[Freesurfer] dt_recon eddy correction fail and freeview errors

2022-10-26 Thread Ward Deferm 
External Email - Use Caution

Dear Freesurfer Developers,



I am trying to perform the dt_recon command for a single participant of my 
dataset. The original data comes from a philips scanner and was in the PAR/REC 
format. I converted these files to nifti’s using dcm2niix. This seemed to have 
worked as I got my nifti files and .bval and .bvec.


However, when I run the dt_recon command it does not give me a hard error, but 
the output is not how it should be. Instead of taking 1-2 hours to complete the 
command, the command is done in about 3 minutes and I’m doubting if the eddy 
corrections are actually performed (fsl seems to be installed properly and is 
recognized when sourcing freesurfer. When trying to view the output with 
freeview I get 2 outcomes. Sometimes all of the file's work but there is no 
eddy correction performed and the FA volume is spread all over the brain when 
looking at this volume using freeview. But other times certain volumes either 
refuse to load or come up as a blank rectangle. In the freeview command line I 
then get the error:


WARNING: 37103 NaNs found in volume 
/home/ward/freesurfer/subjects/testdtrecon/dti/ra.nii.gz


In the attached files you can find the dt_recon log file. As for version and 
operating system I am running:


1) freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275

2)Ubuntu 22.04.1 LTS


Kind regards,


Ward Deferm

dt_recon logfile
wo 26 okt 2022 11:08:11 CEST
VERSION dt_recon 7.3.2
setenv SUBJECTS_DIR /home/ward/freesurfer/subjects/original_data_both_groups
cd /home/ward/freesurfer/subjects/testdtrecon
/home/ward/freesurfer/bin/dt_recon --i DTI_data_FT_WIPDTI_b1300_d60_MB2_20190706092846_13.nii --b DTI_data_FT_WIPDTI_b1300_d60_MB2_20190706092846_13.bval DTI_data_FT_WIPDTI_b1300_d60_MB2_20190706092846_13.bvec --s NT001_T0_MR_STRUCT --o dti --debug
ward-GE72-6QD
ward
/home/ward/fsl/bin/eddy_correct
ECRefTP 0
#@#---
Converting input
wo 26 okt 2022 11:08:11 CEST
cd /home/ward/freesurfer/subjects/testdtrecon
mri_convert /home/ward/freesurfer/subjects/testdtrecon/DTI_data_FT_WIPDTI_b1300_d60_MB2_20190706092846_13.nii /home/ward/freesurfer/subjects/testdtrecon/dti/dwi.nii.gz
mri_convert /home/ward/freesurfer/subjects/testdtrecon/DTI_data_FT_WIPDTI_b1300_d60_MB2_20190706092846_13.nii /home/ward/freesurfer/subjects/testdtrecon/dti/dwi.nii.gz 
reading from /home/ward/freesurfer/subjects/testdtrecon/DTI_data_FT_WIPDTI_b1300_d60_MB2_20190706092846_13.nii...
TR=4000.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.0266673, -0.998596, 0.0457636)
j_ras = (-0.0497214, 0.0470482, 0.997654)
k_ras = (0.998407, -0.0243294, 0.0509062)
writing to /home/ward/freesurfer/subjects/testdtrecon/dti/dwi.nii.gz...


