Re: [Freesurfer] Running Linear Mixed Effects (LME) Model

[Diers, Kersten /DZNE]

On Do, 2018-03-08 at 03:56 +0100, Kaushal, Mayank wrote:
> Your inputs have been very helpful.
>
> Looking at the examples on LME webpage, the contrast for both
> univariate and mass-variate creates 3 rows with 14 columns for
> univariate and 17 for mass-variate analysis. My understanding is that
> 3 rows have been created because there are 4 groups being analyzed
> and applying that rationale to my data would mean that the contrast
> for my analysis would require 2 rows since I comparing 3 groups. Is
> my logic correct here?

Yes, that's correct.

As a side note, it only applies when you want to include all three
groups in a contrast. If you compare only two groups against each
other, then a single line could be sufficient also in your design.

> So, for my analysis if I want to include two random effects, namely,
> intercept and time_from_base_scan, which are given in Column 1 and 2,
> respectively, the contrasts based on M having 6 columns would as
> follows:
> CM.C = [1 1 ; 1 1] zeros(2,4)];
> or
> CM.C = [1 1 0 0 0 0; 1 1 0 0 0 0]

This may be more tricky. It is not necessarily / exclusively the random
effects that are of interest in a longitudinal study, and in general
there are multiple valid contrasts that each test for different
effects. In the above example, it would be the combined effect of the
overall intercept and the time-from-baseline - I have to admit that I
do not know what the interpretation of that effect would be.

So the contrast specification really depends on which question you want
to ask to the data. In designs like yours, this could be the effect of
group, the effect of time, group differences in the effect of time, or
the effect of covariates. You'll then typically set the corresponding
entries in the contrast vector to either '1' or '-1', and zero
otherwise.

Hope this helps,

Kersten

> Mayank
> On Mar 7, 2018, at 3:33 PM, Diers, Kersten /DZNE  de> wrote:
>
> ATTENTION: This email originated from a sender outside of MCW. Use
> caution when clicking on links or opening attachments.
> 
>
> Hi,
>
> let me just mention that my previous comments were directed at the
> design matrix X and not necessarily at the QDEC table. In that sense,
> it is possible, but not necessary to modify the QDEC table prior to
> loading it into Matlab. Alternatively, one might do these
> modifications
> within Matlab, although this would require some additional manual
> coding.
>
> For the present analysis, however, the current qdec table looks fine.
>
>
> About question 1:
>
> If I understood correctly, you have so far loaded the (modified) QDEC
> table and stored the extracted information within the matlab variable
> 'M'.
>
> In addition to that you'd also need to sort the data within each
> subject according to time, and load 'Y', 'lhcortex' and possibly
> 'lhsphere'. For a description of all of these steps please see the
> "mass-univariate" section of the example data analysis on the
> tutorial
> page.
>
>
> About question 2:
>
> Just to be precise, I assume that for this particular case the matlab
> variable 'M' contains the following four columns: time-from-baseline,
> age-at-baseline, group2, group3; where 'group2' and 'group3' indicate
> memberships in groups 2 and 3, respectively.
>
> Then, a design matrix can be created as follows:
>
> X = [ones(length(M),1) M M(:,1).*M(:,3) M(:,1).*M(:,4)];
>
> Then the order of the columns of X is: intercept, time-from-baseline,
> age-at-baseline, group2, group3, time-from-baseline*group2, time-
> from-
> baseline*group3.
>
> Let's keep in mind that the order of columns in X is important for
> the
> formulation of contrasts at a later stage (and is different from the
> tutorial example).
>
> Again, this procedure and the matrices M and X are specific for this
> particular analysis scenario and cannot necessarily be generalized to
> others.
>
> Best regards,
>
> Kersten
>
>
> -Original Message-
> From: "Kaushal, Mayank" mailto:mkaus...@mcw.edu>>
> Reply-to: Freesurfer support list 
> To: Freesurfer support list 
> Subject: Re: [Freesurfer] Running Linear Mixed Effects (LME) Model
> Date: Wed, 7 Mar 2018 15:48:36 +0100
>
> I have made the suggested edits and would appreciate if you could
> take
> a look at the qdec.table.dat file attached to this conversation.
>
> After going over the univariate example on the Freesurfer LME
> webpage,
> I had a couple of questions.
>
> 1. How will data be loaded into Matlab? More specifically, what would
> be the step(s) after the line M = Qdec2num(Qdec);?
>
> 2. Given that column named time_base_scan would be multiplied with
> column named group2 as well as group3, what will be the equation for
> creating the design matrix?
> X = [ones(length(M),1) M M(:,).*M(:,)];
>
>
> Mayank
> On Mar 7, 2018, at 7:14 AM, Diers, Kersten /DZNE  de> wrote:
>
> ATTENTION: This email originated from a sender outside of MCW. Use
> caution when clicking on links or opening att

