Re: [Freesurfer] Longitudinal multimodal processing

2023-10-17 Thread 姜黎黎 
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Thanks for your email.


-原始邮件-
发件人:"gabriel robert" 
发送时间:2023-10-16 15:06:38 (星期一)
收件人: "Freesurfer support list" , "Vaidya, 
Nilakshi" 
抄送:
主题: Re: [Freesurfer] Longitudinal multimodal processing



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Dear Prof Greve,


Many thanks for your reply,
Could you please confirm also the second part of the sentence ? " [...] given 
the sample size this is likely to be marginal compared to the effect size and 
results would still be interpretable... "
Sorry but experts are th only way to get a feeling about those analyses without 
ground truth..
Best wishes


Gabriel Robert, MD, PhD, HDR

PU-PH, Pôle Hospitalo-Universitaire de Psychiatrie Adulte (PHUPA)

Psychiatrie de la personne âgée
Centre Hospitalier Guillaume Régnier, Rennes, France

U1228, UMR 60274 IRISA, Campus Beaulieu, Rennes, France 

Google Scholar
Journées de Psychiatrie de la Personne âgée

Société de Psychogériatrie et de Psychiatrie de la Personne Âgée (SF3PA)
Institut de Neuroscience Clinique de Rennes







Le lun. 16 oct. 2023 à 04:55, Douglas N. Greve  a écrit 
:

yes, I think so too


On 9/19/2023 5:07 PM, gabriel robert wrote:


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Dear experts in longitudinal neuroimaging


We carefully read the papers about possible biases introduced by treating 
timepoints images differently (Reuter and Fischl NI 2011, for example) to 
estimate unbiased anatomical and functional changes of brain development in 
healthy individuals. We took good note that treating each time point 
independently would remove asymmetry biases at the cost of reduced power.


In our project, we would like to analyze about 800 scans both 3DT1, diffusion 
(FA preprocessed with fsl TBSS) and functional task BOLD at 3 time points (14 
years-old, 19 years-old and 23 years-old).


Each time point scans are preprocessed individually and normalized to a 
specific group-based template at the corresponding time point (not a 
within-subject midpoint symmetric space) and to the standard MNI space.  


Our question: We'd like to use a home-made study-specific multimodal atlas to 
resample ROI BOLD mean contrasts and fractional anisotropy at each time point 
but this atlas is based on the last time point only (23 years-old). Does this 
situation fall into the 'asymmetry-induced bias in longitudinal processing' ?


Our feeling is most probably yes but given the sample size this is likely to be 
marginal compared to the effect size and results would still be 
interpretable... ?


Many thanks for time, interest and insight,


Best wishes


Gabriel




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[Freesurfer] Atrophy Maps on Coronal Slices

2023-10-17 Thread Daniel Gutstein 
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Is there a methodology in FreeSurfer for creating atrophy maps and displaying 
them on individual coronal slices?
Thank you.


Daniel Gutstein

Research Data Analyst

Northwestern University | Mesulam Center for Cognitive Neurology & Alzheimer's 
Disease

300 E. Superior Street | Tarry 8-734 | Chicago, IL 60611

daniel.gutst...@northwestern.edu | 
(312) 503 - 8150
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[Freesurfer] Common space

2023-10-17 Thread Alberto Del Cerro Leon 
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Good morning, I would be interested in observing regional differences in
cortical thickness without using predefined regions. However the results
offered by FreeSurfer arrange the thickness results etc. in an individual
space which is difficult to compare between subjects before labeling. Is
there a possibility to transform the results to a common mesh (like a
template) in order to perform an exploratory analysis?
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Re: [Freesurfer] [WARNING: ATTACHMENT(S) MAY CONTAIN MALWARE]Re: Stools error query

2023-10-17 Thread Diers, Kersten /DZNE 
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Hello,

and thanks for the confirmation.

Then I'll try to make the toolbox run with these image dimensions / resolutions 
also; will take approximately one week, I guess.

Best regards,

Kersten

On Mon, 2023-10-16 at 21:15 +, Elizabeth Haris wrote:

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Hi Kersten,

Ah yes, that would be it. I am using data from a 7T scanner, so wanted it to be 
processed at the best resolution possible, hence using the -cm command.

Many thanks,
Elizabeth

From:freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Diers, Kersten /DZNE 

Date: Tuesday, 17 October 2023 at 12:12 am
To: freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] [WARNING: ATTACHMENT(S) MAY CONTAIN MALWARE]Re: 
Stools error query

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Hello Elizabeth,

thank you for giving the new version of the toolbox a try as well.

Since the error persists: my suspicion is that not all of your images have the 
canonical ("FreeSurfer - conformed") dimensions of 256 x 256 x 256 voxels, 
maybe because they were processed with FreeSurfer's high-resolution processing 
variant / the recon-all ... -cm ... command?

If that's indeed the case, I will try to update the toolbox to be able to deal 
with images that have dimensions different from 256 x 256 x 256.

Best regards,

Kersten

On Sun, 2023-10-15 at 23:37 +, Elizabeth Haris wrote:
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Hi Kersten,

I ran the fsqc, but am still getting the same error for 45 of my 72 
participants (outlined below). I’ve attached the logfile and the csv output if 
that helps.

Starting fsqc for subject 630 at 2023-10-16 10:09 AEDT
Computing white and gray matter SNR for orig.mgz ...
ERROR: SNR computation failed for 630
Reason: index 256 is out of bounds for axis 2 with size 256
Computing white and gray matter SNR for norm.mgz ...
ERROR: SNR computation failed for 630
Reason: index 256 is out of bounds for axis 2 with size 256

Thanks,
Elizabeth

From:freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Diers, Kersten /DZNE 

Date: Thursday, 12 October 2023 at 10:06 pm
To: freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] Stools error query

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Hi Elizabeth,

the qatools / fsqc tools have evolved quite a bit since their inclusion in FS 
7.1.

Would it be possible for you to try their newest version, available from 
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Thanks,

Kersten

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Hi there,

I am running into a problem when using qatools.py to qa my recon-all. Some of 
my participants process ok, but with others I get the error below. Any advice 
on what to do to address this?

Many thanks,
Elizabeth

ERROR:


Computing white and gray matter SNR for orig.mgz ...

Traceback (most recent call last):

 File "/Applications/freesurfer_v7.1.0/python/scripts/qatools.py", line 17, in 


   qatoolspython.run_qatools(subjects_dir, output_dir, subjects, shape, 
screenshots, fornix, outlier, outlier_table)

 File 
"/Applications/freesurfer_v7.1.0/python/packages/qatoolspython/qatoolspython.py",
 line 883, in run_qatools

   _do_qatools(subjects_dir, output_dir, subjects, shape, screenshot

Re: [Freesurfer] FreeSurfer License

2023-10-17 Thread Lauren Stephens 
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Hi Camille,

https://secure-web.cisco.com/1Z0mtk-GdaneIrZnocCICBN5oOIERpgBztEHp89f1GbNPxyx9pDF2yKjprOTG9yU84m_9LhTGAI1I-cUYVbkQ16RRRJWIGiefjRgahDaYRPj7Zp_aYyD1X0FSo8PELG74pf8sPmJdMpwYYm3tSXGpJOKIQIYqASPUWsd6KlvqUtYuMS8Q-CBLmqvXh2_yglCkKUFf-7P-7yDqaccmf4mGtozw0iEygbq6b6UUZSp86ej7UNvDUOezmJAuf25dYAab__A9ZebbWjpPh7KxIoLV-WhJhtWX0zRhz28VS0QISl5IL4WJNRJkwfivbwgX6zjt/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fregistration.html
 Follow this link to download the license.

Best,

Lauren Stephens


Lauren Stephens, MS

Assistant Clinical Research Coordinator

Department of Psychiatry and Behavioral Science

Stanford University School of Medicine

E: laure...@stanford.edu

P: (650)-725-1716


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Camille Fakche 

Sent: Tuesday, October 17, 2023 8:39 AM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: [Freesurfer] FreeSurfer License


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Dear FreeSurfer community,

I would like to obtain a free license to use FreeSurfer, I hope I am sending 
the request in the right place.

Thank you,
Camille.
--
FAKCHE Camille
Post Doctoral Researcher
Centre for Human Brain Health (CHBH)
University of Birmingham, UK
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[Freesurfer] FreeSurfer License

2023-10-17 Thread Camille Fakche 
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Dear FreeSurfer community,

I would like to obtain a free license to use FreeSurfer, I hope I am
sending the request in the right place.

Thank you,
Camille.
-- 
FAKCHE Camille
Post Doctoral Researcher
Centre for Human Brain Health (CHBH)
University of Birmingham, UK
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Re: [Freesurfer] Freeview misaligned surfaces "warning matrixinverse failed"

2023-10-17 Thread Marina Fernández 
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Hi Andrei,

I was referring to .bashrc file located in these directories:
/root/.bashrc
/home/'your_user'/.bashrc
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Re: [Freesurfer] Freeview misaligned surfaces "warning matrixinverse failed"

2023-10-17 Thread Andrei Bieger 
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Indeed, the /usr/local/freesurfer/.bashrc file is empty
Trying to set the FS_DISABLE_LANG to true or false also had no consequences.
But thank you, anyway.

Andrei

Em ter., 17 de out. de 2023 às 07:45, fsbuild 
escreveu:

>
> From what I can see, the freesurfer release 7 installers do not modify the
> shell init file, e.g., bashrc, and neither did the VM provided in the past
> with freesurfer 7.2.0 pre-installed have an entry with FS_DISABLE_LANG set
> in the bashrc file.
>
> - R.
>
> On Oct 17, 2023, at 06:04, Marina Fernández 
> wrote:
>
> External Email - Use Caution
>
> Hi Andrei and Freesurfer experts,
>
> We had the same problem in the past and we noticed there was an extra line
> in the .bashrc file of Ubuntu:
> export FS_DISABLE_LANG="true"
> Deleting this line solves the problem.
>
> The .bashrc file should contain only the following FS lines:
> #Freesurfer:
> export FREESURFER_HOME=/usr/local/freesurfer
> source $FREESURFER_HOME/SetUpFreeSurfer.sh
>
> Make sure you do this for home and root .bashrc files.
>
> Hope this helps.
>
> Best wishes,
> Marina
>
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>
>

-- 
Andrei Bieger
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Re: [Freesurfer] Freeview misaligned surfaces "warning matrixinverse failed"

2023-10-17 Thread fsbuild 
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From what I can see, the freesurfer release 7 installers do not modify the 
shell init file, e.g., bashrc, and neither did the VM provided in the past with 
freesurfer 7.2.0 pre-installed have an entry with FS_DISABLE_LANG set in the 
bashrc file.
- R.

On Oct 17, 2023, at 06:04, Marina Fernández 
 
wrote:External Email - Use 
CautionHi Andrei and Freesurfer 
experts,We had the same problem in the past and we noticed there was an extra 
line in the .bashrc file of Ubuntu: export FS_DISABLE_LANG="true"Deleting 
this line solves the problem. The .bashrc file should contain only the 
following FS lines:#Freesurfer:export 
FREESURFER_HOME=/usr/local/freesurfersource 
$FREESURFER_HOME/SetUpFreeSurfer.shMake sure you do this for home and root 
.bashrc files.Hope this helps.Best 
wishes,Marina___Freesurfer mailing 
listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] Freeview misaligned surfaces "warning matrixinverse failed"

2023-10-17 Thread Marina Fernández 
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Hi Andrei and Freesurfer experts,

We had the same problem in the past and we noticed there was an extra line
in the .bashrc file of Ubuntu:
export FS_DISABLE_LANG="true"
Deleting this line solves the problem.

The .bashrc file should contain only the following FS lines:
#Freesurfer:
export FREESURFER_HOME=/usr/local/freesurfer
source $FREESURFER_HOME/SetUpFreeSurfer.sh

Make sure you do this for home and root .bashrc files.

Hope this helps.

Best wishes,
Marina
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