[Freesurfer] Canon MRI morphometry protocols

[南修司郎]

   External Email - Use Caution


Dear experts


We are trying to take MRI with Canon magnetic resonance for FreeSurfer analysis.

I'd appreciate If you could give me the recommended T1 structural protocol for 
Canon scanners.



Thank you in advance.



Shujiro



Shujiro Minami M.D., Ph.D.
Dpt. of Otolaryngology National Tokyo Medical Center
2-5-1 Higashigaoka, Meguro, Tokyo 152-8902, Japan
E-mail shujiromin...@me.com
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[Freesurfer] question about ventricular volume calculation

[Jiao Qing]

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Dear FreeSurfer Developers:

 

  I want to calculate ventricular volume using the 'recon-all' procedure. 
Would you like to let me know in how the ventricular volumes were calculated?  
Thank you!

   

FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c

Platform:Ubuntu 14.04.

 

Best wishes

Qing Jiao, Ph.D

Department of Radiology

Shandong First Medical University, China








 






 





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Re: [Freesurfer] Recon1 command {Disarmed}

[Kelli Ann Nini]

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Dr. Fischl,
Thank you so much for your reply. The brains I'm using have been processed and 
analyzed numerous times for a variety of projects in our department and are in 
several directories on the same computer. However, I copied only the .nii files 
over to a new directory and set the environment before attempting to run 
recon-1. I'm tasked with teaching FreeSurfer to our incoming lab students, so 
I'd like to keep the copies separate if possible. Any advice is sincerely 
appreciated.
-Kelli


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

Sent: Sunday, November 8, 2020 10:07 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Recon1 command


WARNING: This email originated outside of the University of New Orleans system. 
The sender of this email could not be validated and may not actually be the 
person in the “From” field. Do NOT click links or open attachments if the 
message seems suspicious in any way. Never provide your user ID or password.



HI Kelli



It sounds like you started running at some point but didn’t get very far? Try 
something like:



mv /home/blah/blah/blah/1234 /home/blah/blah/blah/saved.1234

recon-all -subjid 1234 -i 1234.nii -autorecon1



and see if that works (then you can probably delete the saved.1234 dir if you 
want)

cheers

Bruce



From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Kelli Ann Nini
Sent: Saturday, November 7, 2020 5:28 PM
To: Freesurfer support list 
Subject: [Freesurfer] Recon1 command



External Email - Use Caution

Greetings, esteemed Surfers! I have a .nii file that I am trying to run through 
recon1 and I'm not sure I have my commands correct. At first I typed this 
command line and received this error: recon-all -subjid 1234 -i 1234.nii 
-autorecon1

ERROR: You are trying to re-run an existing subject with (possibly)

 new input data (-i). If this is truly new input data, you should delete

 the subject folder and re-run, or specify a different subject name.

 If you are just continuing an analysis of an existing subject, then

 omit all -i flags.



However, if I omit the -i flag, I receive this message: recon-all -subjid 1234 
-autorecon1

Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c

Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c

INFO: SUBJECTS_DIR is /home/scanlab1/Desktop/FSTraining_2020

Actual FREESURFER_HOME /usr/local/freesurfer

Linux SCANLab-Work1 4.15.0-46-generic #49~16.04.1-Ubuntu SMP Tue Feb 12 
17:45:24 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux

'/usr/local/freesurfer/bin/recon-all' -> 
'/home/scanlab1/Desktop/FSTraining_2020/2556/scripts/recon-all.local-copy'

#

#@# MotionCor Tue Nov  3 17:46:26 CST 2020

ERROR: no run data found in /home/blah/blah/blah/1234/mri. Make sure to

have a volume called 001.mgz in  /home/blah/blah/blah/1234/mri/orig.

If you have a second run of data call it 002.mgz, etc.

See also: 
http://secure-web.cisco.com/1K1UWo6yjlzKPnx8ZzHCZXX0yjG2qBUWcvpBNuB8ejSW-zXLDTW8bgvgbe6De7F1Qq0beJU_EEFptKSQq8tGy7g3cwHkHFiVJgUUbGlSfB4RjutUPYWyqJZQnArHU_sw1whyb1Q0pvaXbPYLnOCFZmyWcyBaTbfOtb-nA_5TINewbo_pFx2zcitejPOoIUeJUVDttBiEaSeE2ABkgCL6sjyy5q17cT3OLaRkdcNeHcduLlCXHNhlbjb9_Cr7eVEzXI-RvXYq7_Zz3gHHEu2kNIA/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FConversion

Linux SCANLab-Work1 4.15.0-46-generic #49~16.04.1-Ubuntu SMP Tue Feb 12 
17:45:24 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux



recon-all -s 2556 exited with ERRORS at Tue Nov  3 17:46:26 CST 2020



For more details, see the log file 
/home/scanlab1/Desktop/FSTraining_2020/2556/scripts/recon-all.log

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Re: [Freesurfer] Help with mergecontrasts-sess function

[Paula Maldonado]

External Email - Use Caution

Thanks for your reply, that worked. Can you please tell me where I can find a 
summary table of the activated regions resulting from the conjunction analysis?