[Freesurfer] Eliminate variable which is the same for all patients from FreeSurfer's Design Matrix

[k . ohmstedt]

Dear all,

I am trying to correlate psychometric measurements and the local  
Gyrification Index.
To do so, I use the FreeSurfer pipeline to calculate the lGI and then  
PALM, following the advice in this thread  
(https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2017-March/050703.html).

All my subjects are part of the same group, so I used a FSGD with the  
group "main" to create the design matrix and mask for my data that are  
required by PALM.
Having a closer look at the design matrix that was created, I found  
that there was a variable for the group that was the same for all my  
patients. As it is the same for all patients, I thought eliminating it  
would not be a problem. But after re-running PALM without it, there  
were huge differences in my results and effects were notably larger  
and more significant.

Do any of you have any experience which option is best in this case?  
Is it a valid choice to eliminate the variable for the group, as it is  
the same for each patient anyway?

Furthermore, would you recommend centering for the design matrix? I  
found that this can have an impact, but I am lost on in which cases it  
should be done and in which it shouldn't.


Thank you for your help!


Best regards

Kai Ohmstedt


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[Freesurfer] Brain microstructure MRI postdoc (Italy)

[Jovicich, Jorge]

Hello,

We will soon advertise a 2-year postdoctoral fellowship at the MRI Group 
 of the Center for Mind/Brain Sciences 
(CIMeC ), University of Trento 
, Italy. The focus of this position will 
involve the development, testing and validation of MRI techniques that 
allow quantification of tissue microstructure properties. The successful 
candidate will be part of an international multidisciplinary team 
developing and applying MRI techniques to study brain structure and 
function supporting normal higher cognitive function as well as the 
study of cognitive dysfunction in various neurological and 
neuropsychiatric conditions (including pre-surgical planning, plasticity 
in deaf and blind, novel markers sensitive to the progression of 
neurodegenerative diseases).

Facilities: The CIMeC MRI neuroimaging lab will house a Siemens Prisma 
3T scanner (tentatively May 2018) designed for research and clinical 
studies. The position will allow for training opportunities in pulse 
sequence development, brain anatomy, and translational clinical 
research. The fellow is expected to be able to work independently as 
well as part of a multidisciplinary team with supervisory 
responsibilities of graduate student research. The fellow will support 
research MRI users, will have opportunities to develop new ideas and 
advance their own research interests in an international academic 
environment.

Requirements: Minimum qualifications are a doctoral degree in cognitive 
neurosciences, physics, engineering, computer sciences or related area, 
strong scientific publication record, and demonstrated expertise in MRI 
methods development and applications. The ideal candidates should be 
proficient in programming, such as C++, Matlab. Experience in pulse 
sequence design, particularly on Siemens platform, and/or image 
reconstruction will be a plus. Additional requirements include high 
self-motivation, ability of solving research problems independently, and 
excellent communication skills.

Contact: Interested candidates please contact Jorge Jovicich, Ph.D, 
MSc., Assistant Professor (jorge.jovic...@unitn.it).

-- 
Jorge Jovicich, Ph.D.

