External Email - Use Caution
I fix it by adding --id 'segmentation id' to mri_segstats.
Thanx Douglas.
Le mer. 10 août 2022 à 03:51, Douglas N. Greve a
écrit :
> Can you send the terminal output and the petsuv.segstats.dat? How have you
> verified that the registration is cor
Can you send the terminal output and the petsuv.segstats.dat? How have
you verified that the registration is correct? What version of FS are
you running?
On 8/5/2022 4:44 PM, Bouchra Guelib wrote:
External Email - Use Caution
I want to segment registered PET to T1 MRI to 45 subcortic
External Email - Use Caution
I want to segment registered PET to T1 MRI to 45 subcortical regions as the
regions in aseg.stats of MRI.
I used mri_segstats --seg MRI-floder/mri/aparc+aseg.mgz --reg
Pet2T1.register.dof12.lta --sum petsuv.segstats.dat --i PET-SPM.mgh
--ctab-default
REgister the FDG to the anatomical (mri_coreg --s subject --mov fdg.nii
--reg fdg.reg.lta), sample the FDG into the anatomical space
(mri_vol2vol --mov fdg.nii --reg fdg.reg.lta --fstarg --o fdg.anat.mgz),
the use mri_segstats --seg
rh.hippoAmygLabels-T1.v21.FS60.FSvoxelSpace.mgz --i fdg.anat.m
External Email - Use Caution
Dear Freesurfer Development Team
I've used freesurfer with hippocampal subfields module to get GM and
Thickness in this region in detail. but now I need this subfields' mask to
use it on my PET data. So I'll appreciate it if you tell me how I can get
t
Sorry, we don't have any tools to convert from PET formats. Not sure where to
go for that ...
On 11/19/2020 8:27 AM, Marina Fernández wrote:
External Email - Use Caution
Dear experts!
I am using PetSurfer and I have a PET dataset that is in ecat format (.v). I
would like to convert th
External Email - Use Caution
Dear experts!
I am using PetSurfer and I have a PET dataset that is in ecat format (.v).
I would like to convert the images to nifti format to start processing the
data.
What function can I use to convert the images?
How can I check that the left-right
I would use unstripped, but it probably won't make much difference. Just
make sure that the registration is good.
On 9/17/19 1:48 PM, Jane Tseng wrote:
>
> External Email - Use Caution
>
> Dear Freesurfer experts,
>
> I was wondering if there is any recommendation on the PET input file
>
External Email - Use Caution
Dear Freesurfer experts,
I was wondering if there is any recommendation on the PET input file for
partial volume correction using mri_gtmpvc? Should I use a
non-skullstripped SUV or a skullstripped SUV? If a skullstripped SUV can be
used, would a tight
On 1/29/19 11:21 AM, Adam Martersteck wrote:
>
> External Email - Use Caution
>
> Hi FreeSurfer team,
> I have two comments/questions about PET PVC & Doug’s 2016 Neuroimage
> paper:
>
> 1) It looks like the 2 rigid transforms created during mri_gtmpvc
> found at [$pvc_directory/aux/anat
External Email - Use Caution
Hi Freesurfer team,
Just wanted to bump this to see if anyone had any thoughts.
Thanks,
Adam
On Tue, Jan 29, 2019 at 10:21 AM Adam Martersteck
wrote:
> Hi FreeSurfer team,
> I have two comments/questions about PET PVC & Doug’s 2016 Neuroimage paper
It could make sense to apply it to WM. CSF I'm not so sure. Are you
really trying to measure the signal in CSF?
On 10/10/18 6:08 PM, David.Mackarthy wrote:
> External Email - Use Caution
>
> Dear Dr Greve, thank you for the response
> This is for a map-based study. Absolutely, this is cl
External Email - Use Caution
Dear Dr Greve, thank you for the response
This is for a map-based study. Absolutely, this is clear, I appreciate the
response. I just have one additional question and I appreciate your patience.
Is it recommended to apply PVC on white matter or csf? d
Is this for an ROI-based study or a map-based study? For ROI, we use the
GTM, and it PV corrects for all structures (including WM and CSF). For
map-based, we use MG. MG removes WM (and CSF) entirely. In theory, it
can be run in a way to keep WM and throw GM and CSF away, but that is
not impleme
External Email - Use Caution
Dear Dr Greeve,
I am following petsurfer pipeline to do surface based analysis of PET-FDG data
and I have interest in doing partial volume correction. I would like to inquire
about:
1) Can partial volume correction be applied on white mater, or just
It is a little tricky because you don't want to use different masks for
different subjects. I recommend using CVS where I've created a
subcoritcal mask in 2mm space (mri.2mm). So the idea would be that you
map your subcortical MG map to CVS space, then smooth it (mri_fwhm)
specifying the subcor
Dear Dr Greve,
Thank you so much for the quick response.