#@#---
Eddy/Motion Correct
wo 26 okt 2022 11:08:16 CEST
cd /home/ward/freesurfer/subjects/testdtrecon/dti/ectmp
eddy_correct /home/ward/freesurfer/subjects/testdtrecon/dti/dwi.nii.gz /home/ward/freesurfer/subjects/testdtrecon/dti/dwi-ec.nii.gz 0
processing /home/ward/freesurfer/subjects/testdtrecon/dti/dwi-ec_tmp
processing /home/ward/freesurfer/subjects/testdtrecon/dti/dwi-ec_tmp0001
processing /home/ward/freesurfer/subjects/testdtrecon/dti/dwi-ec_tmp0002
processing /home/ward/freesurfer/subjects/testdtrecon/dti/dwi-ec_tmp0003
processing /home/ward/freesurfer/subjects/testdtrecon/dti/dwi-ec_tmp0004
processing /home/ward/freesurfer/subjects/testdtrecon/dti/dwi-ec_tmp0005
processing /home/ward/freesurfer/subjects/testdtrecon/dti/dwi-ec_tmp0006
processing /home/ward/freesurfer/subjects/testdtrecon/dti/dwi-ec_tmp0007
processing /home/ward/freesurfer/subjects/testdtrecon/dti/dwi-ec_tmp0008
processing /home/ward/freesurfer/subjects/testdtrecon/dti/dwi-ec_tmp0009
processing /home/ward/freesurfer/subjects/testdtrecon/dti/dwi-ec_tmp0010
processing /home/ward/freesurfer/subjects/testdtrecon/dti/dwi-ec_tmp0011
processing /home/ward/freesurfer/subjects/testdtrecon/dti/dwi-ec_tmp0012
processing /home/ward/freesurfer/subjects/testdtrecon/dti/dwi-ec_tmp0013
processing /home/ward/freesurfer/subjects/testdtrecon/dti/dwi-ec_tmp0014
processing /home/ward/freesurfer/subjects/testdtrecon/dti/dwi-ec_tmp0015
processing /home/ward/freesurfer/subjects/testdtrecon/dti/dwi-ec_tmp0016
processing /home/ward/freesurfer/subjects/testdtrecon/dti/dwi-ec_tmp0017
processing /home/ward/freesurfer/subjects/testdtrecon/dti/dwi-ec_tmp0018
processing /home/ward/freesurfer/subjects/testdtrecon/dti/dwi-ec_tmp0019
processing /home/ward/freesurfer/subjects/testdtrecon/dti/dwi-ec_tmp0020
processing /home/ward/freesurfer/subjects/testdtrecon/dti/dwi-ec_tmp0021
processing /home/ward/freesurfer/subjects/testdtrecon/dti/dwi-ec_tmp0022
processing /home/ward/freesurfer/subjects/testdtrecon/dti/dwi-ec_tmp0023
processing /home/ward/freesurfer/subjects/testdtrecon/dti/dwi-ec_tmp0024
processing /home/ward/freesurfer/subjects/testdtrecon/dti/dwi-ec_tmp0025
processing /home/ward/freesurfer/subjects/testdtrecon/dti/dwi-ec_tmp0026
processing /

[Freesurfer] PostDoc (or qualified PhD) in Cognitive Computational Modeling (fMRI) in Copenhagen

2022-10-26 Thread David Meder 
External Email - Use Caution

We are hiring a PostDoc (or qualified PhD student) on cognitive computational 
neuroimaging. 
This position is for you if you are interested in how the dopamine system works 
and like computational modeling. You would be part of a small and dynamic 
research project on the reward and motor systems in Parkinson’s Disease, 
embedded in the Movement Disorders research group at the Danish Research Centre 
for Magnetic Resonance.
And all of that in the most liveable city in the world.

For any inquiries or questions, write to dav...@drcmr.dk 
.

Follow this link for all details and for the application: 
https://secure-web.cisco.com/1P2UVw0p3pRPifdvgHBVRQ_b0Gh8fhcwt4AnFZTaVc0kpCRc08SGhqteek4-saU0gK2d1IrYvxh7WrpMqHdVcUK2-4D4sRwCzlogvpv6l9SIuQXt9bNKMKHFPGMSqp35X6q94i-8-HN2geMcbuDxl4YButWlvPcpk9naaoLHc2xEtJsNI18nMEYJKeE72FNf8GdosRDpoK3obIehuVYRU14Pnq79ys7YEXFPuB25dvaR3g1mVBtgmL_7bFXDS15shWCkHuo4lEzL72_sZy0oTjS6WrVr3MisvAtfwwl4efoUsgplLJAYByZtUDuQb8Eij/https%3A%2F%2Fwww.drcmr.dk%2Fvacancies%2Fitem%2F1270-a-postdoc-or-qualified-phd-in-cognitive-computational-modeling-of-neuroimaging-data
 

 

Deadline is Nov. 13th


David Meder
Research Fellow
Danish Research Centre for Magnetic Resonance DRCMR, Section 714
Copenhagen University Hospital Amager and Hvidovre
Kettegaard Alle 30, 2650 Hvidovre, Denmark

http://secure-web.cisco.com/15MpSS7cf-43ZjZWVO4wi088tGjgBnwHuBnw3d2e1b5falw4mp8cFmX3W7qnSMhKxQPdB-Le6PL7kAF7m0uquInUlyyHztLPG0H3rCqN7stu4mGyCj0dsneAJCYt3SUuYVPlgbxs463a-1cpO7SbaVqvRNWqzJ0d2WSujwymCIOjYfBY_JNflnafMYQ0rqJdXtWyLKeaaYDWpotUYhvsNX69a-pLPO5_IhdahDvYmXxP6l9Q6lu0sVvkBXOTadSQ0OTjIRZOm6EX0bzMEehfEmw9xDFiKlG4ZATc80iG7wzTVIyR87pDjopGazTaPwlXs/http%3A%2F%2Fwww.drcmr.dk

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Re: [Freesurfer] MRI recon-all failed at talairach

2022-10-26 Thread Douglas N. Greve 
What is the error? The funny characters? Can you just send the entire 
logs (recon-all and avi.log)?


