[Freesurfer] Extract the ROI mapping

2019-04-18 Thread 2016102110...@whu.edu.cn 
External Email - Use Caution

Hello Freesurfer developers,

After I recon-all my subjects, the label files are generated. Could you please 
kindly help me how can I extract the special brain region from these label 
files by matlab:


But I don't know if it is the mean thickness for brain region BA1. Where can I  
get the detail information for these label files, such as 'lh.BA1.label'.

Best Regards and thanks,
Henry



2016102110...@whu.edu.cn
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] CORRECTING DEFECT 1 problem

2019-04-18 Thread Abby tang 
External Email - Use Caution

Hello，Bruce
I attached my subjects. Please help me.
Thank you.
Abby
 2851A_T1_w4.nii


Bruce Fischl  于2019年4月18日周四 下午10:53写道：

> Hi Abby
>
> it's hard to tell from the image, but it looks like there is a big I/S
> bias field as well as large amounts of pathology.
>
> If you upload the subject to our ftp site we will take a look
>
> cheers
> Bruce
> On Thu, 18 Apr
> 2019, Abby
> tang wrote:
>
> >
> > External Email - Use Caution
> >
> > Hello FreeSurfer Developers,
> >
> > I'm attempting to recon_all my subjects which is .nii file. But I
> usually meet this error.
> >
> > CORRECTING DEFECT 0 (vertices=67, convex hull=73, v0=950)
> > After retessellation of defect 0 (v0=950), euler #=20
> (87340,255044,167724) : difference with theory
> >  (-32) = -52
> >
> > CORRECTING DEFECT 1 (vertices=46367, convex hull=8524, v0=962)
> > Segmentation fault (core dumped)
> > Linux abby-virtual-machine 4.15.0-47-generic #50-Ubuntu SMP Wed Mar 13
> 10:44:52 UTC 2019 x86_64 x86_
> > 64 x86_64 GNU/Linux
> >
> > recon-all -s 2851A_T1_w4 exited with ERRORS at Thu Apr 18 20:25:16 CST
> 2019
> >
> > To report a problem, see
> http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> >
> > I check files in blow command and attached picture.
> >
> > freeview -v 2851A_T1_w4/mri/norm.mgz -f 2851A_T1_w4/surf/lh.orig.nofix
> 2851A_T1_w4/surf/lh.inflated.
> > nofix
> >
> > almost all of subjects go wrong. I need your help.
> >
> > please give some advises with program statements in detail.
> >
> > I really appreciate your help
> >
> > 1) FreeSurfer version: freesurfer-linux-centos7_x86_64-dev.tar.gz
> > 2) Platform: ubuntu 18
> > 3) recon-all.log:see attached
> >
> >___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] issue running trac-all longitudinal

2019-04-18 Thread Daniel Callow 
External Email - Use Caution

Sorry, the beginning of the email seems to have been cut off. I was trying
to run trac-all on one of my subjects to troubleshoot running the following
command.

trac-all -prep -c /Volumes/DANIEL/dmrirc.long.example.single.sh


I posted the errors and attached the dmrirc file I used below.


There seems to be an issue with











writing to 
/Volumes/DANIEL/dti_freesurf/trac/Ex.AES101.long.base_AES101/dmri/dwi_orig.nii.gz...

Saving bvals and bvecs

mv -f 
/Volumes/DANIEL/dti_freesurf/trac/Ex.AES101.long.base_AES101/dmri/dwi_orig.voxel_space.bvecs
/Volumes/DANIEL/dti_freesurf/trac/Ex.AES101.long.base_AES101/dmri/dwi_orig.bvecs

mri_probedicom --i
/Volumes/DANIEL/dti_freesurf/diffusion_recons//AES101.Ex/image01.dcm
> /Volumes/DANIEL/dti_freesurf/trac/Ex.AES101.long.base_AES101/dmri/dcminfo.dat

mv -f 
/Volumes/DANIEL/dti_freesurf/trac/Ex.AES101.long.base_AES101/dmri/bvecs.tmp
/Volumes/DANIEL/dti_freesurf/trac/Ex.AES101.long.base_AES101/dmri/dwi_orig.bvecs

mv -f 
/Volumes/DANIEL/dti_freesurf/trac/Ex.AES101.long.base_AES101/dmri/bvals.tmp
/Volumes/DANIEL/dti_freesurf/trac/Ex.AES101.long.base_AES101/dmri/dwi_orig.bvals

orientLAS 
/Volumes/DANIEL/dti_freesurf/trac/Ex.AES101.long.base_AES101/dmri/dwi_orig.nii.gz
/Volumes/DANIEL/dti_freesurf/trac/Ex.AES101.long.base_AES101/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


Abort

ERROR: input file must be in NIfTI format


The error does not seem to be due to dwi_orig.nii.gz being missing as
I see it in the folderr after it has been written there in a previous
command.