Just to confirm that I understood the procedure correctly. The analysis is
volume based (i.e. voxel-wise) for the subcortical structures using mask
created by freesurfer's "mri_binarize" for these regions.
Correct?
Original Mess
It is volume-based for subcortical
On 1/12/18 8:17 AM, John Anderson wrote:
Dear Dr Greeve,
I interestingly read the manuscript "Different partial volume
correction methods lead to different conclusions: An (18)F-FDG-PET
study of aging" Thank you for publishing this data.
I understood from
Dear Dr Greeve,
I interestingly read the manuscript "Different partial volume correction
methods lead to different conclusions: An (18)F-FDG-PET study of aging" Thank
you for publishing this data.
I understood from this paper that he recommended stream for PVC is to correct
the PET images using
Hi John
Doug is out of touch for a week. Maybe you can post this again at the end
of next week or early the following if he hasn't responded?
cheers
Bruce
On Fri, 12 Jan 2018, John Anderson
wrote:
Dear Dr Greeve,
I interestingly read the manuscript "Different partial volume correction
m
Dear Dr Greeve,
I interestingly read the manuscript "Different partial volume correction
methods lead to different conclusions: An (18)F-FDG-PET study of aging" Thank
you for publishing this data.
I understood from this paper that he recommended stream for PVC is to correct
the PET images using
ht-F3orb not set
Failed tissue type check
Any help with this would be very much appreciate it!
Thanks!
Elena
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve
[gr...@nmr.mgh.harvard.edu]
Sent: Th
Hi Elena, it looks like the aseg.mgz has several unexpected segments in
it. The aseg.auto.mgz looks ok, so I think FS is working properly. It
looks like you made some changes to the aseg. What did you do?
On 12/06/2017 03:51 PM, Douglas N Greve wrote:
> Did you run this through the standard FS
Did you run this through the standard FS pipeline? If so, can you send
me the FS analysis for this subject? You can upload it here
https://gate.nmr.mgh.harvard.edu/filedrop2
On 12/06/2017 09:46 AM, Herranz Muelas, Elena wrote:
> Dear Freesurfers,
>
>
> I am trying to apply partial volume correc
Dear Freesurfers,
I am trying to apply partial volume correction to my PET images, following
the steps explained in the PetSurfer wiki.
When I run the mri_gtmpvc command, it works fine for most of the subjects but
for some of them I get the following error message:
/autofs/space/alicudi_00
There is not time.dat file. CAn you send it?
On 11/13/17 4:28 PM, Conchy PF wrote:
Dear Douglas,
I did not save the full output from the beginning when I processed
this subject. I can send you what I get when I run the
mri_glmfit command. If you need this output, I can run another subject
Dear Douglas,
I run another participant with PET Surfer. This time I converted the
original PET image from .hdr/.img to nii.gz using mri_convert. I had the
same problem when I run MRTM1. Please, find attached the log from the
beginning.
Thank you and kind regards,
CP
On Mon, Nov 13, 2017 at 9:3
Sorry, I forgot the time.dat file. Here it goes.
Thank you,
CP
On Mon, Nov 13, 2017 at 9:28 PM, Conchy PF wrote:
> Dear Douglas,
>
> I did not save the full output from the beginning when I processed this
> subject. I can send you what I get when I run the
>
> mri_glmfit command. If you need t
Dear Douglas,
I did not save the full output from the beginning when I processed this
subject. I can send you what I get when I run the
mri_glmfit command. If you need this output, I can run another subject from
the beginning. Please, find attached the original pet data, .nii.gz,
time.dat, and .d
Can you send the full terminal output? ie, evverything that is printed
to the screen until the program exists? Also, can you send the nii.gz,
.dat, and time.dat file?
