Re: [Freesurfer] Hippocampal subfield validation

[Dawn C. Matthews]

External Email - Use Caution

 

Dear Freesurfer Team, 

This is a follow on to the question regarding manual validation results for the 
FS 6.0 hippocampal subfield total mask.  Could you please also comment on the 
similarities and differences between the hippocampal subfield summation (ORing 
of the subfields) and the HARP manual protocol definition, and whether FS 6.0 
aseg hippocampus and the subfield summation have been directly compared to the 
HarP validation set (Boccardi et al, 2015) using a DICE approach on same 
subjects?  These questions pertain to the hippocampal subfield segmentation 
atlas prior to the more recent inclusion of amygdala, but the same questions 
regarding manual validation images and masks would apply for the latter as well.

Thanks again,

Dawn Matthews

 

 

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Re: [Freesurfer] [EXT] Re: Freeview froze when trying to open volume file

[Hoopes, Andrew]

You can try updating your version of freeview following the instructions at 
https://surfer.nmr.mgh.harvard.edu/fswiki/UpdateFreeview. The freeview version 
shipped with FS 6.0 uses some pretty old Qt libraries, so upgrading might fix 
this… hopefully
Andrew

From:  on behalf of "Tarui, Tomo" 

Reply-To: FS Help 
Date: Thursday, January 23, 2020 at 3:15 PM
To: FS Help 
Subject: Re: [Freesurfer] [EXT] Re: Freeview froze when trying to open volume 
file


External Email - Use Caution
Thank you very much for your prompt advice. I have granted freeview the 
permission to access all files through System Preferences —> Security & Privacy 
—> Privacy (then restarted computer).
Unfortunately, the freeview still freezes when attempting to open a new file. 
Following are additional lines of error messages.
I would appreciate for your advice again.

[Tomo-no-iMac:~] tomotarui% freeview
2020-01-23 15:05:44.369 Freeview[876:10904] -_continuousScroll is deprecated 
for NSEventTypeScrollWheel. Please use -hasPreciseScrollingDeltas.
2020-01-23 15:05:44.369 Freeview[876:10904] -deviceDeltaX is deprecated for 
NSEventTypeScrollWheel. Please use -scrollingDeltaX.
2020-01-23 15:05:44.369 Freeview[876:10904] -deviceDeltaY is deprecated for 
NSEventTypeScrollWheel. Please use -scrollingDeltaX.
2020-01-23 15:05:44.369 Freeview[876:10904] -deviceDeltaZ is deprecated for 
NSEventTypeScrollWheel. Please use -scrollingDeltaX.
2020-01-23 15:05:50.197 Freeview[876:10904] modalSession has been exited 
prematurely - check for a reentrant call to endModalSession:

** I force closed freeview here **

020-01-23 15:11:19.499 Freeview[876:10904] WARNING:  found it necessary to prepare implicitly; please prepare panels 
using NSSavePanel rather than NSApplication or NSWindow.
2020-01-23 15:11:19.518 Freeview[876:10904] WARNING:  found it necessary to start implicitly; please start panels 
using NSSavePanel rather than NSApplication or NSWindow.
2020-01-23 15:11:19.518 Freeview[876:10904] WARNING:  running implicitly; please run panels using NSSavePanel rather 
than NSApplication.
2020-01-23 15:11:19.519 Freeview[876:10904] -[NSApplication runModalSession:]: 
Use of freed session detected. Do not call runModalSession: after calling 
endModalSesion:.
2020-01-23 15:11:19.548 Freeview[876:10904] modalSession has been exited 
prematurely - check for a reentrant call to endModalSession:

Tomo


On Jan 23, 2020, at 14:21, Ruopeng Wang 
mailto:rpw...@nmr.mgh.harvard.edu>> wrote:

EXTERNAL MESSAGE - TREAT LINKS/FILES WITH CARE
You probably need to grant freeview permission to access your files and folders 
if you have not. You can check in System Preferences.
Ruopeng
On 1/23/20 2:16 PM, Tarui, Tomo wrote:
External Email - Use Caution
Dear Freesurfer community,

I have been also experiencing problem that freeview froze when I tried to 
select and open a new volume file.
This started after I upgraded mac OS X to Catalina. Until that I have been 
using freeview fine for five years.