What could be leading to these issues?

*Daniel Callow*
*PhD Student, Neuroscience and Cognitive Science*
Exercise for Brain Health Lab
University of Maryland, College Park
*ddcc2...@gmail.com *
443-254-6298


On Thu, Apr 18, 2019 at 3:18 PM Daniel Callow  wrote:

> Hello,
>
> trac-all -prep -c /Volumes/DANIEL/dmrirc.long.example.single.sh with the
> attached configuration file.
>
>
> I get the following error message
>
>
>
> INFO: no Siemens slice order reversal detected (good!).
>
> TR=6300.00, TE=106.00, TI=-1.00, flip angle=90.00
>
> i_ras = (-1, -0, 0)
>
> j_ras = (-0, -1, 0)
>
> k_ras = (-0, -0, 1)
>
> writing to
> /Volumes/DANIEL/dti_freesurf/trac/Rest.AES101.long.base_AES101/dmri/dwi_orig.nii.gz...
>
> Saving bvals and bvecs
>
> mv -f
> /Volumes/DANIEL/dti_freesurf/trac/Rest.AES101.long.base_AES101/dmri/dwi_orig.voxel_space.bvecs
> /Volumes/DANIEL/dti_freesurf/trac/Rest.AES101.long.base_AES101/dmri/dwi_orig.bvecs
>
> mri_probedicom --i
> /Volumes/DANIEL/dti_freesurf/diffusion_recons//AES101.Rest/image01.dcm
> >
> /Volumes/DANIEL/dti_freesurf/trac/Rest.AES101.long.base_AES101/dmri/dcminfo.dat
>
> mv -f
> /Volumes/DANIEL/dti_freesurf/trac/Rest.AES101.long.base_AES101/dmri/bvecs.tmp
> /Volumes/DANIEL/dti_freesurf/trac/Rest.AES101.long.base_AES101/dmri/dwi_orig.bvecs
>
> mv -f
> /Volumes/DANIEL/dti_freesurf/trac/Rest.AES101.long.base_AES101/dmri/bvals.tmp
> /Volumes/DANIEL/dti_freesurf/trac/Rest.AES101.long.base_AES101/dmri/dwi_orig.bvals
>
> orientLAS
> /Volumes/DANIEL/dti_freesurf/trac/Rest.AES101.long.base_AES101/dmri/dwi_orig.nii.gz
> /Volumes/DANIEL/dti_freesurf/trac/Rest.AES101.long.base_AES101/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
>
>
> Abort
>
> ERROR: input file must be in NIfTI format
>
> Darwin 255a-280.umd.edu 18.2.0 Darwin Kernel Version 18.2.0: Thu Dec 20
> 20:46:53 PST 2018; root:xnu-4903.241.1~1/RELEASE_X86_64 x86_64
>
>
> trac-preproc exited with ERRORS at Thu Apr 18 15:16:47 EDT 2019
>
>
>
> and after that I get
>
>
> --
>
> SUBJECT base_AES101
>
> DATE Thu Apr 18 15:11:44 EDT 2019
>
> USER amos
>
> HOST 255a-280.umd.edu
>
> PROCESSOR x86_64
>
> OS Darwin
>
> Darwin 255a-280.umd.edu 18.2.0 Darwin Kernel Version 18.2.0: Thu Dec 20
> 20:46:53 PST 2018; root:xnu-4903.241.1~1/RELEASE_X86_64 x86_64
>
> $Id: FreeSurferEnv.csh,v 1.89 2016/06/09 14:54:31 zkaufman Exp $
>
> /Applications/freesurfer//bin/trac-preproc
>
> PWD /Volumes/DANIEL/dti_freesurf
>
> CMD cp
> /Volumes/DANIEL/dti_freesurf/trac/Ex.AES101.long.base_AES101/dmri/xfms/mni2anatorig.mat
> /Volumes/DANIEL/dti_freesurf/trac/Ex.AES101.long.base_AES101/dmri/xfms/anatorig2mni.mat
>