On 11/13/2017 03:16 PM, Conchy PF wrote:
> Dear Douglas,
>
> I checked km.ref.tac.dat and these are the values (I also copied th
Dear Douglas,
I checked km.ref.tac.dat and these are the values (I also copied the values
from km.hb.tac.dat):
hbref
26.73126411 -4.761529326
-51.51094818 9.139505029
-44.41317749 -30.22258914
220.9154358 14.15057564
-148.9746399 -43.47668242
616.010437 693.7505493
3824.4064
Please check the reference TAC. Also, please send the full terminal output
On 11/11/2017 06:07 AM, Conchy PF wrote:
> Dear Douglas,
>
> I had the same problem as Jonathan described in his post "PET
> processing seg fault with mri_glmfit --mrtm1"
> (https://mail.nmr.mgh.harvard.edu/pipermail//fr
Dear Douglas,
I had the same problem as Jonathan described in his post "PET processing
seg fault with mri_glmfit --mrtm1" (
https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2016-January/043144.html
).
In my case, I used this command:
mri_glmfit --y gtmpvc/km.hb.tac.nii.gz --mrtm1 gtmpvc/km
PVC will increase signal in some regions and will decrease it in others.
Eg, for FDG it will increase it in GM and decrease it in WM. The reason
you are seeing such a wide range is that the MG correction subtracts the
WM then divides by the GM partial volume fraction (PVF, a number
between 0 a
Hi Dr Greve, Thank you very much for the great answers.
Kindly, I have one last question.
The range of the signal intensity within the voxels in the original SUV maps is
min=0.00 and max=3.017629
For the mgx images it is min=-43.74384 and max=88.468712
The difference in the range of signal inten
On 8/18/17 10:20 AM, John Anderson wrote:
Hi Dr Greve,
I followed the steps in WIKI to do SUV-surface based analyses + PVC. I
have the following questions and I highly appreciate your input:
1. Why the dimension of the images (mgx.gm, mgx.ctx.gm and
mgx.ctx.subgm) is not like the original
Hi Dr Greve,
I followed the steps in WIKI to do SUV-surface based analyses + PVC. I have the
following questions and I highly appreciate your input:
1. Why the dimension of the images (mgx.gm, mgx.ctx.gm and mgx.ctx.subgm) is
not like the original SUV image that has been fed to the pipeline. i.
Hi Dr Greve,
Thanks again for the great explanation and for clarifying how smoothing may
exacerbate the partial volume effects.
I have additional question and I appreciate your answer:
In the literature of the voxel-wise analysis using FSL/randomise to study the
difference between two groups
On 08/10/2017 11:35 AM, John Anderson wrote:
>
> Dear Dr Greve,
>
> Thank you very much for the great explanation. I will definitely
> correct for PVC using PET surfer.
>
> Kindly I have one follow-up question and I highly appreciate your input.
>
> I have PET data for two groups. I studied the
Dear Dr Greve,
Thank you very much for the great explanation. I will definitely correct for
PVC using PET surfer.
Kindly I have one follow-up question and I highly appreciate your input.
I have PET data for two groups. I studied the difference in PET signal using
voxel-wise ( FSL/randomise) a
The PET signal can change with a lot of anatomical changes in the brain
including thickness, surface area, and gyrification. There is no known
regressor that will account for this. Right right way to account for it
is with partial volume correction (PVC). It is best to do PVC
simultaneously w
Hi Dr Greve,
I have PET data for two groups and I used PET surfer in FSV 6.0 to run the
analyses. The pipeline is straightforward and the analysis ran smoothly without
any issues.
Is it correct procedure to adjust PET signal to differences in gray matter
volume or cortical thinness between two
This is a little tricky to do, but I can probably step you thru the
process. The first thing you have to do is to transfer your ROI from
fsaverage space to the individual using mri_label2label with the
--regmethod surface option (view it on the surface to make sure it is ok).
The next thing to
?Hello FreeSurfer Developers,
I have done partial volume correction of PET data as described in PETSurfer
stream. Now, I want to extract a mean intensity value of my ROI for each
subject. This ROI is defined in the fsaverage space and saved as a label. What
would be the best way to do it? Shou
Hi Adam, it might depend on which version you are running. I've been
working on it over the last year and made some changes related to
choroid plexus. The version that I have now does not merge CP with CSF.
You can check in your analysis by running
cd gtmdir/aux
mri_binarize --i seg.nii.gz --m
Hi,
Just want to bump this to the top now that the weekend is over!
