[Freesurfer] Segmentation Query

[Fariha Muazzam]

External Email - Use Caution

Hi

I am working in Freesurfer for subcortical segmentation of brain, I did
segmentation of a volume and I got around 45 regions. Is it possible that I
could customize the regions I want or number of segments that I want?

Thank You

Regards

*Fariha Muazzam*
Research Officer

--
Al-Khawarizmi Institute of Computer Science (KICS)

University of Engineering and Technology (UET), Lahore

*Email:* fariha.muaz...@kics.edu.pk * |* *Web:* www.
kics.edu.pk
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Re: [Freesurfer] GPU/supercomputer adaptation of freesurfer?

[R Edgar]

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Sorry I'm coming to this a bit late I'm not sure that the CUDA
implementation is supported these days. I've not done much work on em_
and ca_register since 2012; I'm not sure about the surface stream (I
didn't do that port). Furthermore, I don't see CUDA being included in
the new CMake build system. Some differences to the CPU stream are
inevitable (floating point arithmetic and all that), but if the
workflow in those binaries has changed since when I was working on
them, then those changes may not be reflected in the GPU code.

Regards,

Richard

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Re: [Freesurfer] Error in running make_average_subject

[Bruce Fischl]

Hi Emanuel,

can you include the full command line and output?

cheers
Bruce
On Wed, 12 Dec 2018, 
Emanuel Alvaredo wrote:




External Email - Use Caution

Thanks for your answer Douglas. I replaced the make_average_surface  file with 
the new one but  I
have the same message error.
ASeg Vox2RAS: ---
-1.0   0.0   0.0   128.0;
 0.0   0.0   1.0  -128.0;
 0.0  -1.0   0.0   128.0;
 0.0   0.0   0.0   1.0;
mghRead(mri/norm.mgz, -1): could not open file
-

Labeling Slice
relabeling unlikely voxels in interior of white matter
mri/norm.mgz: could not load norm volume from (null)

Linux neuroWorkstation00 4.4.0-138-generic #164-Ubuntu SMP Tue Oct 2 17:16:02 
UTC 2018 x86_64 x86_64
x86_64 GNU/Linux

Thanks

Emanuel


On Tue, Dec 11, 2018 at 1:10 PM Greve, Douglas N.,Ph.D. 
 wrote:
  Sorry, the disk that held that patch failed and we did not have a backup 
so not
  everything was restored. I just put this file there:

  
https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-patch/make_average_surface

  Copy it to $FREESURFER_HOME/bin. Let me know how it goes


  On 12/10/18 12:48 PM, Emanuel Alvaredo wrote:

  External Email - Use Caution

  Thanks Bruce. The following is the command.

 make_average_subject --out avgsubjectPRUEBAESTASIEmac --subjects  subject1 
subject2 subject3


And I made a mistake in may last mail. I use the word path instead of patch

I have found this page with a patch for de issue

https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2018-February/056008.html

But I dont know how to apply the patch. Can you give some information about 
this?


Emanuel


On Fri, Dec 7, 2018 at 4:54 PM Bruce Fischl  wrote:
  Hi Emanuel

  you need to send us the full command you ran and output of it if you want
  us to be able to help you

  cheers
  Bruce
  On Fri, 7 Dec 2018, Emanuel Alvaredo wrote:

  >
  > External Email - Use Caution
  >
  > Hello!, I am getting the following error using the
  command make_average_subject 
  >
  > mri/norm.mgz: could not load norm volume from (null)
  >
  > I have found this page with a path for de issue
  >
  >
  
https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2018-February/056008.html
  >
  > But I dont know how to apply the path. Can you give some information 
about
  this?
  >
  > Thanks!
  >
  >
  >
  > Emanuel
  >
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Re: [Freesurfer] Power analysis

[Laura Ferrero]