On 10/25/2022 11:49 AM, Jonany, Vincent Joe wrote:


External Email - Use Caution


Dear FreeSurfer Developers,

I am encountering a weird error in performing recon-all in my dicom 
directory. I believe the problem is here (snippet copied from 
talairach_avi.log. I have also attached here the recon-all.log, as 
well as the talaraich_avi.log. Does anyone know or have seen this 
problem before? I will appreciate any kind of help, please let me know 
if I need to provide anything else.


FreeSurfer version: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c
Platform: MacOS Monterey (apple silicon)

$Id: imgreg_4dfp.c,v 1.4 2010/02/27 01:41:53 nicks Exp $
/Applications/freesurfer/6/average/3T18yoSchwartzReactN32_as_orig.4dfp.img
256 256 256 1
1.00 1.00 1.00
orientation T byte_order littleendian
Reading image: 
/Applications/freesurfer/6/average/3T18yoSchwartzReactN32_as_orig.4dfp.img

dimensions: 256 256 256
mmppix: 1. -1. -1.
center: 128. -129. -129.
talsrcimg_g11.4dfp.img
256 256 256 1
1.00 1.00 1.00
orientation T byte_order littleendian
Reading image: talsrcimg_g11.4dfp.img
dimensions: 256 256 256
mmppix: 1. -1. -1.
center: 128. -129. -129.
t4_read: talsrcimg_to_3T18yoSchwartzReactN32_as_orig_t4pupuÀþN
èEÑ�àÔ�àÔ7SÎ0°þN
#Öô>ÖxþN
°þN
�þN
SÎðþN

þN
Ñ@
àþN
�
Ñ read error
t4_read: transform initialized to I4
rotation matrix determinant 1.00

Thank you in advance! I appreciate any help!

Best,

Vincent

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Re: [Freesurfer] Preproc-sess crashed - 3dvolreg.afni error

2022-10-26 Thread Douglas N. Greve 
What  happens when your run 3dvolreg.afni by itself (no options) from 
the command line?


On 10/25/2022 4:41 PM, Gillian Grennan wrote:


External Email - Use Caution

Hello FreeSurfer Developers,

I downloaded Freesurfer v7.3.2 
 
onto my local drive and am attempting to run preprocessing through 
FSFAST. I wasn't able to get access to the .tar.gz Darwin file but 
downloaded Xquartz, Freesurfer, FSL, and Matlab individually and was 
able to source Freesurfer using the following commands:


export FREESURFER_HOME=/Applications/freesurfer/7.3.2

export 
PROJECT_DIR=/Users/angelafang/Library/CloudStorage/OneDrive-UW/VicExt


export SUBJECTS_DIR=$PROJECT_DIR/subjects

source $FREESURFER_HOME/SetUpFreeSurfer.sh


However, when I run preproc-sess in my analysis folder I get the 
following error:



command: preproc-sess -sf subjectlist -fsd bold -stc siemens -surface 
fsaverage lhrh -mni305 -fwhm 5 -per-run



error message:

++ Initializing alignment base

Choleski factorization failure in startup_lsqfit

mri_startup_lsqfit: bad call to startup_lsqfit!

++ Starting final pass on 44 sub-bricks: 0

Fatal Signal 11 (SIGSEGV) received

mri_3dalign_one

3dvolreg main

Bottom of Debug Stack

** AFNI version = AFNI_2011_12_21_1014Compile date = May 22 2013

** [[Precompiled binary macosx_10.7_Intel_64: May 22 2013]]

** Program Abort **

** If you report this crash to the AFNI message board,

** please copy the error messages EXACTLY, and give

** the command line you used to run the program, and

** any other information needed to repeat the problem.

** You may later be asked to upload data to help debug.

ERROR: 3dvolreg.afni

Invalid null command.


I'm confused on what more I need to install? Is there a way I can get 
an updated link to the tar file with the relevant software packages 
needed to run FSFAST?