[Freesurfer] MRI RA position available at Ohio State Buckeye Brain Aging Lab

2019-04-18 Thread Hayes, Scott M. 
External Email - Use Caution

Research Assistant Position

The Buckeye Brain Aging Lab (B-BAL)

Department of Psychology

Ohio State University

Applications are being sought for a full-time research assistant position in 
the Buckeye Brain Aging Lab (B-BAL; https://u.osu.edu/bbal/) directed by Dr. 
Scott Hayes. The B-BAL studies the relationships among aging, physical 
activity, cognition and the brain [using Magnetic Resonance Imaging (MRI) 
metrics]. We also examine neural correlates of memory in healthy and clinical 
populations. The Research Assistant 1 assists in the general coordination and 
conduct of research in the B-BAL, including administration of 
neuropsychological tests and/or questionnaires to young and older adults; 
recruits, screens, and schedules human subjects, including coordination of 
subject appointments (cognitive, MRI, and physical fitness assessments), 
subject payments, and submission of IRB amendments; assists with participant 
recruitment efforts between the laboratory and community partners; assists with 
research lab purchases and maintains lab supplies; assists with cognitive, MRI, 
and physical fitness data collection, including obtaining informed consent, 
cognitive testing (computer and paper and pencil based testing), MRI data 
acquisition, and record keeping; assists with cognitive and MRI data processing 
and analyses, supervises undergraduate research assistants.


Desired qualifications include: Bachelor's degree in psychology, neuroscience, 
computer science, engineering, or physics; programming experience in unix, 
python, matlab, as well as experience in neuroimaging data analyses; knowledge 
of software packages, such as FreeSurfer, FSL, AFNI, SPM, CONN, R. The position 
is available for one year with the possibility of extension for additional 
years based on satisfactory performance and availability of funds.


If you are interested in being considered for the position, please apply online 
at https://www.jobsatosu.com,under job listing #448534 (application portal 
opens this weekend) and submit a cover letter, writing sample (research paper 
from course, poster presented at a conference), current CV and arrange to have 
two reference letters emailed to b...@osu.edu .

If you have questions about the position or the lab, please email 
b...@osu.edu .



To build a diverse workforce, The Ohio State University encourages applications 
from all individuals. Ohio State is an Equal Opportunity/Affirmative Action 
Employer. All qualified applicants will receive consideration for employment 
without regard to age, race, color, religion, sex, sexual orientation, gender 
identity, national origin, disability status, or protected veteran status.



Best,

Scott


__

Scott M. Hayes, Ph.D.

Assistant Professor

Department of Psychology

Chronic Brain Injury, Discovery Themes

The Ohio State University

http://u.osu.edu/bbal/

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] issue running trac-all longitudinal

2019-04-18 Thread Daniel Callow 
External Email - Use Caution

Hello,

trac-all -prep -c /Volumes/DANIEL/dmrirc.long.example.single.sh with the
attached configuration file.


I get the following error message



INFO: no Siemens slice order reversal detected (good!).

TR=6300.00, TE=106.00, TI=-1.00, flip angle=90.00

i_ras = (-1, -0, 0)

j_ras = (-0, -1, 0)

k_ras = (-0, -0, 1)

writing to
/Volumes/DANIEL/dti_freesurf/trac/Rest.AES101.long.base_AES101/dmri/dwi_orig.nii.gz...

Saving bvals and bvecs

mv -f
/Volumes/DANIEL/dti_freesurf/trac/Rest.AES101.long.base_AES101/dmri/dwi_orig.voxel_space.bvecs
/Volumes/DANIEL/dti_freesurf/trac/Rest.AES101.long.base_AES101/dmri/dwi_orig.bvecs

mri_probedicom --i
/Volumes/DANIEL/dti_freesurf/diffusion_recons//AES101.Rest/image01.dcm
>
/Volumes/DANIEL/dti_freesurf/trac/Rest.AES101.long.base_AES101/dmri/dcminfo.dat

mv -f
/Volumes/DANIEL/dti_freesurf/trac/Rest.AES101.long.base_AES101/dmri/bvecs.tmp
/Volumes/DANIEL/dti_freesurf/trac/Rest.AES101.long.base_AES101/dmri/dwi_orig.bvecs

mv -f
/Volumes/DANIEL/dti_freesurf/trac/Rest.AES101.long.base_AES101/dmri/bvals.tmp
/Volumes/DANIEL/dti_freesurf/trac/Rest.AES101.long.base_AES101/dmri/dwi_orig.bvals

orientLAS
/Volumes/DANIEL/dti_freesurf/trac/Rest.AES101.long.base_AES101/dmri/dwi_orig.nii.gz
/Volumes/DANIEL/dti_freesurf/trac/Rest.AES101.long.base_AES101/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