External Email - Use Caution

After using MRIread from Matlab in file gamma.mgh, I obtain the following:
mri = 

  struct with fields:

   srcbext: ''
analyzehdr: []
  bhdr: []
   vol: []
 fspec: 'gamma.mgh'
   pwd: '/Users/lauraferrero/Documents/MATLAB'
flip_angle: 0
tr: 0
te: 0
ti: 0
  vox2ras0: [4×4 double]
   volsize: [1 34 1]
height: 1
 width: 34
 depth: 1
   nframes: 1
   vox2ras: [4×4 double]
   nvoxels: 34
 xsize: 1
 ysize: 1
 zsize: 1
   x_r: 1
   x_a: 0
   x_s: 0
   y_r: 0
   y_a: 1
   y_s: 0
   z_r: 0
   z_a: 0
   z_s: 1
   c_r: 0
   c_a: 0
   c_s: 0
  vox2ras1: [4×4 double]
   Mdc: [3×3 double]
volres: [1 1 1]
tkrvox2ras: [4×4 double]

But I do not know which field corresponds to the mean for the effect size.
Regards,
Laura


> El 11 dic 2018, a las 18:21, Laura Ferrero  
> escribió:
> 
> Dear Douglas,
> 
> I performed the statistical analysis using stats files so I do not have 
> vertex information, I assume it will be cortical regions information. Is the 
> approach to read them the same?
> Thank you,
> Laura
> 
> 
> 
> 
>> El 11 dic 2018, a las 16:54, Greve, Douglas N.,Ph.D. 
>>  escribió:
>> 
>> The gamma and gammavar files are vertex-wise values. You can load them 
>> in matlab with something like
>> g = MRIread('gamma.mgh');
>> gv = MRIread('gammavar.mgz');
>> but you will need the vertex that you are interested in (or do for all 
>> vertices).
>> You can use fast_glm_power.m in the FSFAST toolbox to compute the power 
>> (requires stats toolbox).
>> 
>> 
>> On 12/11/18 6:39 AM, Laura Ferrero wrote:
>>>External Email - Use Caution
>>> 
>>> Hi,
>>> I want to perform a power analysis and I read that I need 3 of 4 things:
>>> 1. Effect size (mean/std)
>>> 2. False positive rate
>>> 3. Number of subjects
>>> 4. True positive rate
>>> 
>>> I also read that the effect size can be calculated using gamma.mgh and 
>>> gammavar.mgh files but I do not know how to open them in order to get the 
>>> numbers.
>>> 
>>> Thank you,
>>> Laura
>>> 
>>> ___
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>> 
>> 
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> 


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[Freesurfer] Job ad: small animal MRI faculty position

[Keith Schneider]

External Email - Use Caution

Associate Professor, Behavioral Neuroscience
University of Delaware: College of Arts & Sciences: Psychological & Brain 
Sciences
Location: Newark, DE
The University of Delaware invites applications for a tenured associate 
professor (or assistant professor nearing tenure) in behavioral neuroscience to 
begin September 1, 2019. We are seeking to hire a scholar with a solid 
background in small animal fMRI and/or DTI at ultrahigh fields for linking 
systems neuroscience and brain MR imaging (the university has a 9.4T/30cm 
Bruker MRI for animal research). The exact discipline area is open for this 
position as scholarly excellence will be the primary consideration. Ideal 
candidates will have extensive experience in brain science-oriented MR 
research, demonstrate outstanding and innovative scholarship, and have 
collaborative and synergistic possibilities with existing researchers at UD. 
The candidate should enjoy collaborating with researchers from various 
disciplines (e.g., medical engineering, biochemistry) and helping researchers 
new to MRI.

This is an outstanding opportunity for a scholar to join and strengthen the 
growing Department of Psychological and Brain Sciences 
(https://www.psych.udel.edu ) and University of 
Delaware (https://www.udel.edu ) that already has a 
promising core of interdisciplinary researchers utilizing cutting edge 
methodologies.

