[Freesurfer] Binary Mask Overlay

[Dincer, Aylin]

Hi FreeSurfer Team,


I used QDEC to do a group analysis and from that I generated a surface-based 
mask using the command "mri_binarize --i sig.mgh --min 3 --o mask.mgz" 
Ultimately, I would like to overlay this mask on an individual subject (other 
than the fsaverage "lh.inflated" surface).  Using freeview, I uploaded the 
lh.inflated surface of an individual subject and tried to overlay the 
"mask.mgz" file, but it doesn't seem to work.  There are no error messages and 
it is visible in the "overlay" drop down menu.  However, nothing appears on the 
surface. The chosen subject was in the QDEC group analysis and all subjects 
were run with FreeSurfer v5.3. I did try this on the fsaverage surface and the 
mask is visible.  What are your suggestions for this overlay issue?


Let me know if you need any more information!


Best,

Aylin


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[Freesurfer] Monte Carlo threshold p-values

[Dincer, Aylin]

External Email - Use Caution

Hello FreeSurfer experts,


In the FreeSurfer wiki page regarding multiple comparisons 
(https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/QdecMultipleComparisons
) under "Simulation", it mentions the common Monte Carlo thresholds and their 
associated p-values.  Would you be able to explain how the associated p values 
for each z threshold was calculated? (Ex. The associated p-value for z=1.3 is 
0.05)


Thank you!

Aylin


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[Freesurfer] Monte Carlo simulation - vertex wise threshold question

[Dincer, Aylin]

External Email - Use Caution

Hi FreeSurfer experts,


I am trying to understand the Monte Carlo Z simulation in FreeSufer 
(mri_glmfit-sim) and have a question about the vertex wise /cluster forming 
threshold.


In the simulation, a vertex wise threshold (ex. -cache 3 abs) is set and the 
threshold is applied to a z map. Is the 3 threshold (p value of 0.001) 
converted to a z score using the z table before it is applied to the map?


Thanks!

Aylin


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[Freesurfer] hardware upgrade affect Freesurfer?

[Dincer, Aylin]

External Email - Use Caution

Hi FreeSurfer Experts,

Would upgrading computer hardware affect FreeSurfer output?  We are using 
FreeSurfer version 5.3-HCP and we are considering upgrading our server.  It 
will have the same operating system but different computer specs (memory, cpu, 
graphics, etc.).

Thank you!
Aylin



_
Aylin Dincer
Senior Research Technician
NeuroImaging Laboratories
Imaging Core, Benzinger Lab
314-362-3629



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[Freesurfer] PetSurfer reference region

[Dincer, Aylin]

External Email - Use Caution

Hello PetSurfer experts,

We are using the cerebellum cortex as our reference region, but noticed that 
the SUVR values for lh/rh cerebellum cortex do not have a value of 1 (which is 
what we were expecting). The actual SUVR values are 1.31 for the lh and 1.35 
for the rh cerebellum cortex. I attached the stats file (gtm.stats.dat) and 
below is the command we ran.

mri_gtmpvc --i regmean.nii.gz --reg regmean_template.reg.lta --psf ${FWHM} 
--seg ${MR_ID}/mri/gtmseg.mgz --default-seg-merge --auto-mask PSF+2 .01 --mgx 
.01 --rescale 8 47 -o regmean_gtmpvc_output

Let me know if you need any more details.

Thanks so much,
Aylin



_
Aylin Dincer
Senior Research Technician
NeuroImaging Laboratories
Imaging Core, Benzinger Lab
314-362-3629



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gtm.stats.dat
Description: gtm.stats.dat
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Re: [Freesurfer] PetSurfer reference region

[Dincer, Aylin]

External Email - Use Caution

Thanks for the quick reply. I attached the terminal output to this email. We 
are running this on v6.

Best,
Aylin

___
Message: 9
Date: Fri, 6 Mar 2020 11:50:51 -0500
From: "Douglas N. Greve" 
Subject: Re: [Freesurfer] PetSurfer reference region
To: 
Message-ID: <64d6089e-f818-e30e-deff-98a812b72...@mgh.harvard.edu>
Content-Type: text/plain; charset="windows-1252"

I cannot replicate this in either v6 or v7beta. Can you send the
terminal output?

On 3/5/2020 1:32 PM, Dincer, Aylin wrote:
>
> External Email - Use Caution
>
> Hello PetSurfer experts,
>
> We are using the cerebellum cortex as our reference region, but
> noticed that the SUVR values for lh/rh cerebellum cortex do not have a
> value of 1 (which is what we were expecting). The actual SUVR values
> are 1.31 for the lh and 1.35 for the rh cerebellum cortex. I attached
> the stats file (gtm.stats.dat) and below is the command we ran.
>
> mri_gtmpvc --i regmean.nii.gz --reg regmean_template.reg.lta --psf
> ${FWHM} --seg ${MR_ID}/mri/gtmseg.mgz --default-seg-merge --auto-mask
> PSF+2 .01 --mgx .01 --rescale 8 47 ?o regmean_gtmpvc_output
>
> Let me know if you need any more details.
>
> Thanks so much,
>
> Aylin
>
> 
>
> _
>
> Aylin Dincer
>
> Senior Research Technician
>
> NeuroImaging Laboratories
>
> Imaging Core, Benzinger Lab
>
> 314-362-3629
>
> 
>
> 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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pet_regmiddle_pvc_rerun_2020_03_06.log
Description: pet_regmiddle_pvc_rerun_2020_03_06.log
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Re: [Freesurfer] PetSurfer reference region

[Dincer, Aylin]

External Email - Use Caution

Hello PetSurfer experts,

We found the SUVR values for the reference region (lh/rh cerebellum cortex) 
does not equal 1 in the gtm.stat.dat file.

We tried a few things:
1) leaving the PET image as multi-frames (ref region SUVR about 1.34)
2) concatenating the frames as suggested in the previous response (ref region 
SUVR about 1.34)
3) running with the SUV image (ref region SUVR about 1.003).

I attached the terminal output and the gtm.stat.dat file from the concatenated 
image run.

Here is the command we ran using v6:
mri_gtmpvc --i regmean.nii.gz --reg regmean_template.reg.lta --psf 8--seg 
${MR_ID}/mri/gtmseg.mgz --default-seg-merge --auto-mask PSF+2 .01 --mgx .01 
--rescale 8 47 -o regmean_gtmpvc_output

Let me know if you have suggestions.

Thanks so much,
Aylin

___

Message: 11
Date: Fri, 6 Mar 2020 16:59:53 -0500
From: "Douglas N. Greve" 
Subject: Re: [Freesurfer] PetSurfer reference region
To: 
Message-ID: <8c262861-3272-151b-ae18-906898408...@mgh.harvard.edu>
Content-Type: text/plain; charset="windows-1252"

I think the issue is that your input has multiple frames (6). It will
compute the scaling from all 6 whereas the gtm.stats file is only from
the first frame. Try running it with a single frame. Note that the
gtm.nii.gz will have all the frames for each ROI.


On 3/6/2020 3:56 PM, Dincer, Aylin wrote:
>  External Email - Use Caution
>
> Thanks for the quick reply. I attached the terminal output to this email. We 
> are running this on v6.
>
> Best,
> Aylin
>
> ___
> Message: 9
> Date: Fri, 6 Mar 2020 11:50:51 -0500
> From: "Douglas N. Greve" 
> Subject: Re: [Freesurfer] PetSurfer reference region
> To: 
> Message-ID: <64d6089e-f818-e30e-deff-98a812b72...@mgh.harvard.edu>
> Content-Type: text/plain; charset="windows-1252"
>
> I cannot replicate this in either v6 or v7beta. Can you send the
> terminal output?
>
> On 3/5/2020 1:32 PM, Dincer, Aylin wrote:
>> External Email - Use Caution
>>
>> Hello PetSurfer experts,
>>
>> We are using the cerebellum cortex as our reference region, but
>> noticed that the SUVR values for lh/rh cerebellum cortex do not have a
>> value of 1 (which is what we were expecting). The actual SUVR values
>> are 1.31 for the lh and 1.35 for the rh cerebellum cortex. I attached
>> the stats file (gtm.stats.dat) and below is the command we ran.
>>
>> mri_gtmpvc --i regmean.nii.gz --reg regmean_template.reg.lta --psf
>> ${FWHM} --seg ${MR_ID}/mri/gtmseg.mgz --default-seg-merge --auto-mask
>> PSF+2 .01 --mgx .01 --rescale 8 47 ?o regmean_gtmpvc_output
>>
>> Let me know if you need any more details.
>>
>> Thanks so much,
>>
>> Aylin
>>
>> 
>>
>> _
>>
>> Aylin Dincer
>>
>> Senior Research Technician
>>
>> NeuroImaging Laboratories
>>
>> Imaging Core, Benzinger Lab
>>
>> 314-362-3629


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gtm.stats.dat
Description: gtm.stats.dat


mri_gtmpvc.log
Description: mri_gtmpvc.log
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[Freesurfer] tkmedit in FreeSurfer 7.0

[Dincer, Aylin]

External Email - Use Caution

Hi FreeSurfer Experts,

We are unable to use tkmedit using FreeSurfer 7.0 (centos 7).  In the 
.xdebug_tkmedit file, it outputs the following error:

"Tcl_Init returned 1: Can't find a usable init.tcl in the following 
directories: /usr/pubsw/packages/tcltktixblt/current/lib/tcl8.4"

It looks like when we manually set the environmental variable TCL_LIBRARY to 
point to the tcl location in the $FREESURFER_HOME folder, tkmedit will open. Is 
there a way to fix this so it automatically sets this environmental variable?

Thanks!
Aylin
_
Aylin Dincer
Senior Research Technician
NeuroImaging Laboratories
Imaging Core, Benzinger Lab
314-362-3629



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[Freesurfer] FreeSurfer 7.1 patch question

[Dincer, Aylin]

External Email - Use Caution

Hi FreeSurfer Experts,

Is there a tentative date when the FreeSurfer 7.1 patch and docker 
implementation is going to be released?

Thanks!
Aylin

_
Aylin Dincer
Senior Research Technician
NeuroImaging Laboratories
Imaging Core, Benzinger Lab
314-362-3629



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[Freesurfer] freesurfer flag for multiple edited volumes

[Dincer, Aylin]

External Email - Use Caution

Hello FreeSurfer Experts,

If I need to manually edit both the brainmask.mgz and the wm.mgz in a 
FreeSurfer, what are the recommended flags when rerunning recon-all with the 
edits (-all, -autorecon2, etc)? Or is it recommended to run an edited volume 
through recon-all one at a time (i.e. editing the brainmask.mgz first, running 
recon-all using autorecon2-pial flag, editing the wm.mgz afterwards, then 
running recon-all again with autorecon2-wm)?

Thank you for the help!
Aylin


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Re: [Freesurfer] freesurfer flag for multiple edited volumes

[Dincer, Aylin]

External Email - Use Caution

Hi Jackson,

Thank you for the reply!

I appreciate the explanation. It makes sense the wm.mgz edits need to be run 
before the brainmask.mgz edits through the recon-all pipeline. Just to clarify, 
would it be preferred to run:

"recon-all -s subject -autorecon2 -autorecon3" or "recon-all -s subject 
-autorecon2-wm -autorecon3"

when running both the wm.mgz edits and brainmask.mgz edits through the 
recon-all pipeline?

Both -autorecon2 and autorecon2-wm flags run the the wm steps first followed by 
the pial surface steps.  However, since the -autorecon2 flag starts at an 
earlier step in the pipeline 
(https://secure-web.cisco.com/1C4E49kpOyvSIiWbEQGdFRU0QrTinsX1IjQbhSQ0_sfxXo1KWkfjCsNJF-XzE_Gwa97tofoWaO-D1fQ0GImnfD_ExaIccQf5z3-U1TNRUhLDw6JTb-X9xh2_DIlXwP4v-Cttq3jm_Izd0z00BzKxTYujqg3DsR7fz7PGgpxCPXtCinmZBlfpxYkeT-rkPuf1WCCgDzgSf0WEl4WBJ-mvc4eDDeIuTvdRwJObhAQ9f7rv9GVCKfH4D7sp3pdQ3X5wN/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2Frecon-all%23Manual-InterventionWorkflowDirectives),
 would there be a chance it would ignore/erase any of the manual edits done?

Thank you in advance for the clarification!
Aylin




Aylin Dincer
aylin.din...@wustl.edu<mailto:aylin.din...@wustl.edu>

From: Nolan, Jackson [mailto:jnol...@mgh.harvard.edu]
Sent: Wednesday, January 13, 2021 10:31 AM
To: freesurfer@nmr.mgh.harvard.edu; Dincer, Aylin 
Subject: Re: freesurfer flag for multiple edited volumes

* External Email - Caution *
Greetings Aylin,

If you have made edits to both the brainmask.mgz and wm.mgz files, I would 
recommend running recon-all with the -autorecon2 and -autorecon3 flags.

Each step in the FreeSurfer recon-all process draws on files generated in 
previous steps. So, if you have made edits to the wm.mgz volume, you will need 
to re-run the portion of the recon-all pipeline to incoperate you wm.mgz edits 
before you run the edits you made to brainmask.mgz through recon-all. This is 
because the pial surface processing happens after the white matter segmentation.

Below is a link to the FreeSurfer wiki page about recon-all. The section 
"Manual Intervention Workflow Directives" gives a breakdown of the steps in the 
recon-all pipeline.

https://secure-web.cisco.com/1C4E49kpOyvSIiWbEQGdFRU0QrTinsX1IjQbhSQ0_sfxXo1KWkfjCsNJF-XzE_Gwa97tofoWaO-D1fQ0GImnfD_ExaIccQf5z3-U1TNRUhLDw6JTb-X9xh2_DIlXwP4v-Cttq3jm_Izd0z00BzKxTYujqg3DsR7fz7PGgpxCPXtCinmZBlfpxYkeT-rkPuf1WCCgDzgSf0WEl4WBJ-mvc4eDDeIuTvdRwJObhAQ9f7rv9GVCKfH4D7sp3pdQ3X5wN/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2Frecon-all%23Manual-InterventionWorkflowDirectives
recon-all - Free Surfer 
Wiki<https://secure-web.cisco.com/1C4E49kpOyvSIiWbEQGdFRU0QrTinsX1IjQbhSQ0_sfxXo1KWkfjCsNJF-XzE_Gwa97tofoWaO-D1fQ0GImnfD_ExaIccQf5z3-U1TNRUhLDw6JTb-X9xh2_DIlXwP4v-Cttq3jm_Izd0z00BzKxTYujqg3DsR7fz7PGgpxCPXtCinmZBlfpxYkeT-rkPuf1WCCgDzgSf0WEl4WBJ-mvc4eDDeIuTvdRwJObhAQ9f7rv9GVCKfH4D7sp3pdQ3X5wN/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2Frecon-all%23Manual-InterventionWorkflowDirectives>
Description. Performs all, or any part of, the FreeSurfer cortical 
reconstruction process. This help only gives some simple information. See also 
ReconAllDevTable.. Basic usages: 1. Subject dir does not exist:
surfer.nmr.mgh.harvard.edu

Best,
Jackson


From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Dincer, Aylin 
mailto:aylin.din...@wustl.edu>>
Sent: Wednesday, January 6, 2021 1:05 PM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] freesurfer flag for multiple edited volumes


External Email - Use Caution

Hello FreeSurfer Experts,



If I need to manually edit both the brainmask.mgz and the wm.mgz in a 
FreeSurfer, what are the recommended flags when rerunning recon-all with the 
edits (-all, -autorecon2, etc)? Or is it recommended to run an edited volume 
through recon-all one at a time (i.e. editing the brainmask.mgz first, running 
recon-all using autorecon2-pial flag, editing the wm.mgz afterwards, then 
running recon-all again with autorecon2-wm)?



Thank you for the help!

Aylin





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contains 

[Freesurfer] Research Assistant Positions at Washington University School of Medicine

[Dincer, Aylin]

External Email - Use Caution

The Benzinger Imaging Core Laboratory at 
Washington University School of Medicine is looking for full-time Research 
Assistants (multiple openings available!) to work with us on magnetic resonance 
imaging and positron emission tomography studies of Alzheimer disease.

Your responsibilities will include:

1. Processing of imaging data using neuroimaging software 
toolkits (FreeSurfer, MATLAB, R, SAS, SPSS)

2.Performing QC / QA on imaging data and preliminary analyses

3.Opportunities to work on your own research projects and perform 
statistical analyses.

4.Assisting with research studies, collection of data, set-up and 
maintenance of equipment.

The ideal candidate will be able to work independently, communicate with 
laboratory staff and investigators, and maintain complete and organized 
records/reports.  They'll have working knowledge of computer software and a 
familiarity with command line interface computer processing (Linux). They are 
interested in psychology and/or neuroscience.

Apply with one of the links below interested!
RTII Posting 
50550
RTII Posting 
50947

All the best,
Aylin

Aylin Dincer, Neuroimaging Engineer
Benzinger Lab | Mallinckrodt Institute of Radiology | Neuroimaging Laboratory
Pronouns: she/her/hers

Washington University School of Medicine
4525 Scott Ave.
St. Louis, MO 63110
aylin.din...@wustl.edu





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