Abort

ERROR: input file must be in NIfTI format

Darwin 255a-280.umd.edu 18.2.0 Darwin Kernel Version 18.2.0: Thu Dec 20
20:46:53 PST 2018; root:xnu-4903.241.1~1/RELEASE_X86_64 x86_64


trac-preproc exited with ERRORS at Thu Apr 18 15:16:47 EDT 2019



and after that I get


--

SUBJECT base_AES101

DATE Thu Apr 18 15:11:44 EDT 2019

USER amos

HOST 255a-280.umd.edu

PROCESSOR x86_64

OS Darwin

Darwin 255a-280.umd.edu 18.2.0 Darwin Kernel Version 18.2.0: Thu Dec 20
20:46:53 PST 2018; root:xnu-4903.241.1~1/RELEASE_X86_64 x86_64

$Id: FreeSurferEnv.csh,v 1.89 2016/06/09 14:54:31 zkaufman Exp $

/Applications/freesurfer//bin/trac-preproc

PWD /Volumes/DANIEL/dti_freesurf

CMD cp
/Volumes/DANIEL/dti_freesurf/trac/Ex.AES101.long.base_AES101/dmri/xfms/mni2anatorig.mat
/Volumes/DANIEL/dti_freesurf/trac/Ex.AES101.long.base_AES101/dmri/xfms/anatorig2mni.mat
/Volumes/DANIEL/dti_freesurf/trac/base_AES101/dmri/xfms



Any idea what might be causing the issue?


Best,



*Daniel Callow*
*PhD Student, Neuroscience and Cognitive Science*
Exercise for Brain Health Lab
University of Maryland, College Park
*ddcc2...@gmail.com *
443-254-6298
#
# dmrirc.long.example
#
# This example is applicable to longitudinal studies, where DWI data from
# multiple time points are available for each subject. For a simple example
# with a single DWI data set per subject, see dmrirc.example instead.
#
# This file contains commands that will be run by trac-all before an analysis.
# It is used to set all parameters needed for the analysis.
#
# Remove a parameter from your dmrirc file if you want use the default value.
# Parameters that don't have default values must be specified.
#
# Any other commands that you might want to run before an analysis can be added
# to this file.
#
# Original Author: Anastasia Yendiki
# CVS Revision Info:
#$Author: zkaufman $
#$Date: 2016/12/20 17:04:05 $
#$Revision: 1.3.2.1 $
#
# Copyright © 2011 The General Hospital Corporation (Boston, MA) "MGH"
#
# Terms and conditions for use, reproduction, distribution and contribution
# are found in the 'FreeSurfer Software License Agreement' contained
# in the file 'LICENSE' found in the FreeSurfer distribution, and here:
#
# https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferSoftwareLicense
#
# Reporting: freesurfer@nmr.mgh.harvard.edu
#
#

# FreeSurfer SUBJECTS_DIR
# T1 images and FreeSurfer segmentations are expected to be found here
# 
setenv SUBJECTS_DIR /Volumes/DANIEL/freesurfer/

# Output directory where trac-all results will be saved
# Default: Same as SUBJECTS_DIR
#
set dtroot = /Volumes/DANIEL/dti_freesurf/trac

# Subject IDs (one per time point per subject)
#
set subjlist = (Ex.AES101 Rest.AES101)

# Longitudinal base template subject IDs (one for each time point above)
#
set baselist = (base_AES101 base_AES101)

# In case you want to analyze only Huey and Louie
# Default: Run analysis on all time points and subjects
#
set runlist = ()

# Input diffusion DICOMs (file names relative to dcmroot)
# If original DICOMs don't exist, these can be in other image format
# but then the gradient table and b-value table must be specified (see below)
#
set dcmroot = /Volumes/DANIEL/dti_freesurf/diffusion_recons/
set