An innovative leader in research and teaching, the University of Delaware 
combines a rich historic legacy with a commitment to education and the latest 
in advanced technology. With external funding exceeding $200 million per year, 
the University ranks among the top 100 universities in federal R support for 
science and engineering. Enhanced by state-of-the-art facilities, research is 
conducted across all seven colleges and numerous interdisciplinary institutes 
and centers. Relevant facilities on campus include the new 11,600 square foot 
Center for Biomedical and Brain Imaging, housing the 9.4T/30cm Bruker MRI, a 3T 
Siemens Magnetom Prisma, and transcranial magnetic stimulation machine; a 
103,000 square foot Health Sciences Complex, a facility that includes labs for 
small animal and human-based studies, and an active outpatient clinic; a 
194,000 square foot Interdisciplinary Science and Engineering Laboratory; and 
the Delaware Technology Park, where entrepreneurial and academic research labs 
are co-located. The Delaware Health Sciences Alliance (DHSA), a partnership 
among the University of Delaware, Christiana Care Health System 
, Nemours/Alfred I. du Pont Hospital for 
Children , and Thomas Jefferson University 
, provides infrastructure and opportunity for innovative 
clinical and translational collaborations.

The University of Delaware is located in Newark, Delaware, which is only a 
short drive or train commute from Philadelphia, PA. UD is also within driving 
distance of New York City, Baltimore, Washington DC, the Poconos and some of 
the finest beaches in the country, making it an ideal location for day or 
weekend trips.

QUALIFICATIONS

Applicants for this position must have earned a Ph.D., tenure (or be nearing 
tenure), have a history of high-level publications in behavioral neuroscience 
or related fields, and conduct fundable research. 

APPLICATION INSTRUCTIONS

Using the Interfolio system at UD, http://apply.interfolio.com/58701 
, applicants submit a cover letter, a 
statement of research, a current curriculum vitae, three representative 
publications, and three confidential letters of reference. Inquiries, but not 
application materials, should be emailed to Jeffrey Rosen, Chair of the small 
animal MRI Faculty Search committee, jro...@psych.udel.edu. Review of 
applications will begin on January 15, 2019 and will continue until the 
position is filled.

The University of Delaware is an Equal Opportunity Employer which encourages 
applications from minority group members and women.  The University's Notice of 
Non-Discrimination can be found at 
http://www.udel.edu/aboutus/legalnotices.html.

-
Keith Schneider
Director, Center for Biomedical and Brain Imaging
Associate Professor
Department of Psychological and Brain Sciences
University of Delaware

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Re: [Freesurfer] Error in running make_average_subject

[Emanuel Alvaredo]

External Email - Use Caution

Thanks for your answer Douglas. I replaced the make_average_surface  file
with the new one but  I have the same message error.

ASeg Vox2RAS: ---
-1.0   0.0   0.0   128.0;
 0.0   0.0   1.0  -128.0;
 0.0  -1.0   0.0   128.0;
 0.0   0.0   0.0   1.0;
mghRead(mri/norm.mgz, -1): could not open file
-

Labeling Slice
relabeling unlikely voxels in interior of white matter
mri/norm.mgz: could not load norm volume from (null)

Linux neuroWorkstation00 4.4.0-138-generic #164-Ubuntu SMP Tue Oct 2
17:16:02 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux

Thanks

Emanuel


On Tue, Dec 11, 2018 at 1:10 PM Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> wrote:

> Sorry, the disk that held that patch failed and we did not have a backup
> so not everything was restored. I just put this file there:
>
>
> https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-patch/make_average_surface
>
> Copy it to $FREESURFER_HOME/bin. Let me know how it goes
>
>
> On 12/10/18 12:48 PM, Emanuel Alvaredo wrote:
>
> External Email - Use Caution
> Thanks Bruce. The following is the command.
>
>
>  make_average_subject --out avgsubjectPRUEBAESTASIEmac --subjects
> subject1  subject2 subject3
>
>
> And I made a mistake in may last mail. I use the word path instead of patch
>
> I have found this page with a *patch* for de issue
>
>
> https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2018-February/056008.html
>
> But I dont know how to apply the *patch*. Can you give some information
> about this?
>
>
> Emanuel
>
>
> On Fri, Dec 7, 2018 at 4:54 PM Bruce Fischl 
> wrote:
>
>> Hi Emanuel
>>
>> you need to send us the full command you ran and output of it if you want
>> us to be able to help you
>>
>> cheers
>> Bruce
>> On Fri, 7 Dec 2018, Emanuel Alvaredo wrote:
>>
>> >
>> > External Email - Use Caution
>> >
>> > Hello!, I am getting the following error using the
>> command make_average_subject
>> >
>> > mri/norm.mgz: could not load norm volume from (null)
>> >
>> > I have found this page with a path for de issue
>> >
>> >
>> https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2018-February/056008.html
>> >
>> > But I dont know how to apply the path. Can you give some information
>> about this?
>> >
>> > Thanks!
>> >
>> >
>> >
>> > Emanuel
>> >
>> >___
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>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
> ___
> Freesurfer mailing 
> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> ___
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Re: [Freesurfer] recon-all ERROR: killed