Thanks for any insights about the CSF estimation,
Adam
On Fri, Oct 21, 2016 at 1:03 PM, Adam Martersteck
wrote:
> Thanks for replying Doug,
>
> Yes, I would like to use my own mask if the choroid plexus is included but
> *only
Thanks for replying Doug,
Yes, I would like to use my own mask if the choroid plexus is included but
*only* for Tau PET. There is high off-target binding of the new tau PET
ligand AV1451 (formerly called T807) in choroid plexus. I wanted to avoid
that high signal when estimating CSF.
I think chor
What do you mean? You have your own CSF segmentation and you want to use
that instead of the one created by gtmseg?
On 10/20/2016 11:32 AM, Adam Martersteck wrote:
> Hi FreeSurfer team,
>
> Hopefully Doug or someone familiar with the new PET PVC implementation
> can answer a few things I can't
Hi FreeSurfer team,
Hopefully Doug or someone familiar with the new PET PVC implementation can
answer a few things I can't seem to find on
http://surfer.nmr.mgh.harvard.edu/fswiki/PetSurfer or either of Doug's PVC
publications (2013 or 2016).
1) Is the choroid plexus included in the binarized the
you need to go back to the source data. At some point someone set or
changed the voxel size to the wrong thing. This can sometimes happen in
PET as reconstruction into volumes is not all that standardizeed
On 10/12/2016 06:12 PM, Matthieu Vanhoutte wrote:
>
> Thank you for your diagnosis Dougla
Thank you for your diagnosis Douglas. How could I get the voxel sizes right
from input nifti pet and mri data ?
Best regards,
Matthieu
Le 12 oct. 2016 10:05 PM, "Douglas N Greve" a
écrit :
> The problem appears to be that the PET or the MRI (or both) have
> incorrect voxel sizes (about 15%). Yo
The problem appears to be that the PET or the MRI (or both) have
incorrect voxel sizes (about 15%). You need to fix the problem. You can
get a decent registration using something like
mri_coreg --mov BS7_PET.lps.nii.gz --s 207118_FS_Filedrop --reg
dof9.wb.lta --dof 9 --no-ref-mask --ref mri/or
not yet. I'm on vacation until Wed, so it might be a while.
On 10/6/16 2:50 PM, Matthieu Vanhoutte wrote:
Hi Douglas,
Dis you have time to take a look at ?
Best regards,
Matthieu
Le 3 oct. 2016 6:25 PM, "Matthieu Vanhoutte"
mailto:matthieuvanhou...@gmail.com>> a
écrit :
Hi Douglas,
Hi Douglas,
Dis you have time to take a look at ?
Best regards,
Matthieu
Le 3 oct. 2016 6:25 PM, "Matthieu Vanhoutte"
a écrit :
> Hi Douglas,
>
> I have just sent it to you on Filedrop.
>
> Best regards,
> Matthieu
>
> 2016-10-03 17:45 GMT+02:00 Douglas Greve :
>
>> Can you tar up the FS anat
Hi Douglas,
I have just sent it to you on Filedrop.
Best regards,
Matthieu
2016-10-03 17:45 GMT+02:00 Douglas Greve :
> Can you tar up the FS anat analysis and BS7_PET.lps.nii.gz and send it to
> me on our filedrop?
>
> On 10/3/16 6:55 AM, Matthieu Vanhoutte wrote:
>
> Hi Douglas,
>
> Please fi
Can you tar up the FS anat analysis and BS7_PET.lps.nii.gz and send it
to me on our filedrop?
On 10/3/16 6:55 AM, Matthieu Vanhoutte wrote:
Hi Douglas,
Please find below the mri_coreg terminal output :
/
/
/$Id: mri_coreg.c,v 1.27 2016/04/30 15:11:49 greve Exp $/
/cwd /NAS/tupac/matthieu/FS5.
Hi Douglas,
Please find below the mri_coreg terminal output :
*$Id: mri_coreg.c,v 1.27 2016/04/30 15:11:49 greve Exp $*
*cwd /NAS/tupac/matthieu/FS5.3/207118_M0_2014-01-29/pet*
*cmdline mri_coreg --s 207118_M0_2014-01-29 --mov BS7_PET.lps.nii.gz --reg
Pet2T1.BS7.register.dof6.mri_coreg.lta --regd
Can you send the mri_coreg terminal output?
