Re: [Freesurfer] TIV should be considered as a covariant for thickness, volume and area analyses

2018-06-29 Thread Ting Li 
External Email - Use Caution

Thank you so much!

Ting
> On Jun 29, 2018, at 2:10 PM, Douglas Greve  wrote:
> 
> Yes, for area and volume, no for thickness
> 
> On 6/29/18 3:06 PM, Ting Li wrote:
>> External Email - Use Caution
>> 
>> Hi FreeSurfer Experts,
>> 
>> I would like to do the surface analysis among two groups, like the 
>> thickness, volume and area. When I run the GLM, do I have to consider the 
>> eTIV as a covariant or not? Thanks a lot!
>> 
>> Best wishes,
>> Ting
>> 
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[Freesurfer] After v.5.3 to v.6.0 update octave set up doesn't work

2018-06-29 Thread Patrycja Naumczyk 
External Email - Use Caution

Hi all,

I just switched from FS 5.3 to 6.0 on Gentoo Linux. Previously Freesurfer
worked fine under octave setup (as specified here:
https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2012-January/022135.html),
but after the update, when I tried testing a MATLAB related function I get
an error:

mkcontrast-sess -analysis PASAT.sm5.lh -contrast test -a 1 -c 0
INFO: Found 2 Non-Null Conditions
INFO: Found 3 Delays
Condition Weights: 1. 0
mkcontrast2 -config PASAT.sm5.lh/test.config -anadir PASAT.sm5.lh -wcond
1. 0 -sumconds -o PASAT.sm5.lh/test.mat -wdelay 1 0 0
-octave
  $Id: mkcontrast2,v 1.3 2016/03/11 23:46:48 greve Exp $
cmtxfile  PASAT.sm5.lh/test.mat
nconds2,  wcond  1. 0
ndelays   3, wdelay 1 0 0
ndelays   3, wpsa
sumconds  1
sumdelays 0
nircorr   0
TER   0.05
rdelta
rtau
ERROR: cannot find matlab. Is it in your path?
ERROR running mkcontrast
mkcontrast2 -config PASAT.sm5.lh/test.config -anadir PASAT.sm5.lh -wcond
1. 0 -sumconds -o PASAT.sm5.lh/test.mat -wdelay 1 0 0
-octave
Fri Jun 29 21:21:16 CEST 2018

It seems that the environment variable (FS_USE_OCTAVE) is recognized
correctly (the function runs with "-octave" flag), but somehow is omitted
during execution? What can I do about it?

I checked that v.5.3 used mkcontrast, whereas v.6.0 uses mkcontrast2 which
does not seem to support octave? Is it possible to force calling mkcontrast
instead of mkcontrast2?

Best regards,
Patrycja
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[Freesurfer] Eddy correct command not found

2018-06-29 Thread Renew Andrade 
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Dear community:
I have a problem with trac-all processing with the tutorial data. 

sh-3.2# trac-all -prep -c $TUTORIAL_DATA/diffusion_tutorial/dmrirc.tutorial
INFO: SUBJECTS_DIR is 
/Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_recons
INFO: Diffusion root is 
/Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial
Actual FREESURFER_HOME /Applications/freesurfer
INFO: FreeSurfer build stamps do not match
Subject Stamp: freesurfer-Linux-centos6_x86_64-dev-20130423
Current Stamp: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c
flirt: Command not found.
INFO: current FREESURFER_HOME does not match that of previous processing.
Current: /Applications/freesurfer
Previous: /usr/local/freesurfer/dev
trac-preproc -c 
/Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/scripts/dmrirc.local
 -log 
/Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/scripts/trac-all.log
 -cmd 
/Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/scripts/trac-all.cmd
#-
/Applications/freesurfer/bin/trac-preproc 
#-
#@# Image corrections Fri Jun 29 21:19:12 CEST 2018
mri_convert --bvec-voxel 
/Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/orig/656000-11-1.dcm
 
/Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/dmri/dwi_orig.nii.gz
mri_convert.bin --bvec-voxel 
/Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/orig/656000-11-1.dcm
 
/Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/dmri/dwi_orig.nii.gz
 
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from 
/Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/orig/656000-11-1.dcm...
Getting Series No 
INFO: Found 75 files in 
/Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/orig
INFO: Scanning for Series Number 11
Scanning Directory 
INFO: found 70 files in series
INFO: loading series header info.