Re: [Freesurfer] fixing errors with pial boundary

2019-04-18 Thread Greve, Douglas N.,Ph.D. 
This often happens because the white surface is in accurate and fixing 
the white surface will fix the pial. Is the white surf ok? Sending pics 
would be helpful

On 4/18/19 1:28 PM, Morgan Botdorf wrote:
>
> External Email - Use Caution
>
> Dear Freesurfer Experts,
>
> I asked about this a few months ago, but didn't receive a reply so 
> thought I would ask again! We have come across several subjects where 
> the pial boundary line does not extend far enough outward and misses 
> some gray matter. We know that control points can be used to fix a 
> similar issue with white matter boundaries. Are there any tools that 
> can be used to fix this type of gray matter error?
>
> Thank you,
> Morgan Botdorf
>
> -- 
>
> Morgan Botdorf, M.S.
>
> Graduate Student
>
> Neurocognitive Development Lab
>
> University of Maryland, College Park
>
> mbotd...@terpmail.umd.edu 
>
> Office: 301.405.5922 
>
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] fixing errors with pial boundary

2019-04-18 Thread Morgan Botdorf 
External Email - Use Caution

Dear Freesurfer Experts,

I asked about this a few months ago, but didn't receive a reply so thought
I would ask again! We have come across several subjects where the pial
boundary line does not extend far enough outward and misses some gray
matter. We know that control points can be used to fix a similar issue with
white matter boundaries. Are there any tools that can be used to fix this
type of gray matter error?

Thank you,
Morgan Botdorf

-- 

Morgan Botdorf, M.S.

Graduate Student

Neurocognitive Development Lab

University of Maryland, College Park
mbotd...@terpmail.umd.edu

Office: 301.405.5922
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] convert aseg to functional space

2019-04-18 Thread Sam W. 
External Email - Use Caution

Thanks again Doug, that makes sense. I was aware that the matrix could be
inverted but I thought we would need --inv for that. Does mri_label2vol
also convert label-to-temp when --label is used, or is this specific to
seg-to-temp conversion?
I'm asking because I also created labels with mri_annotation2label and
tried to convert them to functional space with this command:
mri_label2vol --label labels/lh.precuneus.label --reg reg.dat --subject s01
--o label-in-func.nii --temp example_func.nii --fill-ribbon --hemi lh#
reg.dat comes from bbregister -mov example_func.nii
but this did not work. The label-in-func.nii kept the voxel size and
orientation of the orig.mgz.
Do you have any idea what I'm doing wrong?
Best regards,
Sam

On Thu, Apr 18, 2019 at 6:13 PM Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> wrote:

> The registration actually goes from anat to func. mri_label2vol knows
> this. In any case, it is just a matrix that can easily be inverted.
>
> On 4/18/19 11:58 AM, Sam W. wrote:
> >
> > External Email - Use Caution
> >
> > Hi Doug,
> > Thanks! After registering with bbregister -mov example_func.nii (to
> > get reg.dat), I tried
> > mri_label2vol --seg s01/mri/aseg.mgz --reg reg.dat --subject s01 --o
> > aseg-in-func.nii --temp example_func.nii
> > the result looks good, but I'm wondering why it worked. The reg.dat
> > specifies the conversion from func to orig doesn't it? And the
> > mri_label2vol command above does the registration from seg to
> > example_func, which is the opposite direction to what reg.dat encodes.
> > Could you clarify that to me please?
> > Best regards,
> > Sam
> >
> >
> > On Wed, Apr 17, 2019 at 11:27 PM Greve, Douglas N.,Ph.D.
> > mailto:dgr...@mgh.harvard.edu>> wrote:
> >
> > If you want to transfer a segmentation, then it is better to use
> > mri_label2vol with the --seg option. Run it with --help to get
> > examples.
> > Probably even better is to transfer your functional to anatomical
> > space
> > (mri_vol2vol) so that it is in registration with the anatomical;
> > transferring it to anat space handles partial voluming better.
> >
> > On 4/16/19 8:21 PM, Sam W. wrote:
> > >
> > > External Email - Use Caution
> > >
> > > Hi,
> > >
> > > I just finished reconall and now I'd like to convert the
> > aseg.mgz to
> > > native functional space.
> > > My first thought was to simply convert the aseg.mgz to native
> > > functional space with mri_vol2vol:
> > > mri_vol2vol --mov sub001/mri/aseg.mgz --targ example_func.nii.gz
> > --o
> > > aseg-in-rawavg.nii --regheader
> > > Is this a valid procedure to convert the aseg to functional space?
> > > I think the recommended way is to register the example_func to
> > > anatomical first:
> > > bbregister --mov example_func.nii.gz --s sub001 --reg reg.dat
> > > and then use mri_vol2vol with the --inv flag
> > > mri_vol2vol --mov sub001/mri/aseg.mgz --targ example_func.nii.gz
> > --o
> > > aseg-in-rawavg.nii --regheader --inv
> > > But I'm not sure... Could someone confirm which of the above  (or
> > > maybe none of them) is correct?
> > >
> > > Best regards,
> > > Sam
> > >
> > >
> > > ___
> > > Freesurfer mailing list
> > > Freesurfer@nmr.mgh.harvard.edu
> > 
> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu  Freesurfer@nmr.mgh.harvard.edu>
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] convert aseg to functional space

