Re: [Freesurfer] Structural resolution and longitudinal processing

[Martin Reuter]

Mike,

I see. Currently it is not possible to insert different images into 
individual components of the stream in a convenient way. Both the -base 
and -long processing take their data from cross. There could be ways of 
manually stopping the stream (e.g. after the motion correct in -long) 
and then replacing the timepoint.long.base/mri/001.mgz with the updated 
one and continuing the stream. This only works if the old and fixed 
images are exactly on top of each other (no shift or scaling), only 
different slicing.

You could try that in a few cases and see what happens. I never tested 
it. A simple first test could be to put the fixed images through the 
-motioncor step (e.g. a cross sectional call) and compare this orig.mgz 
with the one derived from the old inputs. There should be no movement 
(you can use the opacity slider in freeview to blend between two images 
and detection motion).

Best, Martin



On 04/04/2016 04:56 PM, Angstadt, Mike wrote:
> Martin,
>
> The problem is not due to a different acquired resolution, but different 
> reconstruction scripts being used at the scanner, so the underlying DICOM 
> data is actually the same dimensions throughout the study.
>
> This means that some subjects have a bit of squishing in the x/y dimensions. 
> And since it's a non-uniform effect in x/y only, that means the degree of 
> effect depends on the participant's head's orientation in the scanner.
>
> When you say that if it was different processing after scanning it could be 
> fixed, are you suggesting there's something we could do to fix it while still 
> maintaining our original cross-sectional processing and edits, or are you 
> just suggesting that it could be fixed by correcting the dimensions and then 
> re-running cross-sectional processing.  We were hoping to avoid the latter as 
> it's several hundred scans, but I suspect that's ultimately what will need to 
> happen.
>
> -Mike
>
>
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Martin Reuter
> Sent: Monday, April 04, 2016 4:35 PM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] Structural resolution and longitudinal processing
>
> Hi Mike,
>
> you can't change this retrospectively. It means that different protocols were 
> used when scanning (or different processing after scanning, before passing it 
> to freesurfer-in that case it could be fixed). It would be good to try to 
> understand what exactly changed between acquisitions (is this on the same 
> scanner/headcoil)? If it is the same scanner and no parameters that affect 
> the image intensity changed, I would not worry too much about this small 
> difference in voxel size.
> You may also want to check if this happens in all subjects, or only some. And 
> if in some, are they all in one of your groups or distributed across groups, 
> to avoid potential bias.
>
> Best, Martin
> On 04/04/2016 12:07 PM, Angstadt, Mike wrote:
> We have a large number of scans that have been processed through the standard 
> cross-sectional stream. Subjects have a number of repeated scans, so we now 
> want to take advantage of the longitudinal stream.
>   
> When first beginning to run subjects through longitudinal template creation, 
> we noticed a warning message in some cases in the log:
> ***
> WARNING: Image geometries differ across time, maybe due to aquisition changes?
>   This can potentially bias a longitudinal study! Will continue in 
> 10s.
> ***
>   
> Looking into it, there does indeed appear to have been a change in the 
> reconstruction stream that led to images at different times during the study 
> to have slightly different voxel dimensions, changing from 1x1x1.2 to 
> 1.01x1.01x1.2mm voxels.
>   
> Our question is if there is some way to fix this prior to starting the 
> longitudinal stream but without having to redo the original cross-sectional 
> processing and editing that has been completed?
>   
>   
> --
>Mike Angstadt
>Research Computer Specialist / PANLab Lab Manager
>Department of Psychiatry / University of Michigan
>(734) 936-8229
>   
> **
> Electronic Mail is not secure, may not be read every day, and should not be 
> used for urgent or sensitive issues
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>

-- 
Martin Reuter, PhD
Assistant Professor of Radiology, Harvard Medical School
Assistant Professor of Neurology, Harvard Medical School
A.A.Martinos Center for Biomedical Imaging
Massachusetts General Hospital
Research Affiliate, CSAIL, MIT
Phone: +1-617-724-5652
Web  : http://reuter.mit.edu

___

Re: [Freesurfer] Structural resolution and longitudinal processing

[Angstadt, Mike]

Martin,

The problem is not due to a different acquired resolution, but different 
reconstruction scripts being used at the scanner, so the underlying DICOM data 
is actually the same dimensions throughout the study. 