RunNo = 10
WARNING: Run 1 appears to be truncated
  Files Found: 70, Files Expected (lRep+1): 120
FileName
/Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/orig/656000-11-1.dcm
Identification
NumarisVersyngo MR 2004A 4VA25A 
ScannerModel  Trio
PatientName   Trio_calib_002_run2 
Date and time
StudyDate 20050905
StudyTime 100821.656000 
SeriesTime104226.748000 
AcqTime   104209.522496 
Acquisition parameters
PulseSeq  ep_b0#0 
Protocol  DIFFUSION_HighRes 
PhEncDir  COL
EchoNo0
FlipAngle 90
EchoTime  100
InversionTime -1
RepetitionTime10100
PhEncFOV  256
ReadoutFOV256
Image information
RunNo 10
SeriesNo  11
ImageNo   1
NImageRows1024
NImageCols1024
NFrames   70
SliceArraylSize   60
IsMosaic  1
ImgPos1048.1801 1002.6923 -265.4914 
VolRes  2.   2.   2. 
VolDim128  128   60 
Vc -0.9997   0.0244   0.0005 
Vr -0.0238  -0.9764   0.2147 
Vs  0.0057   0.2147   0.9767 
VolCenter   0.   0.   0. 
TransferSyntaxUID unknown
INFO: sorting.
INFO: (128 128  60), nframes = 70, ismosaic=1
sdfi->UseSliceScaleFactor 0
datatype = 4, short=4, float=3
Numaris Version: syngo MR 2004A 4VA25A  Maj = 4, Min=2, MinMin = 5 
Repetition Time = 10100, TR = 10100 ms
PE Dir COL COL
AutoAlign matrix detected 
AutoAlign Matrix - 
 0.99970   0.02376  -0.00570  -0.49480;
-0.02443   0.97638  -0.21466  -40.55519;
 0.00047   0.21474   0.97667   12.50291;
 0.0   0.0   0.0   1.0;

FileName
/Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/orig/656000-11-1.dcm
Identification
NumarisVersyngo MR 2004A 4VA25A 
ScannerModel  Trio
PatientName   Trio_calib_002_run2 
Date and time
StudyDate 20050905

Re: [Freesurfer] TIV should be considered as a covariant for thickness, volume and area analyses

2018-06-29 Thread Douglas Greve 
Yes, for area and volume, no for thickness

On 6/29/18 3:06 PM, Ting Li wrote:
>  External Email - Use Caution
>
> Hi FreeSurfer Experts,
>
> I would like to do the surface analysis among two groups, like the thickness, 
> volume and area. When I run the GLM, do I have to consider the eTIV as a 
> covariant or not? Thanks a lot!
>
> Best wishes,
> Ting
>
> ___
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[Freesurfer] TIV should be considered as a covariant for thickness, volume and area analyses

2018-06-29 Thread Ting Li 
External Email - Use Caution

Hi FreeSurfer Experts,

I would like to do the surface analysis among two groups, like the thickness, 
volume and area. When I run the GLM, do I have to consider the eTIV as a 
covariant or not? Thanks a lot!

Best wishes,
Ting

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Re: [Freesurfer] mri_glmfit question

2018-06-29 Thread Douglas Greve 
You can create a surface overlay in matlab and display it using 
freeview.  See 
https://gate.nmr.mgh.harvard.edu/safelinks/greve/annotval2surfoverlay.m

To read it into matlab, you can run
pcc = MRIread('pcc.mgh');

You can convert it to text with mri_convert --ascii pcc.mgh outputtextfile

On 6/28/18 4:42 PM, Nillo, Ryan Michael R wrote:


External Email - Use Caution

Hello FreeSurfer Users,


I want to run an ROI-based analysis on mri_glmfit as opposed to 
vertex-based. I know that if I run mri_glmfit with the --table flag 
and give it the output of asegstats2table or aparcstats2table, it will 
run the analysis on the ROIs and output tables showing significance. 
In each contrast directory that was created from mri_glmfit, I see 
there is a pcc.mgh. Is there any way to display this on the surface or 
put it into a table format?



Mahalo,


Ryan M Nillo

Staff Research Associate I

UCSF Department of Radiology and Biomedical Imaging



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Re: [Freesurfer] Freeview not showing images

2018-06-29 Thread Mark Wagshul 
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Yes, that shows up fine.


