Re: [Freesurfer] Monte-Carlo in LME

2017-07-21 Thread Jordi Pegueroles 
Thank you Doug. So, instead of running mri_surfcluster I should run 
mri_glmfit-sim with the --fwhm-override with the smoothing obtained from 
the residuals of the lme model.

Thanks again,

A 2017-07-18 22:09, Douglas N Greve escrigué:
> Not sure. It might be more accurate. Once you have the FWHM you want,
> you can run mri_glmfit-sim with --fwhm-override
> 
> 
> On 07/17/2017 05:43 PM, Jordi Pegueroles wrote:
>> Dear FS experts,
>> 
>> I was wondering if someone had performed multiple comparisons (ie 
>> monte-carlo) with the LME analyses. I have found a thread 
>> (https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg40195.html) 
>> where Doug recommends to run a GLM fit with the same data and then 
>> overwrite the sig.mgh file with the LME one.
>> 
>> My question is if is not more accurate to estimate the residuals from 
>> the LME model, then compute the relative smooth of the data with the 
>> mris_fwhm command and pass it as an argument in the mri_surfcluster 
>> command (mri_surfcluster --in $direct1/sig.mgh --csd 
>> /Applications/freesurfer/average/mult-comp-cor/fsaverage/${hemi}/cortex/fwhm${rfwhm}/abs/th13/mc-z.csd
>>  
>> --cwsig $direct1/mc.abs.th13.sig.cluster.mgh --vwsig 
>> $direct1/abs.th13.sig.vertex.mgh --cwpvalthresh 0.05 --surf white).
>> 
>> Thanks in advance.
>> 
> 
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
> 
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: 
> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
> 
> 
> 
> The information in this e-mail is intended only for the person to whom 
> it is
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-- 
Jordi.
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[Freesurfer] tracula error message

2017-07-21 Thread Marissa Pifer 
Hi Freesurfers,

Could you help me interpret this error message? I am attempting to run
TRACULA using version 6 on a MacBook Pro OS X El Capitan Version 10.11.3

helpdesks-MacBook-Pro-2:R01_DTI crc$ trac-all -prep -c dmrirc.example1

INFO: SUBJECTS_DIR is /Users/crc/Documents/myprojects/R01_DTI

INFO: Diffusion root is /Users/CRC/Documents/myprojects/R01_DTI/tracresults

Actual FREESURFER_HOME /Applications/freesurfer

trac-preproc -c
/Users/CRC/Documents/myprojects/R01_DTI/tracresults/NAH001-1/scripts/dmrirc.local
-log
/Users/CRC/Documents/myprojects/R01_DTI/tracresults/NAH001-1/scripts/trac-all.log
-cmd
/Users/CRC/Documents/myprojects/R01_DTI/tracresults/NAH001-1/scripts/trac-all.cmd

#-

/Applications/freesurfer/bin/trac-preproc

#-

#@# Image corrections Fri Jul 21 09:28:12 EDT 2017

mri_convert --bvec-voxel
/Users/CRC/Documents/myprojects/R01_DTI/NAH001-1/DTI/nifty.nii.gz
/Users/CRC/Documents/myprojects/R01_DTI/tracresults/NAH001-1/dmri/dwi_orig.nii.gz

mri_convert.bin --bvec-voxel
/Users/CRC/Documents/myprojects/R01_DTI/NAH001-1/DTI/nifty.nii.gz
/Users/CRC/Documents/myprojects/R01_DTI/tracresults/NAH001-1/dmri/dwi_orig.nii.gz

$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $

reading from
/Users/CRC/Documents/myprojects/R01_DTI/NAH001-1/DTI/nifty.nii.gz...