Error message said

Last login: Thu Jan 23 13:43:03 on ttys000
[tup09900bj11:~] tomotarui% setenv FREESURFER_HOME /Applications/freesurfer
[tup09900bj11:~] tomotarui% source $FREESURFER_HOME/SetUpFreeSurfer.csh
 freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c 
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME   /Applications/freesurfer
FSFAST_HOME   /Applications/freesurfer/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR  /Applications/freesurfer/subjects
MNI_DIR   /Applications/freesurfer/mni
FSL_DIR   /usr/local/fsl
[tup09900bj11:~] tomotarui% freeview
2020-01-23 13:54:35.305 Freeview[3205:65482] modalSession has been exited 
prematurely - check for a reentrant call to endModalSession:

I do have read permissions for those volume files when I checked with ls -l and 
mri_info.
I have tried cleaned up and reinstall freesurfer, which did not solve the 
problem.
It may be unique to my computer, but I would appreciate very much for any 
recommendation.
Tomo


The information in this e-mail is intended only for the person to whom it is 
addressed. If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Tufts Medical Center HIPAA 
Hotline at (617) 636-4422. If the e-mail was sent to you in error but does not 
contain patient information, contact the sender and properly dispose of the 
e-mail.

Please consider the environment and the security of the information contained 
within or attached to this e-mail before printing or saving to an insecure 
location.



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[Freesurfer] Hippocampal subfield validation

[Dawn C. Matthews]

External Email - Use Caution

Dear Freesurfer Team, 

Thank you for your work on the segmentation and analysis tools that have been 
provided through Freesurfer and that have been used so widely. We are wondering 
if there is a T1 image data set available for which manual delineation of the 
boundaries of the hippocampal subfield summation has been performed, and 
whether the images and masks might be available for DICE comparison to the 
masks and volume produced by FS in users’ hands? We note that the subfield 
summation does not include the alveus and therefore direct comparison to masks 
generated using standard manual hippocampal segmentation protocols is not 
straightforward.

With thanks and best regards,

Dawn Matthews

 

 

Dawn C. Matthews

CEO, ADM Diagnostics, Inc.

555 Skokie Blvd., Suite 500

Northbrook, Illinois  60062

dmatth...@admdx.com 

 

 

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[Freesurfer] different target image for registration

[Sam W]

External Email - Use Caution

Hello!

I would like to register my dwidata to the anatomical image (rawavg.mgz). I
have run bbregister, but how can I specify a different target image?
bbregister uses the orig.mgz right?

These are the commands I used:
bbregister --s sub001 --mov nodif.nii.gz --reg nodif2orig.dat --dti
--init-fsl

mri_vol2vol --fstarg --reg nodif2orig.dat --mov dwidata.nii --o
dwialigned.nii

mri_label2vol --regheader dwialigned.nii.g --temp mri/rawavg.mgz
--aparc+ageg  --o labels.nii

I'm not sure if the last command is valid, because I think bbregister and
mri_vol2vol use the orig.mgz, whereas mri_label2vol uses rawavg.

Best regards,
Sam
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[Freesurfer] mri_robust_template Internal Error: Rotation should not scale

[Biles, Mandy K]

External Email - Use Caution

Hello FreeSurfer Developers,



I'm attempting to run the longitudinal pipeline for recon-all outside of 
fmriprep. The first step, cross, ran fine and I received the expected outputs. 
I started the base step and for most of my subjects it appears to be working 
but for some of my subjects I get the following error when running the 
mri_robust_template command:



 Internal Error for tp 0 -> template

 Rotation should not scale ( 1.23014e-05 )



I've searched the list and no similar errors have been reported outside of 
fmriprep forums that I can find. Does anyone have any thoughts on how to 
troubleshoot this issue? Also, I’ve attached the recon-all.log in case it's of 
any use.



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

2) Platform: Red Hat Enterprise Linux Server, VERSION=7.7 (Maipo). This is 
being run on a HPC server.

3) uname -a: Linux c0072 3.10.0-1062.9.1.el7.x86_64 #1 SMP Mon Dec 2 08:31:54 
EST 2019 x86_64 x86_64 x86_64 GNU/Linux

4) recon-all.log: see attached



Thank you,
Mandy


Mandy K. Biles, MS | PhD Candidate

Psychology/Behavioral Neuroscience Program

UAB | The University of Alabama at Birmingham

CIRC Suite 252A | 1719 6th Avenue South | Birmingham, AL 35294

P: 205.975.4060 | mkbi...@uab.edu


uab.edu



recon-all.log
Description: recon-all.log
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Re: [Freesurfer] [EXT] Re: Freeview froze when trying to open volume file

[Tarui, Tomo]

External Email - Use Caution

Thank you very much for your prompt advice. I have granted freeview the 
permission to access all files through System Preferences —> Security & Privacy 
—> Privacy (then restarted computer).
Unfortunately, the freeview still freezes when attempting to open a new file. 
Following are additional lines of error messages.
I would appreciate for your advice again.

[Tomo-no-iMac:~] tomotarui% freeview
2020-01-23 15:05:44.369 Freeview[876:10904] -_continuousScroll is deprecated 
for NSEventTypeScrollWheel. Please use -hasPreciseScrollingDeltas.
2020-01-23 15:05:44.369 Freeview[876:10904] -deviceDeltaX is deprecated for 
NSEventTypeScrollWheel. Please use -scrollingDeltaX.
2020-01-23 15:05:44.369 Freeview[876:10904] -deviceDeltaY is deprecated for 
NSEventTypeScrollWheel. Please use -scrollingDeltaX.
2020-01-23 15:05:44.369 Freeview[876:10904] -deviceDeltaZ is deprecated for 
NSEventTypeScrollWheel. Please use -scrollingDeltaX.
2020-01-23 15:05:50.197 Freeview[876:10904] modalSession has been exited 
prematurely - check for a reentrant call to endModalSession:

** I force closed freeview here **

020-01-23 15:11:19.499 Freeview[876:10904] WARNING:  found it necessary to prepare implicitly; please prepare panels 
using NSSavePanel rather than NSApplication or NSWindow.
2020-01-23 15:11:19.518 Freeview[876:10904] WARNING:  found it necessary to start implicitly; please start panels 
using NSSavePanel rather than NSApplication or NSWindow.
2020-01-23 15:11:19.518 Freeview[876:10904] WARNING:  running implicitly; please run panels using NSSavePanel rather 
than NSApplication.
2020-01-23 15:11:19.519 Freeview[876:10904] -[NSApplication runModalSession:]: 
Use of freed session detected. Do not call runModalSession: after calling 
endModalSesion:.
2020-01-23 15:11:19.548 Freeview[876:10904] modalSession has been exited 
prematurely - check for a reentrant call to endModalSession:

Tomo

On Jan 23, 2020, at 14:21, Ruopeng Wang 
mailto:rpw...@nmr.mgh.harvard.edu>> wrote:


EXTERNAL MESSAGE - TREAT LINKS/FILES WITH CARE


You probably need to grant freeview permission to access your files and folders 
if you have not. You can check in System Preferences.

Ruopeng

On 1/23/20 2:16 PM, Tarui, Tomo wrote:

External Email - Use Caution

Dear Freesurfer community,

I have been also experiencing problem that freeview froze when I tried to 
select and open a new volume file.
This started after I upgraded mac OS X to Catalina. Until that I have been 
using freeview fine for five years.