On 09/29/2016 11:19 AM, Matthieu Vanhoutte wrote:
> Dear Freesurfer's experts,
>
> I would like to register PET image onto T1 anatomical. I used
> bbregister with the following command and it failed :
> /bbregister --s SUBJID --init-fsl --t2 --mov PET
Dear Freesurfer's experts,
I would like to register PET image onto T1 anatomical. I used bbregister
with the following command and it failed :
*bbregister --s SUBJID --init-fsl --t2 --mov PET.nii.gz --reg
Pet2T1.register.dof6.dat --lta Pet2T1.register.dof6.lta --init-reg-out
Pet2T1.init.register.
Hi Doug,
Thank you. I ran sampled the data and ran mri_glmfit as you suggested, although
the resulting bp file seems to only have binary clusters (in the attached image
the red cluster all have a value of 1 and everywhere else is 0). Is this the
normal output? I expected a more varying map.
Sample the raw TAC data onto the surface (and not the BPs), then smooth
on the surface, then run the mrtm2 with all the same arguments except
use the surface data as the input (--y) instead of the ROI data.
On 08/23/2016 05:13 PM, Jonathan DuBois wrote:
> Hi,
>
> I’m trying to use the PETsurfer
Hi,
I’m trying to use the PETsurfer Pipeline to perform BP analysis, but I’m not
sure at which point in the pipeline to sample the data to the surface and what
registration to use?
I tried running the pipeline using dynamic kinetic modeling as described here:
http://surfer.nmr.mgh.harvard.ed
On 04/15/2016 08:31 PM, Elijah Mak wrote:
> No, more like running the voxelwise comparisons only on voxels that
> have positive BP between 2 group. Is that possible?
I'm still not sure what you mean by "positive BP between 2 group". Do
you mean masking out voxels where either group is less tha
No, more like running the voxelwise comparisons only on voxels that have
positive BP between 2 group. Is that possible?
On another note, I am running into a puzzling "Segmentation fault" error
with the following command:
mri_glmfit-sim --glmdir lh_ad_hc.glmdir --cache 2 neg --cwp 0.05
--2spac
what do you want to do exactly? Exclude all voxels if any subject has a
neg BP?
On 04/15/2016 11:55 AM, Elijah Mak wrote:
> Dear Doug,
>
> One more question:
>
> There are many voxels with negative binding potentials in this
> dataset, mostly in the CSF/ventricular regions. Can I restrict the
Dear Doug,
One more question:
There are many voxels with negative binding potentials in this dataset,
mostly in the CSF/ventricular regions. Can I restrict the mri_glmfit to
focus only on the voxels with positive BP?
Best Wishes,
Elijah
___
Freesurfer
Hi Doug,
I edited the registration by hand (after bbregister) in Freeview,
saving the PET_2_T1 volume.
In Freeview (dev FS6) : Tools -> Transform Volume --> Tweaked rotation
and translation --> Save Volume As --> Clicked "Do not resample voxel
data when saving (only update header)"
Using this
How did you edit the registration? Does it work with the unedited version?
On 04/13/2016 10:21 AM, Elijah Mak wrote:
> Hi Doug,
>
> One more question about feeding the -reg to mri_vol2surf, please.
>
> I am specifying the registration .lta because I have made edits to it,
>
> mri_vol2surf --src FS
Hi Doug,
One more question about feeding the -reg to mri_vol2surf, please.
I am specifying the registration .lta because I have made edits to it,
mri_vol2surf --src FS6_24551_MPRAGE_Neuro.nii/pet/pet2free_fsl.mgz --out
FS6_24551_MPRAGE_Neuro.nii/surf/lh.PETSurfce.mgh --projfrac 0.5 --hemi lh
--r
No, you'll need to pass the new registration to mri_vol2surf. You should
also check that freeview is producing the correct registration file.
We've had several problems with it that are definitely fixed in 6.0, but
not sure about 5.3. Try loading it in tkregister (--lta your.lta --reg
your.reg
On 3/23/16 9:07 AM, Elijah Mak wrote:
mri_concat --f pib_lh_fsaverage (textfile of subjects and their
images) --o concat_lh_pet.mgh
Should I add -mean here for the GLM?
No, that is handled by glmfit
mri_glmfit --y concat_lh_pet.mgh --fsgd pib_fsgd --C
group1.group2.mtx --surf fsaver
mri_concat --f pib_lh_fsaverage (textfile of subjects and their images) --o
concat_lh_pet.mgh
Should I add -mean here for the GLM?
mri_glmfit --y concat_lh_pet.mgh --fsgd pib_fsgd --C group1.group2.mtx
--surf fsaverage lh --cortex --glmdir lh.pet.glmdir
My simple 2 group-no-covariates FS
Hi Doug,
Thanks!