Best,

Gillian Grennan


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Re: [Freesurfer] dt_recon eddy correction fail and freeview errors

2022-10-26 Thread Douglas N. Greve 
Do you see a filed called dwi-ec.nii.gz? That should be the output of 
eddy_correct. The log file says it is running it. Two min does seem a 
little fast for 60 directions; I have another case that does 340 in 
about 40min. Try running eddy_correct outside of dt_recon and see what 
happens.,


On 10/26/2022 5:53 AM, Ward Deferm wrote:


External Email - Use Caution

Dear Freesurfer Developers,



I am trying to perform the dt_recon command for a single participant 
of my dataset. The original data comes from a philips scanner and was 
in the PAR/REC format. I converted these files to nifti’s using 
dcm2niix. This seemed to have worked as I got my nifti files and .bval 
and .bvec.



However, when I run the dt_recon command it does not give me a hard 
error, but the output is not how it should be. Instead of taking 1-2 
hours to complete the command, the command is done in about 3 minutes 
and I’m doubting if the eddy corrections are actually performed (fsl 
seems to be installed properly and is recognized when sourcing 
freesurfer. When trying to view the output with freeview I get 2 
outcomes. Sometimes all of the file's work but there is no eddy 
correction performed and the FA volume is spread all over the brain 
when looking at this volume using freeview. But other times certain 
volumes either refuse to load or come up as a blank rectangle. In the 
freeview command line I then get the error:



WARNING: 37103 NaNs found in volume 
/home/ward/freesurfer/subjects/testdtrecon/dti/ra.nii.gz



In the attached files you can find the dt_recon log file. As for 
version and operating system I am running:



1) freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275

2)Ubuntu 22.04.1 LTS


Kind regards,


Ward Deferm



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Re: [Freesurfer] Issue with rotation during longitudinal base creation

2022-10-26 Thread Huang, Yujing 
Hi Nathan,

Can you confirm that the error was from mri_robust_template?

Not sure what your command line options. I think these options ‘—inittp <>’, 
‘--fixtp’, ‘—seed <>’ might help.

Best,

Yujing


 Forwarded Message 
Subject:
[Freesurfer] Issue with rotation during longitudinal base creation
Date:
Wed, 12 Oct 2022 16:54:29 +
From:
Nathan Kindred (PGR) 

Reply-To:
Freesurfer support list 

To:
freesurfer@nmr.mgh.harvard.edu 



External Email - Use Caution
Hi,

I have been processing longitudinal data using the longitudinal processing 
stream but for some subjects I am having getting this error when creating the 
base:

Input rotation's max deviation from rotation is: 0.000258493
MyMatrix::RotationMean input(s) not rotation

What would be the best way to fix this?

Best,
Nathan

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Re: [Freesurfer] Preproc-sess crashed - 3dvolreg.afni error

2022-10-26 Thread Gillian Grennan 
External Email - Use Caution

It says "command not found" (when I run 3dvolreg and 3dvolreg.afni)!

On Wed, Oct 26, 2022 at 7:24 AM Douglas N. Greve 
wrote:

> What  happens when your run 3dvolreg.afni by itself (no options) from the
> command line?
>
> On 10/25/2022 4:41 PM, Gillian Grennan wrote:
>
> External Email - Use Caution
> Hello FreeSurfer Developers,
>
> I downloaded Freesurfer v7.3.2 [secure-web.cisco.com]
> 
> onto my local drive and am attempting to run preprocessing through FSFAST.
> I wasn't able to get access to the .tar.gz Darwin file but downloaded
> Xquartz, Freesurfer, FSL, and Matlab individually and was able to source
> Freesurfer using the following commands:
>
> export FREESURFER_HOME=/Applications/freesurfer/7.3.2
>
> export
> PROJECT_DIR=/Users/angelafang/Library/CloudStorage/OneDrive-UW/VicExt
>
> export SUBJECTS_DIR=$PROJECT_DIR/subjects
>
> source $FREESURFER_HOME/SetUpFreeSurfer.sh
>
>
> However, when I run preproc-sess in my analysis folder I get the following
> error:
>
>
> command: preproc-sess -sf subjectlist -fsd bold -stc siemens -surface
> fsaverage lhrh -mni305 -fwhm 5 -per-run
>
>
> error message:
>
> ++ Initializing alignment base
>
> Choleski factorization failure in startup_lsqfit
>
> mri_startup_lsqfit: bad call to startup_lsqfit!
>
> ++ Starting final pass on 44 sub-bricks: 0
>
> Fatal Signal 11 (SIGSEGV) received
>
>mri_3dalign_one
>
>   3dvolreg main
>
>  Bottom of Debug Stack
>
> ** AFNI version = AFNI_2011_12_21_1014  Compile date = May 22 2013
>
> ** [[Precompiled binary macosx_10.7_Intel_64: May 22 2013]]
>
> ** Program Abort **
>
> ** If you report this crash to the AFNI message board,
>
> ** please copy the error messages EXACTLY, and give
>
> ** the command line you used to run the program, and
>
> ** any other information needed to repeat the problem.
>
> ** You may later be asked to upload data to help debug.
>
> ERROR: 3dvolreg.afni
>
> Invalid null command.
>
>
> I'm confused on what more I need to install? Is there a way I can get an
> updated link to the tar file with the relevant software packages needed to
> run FSFAST?
>
>
> Best,
>
> Gillian Grennan
>
> ___
> Freesurfer mailing 
> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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>
>
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Re: [Freesurfer] MRI recon-all failed at talairach