2019-04-18 Thread Greve, Douglas N.,Ph.D. 
The registration actually goes from anat to func. mri_label2vol knows 
this. In any case, it is just a matrix that can easily be inverted.

On 4/18/19 11:58 AM, Sam W. wrote:
>
> External Email - Use Caution
>
> Hi Doug,
> Thanks! After registering with bbregister -mov example_func.nii (to 
> get reg.dat), I tried
> mri_label2vol --seg s01/mri/aseg.mgz --reg reg.dat --subject s01 --o 
> aseg-in-func.nii --temp example_func.nii
> the result looks good, but I'm wondering why it worked. The reg.dat 
> specifies the conversion from func to orig doesn't it? And the 
> mri_label2vol command above does the registration from seg to 
> example_func, which is the opposite direction to what reg.dat encodes. 
> Could you clarify that to me please?
> Best regards,
> Sam
>
>
> On Wed, Apr 17, 2019 at 11:27 PM Greve, Douglas N.,Ph.D. 
> mailto:dgr...@mgh.harvard.edu>> wrote:
>
> If you want to transfer a segmentation, then it is better to use
> mri_label2vol with the --seg option. Run it with --help to get
> examples.
> Probably even better is to transfer your functional to anatomical
> space
> (mri_vol2vol) so that it is in registration with the anatomical;
> transferring it to anat space handles partial voluming better.
>
> On 4/16/19 8:21 PM, Sam W. wrote:
> >
> > External Email - Use Caution
> >
> > Hi,
> >
> > I just finished reconall and now I'd like to convert the
> aseg.mgz to
> > native functional space.
> > My first thought was to simply convert the aseg.mgz to native
> > functional space with mri_vol2vol:
> > mri_vol2vol --mov sub001/mri/aseg.mgz --targ example_func.nii.gz
> --o
> > aseg-in-rawavg.nii --regheader
> > Is this a valid procedure to convert the aseg to functional space?
> > I think the recommended way is to register the example_func to
> > anatomical first:
> > bbregister --mov example_func.nii.gz --s sub001 --reg reg.dat
> > and then use mri_vol2vol with the --inv flag
> > mri_vol2vol --mov sub001/mri/aseg.mgz --targ example_func.nii.gz
> --o
> > aseg-in-rawavg.nii --regheader --inv
> > But I'm not sure... Could someone confirm which of the above  (or
> > maybe none of them) is correct?
> >
> > Best regards,
> > Sam
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> 
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu 
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] convert aseg to functional space

2019-04-18 Thread Sam W. 
External Email - Use Caution

Hi Doug,
Thanks! After registering with bbregister -mov example_func.nii (to get
reg.dat), I tried
mri_label2vol --seg s01/mri/aseg.mgz --reg reg.dat --subject s01 --o
aseg-in-func.nii --temp example_func.nii
the result looks good, but I'm wondering why it worked. The reg.dat
specifies the conversion from func to orig doesn't it? And the
mri_label2vol command above does the registration from seg to example_func,
which is the opposite direction to what reg.dat encodes. Could you clarify
that to me please?
Best regards,
Sam


On Wed, Apr 17, 2019 at 11:27 PM Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> wrote:

> If you want to transfer a segmentation, then it is better to use
> mri_label2vol with the --seg option. Run it with --help to get examples.
> Probably even better is to transfer your functional to anatomical space
> (mri_vol2vol) so that it is in registration with the anatomical;
> transferring it to anat space handles partial voluming better.
>
> On 4/16/19 8:21 PM, Sam W. wrote:
> >
> > External Email - Use Caution
> >
> > Hi,
> >
> > I just finished reconall and now I'd like to convert the aseg.mgz to
> > native functional space.
> > My first thought was to simply convert the aseg.mgz to native
> > functional space with mri_vol2vol:
> > mri_vol2vol --mov sub001/mri/aseg.mgz --targ example_func.nii.gz --o
> > aseg-in-rawavg.nii --regheader
> > Is this a valid procedure to convert the aseg to functional space?
> > I think the recommended way is to register the example_func to
> > anatomical first:
> > bbregister --mov example_func.nii.gz --s sub001 --reg reg.dat
> > and then use mri_vol2vol with the --inv flag
> > mri_vol2vol --mov sub001/mri/aseg.mgz --targ example_func.nii.gz --o
> > aseg-in-rawavg.nii --regheader --inv
> > But I'm not sure... Could someone confirm which of the above  (or
> > maybe none of them) is correct?
> >
> > Best regards,
> > Sam
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] CORRECTING DEFECT 1 problem

2019-04-18 Thread Bruce Fischl 

Hi Abby

it's hard to tell from the image, but it looks like there is a big I/S 
bias field as well as large amounts of pathology.


If you upload the subject to our ftp site we will take a look

cheers
Bruce
On Thu, 18 Apr 
2019, Abby 
tang wrote:




External Email - Use Caution

Hello FreeSurfer Developers,

I'm attempting to recon_all my subjects which is .nii file. But I usually meet 
this error.

CORRECTING DEFECT 0 (vertices=67, convex hull=73, v0=950)
After retessellation of defect 0 (v0=950), euler #=20 (87340,255044,167724) : 
difference with theory
 (-32) = -52 


CORRECTING DEFECT 1 (vertices=46367, convex hull=8524, v0=962)
Segmentation fault (core dumped)
Linux abby-virtual-machine 4.15.0-47-generic #50-Ubuntu SMP Wed Mar 13 10:44:52 
UTC 2019 x86_64 x86_
64 x86_64 GNU/Linux

recon-all -s 2851A_T1_w4 exited with ERRORS at Thu Apr 18 20:25:16 CST 2019

To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

I check files in blow command and attached picture. 


freeview -v 2851A_T1_w4/mri/norm.mgz -f 2851A_T1_w4/surf/lh.orig.nofix 
2851A_T1_w4/surf/lh.inflated.
nofix

almost all of subjects go wrong. I need your help. 


please give some advises with program statements in detail.

I really appreciate your help

1) FreeSurfer version: freesurfer-linux-centos7_x86_64-dev.tar.gz
2) Platform: ubuntu 18
3) recon-all.log:see attached

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] mri_glmfit-sim error correcting for MC for LGI analysis

2019-04-18 Thread amirhossein manzouri 
External Email - Use Caution

Hi Freesurfer,
I am also experiencing the same problem and everything regarding FREESURFER
path looks ok just getting error that says:
Reading source surface
/storage/affective/ume2/confined/Amir/FS/fsaverage/surf/rh.white
MRISread(): could not open file
No such file or directory
mri_surfcluster: could not read surface
/storage/affective/ume2/confined/Amir/FS/fsaverage/surf/rh.white
No such file or directory
I wonder if you found the reason and solution?

Best regards,
Amirhossein Manzouri





On Thu, Dec 6, 2018 at 6:57 PM Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> wrote:

>
>
> On 11/27/2018 06:46 AM, C.P.E. Rollins wrote:
> > External Email - Use Caution
> > Hi Douglas,
> >
> > Thanks a lot for your answers.
> >
> > 1) For the permutations, would you recommend using this for
> > controlling for MC in cortical thickness analyses too?
> Yes
> > Why is it recommended to use permutation simulation as opposed to Z
> > Monte Carlo simulation for an LGI analysis?
> Because the spatial correlations are very high (which makes MCZ less
> accurate)
> >
> > 2) I've attached here the output from ls -Rl
> > $FREESURFER_HOME/subjects/fsaverage.
> It looks like there is a difference in where you think FREESURFER_HOME
> is. Below, you say it is in /home/cper2/BeneMin/Freesurfer, but the
> attached file says it is in /applications/freesurfer/freesurfer_6.0.0.
> Which one is it?
>
>
> >
> > Thanks again,
> > Colleen
> >
> > On 2018-11-23 16:26, C.P.E. Rollins wrote:
> >> Dear Freesurfer Developers,
> >> I have a 2-part question:
> >> 1) I was advised to use permutation to control for multiple
> >> comparisons in an LGI analysis, would you mind elaborating how to do
> >> this in command line (in terms of command and parameters)?
> >> 2) In running "mri_glmfit-sim --glmdir lh.5.lgi_MAN_new.glmdir --cache
> >> 1.3 pos --cwp 0.05 --2spaces --debug", I receive the following error
> >> (attached). I was wondering if you might have any advice? The file
> >> /home/cper2/BeneMin/Freesurfer/fsaverage/surf/lh.white exists and I can
> >> view it in freeview.
> >>
> >> Many thanks,
> >> Colleen
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] Issue with longitudinal surfaces

2019-04-18 Thread Martin Reuter 
Hi Maxime, 

also how do the surfaces look on their respective time point images
from long? Do they look accurate there? Could be that there are
differences across the time points that cause the surfaces to differ
this much. Was the same hardware (scanner, coil) and same protocol used
for both time points?

Best, Martin


On Tue, 2019-04-09 at 11:04 +, maxime GUILLAUME wrote:
> External Email - Use Caution
> Dear freesurfer experts, 
> 
> I re-send this question because i didn't received (or missed) the
> answer from the first time i sent it.
>  
> I am performing a longitudinal study (2 time points, 1 year apart) in
> patients with Multiple Sclerosis using freesurfer 6.0.
>  
> After following the tutorial for the CROSS, the BASE (where I only
> performed few manual edits of the surfaces) and the LONG steps, I am
> facing a problem with the results of the longitudinal pipeline:
>  
> If I overlay the final surfaces of the different time points (the
> white and pial surfaces of the LONG step) on the BASE template using
> the command given in the fs tutorial, there are important differences
> between the two time points (see figure attached). This happened only
> on a subset of my subjects.
> One of our collaborators in this study suggested that this might be
> because the patient was positioned differently in the two time
> points, in particular with respect to the z axis (and indeed the
> major differences between the two surfaces are in the topmost area of
> the brain).
> Does anybody have experienced the same problem? And how can I correct
> for it?
>  
> Thank you in advance for your help.
> 
> (*in the captures surfaces of the first visit are in red and blue and
> in lighter tones for the second visit) 
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] Thalamic segmentation

2019-04-18 Thread Iglesias Gonzalez, Eugenio 
External Email - Use Caution

Dear Zheng
One of the other developers can help you with Freeview.
But, as a workaround, you can always use an earlier version of Freeview, and 
load the lookup table of the Dev version.
Cheers
Eugenio

Sent from mobile, please excuse brevity and typos

--

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





From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of 郑凤莲 

Sent: Thursday, April 18, 2019 5:59:15 AM
To: Freesurfer support list
Subject: [Freesurfer] Thalamic segmentation


External Email - Use Caution

Hi Expert,

In the latest version of FS, I have segmented the thalamic successfully. But I 
can't use Freeview to show the segmentation map. There is an error :"freeview: 
/usr/lib/libpng15.so.15:version 'PNG15_0' not found (required by 
/opt/freesurfer/bin/../lib/qt/lib/libQt5Gui.so.5)". May be I didn't install the 
latest version of Freeview. However, I can't find this version on 
Freesurferwiki.  Could you share me the install steps and the latest version? 
Thanks very much for your help.

Sincerely,
Zheng





___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] Thalamic segmentation

2019-04-18 Thread 郑凤莲 
External Email - Use Caution

Hi Expert,


In the latest version of FS, I have segmented the thalamic successfully. But I 
can't use Freeview to show the segmentation map. There is an error :"freeview: 
/usr/lib/libpng15.so.15:version 'PNG15_0' not found (required by 
/opt/freesurfer/bin/../lib/qt/lib/libQt5Gui.so.5)". May be I didn't install the 
latest version of Freeview. However, I can't find this version on 
Freesurferwiki.  Could you share me the install steps and the latest version? 
Thanks very much for your help.


Sincerely,
Zheng

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer