Re: [Freesurfer] Freesurfer edits

[Zollei, Lilla,Ph.D.]

Hi Jim,
Did you use the infant or the regular pipeline here?
Lilla

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Alexopoulos, Dimitrios 

Sent: Tuesday, October 20, 2020 11:24 AM
To: Freesurfer support list 
Subject: [Freesurfer] Freesurfer edits


External Email - Use Caution

Hi freesurfer editing experts.



Below are snapshots of the brainmask, aseg and wm.mgz for a 2 year old run 
through FS 7.1.1

I’m hoping for feedback on the best way to make the relevant edits to the three 
blue-circled regions.



1.   In the superior regions I think control points will help to pick up 
some WM to help fuill

2.   In the left hemisphere medial prefrontal (gyrus rectus) regions, the 
WM is overestimated. I presume removing WM voxels from the wm.mgz is the best 
approach?

3.   The left temporal pole region is missing GM/cortex and there really 
isn’t any WM that would help with controls points or adding WM voxels. How can 
I add GM to this area?



[cid:image007.jpg@01D6A6CB.3399D5E0][cid:image008.jpg@01D6A6CB.3399D5E0]





[cid:image009.jpg@01D6A6CB.3399D5E0][cid:image010.jpg@01D6A6CB.3399D5E0]









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[Freesurfer] Group Analysis: Comparing four groups

[Steve Petersen]

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Dear Freesurfer experts,

This is the first time I perform group analysis in Freesurfer. My aim is to
compare the cortical thickness in four groups matched in age, sex and years
of education using the Monte Carlo multiple comparisons correction. I tried
to follow the Freesufer tutorials
 to
perform this group analysis and I would be really grateful whether someone
can verify that all steps are correct. For example, for the cortical
thickness (smooth = 15 FWHM) of the left hemisphere, the four steps that I
followed were:

STEP 1. Assemble the cached Data (mris_preproc) using the fsgd file

mris_preproc --fsgd STUDY_4groups.fsgd \
  --cache-in thickness.fwhm15.fsaverage \
  --target fsaverage \
  --hemi lh \
  --out lh_J4G_thickness.15.mgh \

STEP 2. Perform a GLM Analysis (mri_glmfit)

mri_glmfit \
--y lh_J4G_thickness.15.mgh \
--fsgd STUDY_4groups.fsgd \
--C *group.effect.mtx* \
--surf fsaverage lh \
--cortex \
--glmdir left_hemisphere_thickness_results\


STEP 3. Perform Monte Carlo simulation

mri_glmfit-sim \
  --glmdir left_hemisphere_thickness_results \
  --sim mc-z 1 4 mc-z.abs \
  --sim-sign abs --cwpvalthresh 0.05\
  --overwrite \


*QUESTIONS:*

1. Have I followed the steps to perform the analysis correctly or do you
think I forgot some important flag?


2. Before test differences between two groups (eg. group1 > group 2 with
the vector 1 -1 0 0) I would like to test any group effect. For that
purpose, I created the group.effect.mtx contrast file (see below), is
correct?

1 -1 0 0
0 1 -1 0
0 0 1 -1


Any help would be appreciated.

Best regards,


Steve
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Re: [Freesurfer] please help me

[Fischl, Bruce]

Nifty is a format that a lot of people use (including us) but it is not needed 
for our processing. Pick *one* file in your dicom series and pass it to 
recon-all:


recon-all -i  -s  -sdir  -all

cheers
Bruce

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of saman fouladi
Sent: Wednesday, October 21, 2020 11:57 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] please help me


External Email - Use Caution
hi

Thank you for your response

I have 60 subject MRI that each  contains 174 dcm file. and i want predict age 
of these subjects. in step one i want extract morphology features and in step2 
create a deep learning model that predict age.

According to what I said, what should I do?

If I have to use recon-all with what code can I do this? And what is the use of 
nifty?

On Wednesday, October 21, 2020, 1:06:50 AM GMT+3:30, Fischl, Bruce 
mailto:bfis...@mgh.harvard.edu>> wrote:



Hi Saman



Recon-all will give you a comprehensive assessment of most macroscopically 
visible structures in the brain. You don’t have to convert to nifty first – 
just point recon-all at a single slice in the proper dicom series (for your 3D 
T1-weighted scan), and it will spend a few hours doing stuff



Cheers

Bruce



From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of saman fouladi
Sent: Tuesday, October 20, 2020 4:12 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] please help me



External Email - Use Caution

hi



I want to process MRI images to extract Morphology features.