I manually tweaked the registration of the PET to T1 on a number of
subjects to bring the mincost down to < 0.5. After saving the pet2free
volume in Freeview, I noticed that a new .lta is produced in the same
directory (i.e. pet2free_fsl.mgz.lta).
Will the option --regheader te
That looks ok, but if you want to do a group analysis, you can add
--trgsubject fsaverage and the output surface will be in fsaverage
space. You can then concatenate the data together (mri_concat) into one
stack and then run mri_glmfit etc for your group analysis. You may or
may not want to smo
Hi Freesurfer Community,
I am trying to run a vertex-wise analyses of PET data.
I have already performed bbregister. Next, I did mri_vol2surf for each
subject, left and right hemispheres.
for i in `cat subjects`; do mri_vol2surf --src
FS6_${i}_MPRAGE_Neuro.nii/pet/pet2free_fsl.mgz --out
FS6_${i}
The km.hb.tac.nii.gz is not a volume. It is a single voxel of data
stored in nii format. This format is needed to input to mri_glmfit. Try
loading it in matlab, eg,
hb = fast_vol2mat( MRIread('km.hb.tac.nii.gz'));
plot(hb)
if that is all 0s then it will surely cause mrtm1 to fail.
doug
On 01/
Hi Freesurfer developers,
I’m trying to perform BP analysis with mri_glmfit —mrtm1. I ran mri_gtmpvc
without PVC, which finished without error. However, the km.hb.tac.nii.gz
appears empty when I open it with fslview or tkmedit, although this may be due
to the nature of the file (I’m not sure w
r...@nmr.mgh.harvard.edu>
> <mailto:gr...@nmr.mgh.harvard.edu
<mailto:gr...@nmr.mgh.harvard.edu>>>
> Subject: Re: [Freesurfer] PET tools in FS dev v6.0
> To: freesurfer@nmr.mgh.harvard.edu
<mailto:freesurfer@nmr.mgh.harvar
nd (itk_convert --inv-y --inv-x
> > pet.mnc pet.nii). I couldn't find a good tool to convert directly
> > form ECAT to NIFTI, but perhaps this conversion process interferes
> > with the pet processing?
> >
> > Best,
> > Jonathan
Message: 7
> Date: Mon, 28 Sep 2015 18:07:18 -0400
> From: Douglas N Greve <mailto:gr...@nmr.mgh.harvard.edu>>
> Subject: Re: [Freesurfer] PET tools in FS dev v6.0
> To: freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvar
to NIFTI, but perhaps this conversion
> process interferes with the pet processing?
>
> Best,
> Jonathan
>
>
>> Message: 7
>> Date: Mon, 28 Sep 2015 18:07:18 -0400
>> From: Douglas N Greve
>> Subject: Re: [Freesurfer] PET tools in FS dev v6.0
>> To
7;t find a good
tool to convert directly form ECAT to NIFTI, but perhaps this conversion
process interferes with the pet processing?
Best,
Jonathan
> Message: 7
> Date: Mon, 28 Sep 2015 18:07:18 -0400
> From: Douglas N Greve
> Subject: Re: [Freesurfer] PET tools in FS dev
andubois/data/fssub/epc_02/mri/gtmseg.ctab
> Reading /Users/jonathandubois/data/fssub/epc_02/mri/gtmseg.lta
> Replacing 18
> Pruning ctab
> done with seg vol
> maxFWHM = 3.28205 (voxels), PadThresh=0.0001, nPad=10
> Computing auto mask
> Segmentation fault: 11
>
>
fssub/epc_02/mri/gtmseg.lta
Replacing 18
Pruning ctab
done with seg vol
maxFWHM = 3.28205 (voxels), PadThresh=0.0001, nPad=10
Computing auto mask
Segmentation fault: 11
Message: 13
> Date: Tue, 08 Sep 2015 14:34:11 -0400
> From: Douglas N Greve
> Subject: Re: [Freesurfer] PET tools in FS
Message: 13
Date: Tue, 08 Sep 2015 14:34:11 -0400
From: Douglas N Greve
Subject: Re: [Freesurfer] PET tools in FS dev v6.0
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <55ef2a23.3070...@nmr.mgh.harvard.edu>
Content-Type: text/plain; charset=window
= 3.28205 (voxels), PadThresh=0.0001, nPad=10
Computing auto mask
Segmentation fault: 11
Message: 13
> Date: Tue, 08 Sep 2015 14:34:11 -0400
> From: Douglas N Greve
> Subject: Re: [Freesurfer] PET tools in FS dev v6.0
> To: freesurfer@nmr.mgh.harvard.edu
> Message-ID:
Yes there are both. For KM we have MRTM1 and MRTM2 so far. They are not
well documented yet.
1. To start, run
gtmseg --s subject
This will take a couple of hours and produces some files needed for GTM
PVC (which is used for GTM, MG, RBV).
2. You'd then register the PET to the anatomical with
Hi FS experts,
In FS development package I see that there have been tools added for
partial volume correction of PET data, but I was wondering if there were
also kinetic modeling tools similar to those described in Doug's 2014
paper? If you could let me know what PET processing tools have been
inc
I can when I have a beta version! I'm actively working on putting the
programs together into a package. Check back in a month or so.
doug
On 02/08/2014 03:41 PM, Jonathan DuBois wrote:
> Hi Doug,
>
> Thanks for replying. We are currently working on this analysis, is
> there anyway you could
Hi Doug,
Thanks for replying. We are currently working on this analysis, is there
anyway you could provide a beta version of the PVC code?
Thanks,
Jonathan
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Hi Jonathan, it is not possible in 5.3 to do the PVC. This will be part
of the next major release.
doug
On 02/07/2014 03:45 PM, Jonathan DuBois wrote:
> Hi Freesurfer experts,
>
> I have been using freesurfer for surface-based PET analysis and was
> wondering if the method for voxel-based p
Hi Freesurfer experts,
I have been using freesurfer for surface-based PET analysis and was
wondering if the method for voxel-based partial volume correction, used
in the recent paper (Cortical surface-based analysis reduces bias and
variance in kinetic modeling of brain PET data), was implemente
Dear Freesurfers,
My goal is to evaluate the cortical thinning patterns in some
(cortical
aparc) regions, and to relate that to loss of PET activation in the
same
regions. I would like to clarify the steps of the pipeline in
Freesurfer
(v5.0.0) for this purpose.
>From my reading of previous
A couple of things:
Map aparc+aseg into the PET space:
mri_label2vol --seg aparc+aseg.mgz --reg register.dat --temp
subject.pet.pvf.nii --o subject_bl.petlabel.nii
Use the PET space aparc+aseg when computing the seg stats:
mri_segstats --seg subject_bl.petlabel.nii --sum
/home/corinna/blstats/s
No, that will be fine.
doug
corinna bauer wrote:
> Will I need to re-register the pet to the mri?
>
> On Fri, Jun 10, 2011 at 10:58 AM, Douglas N Greve
> mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>
> you'll need to get a new version then. You won't need to reanalyze
> your anatomicals in
Will I need to re-register the pet to the mri?
On Fri, Jun 10, 2011 at 10:58 AM, Douglas N Greve wrote:
> you'll need to get a new version then. You won't need to reanalyze your
> anatomicals in the new version, but you will need it to run these programs.
>
> doug
>
> corinna bauer wrote:
>
>> I
you'll need to get a new version then. You won't need to reanalyze your
anatomicals in the new version, but you will need it to run these programs.
doug
corinna bauer wrote:
> I'm using 4.4.0
>
> On Fri, Jun 10, 2011 at 10:44 AM, Douglas N Greve
> mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>
>
>
I'm using 4.4.0
On Fri, Jun 10, 2011 at 10:44 AM, Douglas N Greve wrote:
>
> which version are you using? Both should be in both 5.0 and 5.1.
> doug
>
> corinna bauer wrote:
>
>> Hi Doug,
>>
>> I used the mri_compute_volume_fractions and fscalc commands and got this
>> error message:
>>
>> mri_c
Hi Corinna,
what version of FS are you using?
Bruce
On Fri, 10 Jun 2011, corinna bauer wrote:
> Hi Doug,
> I used the mri_compute_volume_fractions and fscalc commands and got this
> error message:
>
> mri_compute_volume_fractions: Command not found.
> fscalc: Command not found.
>
> Other FreeSur
which version are you using? Both should be in both 5.0 and 5.1.
doug
corinna bauer wrote:
> Hi Doug,
> I used the mri_compute_volume_fractions and fscalc commands and got
> this error message:
>
> mri_compute_volume_fractions: Command not found.
> fscalc: Command not found.
>
> Other FreeSurfer
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