2022-10-26 Thread fsbuild 
External Email - Use Caution

It looks like your terminal/character settings are
 messed up in the current terminal session.  That can happen from trying
 to look at a raw binary or image file in the terminal window or running 
something that outputs non-standard
 characters to the terminal (stdout).  I would open a new terminal 
window, source the freesurfer setup script, and try to identify if something 
you run corrupts the display of text in the new terminal window.

  
- R.


On 10/26/22 10:21, Douglas N. Greve (dgr...@mgh.harvard.edu) wrote:




  
  
What is the error? The funny characters? Can you just send the
entire logs (recon-all and avi.log)?






  On 10/25/2022 11:49 AM, Jonany, Vincent
  Joe wrote:




  
  
  
  External Email - Use
  Caution
  

Dear FreeSurfer
Developers,



I am encountering a weird error in performing recon-all in
my dicom directory. I believe the problem is here (snippet
copied from talairach_avi.log. I have also attached here the
recon-all.log, as well as the talaraich_avi.log. Does anyone
know or have seen this problem before? I will appreciate any
kind of help, please let me know if I need to provide
anything else.



FreeSurfer version:
freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c

Platform: MacOS Monterey (apple silicon)



$Id: imgreg_4dfp.c,v 1.4 2010/02/27 01:41:53 nicks Exp $

/Applications/freesurfer/6/average/3T18yoSchwartzReactN32_as_orig.4dfp.img

256 256 256 1

1.00 1.00 1.00

orientation T byte_order littleendian

Reading image:
/Applications/freesurfer/6/average/3T18yoSchwartzReactN32_as_orig.4dfp.img

dimensions: 256 256 256

mmppix: 1. -1. -1.

center: 128. -129. -129.

talsrcimg_g11.4dfp.img

256 256 256 1

1.00 1.00 1.00

orientation T byte_order littleendian

Reading image: talsrcimg_g11.4dfp.img

dimensions: 256 256 256

mmppix: 1. -1. -1.

center: 128. -129. -129.

t4_read:
talsrcimg_to_3T18yoSchwartzReactN32_as_orig_t4pupuÀþN

èEÑ�àÔ�àÔ7SÎ0°þN

#Öô>ÖxþN

°þN

�þN

SÎðþN



þN

Ñ@

àþN

�

Ñ read error

t4_read: transform initialized to I4

rotation matrix determinant 1.00



Thank you in advance! I appreciate any help!



Best,



Vincent


  

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[Freesurfer] acompcor in fsfast

2022-10-26 Thread Addison, Reuben 
Hi,

I am running resting State functional connectivity and I want to run everything 
in freesurfer and fsfast.

I wanted to know is it is possible to run
acompcor in fsfast. If so, how do I go about it.

Thanks.