[Bruce Fischl]

p.s. if you look in the recon-all.log you will see:

  totalusedfree  shared  buff/cache 
available
Mem:4025436 1115872  794808   54712 2114756 
2510316

Swap: 0   0   0

which looks like something else was running on your machine and taking a 
lot of the total RAM


cheers
Bruce


On Thu, 13 Dec 2018, 
张亮军 wrote:




External Email - Use Caution

Hello FreeSurfer Developers,

I'm attempting to use "recon-all -i T1.nii.gz -s zhang -all", but there is a 
ERROR:

saving intensity scales to aseg.auto_noCCseg.label_intensities.txt
saving sequentially combined intensity scales to 
aseg.auto_noCCseg.label_intensities.txt
Killed
Linux ubuntu 4.10.0-37-generic #41~16.04.1-Ubuntu SMP Fri Oct 6 22:42:59 UTC 
2017 x86_64 x86_64 x86_64 GNU
/Linux
recon-all -s zhang exited with ERRORS at Wed Dec 12 22:18:35 CST 2018
For more details, see the log file 
/usr/local/freesurfer/subjects/zhang/scripts/recon-all.log

I've searched the list and no similar errors have been reported. Does anyone 
have any thoughts on how to t
rouble-shoot this one? Also, I've attached the recon-all.log in case it's of any use. 


1) FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
2) Platform: Ubuntu16.04 LTS(VMware Workstations pro)
3) uname -a: Linux ubuntu 4.10.0-37-generic #41~16.04.1-Ubuntu SMP Fri Oct 6 
22:42:59 UTC 2017 x86_64 x86_
64 x86_64 GNU/Linux
4) recon-all.log: killed
Best,
Liangjun.

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Re: [Freesurfer] recon-all ERROR: killed

[Bruce Fischl]

Hi Liangjun.

usually that means you ran out of RAM.

cheers
Bruce


On Thu, 13 Dec 2018, 张亮军 wrote:



External Email - Use Caution

Hello FreeSurfer Developers,

I'm attempting to use "recon-all -i T1.nii.gz -s zhang -all", but there is a 
ERROR:

saving intensity scales to aseg.auto_noCCseg.label_intensities.txt
saving sequentially combined intensity scales to 
aseg.auto_noCCseg.label_intensities.txt
Killed
Linux ubuntu 4.10.0-37-generic #41~16.04.1-Ubuntu SMP Fri Oct 6 22:42:59 UTC 
2017 x86_64 x86_64 x86_64 GNU
/Linux
recon-all -s zhang exited with ERRORS at Wed Dec 12 22:18:35 CST 2018
For more details, see the log file 
/usr/local/freesurfer/subjects/zhang/scripts/recon-all.log

I've searched the list and no similar errors have been reported. Does anyone 
have any thoughts on how to t
rouble-shoot this one? Also, I've attached the recon-all.log in case it's of any use. 


1) FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
2) Platform: Ubuntu16.04 LTS(VMware Workstations pro)
3) uname -a: Linux ubuntu 4.10.0-37-generic #41~16.04.1-Ubuntu SMP Fri Oct 6 
22:42:59 UTC 2017 x86_64 x86_
64 x86_64 GNU/Linux
4) recon-all.log: killed
Best,
Liangjun.

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[Freesurfer] Beta series method in FS?

[Hahn, Emily M.]

Hi, I am interested in using the beta series method 
(https://neuroscape.ucsf.edu/wp-content/uploads/publications/Rissman2004-Measuring-functional-connectivity-during-distinct-stages-of-a-cognitive-task.pdf)
 for intra-subject analysis. Is there a straightforward way to do this in 
FreeSurfer? 

I attempted and the following analysis (code starting @ foreach) and an error 
appeared at the selxavg3-sess step:
ERROR: condition ids are not contiguous

Should I include a positive contrast for each condition (i.e. instead of 
'-no-con-ok', use 'mkcontrast-sess -analysis $analysis -contrast $contrast -a 
$1_to_194') or is something else about the design erroneous? Thank you in 
advance for feedback.

Notes regarding the paradigm file:
(1) treats each condition type as a unique event (i.e. second column consists 
of numbers 1:194; $Nconditions = 194)
(2) stim weight == 1 (i.e. third column all ones) 

foreach cortices ( lh rh )

mkanalysis-sess \
-fsd $fsd \
-surface fsaverage $cortices \
-fwhm $FWHM \
-event-related \
-paradigm $paradigm \
-nconditions $Nconditions \
-spmhrf 0 \
-TR $TR \
-refeventdur $EVENT_DUR \
-nskip $Nskip \
-hpf $HPF \
-analysis bsm.analyses.$cortices \
-per-run \
-nuisreg $MC_nuis -1 \
-tpexclude $MCR_censor \
-force

end

foreach cortices ( lh rh )

selxavg3-sess \
-s $SUBJECT \
-analysis bsm.analyses.$cortices \
-no-con-ok

end

--
Emily M. Hahn | Clinical-Computational Research Coordinator
Division of Neurotherapeutics | A.A. Martinos Center for Biomedical Imaging
Massachusetts General Hospital/Harvard Medical School
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[Freesurfer] Download link for Matlab runtime broken?

[raul perez moraga]

External Email - Use Caution

Hello!

I tried to download the Matlab runtime for Linux to use FSFAST but the link
is broken.

https://surfer.nmr.mgh.harvard.edu/pub/dist/mcr/MCRv83_linux.tar.gz
Not Found

The requested URL /pub/dist/mcr/MCRv83_linux.tar.gz was not found on this
server.
--
Apache/2.2.15 (CentOS) Server at surfer.nmr.mgh.harvard.edu Port 443

Thanks in advance

Raúl
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Re: [Freesurfer] Problems with GM segmentation -- How to solve it

[Rosalia Dacosta Aguayo]

External Email - Use Caution

Hi Bruce,

Already sent:

ftp> put 013.tar.gz
local: 013.tar.gz remote: 013.tar.gz
200 PORT command successful. Consider using PASV.
150 Ok to send data.
226 Transfer complete.
223104380 bytes sent in 808.49 secs (269.4852 kB/s)
ftp>

On Wed, Dec 12, 2018 at 1:39 PM Rosalia Dacosta Aguayo 
wrote:

> Hi Bruce,
>
> Thank you for your reply.
> I am sending now a file called 013.tar.gz via ftp. And this is not the
> worst...there are other with more regions that have not been considered in
> the segmentation process. I would like to know how could I cope with GM
> editions, as I am doing with control points with WM.
>
> Yours sincerely,
> Rosalia
>
> On Tue, Dec 11, 2018 at 5:17 PM Bruce Fischl 
> wrote:
>
>> Hi Rosalia
>>
>> if you upload an example with voxel coordinates of where you see problems
>> we will take a look
>>
>> cheers
>> Bruce
>> On Tue, 11 Dec 2018, Rosalia Dacosta Aguayo wrote:
>>
>> >
>> > External Email - Use Caution
>> >
>> > Dear Free Surfer team and Bruce,
>> >
>> > I have been doing well editing the skull stripping, and using control
>> points
>> > to improve white matter segmentation. Furthermore, the few participants
>> I
>> > had problems with due to large ventricles were solved using the flag you
>> > recommended me to use. I am very grateful for all your help.
>> >
>> > However, I am facing another problem I thought I could solve using
>> control
>> > points as well but this is worsening things instead of improving them. I
>> > refer to grey matter segmentation. I have found that several
>> participants,
>> > more than I would like, are having problems with grey matter
>> segmentation in
>> > the ventral temporal lobes and in the occipital lobe as well.
>> >
>> > I wonder if you could kindly help me with this, telling me how I could
>> solve
>> > this problem so GM and WM segmentation are fine.
>> >
>> > Yours sincerely,
>> > Rosalia
>> >
>> >
>> >
>> >___
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>
>
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Re: [Freesurfer] Problems with GM segmentation -- How to solve it

[Rosalia Dacosta Aguayo]

External Email - Use Caution

Hi Bruce,

Thank you for your reply.
I am sending now a file called 013.tar.gz via ftp. And this is not the
worst...there are other with more regions that have not been considered in
the segmentation process. I would like to know how could I cope with GM
editions, as I am doing with control points with WM.

Yours sincerely,
Rosalia

On Tue, Dec 11, 2018 at 5:17 PM Bruce Fischl 
wrote:

> Hi Rosalia
>
> if you upload an example with voxel coordinates of where you see problems
> we will take a look
>
> cheers
> Bruce
> On Tue, 11 Dec 2018, Rosalia Dacosta Aguayo wrote:
>
> >
> > External Email - Use Caution
> >
> > Dear Free Surfer team and Bruce,
> >
> > I have been doing well editing the skull stripping, and using control
> points
> > to improve white matter segmentation. Furthermore, the few participants I
> > had problems with due to large ventricles were solved using the flag you
> > recommended me to use. I am very grateful for all your help.
> >
> > However, I am facing another problem I thought I could solve using
> control
> > points as well but this is worsening things instead of improving them. I
> > refer to grey matter segmentation. I have found that several
> participants,
> > more than I would like, are having problems with grey matter
> segmentation in
> > the ventral temporal lobes and in the occipital lobe as well.
> >
> > I wonder if you could kindly help me with this, telling me how I could
> solve
> > this problem so GM and WM segmentation are fine.
> >
> > Yours sincerely,
> > Rosalia
> >
> >
> >
> >___
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[Freesurfer] [PETSurfer] Intensity normalization of PET images without PVE correction

[Matthieu Vanhoutte]

External Email - Use Caution

Dear Douglas,

Is it possible to use mri_gtmpvc command in order to intensity normalize
PET images without applying PVE correction by setting --psf to 0 ?

Best,
Matthieu
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[Freesurfer] Robust PET signal projection

[Matthieu Vanhoutte]

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Dear Freesurfer's experts,

In order to have a robust PET signal projection, is it possible compute the
projected PET signal as a weighted average of the PET signal intersecting
with the surfaces ranging from 35 to 65% of the cortical tickness with a
step t=5% ?

More weight would be given to the surfaces located near the mid distance
between the pial and white surfaces as they have a higher probability to be
well located within the cortex (using a normal distribution for example).

Thank you for helping.

Best,
Matthieu
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Re: [Freesurfer] [PETsurfer] Use of MGX and RBV partial volume correction

[Matthieu Vanhoutte]

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Hi Douglas,

Could you help me about my previous mail with questions ?

Thanks,
Matthieu


Le ven. 7 déc. 2018 à 14:31, Matthieu Vanhoutte 
a écrit :

> Hi Douglas,
>
> Thanks for these clarifications. I added some others questions inline
> below.
>
> Best,
> Matthieu
>
> > Le 6 déc. 2018 à 17:25, Greve, Douglas N.,Ph.D. 
> a écrit :
> >
> >
> >
> > On 11/30/2018 07:15 AM, Matthieu Vanhoutte wrote:
> >>
> >> External Email - Use Caution
> >>
> >> Hi Douglas,
> >>
> >> Thank you for answering. Please find below new questions.
> >> Bien cordialement,
> >>
> >>
> >> Le ven. 30 nov. 2018 à 00:00, Greve, Douglas N.,Ph.D.
> >> mailto:dgr...@mgh.harvard.edu>> a écrit :
> >>
> >>Hi Matthieu, sorry for the delay
> >>
> >>On 11/29/2018 12:50 PM, Matthieu Vanhoutte wrote:
> >>>   External Email - Use Caution
> >>>
> >>> Dear Freesurfer's experts,
> >>>
> >>> I tried to use PETSurfer to correct partial volume effect on my
> >>FDG PET images, testing both Muller-Gartner and RBV corrections.
> >>>
> >>> I ran the commands specified in PETSurfer website and used the
> >>two following commands for both MGX and RBV corrections respectively:
> >>>
> >>> mri_gtmpvc --i PET.nii.gz --reg register.dof6.lta --psf-col 5.51
> >>--psf-row 5.51 --psf-slice 5.9 --seg gtmseg.mgz
> >>--default-seg-merge --auto-mask PSF .01 --mgx .01 --o ./gtmpvc.output
> >>>
> >>> mri_gtmpvc --i PET.nii.gz --reg register.dof6.lta --psf-col 5.51
> >>--psf-row 5.51 --psf-slice 5.9 --seg gtmseg.mgz
> >>--default-seg-merge --auto-mask PSF .01 --rbv --o rbv.output.orig
> >>>
> >>> 1) However, I found that cortical output mgx.ctxgm.nii.gz of MGX
> >>correction encompass more than just GM and values at the
> >>boundaries of mgx.ctxgm.nii.gz seem to me very high or aberrant.
> >>This is expected. The MG method gives you a value every place that
> >>there
> >>is GM signal *in the PET volume after partial volume effects*. So
> >>basically, if you were to take the cortical ribbon and smooth it
> >>by your
> >>PSF, every non-zero voxel has some GM in it (which is why the
> >>edges are
> >>so high). When you run it with --mgx .01, it will exclude voxels that
> >>have less than 1% GM after smoothing. If you you are disturbed by the
> >>wide ribbon, just make the threshold higher. In theory, every point
> >>along the surface normal gives you a valid answer, but the further
> >>from
> >>the center of the ribbon, the noisier it is going to be, so we
> >>generally
> >>only sample it at the center (--projfrac 0.5 to mri_vol2surf).
> >>
> >>
> >> Basically, please find below the mgx.ctxgm with threshold set at 0.01:
> >> image.png
> >>
> >> Then threshold set at 0.1:
> >> image.png
> >>
> >> Values at some parts of the cortex (olfactory, visual) are not the
> >> same between the two thresholds. In the first one in these parts of
> >> the brain, values are higher than the second and seem kind of
> >> aberrant. Is there no reason to prefer a threshold at 0.1 than 0.01 ?
> >> For example, in (Douglas et al., 2016, NeuroImage) a threshold of 0.3
> >> has been found to be optimal: how determine visually or quantitatively
> >> this optimal threshold ?
> > So when you click on the same voxel in both images, you get different
> > values? Or is it just that the color scale is changing? The threshold
> > should not change the values, just what is in or out of the final mask.
> > The threshold of 0.3 was chosen mainly because it worked for the ROI
> > analysis. In general, you should use GTM instead of MG for ROI analysis.
> > For surface-based analysis, the threshold is not critical because the GM
> > PVF is generally pretty high in cortex. It will make more of a
> > difference in subcortical analysis.
>
> Yes, thresholding at 0.01 and 0.1 gave me different values in the same
> voxel in both images. Whereas when thresholding between 0.1 and 0.3 gave me
> same values. What could it be due to ?
>
> GTM is always computed in the *.stat file whatever the method specified in
> mri_gtmpvc command ?
>
> If threshold is not critical for cortical surface, how to determine the
> best threshold for subcortical analysis ? Is it better to have more in the
> final mask ?
>
> >>
> >>
> >>>
> >>> 2) Concerning RBV correction, output rbv.nii.gz seems to me
> >>following more precisely the GM ribbon. However contrary to what
> >>is said in PETSurfer website, rbv.nii.gz seems to be in the
> >>anatomical space (not in native PET) at the resolution of
> >>gtmseg.mgz. How then map rbv.nii.gz to the anatomical space when
> >>mapping the volume to the surface ?
> >>Where does it say this? It should be in the anatomical space in the
> >>sense that it shares an RAS space with the conformed volume (aseg
> >>does
> >>gtmseg.mgz). This means that you can use --regheader with
> >>mri_vol2surf
> >>or