Best regards,

Paula




> Il giorno 27 ott 2020, alle ore 22:50, Douglas N. Greve 
>  ha scritto:
> 
> You would just run mkcontrast-sess, eg, if your four conditions are 
> ordered condA, condAcontrol, condB, condBcont, then
> mkcontrast-sess -analysis analysis -contrast contrastname -a 1 -c 2 -c 3 
> -a 4
> If you want it reversed, then just reverse the a's and c's
> 
> On 10/23/2020 4:39 AM, Paula Maldonado wrote:
>> External Email - Use Caution
>> 
>> Dear experts,
>> I am running an fMRI experiment in which I have four conditions: two main 
>> conditions (condition A and condition B) and two respective control 
>> conditions (condition Acontrol and condition Bcontrol).
>> I would like to create a map showing significantly greater activity for 
>> condition A relative to condition B, after subtracting out the activity for 
>> the respective control conditions. In other words, I would like to perform 
>> the following contrast:
>> (condition A - condition A control) - (condition B - condition B control)
>> Then I would like to have a map that shows the reverse contrast 
>> too:(condition B - condition B control) - (condition A - condition A 
>> control).
>> 
>> How do I do that?To obtain the first map: (condition A - condition A 
>> control) - (condition B - condition B control) I have tried with the 
>> mergecontrasts-sess function with the -conjunction flag and the OR option as 
>> detailed below:
>> mergecontrasts-sess -mergedcontrast conjres -conjunction or -analysis 
>> analysisname -map sig -space sph -isxavg fixed -contrast Contrast1 2 pos 0 
>> -contrast Contrast 2 pos 0 -s sessionsfMRI/Sub01/bold -hemi lh
>> 
>> where Contrast1= (condition A - condition A control) and Contrast2= 
>> (condition B - condition B control)
>> however the map I get is exactly the same as (condition A - condition A 
>> control), as if subtracting out Contrast 2 had no impact on the map.
>> 
>> Thanks,
>> 
>> Paula
>> 
>> 
>> 
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Re: [Freesurfer] trac-all -bedp error after successful -prep

[Michele Valotti]

External Email - Use Caution

solved it, turns out symlinks don't like relative paths (which I was using
in the config file for tracula), changing those to absolute paths tracula
finished with no errors

On Fri, 6 Nov 2020 at 11:38, Michele Valotti 
wrote:

> Hi all,
> I am trying to run tract segmentation on a scan and after running trac-all
> -prep without errors, trac-all -bedp can't run because it can't find
> dmri/data. Checking the dir I see a data.nii.gz but it looks like it's a
> broken link, even though the dwi.nii.gz image (which data.nii.gz should
> link to in my understanding) is in the folder. I have attached the log
> which I have skimmed through without seeing any obvious problems. Any help
> is greatly appreciated,
>
> Thank you,
> Michele
>
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Re: [Freesurfer] Freesurfer 7.1.0 on CentOS 8.1 {Disarmed}

[Snedden, Ali]

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Hello,

Thank you for the reply.

1.  Regarding the Nvidia drivers, we don’t have GPUs in most of our nodes 
(which is where I’m running freeview from).  The CPUs should be doing all the 
rendering in this case.
2.  I am the administrator of this cluster, so that isn’t an issue on my end.
3.  I pulled one of our CentOS 8.1.1911 nodes out of the cluster and installed 
freesurfer-CentOS8-7.1.0-1.x86_64.rpm locally using rpm.
4.  When I run /usr/local/freesurfer/7.1.0-1/bin/freeview, I get :


r1pl-hpcf-n09: ~$ /usr/local/freesurfer/7.1.0-1/bin/freeview

QStandardPaths: XDG_RUNTIME_DIR not set, defaulting to '/tmp/runtime-aps003'

MESA-LOADER: failed to open swrast (search paths /usr/lib64/dri)

libGL error: failed to load driver: swrast

Aborted (core dumped)

And the /var/spool/abrt/ccpp-2020-11-10-08\:26\:55-23032/core_backtrace is 
attached.  If you can’t view it, I can paste it into an email.  It looks very 
similar to the original backtrace that I pasted before.  Even with the rpm 
installed as intended (i.e. in /usr/), it seems that not be functioning 
correctly.   It still seems to me that it is failing in the 
vtkXOpenGLRenderWindow::CreateAWindow() function.  The top of the trace is 
glibc, but everything calls glibc in the end.  It isn’t clear if this is a 
glibc, vtk or some other issue.

Thoughts?


Best regards,

Ali

From: fsbuild 
Date: Monday, November 9, 2020 at 6:53 AM
To: "freesurfer@nmr.mgh.harvard.edu" 
Cc: "Snedden, Ali" 
Subject: Re: [Freesurfer] Freesurfer 7.1.0 on CentOS 8.1 {Disarmed}

Hello Ali,

The swrast error can happen if Nvidia grpahics drivers were installed using 
Nvidia’s own packages/download and then subsequently, your CentOS8 kernel was 
updated via the CentOS package management tools, i.e. the Nvidia software may 
then be incompatible with the upgraded system.  I think there are Nvidia 
packages in the CentOS package repos, and using those to re-install the Nvidia 
software could fix those kinds of errors.

Currently the freesurfer RPM install path is not relocatable.  I’m not sure 
relocation would help as I think admin/root privileges would still be needed to 
for the installation process to download and install any system system 
dependent packages the freesurfer RPM indicates are needed.

I would ask your IT folks (with root/admin privileges) to look into updating 
the Nvidia software and also install the freesurfer RPM for you.  They may 
already have a way to share/mount/mirror what the freesurfer RPM will install 
under the unique path /usr/local/freesurfer/7.1.1 from one machine to another.

-R.


On Nov 6, 2020, at 09:29, Snedden, Ali  
wrote:

External Email - Use Caution

Hello,

Thank you for the response.  I am working on a computer cluster where we 
install all user software on a shared filesystem.  Looking at the RPM, it does 
not seem that I can install it in a path of my choosing (i.e. not in /usr).

i.e..
$ rpm -qpi freesurfer-CentOS8-7.1.0-1.x86_64.rpm | head -15 | grep Relocations
Relocations : (not relocatable)

Is there a strategy for installing the rpm in a custom path?

Best,
Ali


From: fsbuild mailto:fsbu...@contbay.com>>
Date: Thursday, November 5, 2020 at 11:47 PM
To: "freesurfer@nmr.mgh.harvard.edu" 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Cc: "Snedden, Ali" 
mailto:ali.sned...@nationwidechildrens.org>>
Subject: Re: [Freesurfer] Freesurfer 7.1.0 on CentOS 8.1

Hello Ali,

I would try using the RPM installer which should at least check some 
dependencies on X packages, system libraries, etc.,

MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" 
claiming to 
behttps://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/7.1.1/freesurfer-CentOS8-7.1.1-1.x86_64.rpm

- R.


On Nov 5, 2020, at 22:39, Snedden, Ali  
wrote:

External Email - Use Caution

Hello,

I’ve seen a couple mentions on the list-serv about difficulties using 
Freesurfer on CentOS 8.   My issue is likely similar, but 

[Freesurfer] Postdoctoral Fellowship in advanced multi-parametric imaging in Parkinson’s disease, Alzheimer’s disease, and healthy aging

[Maurizio Bergamino]

External Email - Use Caution

My Lab, at Barrow Neurological Institute (Phoenix, AZ), is looking for a
Postdoc.
For more information email to:
Ashley M. Stokes, Ph.D.
Assistant Professor // Division of Neuro-Imaging Research Barrow
Neurological Institute
*ashley.sto...@barrowneuro.org*
and/or
Ryan R. Walsh, M.D., Ph.D., FAAN
Associate Professor // Muhammad Ali Parkinson Center Department of
Neurology // Barrow Neurological Institute
*ryan.wa...@barrowneuro.org*


A postdoctoral fellowship position (fully funded for up to three years) is
available at Barrow Neurological Institute (BNI) working with Ashley
Stokes, PhD, and Ryan R. Walsh, MD, PhD, as part of a rapidly growing
collaborative research effort between the Division of Neuro-Imaging
Research, Department of Neurology, and Muhammad Ali Parkinson Center. The
position will primarily focus on the development, application, and analysis
of advanced MRI methods in the context of both Parkinson’s disease and
Alzheimer’s disease, as well as dementia with Lewy bodies and healthy
cognitive aging, expanding upon recent novel approaches developed by this
multi-modal lab. These methods include advanced functional, diffusion,
perfusion, and structural imaging methods, with an emphasis on novel
mathematical/signal processing approaches to provide a more comprehensive
understanding of neurodegenerative diseases and normal brain aging across
structural, functional, and perfusion signatures, including their mutual
interdependence.