Mark Wagshul, PhD
Associate Professor
Gruss Magnetic Resonance Research Center
Albert Einstein College of Medicine
Bronx, NY 10461

Ph: 718-430-4011
FAX: 718-430-3399
Email: mark.wags...@einstein.yu.edu

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From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Ruopeng Wang
Sent: Friday, June 29, 2018 10:43 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Freeview not showing images


What if you run 'glxgears'? Does it render properly?

Ruopeng

On 06/29/2018 09:50 AM, Mark Wagshul wrote:
Yes, I’m running it with Xming on Windows.  Same thing shows up if I load a 
volume.

Mark


Mark Wagshul, PhD
Associate Professor
Gruss Magnetic Resonance Research Center
Albert Einstein College of Medicine
Bronx, NY 10461

Ph: 718-430-4011
FAX: 718-430-3399
Email: mark.wags...@einstein.yu.edu

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From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 

 On Behalf Of Ruopeng Wang
Sent: Friday, June 29, 2018 8:39 AM
To: Freesurfer support list 

Subject: Re: [Freesurfer] Freeview not showing images

This looks like a display artifact. Are you running freeview via some kind of X 
Terminal Emulator on Windows? What if you load a volume?

Ruopeng



On Jun 28, 2018, at 7:33 PM, Mark Wagshul 
mailto:mark.wags...@einstein.yu.edu>> wrote:

Hi.

I’m a newbie to Freeview, hoping that this is a simple problem.  When I open it 
(specifying the lh.pial surface), I get this view:



Anyone have an idea what’s going on here, is it an issue with the screen 
resolution settings?

Thanks,

Mark


Mark Wagshul, PhD
Associate Professor
Gruss Magnetic Resonance Research Center
Albert Einstein College of Medicine
Bronx, NY 10461

Ph: 718-430-4011
FAX: 718-430-3399
Email: mark.wags...@einstein.yu.edu


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Re: [Freesurfer] Freeview not showing images

2018-06-29 Thread Ruopeng Wang 

What if you run 'glxgears'? Does it render properly?

Ruopeng


On 06/29/2018 09:50 AM, Mark Wagshul wrote:


Yes, I’m running it with Xming on Windows. Same thing shows up if I 
load a volume.


Mark


Mark Wagshul, PhD
Associate Professor
Gruss Magnetic Resonance Research Center
Albert Einstein College of Medicine
Bronx, NY 10461

Ph: 718-430-4011

FAX: 718-430-3399

Email: mark.wags...@einstein.yu.edu 

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*From:* freesurfer-boun...@nmr.mgh.harvard.edu 
 *On Behalf Of *Ruopeng Wang

*Sent:* Friday, June 29, 2018 8:39 AM
*To:* Freesurfer support list 
*Subject:* Re: [Freesurfer] Freeview not showing images

This looks like a display artifact. Are you running freeview via some 
kind of X Terminal Emulator on Windows? What if you load a volume?


Ruopeng



On Jun 28, 2018, at 7:33 PM, Mark Wagshul
mailto:mark.wags...@einstein.yu.edu>> wrote:

Hi.

I’m a newbie to Freeview, hoping that this is a simple problem. 
When I open it (specifying the lh.pial surface), I get this view:



Anyone have an idea what’s going on here, is it an issue with the
screen resolution settings?

Thanks,

Mark


Mark Wagshul, PhD
Associate Professor
Gruss Magnetic Resonance Research Center
Albert Einstein College of Medicine
Bronx, NY 10461

Ph: 718-430-4011

FAX: 718-430-3399

Email:mark.wags...@einstein.yu.edu




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Re: [Freesurfer] Proposed addition for Freesurfer - automated control points

2018-06-29 Thread Bruce Fischl 

Hi Chris

can you elaborate a bit? Our intensity normalization is almost entirely an 
automated control point finding tool.


cheers
Bruce


On Fri, 29 Jun 2018, Chris Adamson 
wrote:




External Email - Use Caution

Freesurfer devs,

 

I presented an automated control point adding tool at HBM and a few freesurfer 
lab people
came over and had a look. I was wondering if someone would like to review it 
for either
inclusion or to perhaps reference from the wiki as a tool for people to use if 
they choose?

 

Thanks in advance,

 

Chris.

 

Dr Chris Adamson

Senior Research Officer

Developmental Imaging, Clinical Sciences

 

Murdoch Childrens Research Institute

The Royal Children’s Hospital

Flemington Road, Parkville, VIC 3052 Australia

E chris.adam...@mcri.edu.au 

www.mcri.edu.au

 

 

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Re: [Freesurfer] 3T Intensity Normalization (Re-Submission)

2018-06-29 Thread Bruce Fischl 

Hi David

the -3T flag changes the target atlas to one built from 3T data, and also 
modifies some of the parameters that are passed to nu_correct, I believe 
to make it a bit more aggressive. I think the parameters we use are the 
ones suggested here:

https://www.ncbi.nlm.nih.gov/pubmed/19732839
cheers
Bruce

On Fri, 29 Jun 2018, David S Lee wrote:



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Hello Experts, 
I believe -3T Flag can be used with "recon-all" on scans collected by 3T 
scanners. I believe
it performs intensity normalization to set white matter intensity threshold at 
110. I am
hoping to learn more about the flag option as it produces slightly better 
output for me. 

Would you be able to guide me to a documentation on this -3T flag? 

Thank you!

--
David S. Lee
Associate Research Specialist
Center for Healthy Minds
University of Wisconsin - Madison
(608) 890-1115  

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[Freesurfer] 3T Intensity Normalization (Re-Submission)

2018-06-29 Thread David S Lee 
External Email - Use Caution

Hello Experts,

I believe -3T Flag can be used with "recon-all" on scans collected by 3T
scanners. I believe it performs intensity normalization to set white matter
intensity threshold at 110. I am hoping to learn more about the flag option
as it produces slightly better output for me.

Would you be able to guide me to a documentation on this -3T flag?

Thank you!

-- 
David S. Lee
Associate Research Specialist
Center for Healthy Minds
University of Wisconsin - Madison
(608) 890-1115
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Re: [Freesurfer] Freeview not showing images

2018-06-29 Thread Mark Wagshul 
External Email - Use Caution

Yes, I’m running it with Xming on Windows.  Same thing shows up if I load a 
volume.

Mark


Mark Wagshul, PhD
Associate Professor
Gruss Magnetic Resonance Research Center
Albert Einstein College of Medicine
Bronx, NY 10461

Ph: 718-430-4011
FAX: 718-430-3399
Email: mark.wags...@einstein.yu.edu

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From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Ruopeng Wang
Sent: Friday, June 29, 2018 8:39 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Freeview not showing images

This looks like a display artifact. Are you running freeview via some kind of X 
Terminal Emulator on Windows? What if you load a volume?

Ruopeng


On Jun 28, 2018, at 7:33 PM, Mark Wagshul 
mailto:mark.wags...@einstein.yu.edu>> wrote:

Hi.

I’m a newbie to Freeview, hoping that this is a simple problem.  When I open it 
(specifying the lh.pial surface), I get this view:



Anyone have an idea what’s going on here, is it an issue with the screen 
resolution settings?

Thanks,

Mark


Mark Wagshul, PhD
Associate Professor
Gruss Magnetic Resonance Research Center
Albert Einstein College of Medicine
Bronx, NY 10461

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FAX: 718-430-3399
Email: mark.wags...@einstein.yu.edu


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Re: [Freesurfer] Freeview not showing images

2018-06-29 Thread Ruopeng Wang 
This looks like a display artifact. Are you running freeview via some kind of X 
Terminal Emulator on Windows? What if you load a volume? 

Ruopeng

> On Jun 28, 2018, at 7:33 PM, Mark Wagshul  
> wrote:
> 
> Hi.
>  
> I’m a newbie to Freeview, hoping that this is a simple problem.  When I open 
> it (specifying the lh.pial surface), I get this view:
>  
> 
>  
> Anyone have an idea what’s going on here, is it an issue with the screen 
> resolution settings?
>  
> Thanks,
>  
> Mark
>  
> 
> Mark Wagshul, PhD
> Associate Professor
> Gruss Magnetic Resonance Research Center
> Albert Einstein College of Medicine
> Bronx, NY 10461
> 
> Ph: 718-430-4011
> FAX: 718-430-3399
> Email: mark.wags...@einstein.yu.edu 
>  
> 
> This email message and any accompanying attachments may contain privileged 
> information intended only for the named recipient(s). If you are not the 
> intended recipient(s), you are hereby notified that the dissemination, 
> distribution, and or copying of this message is strictly prohibited. If you 
> receive this message in error, or are not the named recipient(s), please 
> notify the sender at the email address above, delete this email from your 
> computer, and destroy any copies in any form immediately.
>  
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu 
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 
> 
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