MR Lab Head
Center for Mind/Brain Sciences
University of Trento,
Via delle Regole, 101
38100 Mattarello (TN)
Italy

Telephone: +39-0461-28 3064
Fax: +39-0461-28-3066
Email: jorge.jovic...@unitn.it
MRI Methods Group: http://r.unitn.it/en/cimec/mri
CIMEC: http://www.cimec.unitn.it/

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[Freesurfer] Mean Curvature

[Kasper Jessen]

Hej FreeSurfer,

Question regarding the meancurv extracted from the Desikan atlas using 
aparcstats2table.

Is the meancurv the absolute mean curvature? Thus all the values are positive?

Best regards
Kasper

Sent from [ProtonMail](https://protonmail.com), Swiss-based encrypted email.

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Re: [Freesurfer] Mean Curvature

[Bruce Fischl]

Hi Kaspar

I don't think so.

cheers
Bruce
On Thu, 8 Mar 2018, Kasper Jessen wrote:

> Hej FreeSurfer,
> 
> Question regarding the meancurv extracted from the Desikan atlas using 
> aparcstats2table.
> 
> Is the meancurv the absolute mean curvature? Thus all the values are positive?
> 
> Best regards
> Kasper
> 
> Sent from ProtonMail, Swiss-based encrypted email.
> 
> Sent with ProtonMail Secure Email.
> 
> 
>
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[Freesurfer] FreeSurfer Edit Sequence Inquiry

[David S Lee]

Hello FreeSurfer Group,

I am writing to inquire about Editing Sequence.

The "Troubleshooting your output" page (https://surfer.nmr.mgh.
harvard.edu/fswiki/FsTutorial/TroubleshootingData) explains the edits
sequence as brain mask --> wm volume --> white surface --> control points.

Do you suggest people to absolutely stick to this particular sequence?

Thanks for your time,

David
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Re: [Freesurfer] [Freesurfer/Freeview cutting]

[Ruopeng Wang]

Hi,

There is no surface cutting function in freeview. But I’m going to add it. Will 
let you know when I have it ready for testing. 

Best,
Ruopeng

> On Mar 7, 2018, at 11:16 PM, Dave Yas  wrote:
> 
> Hello,
> 
> Can we cut the surface (for flatting later) in freeview? if yes, how? I cant 
> find a tutorial online for that. 
> tksurfer is not working, it crashes by it self. If i cant use freeview to 
> cut, do you suggest another alternative? 
> 
> thank you 
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> 
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Re: [Freesurfer] Eliminate variable which is the same for all patients from FreeSurfer's Design Matrix

[Douglas N. Greve]

can you send your fsgd file so that I have a better idea of what you are 
mentioning?


On 03/08/2018 08:39 AM, k.ohmst...@stud.uni-heidelberg.de wrote:
> Dear all,
>
> I am trying to correlate psychometric measurements and the local
> Gyrification Index.
> To do so, I use the FreeSurfer pipeline to calculate the lGI and then
> PALM, following the advice in this thread
> (https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2017-March/050703.html).
>
> All my subjects are part of the same group, so I used a FSGD with the
> group "main" to create the design matrix and mask for my data that are
> required by PALM.
> Having a closer look at the design matrix that was created, I found
> that there was a variable for the group that was the same for all my
> patients. As it is the same for all patients, I thought eliminating it
> would not be a problem. But after re-running PALM without it, there
> were huge differences in my results and effects were notably larger
> and more significant.
>
> Do any of you have any experience which option is best in this case?
> Is it a valid choice to eliminate the variable for the group, as it is
> the same for each patient anyway?
>
> Furthermore, would you recommend centering for the design matrix? I
> found that this can have an impact, but I am lost on in which cases it
> should be done and in which it shouldn't.
>
>
> Thank you for your help!
>
>
> Best regards
>
> Kai Ohmstedt
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] Running Linear Mixed Effects (LME) Model

[Kaushal, Mayank]

I created the contrast:
CM.C = [1 1 0 0 0 0; 1 1 0 0 0 0]

Then I ran the following:
F_lhstats = lme_mass_F(lhstats,CM);


I received the following error message, which kept on repeating in loop.