BNI is the world’s largest dedicated neurological disease treatment and
research institution, and the Muhammad Ali Parkinson Center at BNI is a
recognized leader in the field. Outstanding institutional resources,
including 1.5T and 3T Philips clinical MRI, a research-dedicated Philips 3T
MRI, a 7T preclinical Bruker MRI, microCT, microPET, and optical imaging
scanners are available at BNI. The Division of Neuro-Imaging Research has a
strong history of imaging excellence and is currently expanding. BNI is a
major hub for neuroscience research, including both basic and translational
neuroscience, with a wide range of internationally-recognized neurology
subspecialties. Barrow Neurological Foundation provides robust
philanthropic support exceeding $18M per annum, 100% of which benefits
patient care, research and education at BNI.

Applicants should have a PhD in physics, engineering, mathematics, computer
science, or a related discipline. Competitive candidates will have
expertise in signal processing and/or functional MRI and be interested in
developing novel approaches to analysis of MRI-based signals. This position
is available immediately and offers competitive compensation and benefits.

Phoenix is the 5th largest metropolitan in the United States and the 2nd
fastest growing city. Phoenix is a beautiful place to live and work,
boasting more days of sunshine and a lower cost of living than most
comparable cities. A rich culture, including theatre, concerts, museums,
sports, and great food, are easily found in Phoenix. With a moderate
climate most of the year, many Phoenicians enjoy an active lifestyle of
hiking, cycling, rock climbing, swimming, and golf.

Interested applicants should send a current CV, including the names of
three references, to both:



*Ashley M. Stokes, Ph.D.Assistant Professor // Division of Neuro-Imaging
Research Barrow Neurological Institute ashley.sto...@barrowneuro.org*



*Ryan R. Walsh, M.D., Ph.D., FAANAssociate Professor // Muhammad Ali
Parkinson Center Department of Neurology // Barrow Neurological Institute
ryan.wa...@barrowneuro.org*
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[Freesurfer] color and sign of sig.mgh data

[Rovai Antonin]

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Hello,

I am creating sig.mgh overlays in a group analysis. On this map, I can
see some blue and red vertices, corresponding to negative and positive
values (respectively) on the map.

On the other hand, I read in the documentation that sig.mgh is a map
created by computing -log(p) (base 10, whatever).

That cannot be true, since 00.

After some exploration I came up with the following guess: sig.mgh is
actually -sign(z)*log(p). (That is of course very useful to quickly
interpret the maps.)

Question 1: is this guess correct?
Question 2: where is the piece of documentation I missed where this is
explained? (I am asking this because I feel like I am missing a lot on
the details on the machinery behind FS commands...)

Cheers
Antonin

Hôpital Erasme - ULB
Cliniques universitaires de Bruxelles
Route de Lennik 808 - B - 1070 Bruxelles
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[Freesurfer] Correlation between thickness and csf_measures: vector

[Steve Petersen]

External Email - Use Caution

Dear Freesurfer experts,

I am conducting a cortical thickness study in three groups. After
performing the between-group analyses, I would like to evaluate the
possible correlation between cortical thickness and the levels of some csf
measures. To do this I included one column in the FSGD file

GroupDescriptorFile 1
Title OSGM
Class N
Class AD_PREC
Class AD_PLUS
Variables CSF_A_measure
Input 4048 N 1730.00
Input 4102 N 2217.00
Input 4122 PREC 652.00
Input 4146 PREC 695.00
Input 4198 PREC 938.00
Input 5049 AD_PLUS 909.00
Input 5080 AD_PLUS 987.00
Input 5096 AD_PLUS 942.00
Input 5101 AD_PLUS 881.00
Input 5232 AD_PLUS 715.00
And so on


In order to test the possible positive relation between the CSF_A_measure
and the cortical thickness, that is, *does the correlation between
thickness and csf_A_measure differ from zero?, *I would use the following
vector and commands for the left hemisphere.



*Question 1.* Please, can you verify if this vector and commands are
correct.

correlation_vector.mtx -> 0 0 0 1 1 1

mris_preproc --fsgd J3.fsgd \
  --cache-in thickness.fwhm10.fsaverage \
  --target fsaverage \
  --hemi lh \
  --out lh_J3G_thickness.10.mgh \

mri_glmfit \
--y lh_J3G_thickness.10.mgh \
--fsgd J3.fsgd \
--C correlation_vector.mtx \
--surf fsaverage lh \
--cortex \
--glmdir 01_lh_thickness_results\

mri_glmfit-sim \
  --glmdir 01_lh_thickness_results \
  --sim mc-z 1 2.3 mc-z.pos \
  --sim-sign pos --cwpvalthresh 0.05\
  --2spaces --overwrite \


*Question 2:* I tried to run these commands with the permutation method but
the terminal gave to me a warning message saying that the matrix is not
orthogonal and if I really want to run the analysis I should add the
--perm-force argument, in this case should I use other method or can I use
the --perm-force safetely?.


Thank you very much for your help in advance.


Best regards,



Steve,
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