Get Outlook for iOS
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[Freesurfer] overlay_threshold is ignored when using custom overlay

2022-10-26 Thread Maya Yablonski 
External Email - Use Caution

Hello,

I'm trying to use a custom colormap for an overlay in Freeview and I can't get 
the threshold option to work. Specifically, I want to display positive values 
with specific colors, and negative values with different colors, similarly to 
using the threshold with the default Heat colorscale ('Hot' for positive and 
'cold' for negative, values outside the threshold do not appear at all).
This is the code I've been using, and it seems to ignore the values provided by 
overlay_threshold:

freeview -f 
/sub-01/surf/lh.inflated:overlay=tmap.curv:overlay_custom=-3,45,0,130,-9,220,210,250,3,255,70,0,9,255,255,0:overlay_threshold=3,9:overlay_color='clearlower','clearhigher'
 -colorscale


This uses the right colors, but creates a continuous colorscale that spans -9 
to 9, including the range [-3 3] which I want to threshold out of the map. I 
tried toggling the overlay_color='clearlower' and 'clearhigher', but couldn't 
find a combination that thresholded the low values around zero and not the 
extreme values (<-9 and >9). I also tested different values and seems like 
overlay_threshold is being completely ignored when overlay_custom is used. I 
couldn't get the right settings even when using the Freeview GUI.

I tested this on Freesurfer versions 7.1.1 and 7.3.2 on MacOS Catalina 
(10.15.7).

I'd appreciate any leads on this!
Thanks,
Maya
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Re: [Freesurfer] overlay_threshold is ignored when using custom overlay

2022-10-26 Thread Wang, Ruopeng 
Hi Maya,

Custom color table is always continuous. So it will not automatically mask out 
a portion in the middle. The overlay_threshold option is not for custom 
colormap. I think we can add an option to allow specifying colors with 4 
components where the last one is for alpha/transparency.

Ruopeng

On Oct 26, 2022, at 7:52 PM, Maya Yablonski 
mailto:ma...@stanford.edu>> wrote:

External Email - Use Caution

Hello,

I'm trying to use a custom colormap for an overlay in Freeview and I can't get 
the threshold option to work. Specifically, I want to display positive values 
with specific colors, and negative values with different colors, similarly to 
using the threshold with the default Heat colorscale ('Hot' for positive and 
'cold' for negative, values outside the threshold do not appear at all).
This is the code I've been using, and it seems to ignore the values provided by 
overlay_threshold:
freeview -f 
/sub-01/surf/lh.inflated:overlay=tmap.curv:overlay_custom=-3,45,0,130,-9,220,210,250,3,255,70,0,9,255,255,0:overlay_threshold=3,9:overlay_color='clearlower','clearhigher'
 -colorscale

This uses the right colors, but creates a continuous colorscale that spans -9 
to 9, including the range [-3 3] which I want to threshold out of the map. I 
tried toggling the overlay_color='clearlower' and 'clearhigher', but couldn't 
find a combination that thresholded the low values around zero and not the 
extreme values (<-9 and >9). I also tested different values and seems like 
overlay_threshold is being completely ignored when overlay_custom is used. I 
couldn't get the right settings even when using the Freeview GUI.
I tested this on Freesurfer versions 7.1.1 and 7.3.2 on MacOS Catalina 
(10.15.7).
I'd appreciate any leads on this!
Thanks,
Maya
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[Freesurfer] conversion of .stats to .csv

2022-10-26 Thread priya padma 
External Email - Use Caution

Dear Team,

I would like to convert the .stats files that are being generated in the
stats folder as an output from recon-all to csv file or excel file. Is
there any way to convert .stats to .csv or .excel format? any help on
this would be much appreciated.

Thank you

-- 
Best Regards
Padma Priya
*AI Developer *

*PhenoMx, Inc.*
*pr...@phenomx.ai  | (+82)10-5405-2685*
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[Freesurfer] Question regarding General Linear Model analysis with Freesurfer

2022-10-26 Thread Lyna Mariam El Haffaf 
External Email - Use Caution

Hi!

I hope you are doing well!


I am working on a paper where we used Freesurfer for whole brain analysis in 
intergroup comparison (g2v1). The objective of the analysis is to see if there 
is an association between neuropsychiatric symptoms and brain regions at 
different stages of Alzheimer's disease (Alzheimer, Mild cognitive impairment 
and cognitively normal participants).

For this objective, a whole-brain analysis was performed using general linear 
model (GLM) analysis with FreeSurfer mri_glmfit for each neuropsychiatric 
symptoms of interest to assess their effect on brain’s cortical volume, 
thickness and area, between the groups (AD vs MCI, CN vs MCI, CN vs AD). We 
performed a Monte-Carlo correction on the results obtained.


I was wondering if it was possible to add another correction for multiple group 
comparison in addition to the Monte-Carlo correction?


Also, is it possible to add covariates by creating additional models using the 
GLM analysis with Freesurfer mri_glmfit?


Thank you in advance!
Lyna El Haffaf

Graduate student in neuropsychology

Université de Montréal


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