TR=3222.00, TE=0.00, TI=0.00, flip angle=0.00

i_ras = (-0.997757, 0.0345085, 0.057362)

j_ras = (0.0453079, 0.978915, 0.19918)

k_ras = (0.0492791, -0.201332, 0.978283)

writing to
/Users/CRC/Documents/myprojects/R01_DTI/tracresults/NAH001-1/dmri/dwi_orig.nii.gz...

cp /Users/CRC/Documents/myprojects/R01_DTI/NAH001-1/DTI/bvec
/Users/CRC/Documents/myprojects/R01_DTI/tracresults/NAH001-1/dmri/dwi_orig.bvecs

cp /Users/CRC/Documents/myprojects/R01_DTI/NAH001-1/DTI/bval
/Users/CRC/Documents/myprojects/R01_DTI/tracresults/NAH001-1/dmri/dwi_orig.bvals

mv -f
/Users/CRC/Documents/myprojects/R01_DTI/tracresults/NAH001-1/dmri/bvecs.tmp
/Users/CRC/Documents/myprojects/R01_DTI/tracresults/NAH001-1/dmri/dwi_orig.bvecs

mv -f
/Users/CRC/Documents/myprojects/R01_DTI/tracresults/NAH001-1/dmri/bvals.tmp
/Users/CRC/Documents/myprojects/R01_DTI/tracresults/NAH001-1/dmri/dwi_orig.bvals

orientLAS
/Users/CRC/Documents/myprojects/R01_DTI/tracresults/NAH001-1/dmri/dwi_orig.nii.gz
/Users/CRC/Documents/myprojects/R01_DTI/tracresults/NAH001-1/dmri/dwi_orig_las.nii.gz

dyld: lazy symbol binding failed: Symbol not found: ___emutls_get_address

  Referenced from:
/Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib

  Expected in: /usr/lib/libSystem.B.dylib


dyld: Symbol not found: ___emutls_get_address

  Referenced from:
/Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib

  Expected in: /usr/lib/libSystem.B.dylib


Trace/BPT trap

ERROR: input file must be in NIfTI format

Darwin helpdesks-MacBook-Pro-2.local 15.3.0 Darwin Kernel Version 15.3.0:
Thu Dec 10 18:40:58 PST 2015; root:xnu-3248.30.4~1/RELEASE_X86_64 x86_64


trac-preproc exited with ERRORS at Fri Jul 21 09:29:59 EDT 2017


helpdesks-MacBook-Pro-2:R01_DTI crc$


It says at the end that the input file needs to be in nifty format, but my
input file is in nifty format. Do you guys have any idea what could be
going on here. I attached my dmrirc.example file for your reference as
well.

Thank you,

Marissa


dmrirc.example1
Description: Binary data
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Re: [Freesurfer] tracula error message

2017-07-21 Thread Yendiki, Anastasia 
Hi Marisa – Did you check the archives of this email list? I believe this error 
has come up before.

a.y

From: 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Marissa Pifer 
mailto:marissapi...@gmail.com>>
Reply-To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Friday, July 21, 2017 at 9:41 AM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] tracula error message

___emutls_get_address
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[Freesurfer] Postdoctoral Position in Cognitive and Clinical Neuroscience, Boston, MA {Disarmed}

2017-07-21 Thread Dustin Clark 
Postdoctoral Position in Cognitive and Clinical Neuroscience

Boston Attention and Learning Lab, VA Boston Healthcare System, Boston, MA



The BALLAB (www. bu.edu/ballab/) at VA Boston is
looking for a neuroimaging post-doctoral fellow starting this coming fall,
2017. Broadly, the BALLAB uses a variety of cognitive neuroscience tools
(fMRI, EEG, TMS, psychophysics, cognitive training) to study attention and
visual cognition, as well as cognitive and brain dysfunction in Veterans
with psychiatric disorders. This specific position is funded by a VA grant
to use fMRI connectomicsto understand and predict cognitive, functional,
and clinical dysfunction in Veterans. Opportunities to work on a wide range
of projects and with collaborators at VA, Boston University, and Harvard
are ample, and new project development is welcome.



Ph.D. in experimental psychology, cognitive neuroscience, neuroscience, or
related field, as well as experience with programming and fMRI required.
Two years of funding are available. If interested, please contact Mike
Esterman (ester...@bu.edu).
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