[Freesurfer] Gray matter volume image per group

[Oana Georgiana Rus]

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Dear Freesurfer Community,

I want to have an image of the average gray matter Volume in each of my 3 
groups, and I did not find a good way to do it.

I easily obtained an image from the GM thickness and area by using 
make_average_subject in each of my 3 groups (young musicians, old musicians and 
old nonmusicians). Thereby in the surf subfolder I could find an image of these 
2 measures. 

Could anybody give some helpful hint. 

I am using FreeSurfer 6.0 on an Ubuntu Machine.18.04.4 LTS.

Best regards,
Georgiana

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Re: [Freesurfer] Gray matter volume image per group

[Douglas N. Greve]

What do you mean by "gray matter Volume"? Do you just want a map where 
the value at a voxel is the fraction of GM in that voxel? What space 
(eg, cvs, fsaverage, mni305) are you planning to make the average in?

On 7/27/2020 4:33 AM, Oana Georgiana Rus wrote:
>  External Email - Use Caution
>
> Dear Freesurfer Community,
>
> I want to have an image of the average gray matter Volume in each of my 3 
> groups, and I did not find a good way to do it.
>
> I easily obtained an image from the GM thickness and area by using 
> make_average_subject in each of my 3 groups (young musicians, old musicians 
> and old nonmusicians). Thereby in the surf subfolder I could find an image of 
> these 2 measures.
>
> Could anybody give some helpful hint.
>
> I am using FreeSurfer 6.0 on an Ubuntu Machine.18.04.4 LTS.
>
> Best regards,
> Georgiana
>
> ___
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Re: [Freesurfer] Coregistration to MNI

[Douglas N. Greve]

This command will allow you to have a registration file and sample into 
MNI152 2mm space


mri_vol2vol --gcam pet.nii.gz register.dof6.lta 
$SUBJECTS_DIR/$subject/cvs/final_CVSmorph_tocvs_avg35_inMNI152.m3z 
$FREESURFER_HOME/subjects/cvs_avg35_inMNI152/mri.2mm/register.lta 0 1 
pet.cvs.2mm.sm00.nii.gz


you can get the registration file with
mri_coreg --mov pet.nii.gz --s $subject --reg register.dof6.lta



On 7/26/2020 9:19 AM, Zollei, Lilla,Ph.D. wrote:

Hi Aldo,
If you have a recon-ned structural MRI corresponding to your PET scan 
then the answer is yes.

Lilla

*From:* freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Camargo, Aldo 


*Sent:* Saturday, July 25, 2020 12:19 AM
*To:* Freesurfer support list 
*Subject:* [Freesurfer] Coregistration to MNI

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Hi Freesurfer experts,

I want to coregister a PET image to the MNI space, can I use 
mri_cvs_register ?


Thanks a lot,

Aldo Camargo

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Re: [Freesurfer] The input for Petsurfer

[Douglas N. Greve]

Sorry, no, not with PETsurfer

On 7/26/2020 1:05 PM, Hengameh Marzbani wrote:


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Thank you for the quick response.
Could I use the T1 weighted MRI of an atlas as an alternative for 
T1-weighted MRI of each subject?
If this solution is not applicable, is there any analysis or solution 
to my problem?

Thank you.
   

On Fri, Jul 24, 2020 at 11:38 PM Douglas N. Greve 
mailto:dgr...@mgh.harvard.edu>> wrote:


It is not really possible. It is designed assuming you have MRIs.

On 7/24/2020 10:06 AM, Hengameh Marzbani wrote:


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Hello Freesurfer developers,
I have PET images for brain and I want to analyze them with
Petsurfer. But I don't have T1-weighted MRI of each subject.
What should I do? Is it possible?
Thank you in advance, Best regards, Hengameh



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Re: [Freesurfer] Working with cortical surface area - parcellation size?

[Douglas N. Greve]

I'm not sure what you are trying to do. If you want to look at 
differences in surface area, wouldn't making all the ROIs the same size 
defeat the purpose?


On 7/24/2020 9:33 AM, Yash Patel wrote:


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Hi Freesurfer colleagues,

I want to analyze regional profiles of differences in cortical surface 
area (SA). However, SA and its group differences in SA depend on 
parcellation size. In order to mitigate this effect, should I create a 
parcellation that has roughly equal area per ROI in FSaverage space, 
or equal number of vtx per ROI in FSaverage space.
Looking at smaller ROIs than the DK atlas - so I will be making the 
parcellation in any case.


Thanks - any advice would be much appreciated
Yash

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Re: [Freesurfer] overlapping/ superimposing regions of one analysis over another

[Douglas N. Greve]

are you asking how to create positive and negative regions or are you 
asking how to operate the visualization?


On 7/25/2020 9:40 AM, Sunil Khokhar wrote:


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Dear Experts,

I have done a between group (2 groups) difference in whole brain voxel 
based cortical thickness using QDEC, which showed significant regional 
differences in certain clusters bilaterally in the brain. I also did a 
correlation between cortical thickness and behavioral scores 
separately in these two groups. Now, I want to superimpose regions 
(clusters) which showed positive and negative correlation on 
the results/ regions I obtained in my between group analysis. How can 
I do this?


Thanks in advance!
Sunil.
___
Sunil K Khokhar
PhD Scholar,
Department of Neuroimaging & Interventional Radiology,
NIMHANS, Bengaluru, INDIA.
khokharsun...@gmail.com 
+91-9413101839

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[Freesurfer] Question about QDEC Design Tab Measurement Parameter

[Sonya Gupta]

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Hi,
Hope you are having a wonderful morning!
In QDEC in the Design tab under the measurement parameter, there are a
variety of options (thickness, area, area.pial, volume, sulc, curv,
white.K, white.H, w-g.pct.mgh, intensity.deep, intensity.superficial,
intensity.deep.mgz, and intensity.superficial.mgz). I was wondering, what
is the difference between these measurement options? I couldn't find much
documentation online.
Thank you!

Sincerely,
Sonya
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[Freesurfer] local gyrification index unit

[Backhausen, Lea]

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Hi FreeSurfer experts,

I have recently been wondering about the correct unit for curvature and local 
gyrification index.

For curvature I find inconsistent information like:
mm^-2 (https://onlinelibrary.wiley.com/doi/epdf/10.1002/ima.20138, page 47),
but also that curvature values are expressed in degrees 
(https://www.sciencedirect.com/science/article/pii/S1053811905006543, page 
1125).

For local gyrification index these papers make it seem like there is just not 
unit:
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5397412/#:~:text=A%20large%20GI%20indicates%20a,was%20then%20extracted%20per%20region.
https://www.jneurosci.org/content/jneuro/31/19/7174.full.pdf

Which are the correct units?
Happy to get some expert input on this, thank you so much!

Best,
Lea

--
Lea Backhausen
Ph.D. Student (M.Sc. Psychology/Neuroscience)

Department of Child and Adolescent Psychiatry, Faculty of Medicine of the TU 
Dresden, Germany
http://www.uniklinikum-dresden.de

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Re: [Freesurfer] Question about QDEC Design Tab Measurement Parameter

[Douglas N. Greve]

area is the area of the white surface. It  is  not as clear a concept 
as, eg, thickness. Basically, when the surface is registered to the 
atlas, it has to be stretched in some places and compressed in others. 
The stretching and compression will be different in different subjects 
and there may be an effect within group. Area allows you to probe this 
possibility. area.pial is the area of the pial surface.


volume is area*thickness

sulc is the sulcal depth -- how much a vertex has to move to get to the 
inflated surface


curv is the curvature. white.{K,H} are two types of curvature

w-g.pct.mgh is the percent difference between the gray and white matter 
intensities


I'm not  sure what the intensity files are; I don't think they are 
created by recon-all.


On 7/27/2020 12:22 PM, Sonya Gupta wrote:


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Hi,
Hope you are having a wonderful morning!
In QDEC in the Design tab under the measurement parameter, there are a 
variety of options (thickness, area, area.pial, volume, sulc, curv, 
white.K, white.H, w-g.pct.mgh, intensity.deep, intensity.superficial, 
intensity.deep.mgz, and intensity.superficial.mgz). I was wondering, 
what is the difference between these measurement options? I couldn't 
find much documentation online.

Thank you!

Sincerely,
Sonya

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Re: [Freesurfer] overlapping/ superimposing regions of one analysis over another

[Sunil Khokhar]

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To operate the visualization and obtain the common regions of my
between-group difference results and the correlation results in one image.
In other words, overlapping/ superimposing my correlation results on the
between-group results (to obtain the common regions from the two separate
analysis).