This means that some subjects have a bit of squishing in the x/y dimensions. 
And since it's a non-uniform effect in x/y only, that means the degree of 
effect depends on the participant's head's orientation in the scanner.

When you say that if it was different processing after scanning it could be 
fixed, are you suggesting there's something we could do to fix it while still 
maintaining our original cross-sectional processing and edits, or are you just 
suggesting that it could be fixed by correcting the dimensions and then 
re-running cross-sectional processing.  We were hoping to avoid the latter as 
it's several hundred scans, but I suspect that's ultimately what will need to 
happen.

-Mike


From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Martin Reuter
Sent: Monday, April 04, 2016 4:35 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Structural resolution and longitudinal processing

Hi Mike,

you can't change this retrospectively. It means that different protocols were 
used when scanning (or different processing after scanning, before passing it 
to freesurfer-in that case it could be fixed). It would be good to try to 
understand what exactly changed between acquisitions (is this on the same 
scanner/headcoil)? If it is the same scanner and no parameters that affect the 
image intensity changed, I would not worry too much about this small difference 
in voxel size.
You may also want to check if this happens in all subjects, or only some. And 
if in some, are they all in one of your groups or distributed across groups, to 
avoid potential bias. 

Best, Martin
On 04/04/2016 12:07 PM, Angstadt, Mike wrote:
We have a large number of scans that have been processed through the standard 
cross-sectional stream. Subjects have a number of repeated scans, so we now 
want to take advantage of the longitudinal stream.
 
When first beginning to run subjects through longitudinal template creation, we 
noticed a warning message in some cases in the log:
***
WARNING: Image geometries differ across time, maybe due to aquisition changes?
 This can potentially bias a longitudinal study! Will continue in 10s.
***
 
Looking into it, there does indeed appear to have been a change in the 
reconstruction stream that led to images at different times during the study to 
have slightly different voxel dimensions, changing from 1x1x1.2 to 
1.01x1.01x1.2mm voxels.
 
Our question is if there is some way to fix this prior to starting the 
longitudinal stream but without having to redo the original cross-sectional 
processing and editing that has been completed?
 
 
--
  Mike Angstadt
  Research Computer Specialist / PANLab Lab Manager
  Department of Psychiatry / University of Michigan
  (734) 936-8229
 
**
Electronic Mail is not secure, may not be read every day, and should not be 
used for urgent or sensitive issues 



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-- 
Martin Reuter, PhD
Assistant Professor of Radiology, Harvard Medical School
Assistant Professor of Neurology, Harvard Medical School
A.A.Martinos Center for Biomedical Imaging
Massachusetts General Hospital
Research Affiliate, CSAIL, MIT
Phone: +1-617-724-5652
Web  : http://reuter.mit.edu 
**
Electronic Mail is not secure, may not be read every day, and should not be 
used for urgent or sensitive issues 


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Re: [Freesurfer] white matter parcellation

[Bruce Fischl]

Hi Laurena

it doesn't use tensor fitting at all.

cheers
Bruce
On Mon, 4 Apr 2016, Holleran, Laurena 
wrote:



Thanks Bruce,

I have not used TRACULA before but I'll look into it. Does the tensor 
estimation have to be carried out using dtirecon for TRACULA or can I input 
tensor calculations from another software?

Thanks

Laurena

From: freesurfer-boun...@nmr.mgh.harvard.edu  
on behalf of Bruce Fischl 
Sent: 04 April 2016 15:45
To: Freesurfer support list
Subject: Re: [Freesurfer] white matter parcellation

Hi  Laurena

yes, this is what TRACULA does. Usually it requires diffusion data, but you
might be able to run it without (which would amount to mapping the tracts
from the atlas onto your individual subject). Perhaps Anastasia can
comment?

cheers
Bruce


On Mon, 4 Apr 2016, Holleran, Laurena
wrote:



Hello experts,


I wanted to know if there are any other white matter parcellation methods
being developed which specifically label white matter tracts? I know that
the wmparc voxel are assigned a label based on the piece of cortex that is
closest too it​, however a significant portion of the white matter remains
unclassified or "unknown". If there are no plans to develop an atlas of this
sort you can just let me know.


