petsurfer now
Usually, an intensive study is done with any new tracer in which they do
arterial sampling and apply various kinetic models to determine which
one fits best (including which regions to use for high binding in
MRTM2). You should find this study for your tracer. For FDG, MRTM2 is
not appropriate
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Hi Doug, thanks for the explanation. My question is more related to how we
might go about knowing what are the high binding regions for any tracer? If I
am going to do an FDG-PET study, will the HB region parameters be different
from a [11C]-PK11195
You should read up on the MRTM2. Basically, when you run MRTM1, it
computes a separate k2 for each voxel eventhough the k2 should be the
same across the entire brain (since it actually refers to the reference
region). With MRTM2, you estimate the single k2 value from high binding
regions.
On 3
The surface resolution is set during the recon-all analysis and is
uninfluenced by the PET data
On 3/7/19 3:16 AM, Matthieu VANHOUTTE wrote:
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>
> Ok so if I well understand surface in the gtmseg space would not have
> finer resolution than surface in native
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