I convert my dcm file to nii format by mri-convert command and then  I used FSL 
software and BET(Best extraction Tool).



Next I do not know what to do to extract morphological features?



My other question is what is the difference between recon-all and use FEAT( in 
FSL software)? What are the uses of each?



Thank you




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[Freesurfer] Traculina availability

[Ngoh Zhen Ming]

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Good Morning!

I understand that the stable release of TRACULInA will be included in the next 
version of freesurfer. Is there an estimate of when that will be? Or if there 
are any versions that are currently openly available for trial?

Thank you and look forward to hearing back!

Zhen Ming, NGOH
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Re: [Freesurfer] Freesurfer edits

[Alexopoulos, Dimitrios]

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These outputs were generated using the regular pipeline 7.1.1

I tried the  infant pipeline as well but results were less desirable.

Get Outlook for Android


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Zollei, Lilla,Ph.D. 

Sent: Wednesday, October 21, 2020, 10:00 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] Freesurfer edits

* External Email - Caution *
Hi Jim,
Did you use the infant or the regular pipeline here?
Lilla

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Alexopoulos, Dimitrios 

Sent: Tuesday, October 20, 2020 11:24 AM
To: Freesurfer support list 
Subject: [Freesurfer] Freesurfer edits


External Email - Use Caution

Hi freesurfer editing experts.



Below are snapshots of the brainmask, aseg and wm.mgz for a 2 year old run 
through FS 7.1.1

I’m hoping for feedback on the best way to make the relevant edits to the three 
blue-circled regions.



1.   In the superior regions I think control points will help to pick up 
some WM to help fuill

2.   In the left hemisphere medial prefrontal (gyrus rectus) regions, the 
WM is overestimated. I presume removing WM voxels from the wm.mgz is the best 
approach?

3.   The left temporal pole region is missing GM/cortex and there really 
isn’t any WM that would help with controls points or adding WM voxels. How can 
I add GM to this area?



[cid:image007.jpg@01D6A6CB.3399D5E0][cid:image008.jpg@01D6A6CB.3399D5E0]





[cid:image009.jpg@01D6A6CB.3399D5E0][cid:image010.jpg@01D6A6CB.3399D5E0]









The materials in this message are private and may contain Protected Healthcare 
Information or other information of a sensitive nature. If you are not the 
intended recipient, be advised that any unauthorized use, disclosure, copying 
or the taking of any action in reliance on the contents of this information is 
strictly prohibited. If you have received this email in error, please 
immediately notify the sender via telephone or return mail.



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or the taking of any action in reliance on the contents of this information is 
strictly prohibited. If you have received this email in error, please 
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Re: [Freesurfer] please help me

[saman fouladi]

External Email - Use Caution

 hi
 Thank you for your response
I have 60 subject MRI that each  contains 174 dcm file. and i want predict age 
of these subjects. in step one i want extract morphology features and in step2 
create a deep learning model that predict age.
According to what I said, what should I do?
 If I have to use recon-all with what code can I do this? And what is the use 
of nifty?

On Wednesday, October 21, 2020, 1:06:50 AM GMT+3:30, Fischl, Bruce 
 wrote:  
 
 #yiv4456525891 #yiv4456525891 -- _filtered {} _filtered {} _filtered 
{}#yiv4456525891 #yiv4456525891 p.yiv4456525891MsoNormal, #yiv4456525891 
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div.yiv4456525891WordSection1 {}#yiv4456525891 
Hi Saman
 
  
 
Recon-all will give you a comprehensive assessment of most macroscopically 
visible structures in the brain. You don’t have to convert to nifty first – 
just point recon-all at a single slice in the proper dicom series (for your 3D 
T1-weighted scan), and it will spend a few hours doing stuff
 
  
 
Cheers
 
Bruce
 
  
 
From: freesurfer-boun...@nmr.mgh.harvard.edu 
On Behalf Of saman fouladi
Sent: Tuesday, October 20, 2020 4:12 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] please help me
 
  
 
External Email - Use Caution
 
hi
 
  
 
I want to process MRI images to extractMorphology features.
 
  
 
I convert my dcm file to nii format by mri-convert command and then  I used FSL 
software and BET(Best extraction Tool).
 



 
Next I do not know what to do to extract morphological features?
 
  
 
My other question is what is the difference between recon-all and use FEAT( in 
FSL software)? What are the uses of each?
 
  
 
Thank you
 
  
 
  
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Re: [Freesurfer] Estimating the memory footprint of Longitudinal Stream?

[Paul Wighton]

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Thanks Doug.  No need to add anything to mri_fuse_segmentations.  I'll keep
digging.

-Paul

On Mon, Oct 19, 2020 at 11:10 AM Douglas N. Greve 
wrote:

> I don't know. Each command will have an fs_time output which will have a
> measure of the peak memory used, though it is not super accurate.
> Alternatively, I could add something to mri_fuse_segmentations to
> periodically print out the peak memory usage
>
> On 10/13/2020 3:01 PM, Paul Wighton wrote:
>
> External Email - Use Caution
> Hi FreeSurfers,
>
> Is there any guidance on how to estimate the memory footprint of the
> Longitudinal steam?
>
> We are trying to process the MacLaren test-retest dataset [1] (40
> timepoints per subject) with the longitudinal stream in v7.1.1 and are
> running into memory errors during `mri_fuse_segmentations`.
>
> Thanks,
>
> -Paul
>
> [1]: https://openneuro.org/datasets/ds000239/versions/1
>
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>
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[Freesurfer] Tracula: Calculation of MD values from other eigenvectors

[Chong, Catherine (Cat), Ph.D.]

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Dear Tracula Experts,

We are trying to address a question from a reviewer who is wondering why we 
included all of the average diffusion parameters in our model  ( i.e. FA, 
MD,FA, RD, and AD) for distinguishing two groups of patients . The reviewer 
comments that MD values are calculated from AD and RD henceforth, including of 
all of the three parameters ( AD, RD, and MD) might have biased our analysis. I 
understand the reviewer’s concern that MD is calculated from adding all three 
eigenvalues/3, but I am uncertain about the relationship between the 
eigenvalues and the calculation of ‘average’ parameters for a given fibertract.

I am looking forward to your guidance,
With kind Regards,
Catherine

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[Freesurfer] lh.white edits

[Wei Koo]

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Hello FreeSurfer Developers,

I am trying to make edits to the white matter segmentation. I have tried making 
edits to wm.mgz and repeating recon2-wm but I was wondering if there is a way 
to make direct edits to lh.white?

I've searched the lists and did not seem to find anything regarding editing the 
surface directly.

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[Freesurfer] Graduate student positions available

[Stephanie Otto]

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Greetings Freesurfer Community!
The Cognitive and Brain 
Sciences (CBS) group in 
the Department of Psychology at the University of Nevada, Reno have graduate 
positions open for Fall 2021, specifically in the labs of Dr. Edward Ester, Dr. 
Lars Strother, Dr. Marian Berryhill, and Dr. Sarah Haigh. The CBS program has a 
strong concentration in vision science with 11 faculty working in different 
areas of vision.
We strongly encourage students from diverse and under-represented backgrounds 
to apply. Please see additional opportunities through the Graduate 
School, including the NSF GAIN Scholars 
program.
Students can apply either to the Cognitive and Brain Sciences Program or the 
Graduate Program in Integrative Neuroscience.
UNR was recently awarded Carnegie R1 status and has a fast-growing 
multi-disciplinary Neuroscience program. Resources for neuroimaging are 
provided through the Center for Integrative Neuroscience (an NIH COBRE award), 
including 3T fMRI, high-density EEG, fNIRS, and Adaptive Optics. The Center 
also houses a research core supporting applications of Virtual and Augmented 
Reality, and a core for Cellular and Molecular Imaging including confocal and 
2-photon microscopy.  Reno is located next to the Sierra Nevada near Lake 
Tahoe, and has been rated one of the best small cities in the US for outdoor 
recreation and overall quality of life.
Read below for information on specific labs that are recruiting graduate 
students:
Dr. Ester is recruiting a student to work on an NSF-funded 
project
 that explores relationships between short-term memory and motor control. The 
student will have the opportunity to learn multiple techniques used to measure 
human brain activity (EEG, fMRI, and tDCS) and gain a strong quantitative skill 
set.
The Strother lab studies visual perception and object recognition using 
behavioral experiments and fMRI. We are currently investigating neural 
mechanisms that allow us to perceive and recognize stimuli and support social 
and linguistic behaviors (e.g. faces, bodies and words). We are seeking Ph.D. 
students to develop and implement: (a) psychophysical experiments that measure 
visual performance during various perceptual tasks; and (b) fMRI experiments 
that rely on multivariate analysis of the data to measure the neural coding of 
visual object information in the brain.
Dr. Berryhill and Dr. 
Haigh are seeking two joint students to work 
on an NIMH-funded project focusing on biomarkers of schizophrenia that are 
evident in individuals with high schizotypy (subclinical individuals who 
exhibit schizophrenia-like behaviors). Students will learn and conduct studies 
using behavioral psychophysics and electroencephalography (EEG), to investigate 
sensory and working memory.

_

Dr. Sarah Haigh
Assistant Professor,
University of Nevada, Reno,
Department of Psychology and Center for Integrative Neuroscience,
1664 N. Virginia Street
Reno, NV 89557-0296
Tel: +1 (775) 682-9885

https://packpages.unr.edu/shaigh/
Follow us @HaighLab

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Re: [Freesurfer] Infant FreeSurfer issues

[Zollei, Lilla,Ph.D.]

Hi Florent,
See for answers below.
Lilla

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of k3...@free.fr 

Sent: Friday, October 2, 2020 4:30 AM
To: Freesurfer support list 
Subject: [Freesurfer] Infant FreeSurfer issues

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Hi FreeSurfer team,

I’ve been using the Infant FreeSurfer pipeline on 3DT1 sequences for few weeks 
now on infants from 0.4 to 5.4 years-old.

I know Infant FreeSurfer is recommended for 0-2 years old infant but standard 
FreeSurfer was failing due to many lacunar infarcts in the white matter.
So I tried Infant FreeSurfer with an age of 2 years old even for 2 to 5.4 
years-old subjects and results look good.
I know standard FreeSurfer has been tested on infant from 4.2 years-old, so 
what would be your recommendation for subjects from 2 to 4.2 years old?

** That is an age range that we are trying to cover at the moment, but we do 
not have a specific atlas representing that age range. If the infant pipeline 
works for you, that is great.

Have you already run Infant FreeSurfer on subjects older than 2 years-old?

** No, we do not recommend it.

I also have some processing issues with my actual data:
  1. Pixels with 0 value => probably out of the brainmask so the pixels are set 
to 0 after masking
 So, sometimes lateral ventricles are miss-segmented 
(https://ibb.co/JpWG9st)
** If there is no intensity value there, it is as if that area was masked out 
so there is not going to be a label assigned to that area.

  2. Thalamus region is missing from the aseg stat export (always equal to 0 
mm3), do you have a fix? Should I fix a LUT file?
** The pipeline that you are using is still labeling the thalamus with an old 
label value. You could switch the labels to the current ones and rerun the 
stats file generation or I can send you an updated script. Below are the steps 
from the mri dir that can change the labels:

mri_binarize --i aseg.mgz --replace 48 49 --replace 9 10 --o aseg.corrected.mgz
rm aseg.mgz
ln -s aseg.corrected.mgz aseg.mgz

  3. Would it be possible to get the non-skullstripped N3 corrected 3D T1 in 
the MNI space (3D iso)? I was not able to find the registered 3DT1 to re-apply 
the N3 correction, I only found the input 3DT1 (mprage.nii.gz) in its native 
space.

** We do not work in the MNI space. Can you give me more details about what you 
are trying to do?

  4. Do you have any workaround for large ventricles segmentation issue 
(https://ibb.co/nnbZcYs)?
 Standard FreeSurfer has a -bigventricle option, do you have a similar 
approach?

** We do not yet have such a flag for infants.

And some additional questions:
• brainstem seems to be split into multiple sub-regions, is it possible get the 
entire brainstem volume in the aseg stat export?

** You would need to do it manually and merge the labels of interest.

• I saw that corpus callosum is not present in the “aseg” segmentation, so is 
this region out of the Infant FreeSurfer atlases?

** With the most recent script, it is.

• Is it possible to get the mean cortical thickness for the labels you are 
providing?

** Yes, they should all be in the surface stats files.

Many thanks as I know there are plenty of questions here :)
Best,
Florent

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