Thanks
___
Sunil K Khokhar
PhD Scholar,
Department of Neuroimaging & Interventional Radiology,
NIMHANS, Bengaluru, INDIA.
khokharsun...@gmail.com
+91-9413101839


On Mon, Jul 27, 2020 at 8:21 PM Douglas N. Greve 
wrote:

> are you asking how to create positive and negative regions or are you
> asking how to operate the visualization?
>
> On 7/25/2020 9:40 AM, Sunil Khokhar wrote:
>
> External Email - Use Caution
> Dear Experts,
>
> I have done a between group (2 groups) difference in whole brain voxel
> based cortical thickness using QDEC, which showed significant regional
> differences in certain clusters bilaterally in the brain. I also did a
> correlation between cortical thickness and behavioral scores separately in
> these two groups. Now, I want to superimpose regions (clusters) which
> showed positive and negative correlation on the results/ regions I obtained
> in my between group analysis. How can I do this?
>
> Thanks in advance!
> Sunil.
> ___
> Sunil K Khokhar
> PhD Scholar,
> Department of Neuroimaging & Interventional Radiology,
> NIMHANS, Bengaluru, INDIA.
> khokharsun...@gmail.com
> +91-9413101839
>
> ___
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>
>
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[Freesurfer] Postdoctoral position in the Haber laboratory at McLean Hospital/Harvard Medical School

[Yendiki, Anastasia]

Dear all - Please see below for a unique opportunity to join the Haber lab in 
Boston. While the amazing work of the Haber lab speaks for itself, I will also 
add here the questionable perk that you might have me as a collaborator. If 
interested, please contact Dr. Haber directly (see below).


Best,

Anastasia.


Postdoctoral position in the Haber laboratory at McLean Hospital/Harvard 
Medical School


The Haber laboratory at McLean Hospital seeks a postdoctoral fellow with a 
background in neuroscience with a particular interest in circuitry.


We are a translational neuroscience laboratory that uses a multidisciplinary 
approach to: 1) delineate anatomic connections of prefrontal cortex and basal 
ganglia that underlie motivation and decision making, 2) and link the 
neurocircuits to structural and functional networks, 3) use this data to 
develop connectivity profiles in the human brain to determine how circuit 
abnormalities in obsessive compulsive disorder, addiction, and depression are 
related to specific connections, and 4) in collaboration with clinical groups, 
identify potential targets for invasive and non-invasion circuit-based 
therapeutic approaches. We use a combination of anatomic tracing data, 
computational tools, and imaging (diffusion MRI, and resting state MRI in both 
animals and humans) to model neural network interactions. The successful 
applicant will join a vibrant and collaborative laboratory and scientific 
community at McLean Hospital. (S)he will have full access to the diverse 
research, financial, and career development opportunities offered through both 
McLean Hospital and Harvard Medical School as a Research Fellow in the 
Department of Psychiatry at Harvard Medical School.


McLean Hospital is a comprehensive psychiatric hospital committed to providing 
easy access to superior quality, cost-effective mental health services in the 
Boston area, Massachusetts and beyond. Since 1811, McLean Hospital has been a 
world leader in the treatment of mental illness and chemical dependency, 
research into the cause of mental illness and the training of generations of 
mental health care providers. McLean's multidisciplinary programs treat a broad 
range of psychiatric illnesses across the full continuum of care.


There are many opportunities for education and growth in our multidisciplinary, 
collaborative research environment at McLean Hospital that brings together a 
diverse group of neurobiologists, clinicians, psychologists and statisticians. 
Please see https://www.mcleanhospital.org/research


Job description:

Major job duties may include microscopic, diffusion and/or resting state MRI 
analyses, and computer analyses.


Qualifications:

PhD or MD/PhD in neuroscience or related discipline, as well as good computer 
skills. The following experience is preferred:

- Circuitry

- Computational neuroscience

- Imaging (Diffusion MRI and/or Functional MRI)


How to apply:

Interested applicants should send a cover letter, CV, and contact information 
(including phone numbers, email addresses) for three reference letters to 
sha...@mclean.harvard.edu. The position is full-time with excellent benefits. 
Salary will be commensurate with experience and follow NIH guidelines.

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Re: [Freesurfer] FreeSurfer 7.1.0 tkmedit not opening - please help

[Douglas N. Greve]

tkmedit is deprecated. Try tkmeditfv

On 7/24/2020 8:03 AM, Nils Böer wrote:


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Hello everyone,

I'm having a problem with tkmedit on the pre-installed Freesurfer 
7.1.0 version for as Ubuntu guest on a Windows 10 host (via Oracle VM).


I did work with the 6.0 version before but changed to Freesurfer 7.1 
and used the .vdi for Oracle VM where Freesurfer is pre-installed. I 
did run recon-all for all my data and now wanted to start to check the 
surfaces with tkmedit. When I try running tkmedit (tkmedit P_01 
brainmask.mgz -aux T1.mgz -surfs) it shows me, that it Converted the 
surfaces but no window is opening. When I'm closing the console it 
shows me, that there is a process running in the background but the 
tkmedit window is missing.


I hope someone knows how to solve the problem.

Best regards,

Nils
--

Nils Böer
Research Assistant with Bachelor Degree (WHB)
*Psychology and Movement*
University of Paderborn
Department of Sports and Health
Warburger Str. 100
33098 Paderborn
Room: Sp 1.401

Email: nils.tobia...@gmail.com / nbo...@mail.uni-paderborn.de 


Web: https://sug.uni-paderborn.de/en/sport/sportpsychologie/team/
https://sug.uni-paderborn.de/department/it/ 



 
	Virenfrei. www.avast.com 
 




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[Freesurfer] FreeSurfer 7.1.1 is released

[Douglas N. Greve]

FreeSurfer 7.1.1 is now available here 
https://surfer.nmr.mgh.harvard.edu/fswiki/rel7downloads


This new version fixes bugs and adds some new features. Unless the new 
features are employed, it will give the same result as 7.1.0; 
consequently, results from subjects analyzed with 7.1.1 CAN be mixed 
with subjects analyzed with 7.1.0.


Bug Fixes:

 *

   Mac-related fixes:
   freeview/ PETSC error is now fixed
   fs_time now runs properly
   mri_cc does not crash when it can't find fornix (usually on mac)
   "preserve=timestamps" error fixed

 * Memory leaks fixed (MRIScomputeMetricProperties). The excessive
   memory usage had caused some jobs to crash

New Features:

 * mris_volmask and mris_place_surface now have parallel
   implementations making recon-all faster
 * tkregisterfv can now be run with --fstal (use this instead of
   tkregister2 to check the talairach registration)
 *

   official FS docker container at
   https://hub.docker.com/r/freesurfer/freesurfer/


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[Freesurfer] fsgd file - glmfit error

[Lab of Autism and Developmental Neuroscience, Lab of Autism and Developmental Neuroscience]

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Dear Freesurfer experts,

Hope this email finds you well. I am having some trouble with the fsgd file
for glmfit and I'm confused why. This is the error I'm getting when running
glmfit:

iMac-Pro:BAP_complete ajobsaid$ mri_glmfit --y mrip.rh_volume_F7_BNB.00.mgh
--fsgd fsgd_8.fsgd --C Cor_2.mtx --surf fsaverage rh --cortex --glmdir
contrast2.rh_volume_BNB.glmdir
gdfRead(): reading fsgd_8.fsgd
ERROR: FSGDF version 0 unsupported (fsgd_8.fsgd)
iMac-Pro:BAP_complete ajobsaid$

If needed, I can send you my fsgd file, but I have triple checked the
design and format of the file (it is saved as .fsgd), and I'm still getting
this error message.

Thank you,
Alex
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Re: [Freesurfer] fsgd file - glmfit error

[Douglas N. Greve]

Please send the fsgd file

On 7/27/2020 11:34 PM, Lab of Autism and Developmental Neuroscience, Lab 
of Autism and Developmental Neuroscience wrote:


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Dear Freesurfer experts,

Hope this email finds you well. I am having some trouble with the fsgd 
file for glmfit and I'm confused why. This is the error I'm getting 
when running glmfit:


iMac-Pro:BAP_complete ajobsaid$ mri_glmfit --y 
mrip.rh_volume_F7_BNB.00.mgh --fsgd fsgd_8.fsgd --C Cor_2.mtx --surf 
fsaverage rh --cortex --glmdir contrast2.rh_volume_BNB.glmdir

gdfRead(): reading fsgd_8.fsgd
ERROR: FSGDF version 0 unsupported (fsgd_8.fsgd)
iMac-Pro:BAP_complete ajobsaid$

If needed, I can send you my fsgd file, but I have triple checked the 
design and format of the file (it is saved as .fsgd), and I'm still 
getting this error message.


Thank you,
Alex

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