Error message said

Last login: Thu Jan 23 13:43:03 on ttys000
[tup09900bj11:~] tomotarui% setenv FREESURFER_HOME /Applications/freesurfer
[tup09900bj11:~] tomotarui% source $FREESURFER_HOME/SetUpFreeSurfer.csh
 freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c 
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME   /Applications/freesurfer
FSFAST_HOME   /Applications/freesurfer/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR  /Applications/freesurfer/subjects
MNI_DIR   /Applications/freesurfer/mni
FSL_DIR   /usr/local/fsl
[tup09900bj11:~] tomotarui% freeview
2020-01-23 13:54:35.305 Freeview[3205:65482] modalSession has been exited 
prematurely - check for a reentrant call to endModalSession:

I do have read permissions for those volume files when I checked with ls -l and 
mri_info.
I have tried cleaned up and reinstall freesurfer, which did not solve the 
problem.
It may be unique to my computer, but I would appreciate very much for any 
recommendation.
Tomo



The information in this e-mail is intended only for the person to whom it is 
addressed. If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Tufts Medical Center HIPAA 
Hotline at (617) 636-4422. If the e-mail was sent to you in error but does not 
contain patient information, contact the sender and properly dispose of the 
e-mail.

Please consider the environment and the security of the information contained 
within or attached to this e-mail before printing or saving to an insecure 
location.



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The information in this e-mail is intended only for the person to whom it is 
addressed. If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Tufts Medical Center HIPAA 
Hotline at (617) 636-4422. If the e-mail was sent to you in error but does not 
contain patient information, contact the sender and properly dispose of the 
e-mail.

Please consider the 

[Freesurfer] Fwd: [All] FW: Post-doctoral Positions in Affective Neuroscience at McLean Hospital/Harvard Medical School

[Greve, Douglas N.,Ph.D.]

-- Forwarded message --
Date: Thu, 23 Jan 2020 03:37:12 +
From: "Pizzagalli, Diego A.,Ph.D." 
To: 'Help Desk -- Sam Mehl' 
Subject: RE: FW: Post-doctoral Positions in Affective Neuroscience at McLean
Hospital/Harvard Medical School

I'd be very grateful if you could forward to the distribution list:

Post-doctoral Positions in Affective Neuroscience at McLean 
Hospital/Harvard Medical School

Two post-doctoral positions are available within the Laboratory for 
Affective and Translational Neuroscience at McLean Hospital/Harvard 
Medical School, directed by Diego A. Pizzagalli, Ph.D.

The laboratory is part of the Center for Depression, Anxiety and Stress 
Research (CDASR), a vibrant research center with over 40 
scientists/staff/students that embraces a multi-disciplinary approach to 
improve our understanding of the psychological, environmental, and 
neurobiological factors associated with depression, anxiety and related 
disorders across the lifespan (http://cdasr.mclean.harvard.edu/).

Currently ongoing studies in Dr. Pizzagalli's laboratory focus on reward 
processing, stress responsivity, and executive functioning in a range of 
populations including individuals with current or past major depression, 
as well as at-risk samples (e.g., offspring of parents with MDD or 
individuals exposed to early life stress). These studies employ a 
variety of approaches, including high-density EEG, fMRI, PET, MRS, 
computational modeling, and assays of hormonal/inflammatory markers. 
Opportunities will be available to pursue independent research and 
interdisciplinary collaborations across Harvard Medical School. 
Depending on research focus, candidates will have access to three 
research-dedicated human MRI scanners (3 T, 4 T) and one animal MRI 
scanner (9.4 T), as well as two high-density EEG systems.

Qualifications: For the first position, a strong background in EEG/ERP 
techniques is required. For the second position, a strong background in 
functional/structural MRI techniques is required. For both positions, 
clinical training, computational modeling expertise (e.g., machine 
learning) and/or experience with a second imaging modality are a plus.

To apply, send a CV, a cover letter describing research interests, as 
well as names and email addresses of three references to Diego A. 
Pizzagalli (d...@mclean.harvard.edu). Review of applications will begin 
immediately (expected start date: Summer 2020, although an earlier start 
will be possible).