Many thanks.







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Re: [Freesurfer] white matter parcellation

[Holleran, Laurena]

Thanks Bruce,

I have not used TRACULA before but I'll look into it. Does the tensor 
estimation have to be carried out using dtirecon for TRACULA or can I input 
tensor calculations from another software?

Thanks

Laurena

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

Sent: 04 April 2016 15:45
To: Freesurfer support list
Subject: Re: [Freesurfer] white matter parcellation

Hi  Laurena

yes, this is what TRACULA does. Usually it requires diffusion data, but you
might be able to run it without (which would amount to mapping the tracts
from the atlas onto your individual subject). Perhaps Anastasia can
comment?

cheers
Bruce


On Mon, 4 Apr 2016, Holleran, Laurena
wrote:

>
> Hello experts,
>
>
> I wanted to know if there are any other white matter parcellation methods
> being developed which specifically label white matter tracts? I know that
> the wmparc voxel are assigned a label based on the piece of cortex that is
> closest too it​, however a significant portion of the white matter remains
> unclassified or "unknown". If there are no plans to develop an atlas of this
> sort you can just let me know.
>
>
> Many thanks.
>
>
>
>
> 
>
>
> 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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Re: [Freesurfer] white matter parcellation

[Bruce Fischl]

Hi  Laurena

yes, this is what TRACULA does. Usually it requires diffusion data, but you 
might be able to run it without (which would amount to mapping the tracts 
from the atlas onto your individual subject). Perhaps Anastasia can 
comment?


cheers
Bruce


On Mon, 4 Apr 2016, Holleran, Laurena 
wrote:




Hello experts, 


I wanted to know if there are any other white matter parcellation methods
being developed which specifically label white matter tracts? I know that
the wmparc voxel are assigned a label based on the piece of cortex that is
closest too it​, however a significant portion of the white matter remains
unclassified or "unknown". If there are no plans to develop an atlas of this
sort you can just let me know. 


Many thanks.

 





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Healthcare Information or other information of a sensitive nature. If you
are not the intended recipient, be advised that any unauthorized use,
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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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Re: [Freesurfer] Structural resolution and longitudinal processing

[Martin Reuter]

Hi Mike,

you can't change this retrospectively. It means that different protocols 
were used when scanning (or different processing after scanning, before 
passing it to freesurfer-in that case it could be fixed). It would be 
good to try to understand what exactly changed between acquisitions (is 
this on the same scanner/headcoil)? If it is the same scanner and no 
parameters that affect the image intensity changed, I would not worry 
too much about this small difference in voxel size.
You may also want to check if this happens in all subjects, or only 
some. And if in some, are they all in one of your groups or distributed 
across groups, to avoid potential bias.


Best, Martin

On 04/04/2016 12:07 PM, Angstadt, Mike wrote:


We have a large number of scans that have been processed through the 
standard cross-sectional stream. Subjects have a number of repeated 
scans, so we now want to take advantage of the longitudinal stream.


When first beginning to run subjects through longitudinal template 
creation, we noticed a warning message in some cases in the log:


***

WARNING: Image geometries differ across time, maybe due to aquisition 
changes?


 This can potentially bias a longitudinal study! Will continue 
in 10s.


***

Looking into it, there does indeed appear to have been a change in the 
reconstruction stream that led to images at different times during the 
study to have slightly different voxel dimensions, changing from 
1x1x1.2 to 1.01x1.01x1.2mm voxels.


Our question is if there is some way to fix this prior to starting the 
longitudinal stream but without having to redo the original 
cross-sectional processing and editing that has been completed?