Warning: Matrix is singular to working precision.
> In matlab.internal.math.mpower.viaMtimes (line 35)
  In parallel_function>make_general_channel/channel_general (line 914)
  In remoteParallelFunction (line 38)

Finally, I had to terminate the operation Ctrl + C, which displayed the 
following:

Operation terminated by user during matlab.internal.math.mpower.viaMtimes (line 
35)

In parallel_function>make_general_channel/channel_general (line 914)
O = F(C{:});

In remoteParallelFunction (line 38)
out = parallel.internal.pool.serialize(feval(channel, channelArgs{:}));

Operation terminated by user during distcomp.remoteparfor/getCompleteIntervals 
(line 127)

In parallel_function>distributed_execution (line 820)
[tags, out] = P.getCompleteIntervals(chunkSize);

In parallel_function (line 587)
R = distributed_execution(...

In lme_mass_F (line 92)
parfor i=1:nv

Mayank
On Mar 8, 2018, at 6:36 AM, Diers, Kersten /DZNE 
mailto:kersten.di...@dzne.de>> wrote:

ATTENTION: This email originated from a sender outside of MCW. Use caution when 
clicking on links or opening attachments.


On Do, 2018-03-08 at 03:56 +0100, Kaushal, Mayank wrote:
Your inputs have been very helpful.

Looking at the examples on LME webpage, the contrast for both
univariate and mass-variate creates 3 rows with 14 columns for
univariate and 17 for mass-variate analysis. My understanding is that
3 rows have been created because there are 4 groups being analyzed
and applying that rationale to my data would mean that the contrast
for my analysis would require 2 rows since I comparing 3 groups. Is
my logic correct here?

Yes, that's correct.

As a side note, it only applies when you want to include all three
groups in a contrast. If you compare only two groups against each
other, then a single line could be sufficient also in your design.

So, for my analysis if I want to include two random effects, namely,
intercept and time_from_base_scan, which are given in Column 1 and 2,
respectively, the contrasts based on M having 6 columns would as
follows:
CM.C = [1 1 ; 1 1] zeros(2,4)];
or
CM.C = [1 1 0 0 0 0; 1 1 0 0 0 0]

This may be more tricky. It is not necessarily / exclusively the random
effects that are of interest in a longitudinal study, and in general
there are multiple valid contrasts that each test for different
effects. In the above example, it would be the combined effect of the
overall intercept and the time-from-baseline - I have to admit that I
do not know what the interpretation of that effect would be.

So the contrast specification really depends on which question you want
to ask to the data. In designs like yours, this could be the effect of
group, the effect of time, group differences in the effect of time, or
the effect of covariates. You'll then typically set the corresponding
entries in the contrast vector to either '1' or '-1', and zero
otherwise.

Hope this helps,

Kersten

Mayank
On Mar 7, 2018, at 3:33 PM, Diers, Kersten /DZNE mailto:kersten.di...@dzne.de>> wrote:

ATTENTION: This email originated from a sender outside of MCW. Use
caution when clicking on links or opening attachments.


Hi,

let me just mention that my previous comments were directed at the
design matrix X and not necessarily at the QDEC table. In that sense,
it is possible, but not necessary to modify the QDEC table prior to
loading it into Matlab. Alternatively, one might do these
modifications
within Matlab, although this would require some additional manual
coding.

For the present analysis, however, the current qdec table looks fine.


About question 1:

If I understood correctly, you have so far loaded the (modified) QDEC
table and stored the extracted information within the matlab variable
'M'.

In addition to that you'd also need to sort the data within each
subject according to time, and load 'Y', 'lhcortex' and possibly
'lhsphere'. For a description of all of these steps please see the
"mass-univariate" section of the example data analysis on the
tutorial
page.


About question 2:

Just to be precise, I assume that for this particular case the matlab
variable 'M' contains the following four columns: time-from-baseline,
age-at-baseline, group2, group3; where 'group2' and 'group3' indicate
memberships in groups 2 and 3, respectively.

Then, a design matrix can be created as follows:

X = [ones(length(M),1) M M(:,1).*M(:,3) M(:,1).*M(:,4)];

Then the order of the columns of X is: intercept, time-from-baseline,
age-at-baseline, group2, group3, time-from-baseline*group2, time-
from-
baseline*group3.

Let's keep in mind that the order of columns in X is important for
the
formulation of contrasts at a later stage (and is different from the
tutorial exa

Re: [Freesurfer] FreeSurfer Edit Sequence Inquiry

[Boyd, Emma]

Hi David,


There is no particular order in which you have to make edits. The order in 
which these edits are described on our wiki is not indicative of any order in 
which they must be made. However, it may help you to understand the overall 
order of the recon-all processing stream so that you know which volumes to edit 
and how your edits will be incorporated. There is more information on this 
underneath each section on the Troubleshooting wiki, and an overview of the 
recon-all stream is located 1) here: 
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TroubleshootingDataV6.0#Implementingfixes
 2) In the slides titled 'Analyzing the Individual subject' on the FsTutorial 
wiki https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial and 3) on the 
recon-all tables: 
https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllTableStableV6.0.


Best,
Emma



From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of David S Lee 

Sent: Thursday, March 8, 2018 10:41:13 AM
To: Freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] FreeSurfer Edit Sequence Inquiry

Hello FreeSurfer Group,

I am writing to inquire about Editing Sequence.

The "Troubleshooting your output" page 
(https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TroubleshootingData) 
explains the edits sequence as brain mask --> wm volume --> white surface --> 
control points.

Do you suggest people to absolutely stick to this particular sequence?

Thanks for your time,

David
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[Freesurfer] Question regarding recon-all

[Levitas, Daniel]

Hello,


I am running recon-all for the first time, and I am wondering when it is proper 
to use the -i option. My current recon-all command includes the -i option: 
recon-all -i T1.nii.gz -s 1020 -all, where T1.nii.gz is a nifti file of all 160 
anatomical dicoms. I've seen some commands like this however: recon-all -s 
subjid -all?.  My question is, is it safer to specify the input, and if I 
choose not to, do I need to create an mri/orig/001.mgz file from mri_convert?


Thank you for the help,


Dan
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Re: [Freesurfer] Question regarding recon-all

[Bruce Fischl]

Hi Dan

yes, we typically use -i and read in the dicoms directly, but you can do 
it for a nifti also. Or you could create the 001.mgz and not use it, but 
there is no reason to (it's just more work).


cheers
Bruce

On Thu, 8 Mar 2018, Levitas, Daniel wrote:



Hello,


I am running recon-all for the first time, and I am wondering when it is proper 
to use the -i
option. My current recon-all command includes the -i option: recon-all -i 
T1.nii.gz -s 1020 -all,
where T1.nii.gz is a nifti file of all 160 anatomical dicoms. I've seen some 
commands like this
however: recon-all -s subjid -all​.  My question is, is it safer to specify the 
input, and if I
choose not to, do I need to create an mri/orig/001.mgz file from mri_convert?


Thank you for the help,


Dan


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Re: [Freesurfer] Question regarding recon-all

[Levitas, Daniel]

Hi Bruce,

Thanks for your response. Just to clarify, I can run recon-all with the -i 
option and not create the 001.mgz file from mri_convert because recon-all will 
perform the conversion anyway?

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Bruce Fischl 

Sent: Thursday, March 8, 2018 1:37 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Question regarding recon-all

Hi Dan

yes, we typically use -i and read in the dicoms directly, but you can do
it for a nifti also. Or you could create the 001.mgz and not use it, but
there is no reason to (it's just more work).

cheers
Bruce

On Thu, 8 Mar 2018, Levitas, Daniel wrote:

>
> Hello,
>
>
> I am running recon-all for the first time, and I am wondering when it is 
> proper to use the -i
> option. My current recon-all command includes the -i option: recon-all -i 
> T1.nii.gz -s 1020 -all,
> where T1.nii.gz is a nifti file of all 160 anatomical dicoms. I've seen some 
> commands like this
> however: recon-all -s subjid -all​.  My question is, is it safer to specify 
> the input, and if I
> choose not to, do I need to create an mri/orig/001.mgz file from mri_convert?
>
>
> Thank you for the help,
>
>
> Dan
>
>
>

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Re: [Freesurfer] Question regarding recon-all

[Bruce Fischl]

yes, exactly.
On Thu, 8 Mar 2018, Levitas, Daniel wrote:


Hi Bruce,

Thanks for your response. Just to clarify, I can run recon-all with the -i 
option and not create the 001.mgz file from mri_convert because recon-all will 
perform the conversion anyway?

From: freesurfer-boun...@nmr.mgh.harvard.edu  
on behalf of Bruce Fischl 
Sent: Thursday, March 8, 2018 1:37 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Question regarding recon-all

Hi Dan

yes, we typically use -i and read in the dicoms directly, but you can do
it for a nifti also. Or you could create the 001.mgz and not use it, but
there is no reason to (it's just more work).

cheers
Bruce

On Thu, 8 Mar 2018, Levitas, Daniel wrote:



Hello,


I am running recon-all for the first time, and I am wondering when it is proper 
to use the -i
option. My current recon-all command includes the -i option: recon-all -i 
T1.nii.gz -s 1020 -all,
where T1.nii.gz is a nifti file of all 160 anatomical dicoms. I've seen some 
commands like this
however: recon-all -s subjid -all​.  My question is, is it safer to specify the 
input, and if I
choose not to, do I need to create an mri/orig/001.mgz file from mri_convert?


Thank you for the help,


Dan





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[Freesurfer] Brainstem registration

[Chungmin Han]

Dear whomever it may concern,

I'm Chungmin, a graduate research assistant in University of Texas at
Austin,
I'm fairly new to using freesurfer, I'd appreciate to get some advice on
what I'm facing,


I have fMRI limited FOV collected on brainstem + little cerebellum/visual
area,
I've tried SPM manual registration to MNI space, falls in 1-2mm (1-2
voxels) away from accurate registering brainstem correctly,


is there a way to create transformation matrix optimized to fit brainstem
in MNI space?
Registering cortical region slightly bit wrong is okay to me at this
moment,

https://surfer.nmr.mgh.harvard.edu/fswiki/BrainstemSubstructures

I've noticed this has been posted pretty recently, but would like to figure
out how to align in standard space for comparison.

I've also thought of inverse registering from MNI to each native space,
however, if the transformation focuses on maximizing registration on the
cortical level (T1) I don't think inverse registration solves the issue,

Thank you in advance :)
Best

Chungmin

Chungmin Han

Graduate Research Assistant
The University of Texas at Austin
204 E. Dean Keeton St Austin TX 78712
Mobile: 512-717-1671
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Re: [Freesurfer] Brainstem registration

[Bruce Fischl]

Hi Chungmin

do you have a whole-brain T1 that you can use for generating anatomical 
models? If so, many more things are possible


cheers
Bruce


On Thu, 8 Mar 2018, Chungmin Han wrote:


Dear whomever it may concern,

I'm Chungmin, a graduate research assistant in University of Texas at Austin,
I'm fairly new to using freesurfer, I'd appreciate to get some advice on what 
I'm facing,


I have fMRI limited FOV collected on brainstem + little cerebellum/visual area,
I've tried SPM manual registration to MNI space, falls in 1-2mm (1-2 voxels) 
away from accurate
registering brainstem correctly,


is there a way to create transformation matrix optimized to fit brainstem in 
MNI space?
Registering cortical region slightly bit wrong is okay to me at this moment,

https://surfer.nmr.mgh.harvard.edu/fswiki/BrainstemSubstructures

I've noticed this has been posted pretty recently, but would like to figure out 
how to align in
standard space for comparison.

I've also thought of inverse registering from MNI to each native space, 
however, if the
transformation focuses on maximizing registration on the cortical level (T1) I 
don't think inverse
registration solves the issue,

Thank you in advance :)
Best

Chungmin

Chungmin Han

Graduate Research Assistant

The University of Texas at Austin
204 E. Dean Keeton St Austin TX 78712
Mobile: 512-717-1671

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Re: [Freesurfer] Mean Curvature

[Kasper Jessen]

Hej Bruce,

Based on the formular for mean curvature stated below and the article by R. 
Pienaar 
(https://surfer.nmr.mgh.harvard.edu/pub/articles/AMethodologyForAnalyzingCurvature.pdf)

H = 0.5(k1 + k2)

i understand the following:

k1 is by definition larger than k2. Thus values of H is primarily driven by k1 
(which primarily describes the curvature in the gyral/sulcal "banks")e. 

therefore:
if k1 is negative: more variation in the outward curvatures  (gyrus) than 
inward curvatures
if k1 is positive: more variation in the inward curvature (sulcus) than outward 
curvatures

Question:
a) So if a H values for a particular ROI (Desikan atlas) is positive, would 
mean that that the variation is 'primarily' in the inward curvature direction 
(sulcus)?
b) The higher value of H, the more 'sharp' the curvature. 

Is this correctly understood?

and again, thank you for the quick reply. 

BW
Kasper

​Sent from ProtonMail, Swiss-based encrypted email.

Sent with ProtonMail Secure Email.​

‐‐‐ Original Message ‐‐‐

On March 8, 2018 4:13 PM, Bruce Fischl  wrote:

> Hi Kaspar
> 
> I don't think so.
> 
> cheers
> 
> Bruce
> 
> On Thu, 8 Mar 2018, Kasper Jessen wrote:
> 
> > Hej FreeSurfer,
> > 
> > Question regarding the meancurv extracted from the Desikan atlas using 
> > aparcstats2table.
> > 
> > Is the meancurv the absolute mean curvature? Thus all the values are 
> > positive?
> > 
> > Best regards
> > 
> > Kasper
> > 
> > Sent from ProtonMail, Swiss-based encrypted email.
> > 
> > Sent with ProtonMail Secure Email.
> 
> The information in this e-mail is intended only for the person to whom it is
> 
> addressed. If you believe this e-mail was sent to you in error and the e-mail
> 
> contains patient information, please contact the Partners Compliance HelpLine 
> at
> 
> http://www.partners.org/complianceline . If the e-mail was sent to you in 
> error
> 
> but does not contain patient information, please contact the sender and 
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> 
> dispose of the e-mail.



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[Freesurfer] Negative areas in mris_sphere, dark in freeview

[Chris Adamson]

Freesurfer devs,

I have a baffling problem in mris_sphere.

I have generated some surfaces using an external tool that uses VTK. After 
converting the surfaces into freesurfer format using a basic format converter, 
then adding volume geometry to the surface file using the image used to create 
it the surface appears dark in freeview. When I do mris_inflate followed by 
mris_sphere, mris_sphere says nearly all the triangles have negative area at 
the end and it never finishes. I verified in MATLAB that the surface normals 
(computed by mris_convert) of the original white surfaces point outwards. The 
darkness in freeview is not fixed by changing the order of the indices of the 
faces (which should invert the normal). I'm at a loss to explain this.

Thanks in advance,

Chris.

Dr Chris Adamson
Senior Research Officer
Developmental Imaging, Clinical Sciences

Murdoch Childrens Research Institute
The Royal Children's Hospital
Flemington Road, Parkville, VIC 3052 Australia
E chris.adam...@mcri.edu.au
www.mcri.edu.au


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