McLean Hospital, which is an affiliate of Harvard Medical School, is an 
Equal Opportunity Employer. As an equal opportunity employer, McLean 
seeks qualified candidates for all posted employment opportunities 
without regard to race, color, age, religion, gender, national origin, 
disability or veteran status. McLean particularly welcomes applications 
from minorities, women, and persons with disabilities.


About the institution
Since 1811, McLean Hospital has been a world leader in scientific 
investigations and treatments of mental illnesses as well as in training 
generations of scientists and clinicians.

McLean Hospital maintains the largest program of research in 
neuroscience and psychiatry of any private psychiatric hospital in the 
United States. McLean Hospital has been ranked as America's best 
freestanding psychiatric hospital for 17th consecutive years by U.S. 
News and World Report.



__
Diego A. Pizzagalli, Ph.D.
Professor of Psychiatry
Harvard Medical School

Director, McLean Imaging Center
Director, Center For Depression, Anxiety and Stress Research
Director of Research, Division of Depression & Anxiety Disorders
Director, Laboratory for Affective and Translational Neuroscience
McLean Hospital

de Marneffe Building, Room 233C
Mailstop 331
115 Mill Street, Belmont, MA 02478-9106
Phone: (617) 855-4230 (Depression Center)
Phone: (617) 855-2797 (Neuroimaging Center)

Fax: (617) 855-4231
e-mail: d...@mclean.harvard.edu
http://cdasr.mclean.harvard.edu
www.mcleanmri.org
__

___
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a...@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/all

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Re: [Freesurfer] Freeview froze when trying to open volume file

[Ruopeng Wang]

You probably need to grant freeview permission to access your files and 
folders if you have not. You can check in System Preferences.


Ruopeng

On 1/23/20 2:16 PM, Tarui, Tomo wrote:


External Email - Use Caution

Dear Freesurfer community,

I have been also experiencing problem that freeview froze when I tried 
to select and open a new volume file.
This started after I upgraded mac OS X to Catalina. Until that I have 
been using freeview fine for five years.


Error message said

Last login: Thu Jan 23 13:43:03 on ttys000
[tup09900bj11:~] tomotarui% setenv FREESURFER_HOME 
/Applications/freesurfer

[tup09900bj11:~] tomotarui% source $FREESURFER_HOME/SetUpFreeSurfer.csh
 freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c 
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME /Applications/freesurfer
FSFAST_HOME /Applications/freesurfer/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR /Applications/freesurfer/subjects
MNI_DIR /Applications/freesurfer/mni
FSL_DIR           /usr/local/fsl
[tup09900bj11:~] tomotarui% freeview
2020-01-23 13:54:35.305 Freeview[3205:65482] modalSession has been 
exited prematurely - check for a reentrant call to endModalSession:


I do have read permissions for those volume files when I checked with 
ls -l and mri_info.
I have tried cleaned up and reinstall freesurfer, which did not solve 
the problem.
It may be unique to my computer, but I would appreciate very much for 
any recommendation.

Tomo


The information in this e-mail is intended only for the person to whom 
it is addressed. If you believe this e-mail was sent to you in error 
and the e-mail contains patient information, please contact the Tufts 
Medical Center HIPAA Hotline at (617) 636-4422. If the e-mail was sent 
to you in error but does not contain patient information, contact the 
sender and properly dispose of the e-mail.


Please consider the environment and the security of the information 
contained within or attached to this e-mail before printing or saving 
to an insecure location.



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[Freesurfer] Freeview froze when trying to open volume file

[Tarui, Tomo]

External Email - Use Caution

Dear Freesurfer community,

I have been also experiencing problem that freeview froze when I tried to 
select and open a new volume file.
This started after I upgraded mac OS X to Catalina. Until that I have been 
using freeview fine for five years.

Error message said

Last login: Thu Jan 23 13:43:03 on ttys000
[tup09900bj11:~] tomotarui% setenv FREESURFER_HOME /Applications/freesurfer
[tup09900bj11:~] tomotarui% source $FREESURFER_HOME/SetUpFreeSurfer.csh
 freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c 
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME   /Applications/freesurfer
FSFAST_HOME   /Applications/freesurfer/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR  /Applications/freesurfer/subjects
MNI_DIR   /Applications/freesurfer/mni
FSL_DIR   /usr/local/fsl
[tup09900bj11:~] tomotarui% freeview
2020-01-23 13:54:35.305 Freeview[3205:65482] modalSession has been exited 
prematurely - check for a reentrant call to endModalSession:

I do have read permissions for those volume files when I checked with ls -l and 
mri_info.
I have tried cleaned up and reinstall freesurfer, which did not solve the 
problem.
It may be unique to my computer, but I would appreciate very much for any 
recommendation.
Tomo


The information in this e-mail is intended only for the person to whom it is 
addressed. If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Tufts Medical Center HIPAA 
Hotline at (617) 636-4422. If the e-mail was sent to you in error but does not 
contain patient information, contact the sender and properly dispose of the 
e-mail.

Please consider the environment and the security of the information contained 
within or attached to this e-mail before printing or saving to an insecure 
location.
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Re: [Freesurfer] Hippocampal subfields FS6 vs. new hippocampus tool (incl Amygdala) FreeSurfer_dev version

[Iglesias Gonzalez, Juan E.]

Hi Rene,
The atlases are slightly different so the outputs will be a bit different. But 
the segmentations will indeed be comparable.
Cheers,
/Eugenio

Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jeiglesias.com


From:  on behalf of Rene Seiger 

Reply-To: Freesurfer support list 
Date: Thursday, 23 January 2020 at 07:48
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: [Freesurfer] Hippocampal subfields FS6 vs. new hippocampus tool (incl 
Amygdala) FreeSurfer_dev version


External Email - Use Caution

Dear all,

I recently saw that the page of the hippocampal module for FS6 
(https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfields) seems to be 
obsolete and it looks as if this module will be replaced by a newer version in 
the near future (now dev version, 
https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldsAndNucleiOfAmygdala).

However, I am not entirely sure how those two modules differ in terms of 
hippocampal subfield segmentation, when the "FS60" parcellation scheme is used 
in the new module. It is stated that 'it mimics the FreeSurfer 6.0 hippocampal 
module', but is the output 1:1 comparable?
Thank you very much and kind regards,
René
--

Dr. René Seiger
Research Associate

Medical University of Vienna
Department of Psychiatry and Psychotherapy
Division of General Psychiatry
NEUROIMAGING LABS (NIL) - PET, MRI, EEG, TMS & Chemical Lab

Waehringer Guertel 18-20, A-1090 Vienna
Phone +43 (0) 1 40400-38250
rene.sei...@meduniwien.ac.at
http://www.meduniwien.ac.at/neuroimaging/


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Re: [Freesurfer] highres fMRI selxavg error

[Nasiriavanaki, Zahra]

Dear Freesurfer experts

Hi

I have a follow up question on this topic.
I am getting this error "Error using /Matrix dimensions must agree. Error in 
fast_selxavg3b (line 566) RescaleFactor = flac0.inorm/gmean;", when I run 
selxavg for one of my subjects. I attached the log file and copied the terminal 
output below.
Discussing it previously, we found out the problem being "global.meanval.dat 
and global.waveform.dat" files becoming empty after running selxavg!
Listening to Doug's recommendation, I did run everything from scratch.
After doing the preprocessing step, I realized the registration of functional 
on anatomical data is not correct using this command: "tkregister-sess -s $subj 
-fsd bold -per-run -bbr-sum".
So I had to run "register-sess -s $subj -per-run -delete-dat -dof 6 -fsd bold 
-init-header -bbr-xopts bbr.xopts -d ." multiple times to make the registration 
correct (with --brute1max starting from 8 and every time I increased it. The 
last time I ran this command, --brute1max was set to 28).  I got normal values 
for "tkregister-sess" and  I ran selxavg and got the error that I attached.
My question is: Do you think running "register-sess" multiple times is causing 
this issue? and I appreciate any suggestions about how to solve this issue.

P.S:This is highres functional MRI data; the functional data is only acquired 
from parietal and occipital lobes; out of several subjects; analysis is run in 
subject's native space.

Thanks a lot
Mona

#@# osre_7T_all ###
/autofs/space/oprah_001/users/zn025/looming_7T/all_subjects/osre_7T_all
-
$Id: fast_selxavg3b.m,v 1.4 2016/05/04 22:16:47 greve Exp $
-
outtop = /autofs/space/oprah_001/users/zn025/looming_7T/all_subjects
Extension format = nii.gz
INFO: key nSliceGroups unrecognized, line 12, skipping
 1 far.mat
 2 far_vs_near.mat
 3 far_vs_nodis.mat
 4 near.mat
 5 near_vs_far.mat
 6 near_vs_nodis.mat
 7 no_disparity.mat
Excluding 5 points
nruns = 8
autostimdur =


outanadir = 
/autofs/space/oprah_001/users/zn025/looming_7T/all_subjects/osre_7T_all/bold3/vis1_native.rh
Excluding 5 points
Excluding 6 points
Excluding 6 points
Excluding 7 points
Excluding 8 points
parfiles condition id list:  1  2  3
Found 1881/138983 ( 1.4) voxels in mask 1
Creating Design Matrix
 ... creation time =  0.020 sec
DoMCFit = 1
ntptot = 640, nX = 107, DOF = 533
Saving X matrix to 
/autofs/space/oprah_001/users/zn025/looming_7T/all_subjects/osre_7T_all/bold3/vis1_native.rh/Xtmp.mat
XCond = 448.137 (normalized)
Computing compensation for resdual AR1 bias
 1  -0.5  -0.4499(t=0.059341)
 2  -0.25  -0.255889(t=0.147506)
 3  0  -0.0718039(t=0.175004)
 4  0.25  0.0955918(t=0.257562)
 5  0.5  0.229844(t=0.289084)
AR1 Correction M: 0.131515 1.4543
Computing contrast matrices
OLS Beta Pass
  run 1t= 0.0
reading data ... 0.629912
Global Mean
  run 2t= 0.8
reading data ... 0.666993
Global Mean
  run 3t= 0.8
reading data ... 0.640162
Global Mean
  run 4t= 0.8
reading data ... 0.646836
Global Mean
  run 5t= 0.8
reading data ... 0.642453
Global Mean
  run 6t= 0.8
reading data ... 0.64432
Global Mean
  run 7t= 0.8
reading data ... 0.63922
Global Mean
  run 8t= 0.8
reading data ... 0.63597
Global Mean
Global In-Mask Mean =  (35.6878)
Error using /
Matrix dimensions must agree.

Error in fast_selxavg3b (line 566)
RescaleFactor = flac0.inorm/gmean;

>> --
ERROR: fast_selxavg3() failed\n




Zahra (Mona) Nasiriavanaki

Postdoctoral Research Fellow

Martinos Center for Biomedical Imaging

Massachusetts General Hospital

149 13th Street, 149-2615

Charlestown, MA, USA, 02129




From: Nasiriavanaki, Zahra 
Sent: Thursday, January 2, 2020 3:40 PM
To: Greve, Douglas N.,Ph.D. ; 
freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] highres fMRI selxavg error

I did run it from the shell and figured out what the problem was!

Thanks a lot!!
Mona


Zahra (Mona) Nasiriavanaki

Postdoctoral Research Fellow

Martinos Center for Biomedical Imaging

Massachusetts General Hospital

149 13th Street, 149-2615

Charlestown, MA, USA, 02129




From: Greve, Douglas N.,Ph.D. 
Sent: Thursday, January 2, 2020 3:25 PM
To: Nasiriavanaki, Zahra ; 
freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] highres fMRI selxavg error

It appears to be dying on this command
mris_fwhm --mask 
/autofs/space/oprah_001/users/zn025/fearcond_7T/all_subjects/ylug_ass_sess01/bold/cond.lh/mask.nii
Can you run it from the shell and send the terminal output?


On 1/2/2020 2:13 PM, Nasiriavanaki, Zahra wrote:
Thanks a lot for your reply.

I have one more question about selxavg error and I appreciate if you could 
reply.
I have another subject which has been scanned in 7T.  When I run selxavg, it 
doesn't go through for the left and right hemi, but it gets perfectly 

[Freesurfer] PhD and MSc Opportunities in Computational Neuroscience and Neuroimaging at the University of Toronto

[John Griffiths]

External Email - Use Caution

The Whole Brain Modelling Group (PI Dr. John Griffiths; www.grifflab.com)
at the CAMH Krembil Centre for Neuroinformatics (
www.krembilneuroinformatics.ca) and University of Toronto is looking for
PhD and MSc students with a strong background in computational neuroscience
and/or neuroimaging.

The focus of the Group’s work is computational models of large-scale brain
activity, with particular emphases on neural dynamics as measured by M/EEG
and fMRI, oscillations, brain stimulation (TMS, TDCS), neural plasticity,
and macro-connectomics.

The student shall conduct research in one or more of these areas. They will
have the opportunity to shape the details of the project based on their
specific interests, as well as to contribute to other ongoing projects on a
range of topics, including: neuroinformatics of whole-brain modelling,
mapping and modelling anatomical connectivity and microstructure with DWI
in relation to ageing and stroke, and multi-scale modelling of the
thalamocortical system in relation to sleep, pharmacological
neuromodulation, and neuropsychiatric disease.

The successful candidate should have, minimally, an undergraduate degree in
neuroscience, engineering, physics, mathematics, psychology, or related
area, and a demonstrable track record of research experience and interest
in computational neuroscience and/or neuroimaging. Expertise in one or more
modern scientific computing programming language (Python, Matlab, Julia, R,
C++) is essential. The candidate should also have familiarity with one or
both of: i) neuroimaging data analysis (s/d/fMRI and/or M/EEG), and ii)
computational modelling using numerical simulations (particularly modelling
of neural population activity with mean-field/neural mass/neural field
techniques, either with custom implementations or with tools such as The
Virtual Brain Platform or Dynamic Causal Modelling).

Full details of the position and application instructions can be found at
www.grifflab.com/positions/

For informal inquiries, please email Dr. John Griffiths at
john.griffi...@camh.ca with the title “PhD in Whole Brain Modelling” in the
subject line

( Note: students interested in a September 2020 start at the University of
Toronto should get in touch immediately to leave time for approaching
application deadlines )

-- 

Dr. John D. Griffiths

Independent Scientist @ Krembil Centre for Neuroinformatics, CAMH, Toronto

Assistant Professor @ Department of Psychiatry, University of Toronto

www.grifflab.com
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[Freesurfer] Hippocampal subfields FS6 vs. new hippocampus tool (incl Amygdala) FreeSurfer_dev version

[Rene Seiger]

   External Email - Use Caution


Dear all,

I recently saw that the page of the hippocampal module for FS6 
(https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfields) seems 
to be obsolete and it looks as if this module will be replaced by a 
newer version in the near future (now dev version, 
https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldsAndNucleiOfAmygdala).


However, I am not entirely sure how those two modules differ in terms of 
hippocampal subfield segmentation, when the "FS60" parcellation scheme 
is used in the new module. It is stated that 'it mimics the FreeSurfer 
6.0 hippocampal module', but is the output 1:1 comparable?


Thank you very much and kind regards,
René
--

*Dr. René Seiger*
Research Associate

*Medical University of Vienna*
Department of Psychiatry and Psychotherapy
Division of General Psychiatry
NEUROIMAGING LABS (NIL) - PET, MRI, EEG, TMS & Chemical Lab

Waehringer Guertel 18-20, A-1090 Vienna
Phone +43 (0) 1 40400-38250
rene.sei...@meduniwien.ac.at
http://www.meduniwien.ac.at/neuroimaging/ 




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