--

  Mike Angstadt

  Research Computer Specialist / PANLab Lab Manager

  Department of Psychiatry / University of Michigan

  (734) 936-8229

**
Electronic Mail is not secure, may not be read every day, and should 
not be used for urgent or sensitive issues




___
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--
Martin Reuter, PhD
Assistant Professor of Radiology, Harvard Medical School
Assistant Professor of Neurology, Harvard Medical School
A.A.Martinos Center for Biomedical Imaging
Massachusetts General Hospital
Research Affiliate, CSAIL, MIT
Phone: +1-617-724-5652
Web  : http://reuter.mit.edu

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[Freesurfer] white matter parcellation

[Holleran, Laurena]

Hello experts, 



I wanted to know if there are any other white matter parcellation methods being developed which specifically label white matter tracts? I know that the wmparc voxel are assigned a label based on the
 piece of cortex that is closest too it​, however a significant portion of the white matter remains unclassified or "unknown". If there are no plans to develop an atlas of this sort you can just let me know. 


Many thanks.



 



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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[Freesurfer] R-Map

[Morenikeji Adebayo]

Hello Freesurfers,

I'm interested in creating a group map where each vertex/voxel represents the 
correlation (as a correlation coefficient) between a task-related BOLD contrast 
values (ces.nii.gz) and a single covariate. This is analogous to a cortical 
thickness GLM with one group and one covariate, but I'd want an r-map instead 
of a log10p-map. 

How exactly might I do this? I’m trying to accomplish this using mri_glmfit, 
but I’m having generating output that is interpretable in terms of  a 
correlation coefficient and in particular, the direction of the effect.

Thanks,
Keji
---
Morenikeji Adebayo
Clinical Research Coordinator
Department of Psychiatric Neuroscience
Massachusetts General Hospital
(p) 617.643.6347
k...@nmr.mgh.harvard.edu

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[Freesurfer] Structural resolution and longitudinal processing

[Angstadt, Mike]

We have a large number of scans that have been processed through the standard 
cross-sectional stream. Subjects have a number of repeated scans, so we now 
want to take advantage of the longitudinal stream.

When first beginning to run subjects through longitudinal template creation, we 
noticed a warning message in some cases in the log:
***
WARNING: Image geometries differ across time, maybe due to aquisition changes?
 This can potentially bias a longitudinal study! Will continue in 10s.
***

Looking into it, there does indeed appear to have been a change in the 
reconstruction stream that led to images at different times during the study to 
have slightly different voxel dimensions, changing from 1x1x1.2 to 
1.01x1.01x1.2mm voxels.

Our question is if there is some way to fix this prior to starting the 
longitudinal stream but without having to redo the original cross-sectional 
processing and editing that has been completed?


--
  Mike Angstadt
  Research Computer Specialist / PANLab Lab Manager
  Department of Psychiatry / University of Michigan
  (734) 936-8229

**
Electronic Mail is not secure, may not be read every day, and should not be 
used for urgent or sensitive issues 
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[Freesurfer] Group level analysis: Specifying contrasts

[Afzal, Afsana]

Hi,

I want to perform a linear regression for a task with 3 different risk 
conditions (low, medium, high) with the following linear trend: low = 1, medium 
= 2, high = 3.

Right now I'm specifying the above weighted under each risk condition in my 
contrast matrix. Is this the correct approach? I want to make sure I am 
calculating a regression and not a weighted average.

Thank you for your help,

Afsana


__
Afsana Afzal
Clinical Research Coordinator
Massachusetts General Hospital
Division of Neurotherapeutics
Department of Psychiatry: Neurosciences
149 13th St, Room 2612
Charlestown, MA 02129
Phone: 617-643-5129
Fax: 617-726-4078
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[Freesurfer] Fwd: QDEC analysis

[Clara Kühn]

Dear FreeSurfer experts,

I am trying to analyze some single time points of my longitudinal data in QDEC. 
I have 3 groups and created a file for the discrete factor "group" with three 
levels (1,2 and 3). I have done the same for gender (with 2 levels). The 
analysis with gender works just fine but when I try to use group as a factor I 
get an error message that factor 1 must have 2 levels:

SUBJECTS_DIR is '/scr/etsch2/kids/ct'
ERROR: QdecGlmDesign::GenerateContrasts: factor 1 must have 2 levels
ninputs = 72
Checking inputs
nframestot = 72
Allocing output
Done allocing
nframes = 72
Writing to /scr/etsch2/kids/ct/qdec/lh.thick10_groupdiffsc1/y.mgh
gdfReadHeader: reading 
/scr/etsch2/kids/ct/qdec/lh.thick10_groupdiffsc1/qdec.fsgd
INFO: gd2mtx_method is dods
Reading source surface /scr/etsch2/kids/ct/87kids_template/surf/lh.white
ERROR: no contrasts specified.
Error in Analyze: command failed: mri_glmfit --y 
/scr/etsch2/kids/ct/qdec/lh.thick10_groupdiffsc1/y.mgh --fsgd 
/scr/etsch2/kids/ct/qdec/lh.thick10_groupdiffsc1/qdec.fsgd dods --glmdir 
/scr/etsch2/kids/ct/qdec/lh.thick10_groupdiffsc1 --surf 87kids_template lh

In the tutorial it doesn't state that QDEC has to have discrete factors with 2 
levels only.
Am I doing something wrong or is there a work-around for that maybe?

Cheers, Clara
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[Freesurfer] mri_vol2surf misaligment

[Francesca Strappini]

Dear Freesurfers,

I run the preprocessing step of some functional data with preproc-sess,
then the Fourier analysis with matlab. Now, I'm trying to plot this data on
the surface:

mri_vol2surf --mov Katkov_OT_45.nii.gz --trgsubject MishaK --hemi lh --reg
register.dof6.dat --o Katkov_OT_45_LH.nii.gz

I used as registration matrix the one produced by the preprocessing step
but when I try to visualize the map on the surface it looks like completely
misaligned.

Thank you
Best
Francesca



-- 
Francesca Strappini, Ph.D.
Neurobiology Department
Weizmann Institute of Science
234 Herzl Street, Rehovot 7610001 Israel
Tel.: +972 58 444 2584
E-mail: francesca.strapp...@weizmann.ac.il
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[Freesurfer] PostDoc Position - Deep Learning in Neuroimaging of AD - Barcelona

[Juan Domingo Gispert López]

The Barcelonaβeta Brain Research Centre (BBRC) welcomes applications for a
full-time research position to develop deep learning methods to predict the
onset of Alzheimer’s disease and its preclinical stage based on
neuroimaging and other wet biomarkers, as part of its clinical research
program.

The full job description can be found here:

https://fpmaragall.org/en/wp-content/uploads/sites/3/2014/07/BBRC_Researcher-Position-deep-learning.pdf

Qualifications:

- PhD in Neuroscience, Medicine, Computer Science, Bioengineering or
related disciplines (It is mandatory for the candidates to hold a PhD)
- Proven experience in modelling and/or deep learning is required.
- Strong understanding of the biological basis of AD and the course of AD
biomarkers is needed.
- Experience in neuroimaging and/or genetic data analysis would be
positively considered.
- Proven record of first authorship and co-authorship on scientific is
required.

Skills:

- Experience working with large and multidisciplinary data sets is required.
- Database manipulation skills, with strong attention to detail.
- Proven ability to lead and orientate a team of computer scientists
- Interest in joining a non-profit organization with a mission of high
social impact.
- Strong interpersonal skills (empathic and focused team-worker).
- Ability to think independently and work collaboratively.

Benefits:
- Starting date: Second quarter 2016.
- The research position is scheduled initially for two years (open to
renewal).
- Salary will depend on experience.

In order to apply:

Please submit a single PDF file containing the following: 1) Cover letter
describing research interests and relevant background; 2) CV with list of
publications; 3) The names of three individuals who could provide reference
letters.

All files or inquiries should be submitted electronically to:
cminguil...@fpmaragall.org

Deadline for submitting applications: April 29th 2016.

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