[Freesurfer] Fwd: Error in Analyze: Couldn't open ... fwhm10.fsaverage.mgz

2019-07-25 Thread Renew Andrade 
External Email - Use Caution

Dear FreeSurfer experts:
I am processing in qdec 3 subjects with the GUI and I have this terminal 
output. 


Error in Analyze: Couldn't open 
/Applications/freesurfer/subjects/IXI_22_Guys_T1/surf/lh.thickness.fwhm10.fsaverage.mgz
 or .mgh file.
lh-Avg-Intercept-thickness ---
Does the average thickness differ from zero?
Nuisance factors: Right-Hippocampus
 1.000   0.000   0.000;



I have executed recon-all -s IXI_20_Guys_T1 -s IXI_22_Guys_T1 -s IXI_25_Guys_T1 
-qcache -target avgsubj20_22_25 -no-isrunning without any errors. Also 
make_average_subject make_average_subject --out avgsubj20_22_25 --subjects 
IXI_20_Guys_T1 IXI_22_Guys_T1 IXI_25_Guys_T1 without any errors. 

The problem is that I only have files like “...fwhm10.fsaverage.mgz" in one 
subject in this case IXI_25_Guys_T1 not in IXI_22_Guys_T1 or IXI_20_Guys_T1. I 
do not know if that is a mistake of processing or myself it seems by the output 
in qdec that I need files like “...fwhm10.fsaverage.mgz” in every subject 
subdirectory “surf”. 


Thanks for your help in advance!___
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Re: [Freesurfer] label to asc

2019-07-25 Thread Sam W. 
External Email - Use Caution

Thanks Bruce, that's helpful! I take it that it's not possible to create a
surface file simply using the information in the label file then?
The reason I'm confused is that "mris_convert lh.white lh.white.asc" will
convert a surface file to asc. The contents of lh.white.asc look similar to
what a label file contains, so I thought you could easily convert a label
into a surface and vice versa.
Also, if the label does not contain information about topology, how are we
able to convert a label to a volume with mri_label2vol?
Thanks in advance!
Sam

On Wed, Jul 24, 2019 at 10:42 PM Bruce Fischl 
wrote:

> Hi Sam
>
> they are not the same. A label is just a list of vertices in the surface
> (with some possibly voxel coordinates and also with a single
> value/vertex).
> It doesn't have to be ever vertex in the surface, and also contains no
> information about topology (e.g. which vertices are connected by an edge)
>
> cheers
> Bruce
>
>
> On Wed, 24 Jul 2019, Sam W. wrote:
>
> >
> > External Email - Use Caution
> >
> > Thanks Bruce. Can I ask you a very basic question? What exactly is the
> > difference between a surface and a label file? I thought the difference
> was
> > that the label file is just a normal text file containing the vertices
> that
> > are used to construct a surface. If so, is there a tool that allows me to
> > create a surface from a label file? mri_label2surf would be my first
> guess,
> > but that doesn't seem to exist.
> > Best regards,
> > Sam
> >
> >
> > On Wed, Jul 24, 2019 at 4:18 PM Bruce Fischl  >
> > wrote:
> >   Hi Sam
> >
> >   the labels are already ascii
> >
> >   cheers
> >   Bruce
> >   On Tue, 23 Jul 2019, Sam W. wrote:
> >
> >   >
> >   > External Email - Use Caution
> >   >
> >   > Hi,
> >   >
> >   > Is it possible to convert a label file like rh.cuneus.label
> >   into asc? I
> >   > tried
> >   > mris_convert --label rh.cuneus.label ctx-rh-cuneus rh.white
> >   rh.cuneus.asc
> >   >
> >   > but got an error:
> >   >
> >   > ERROR: unknown file annot file type specified for output:
> >   rh.cuneus.asc
> >   >
> >   > Thanks!
> >   > 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
___
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Re: [Freesurfer] Error running recon-all

2019-07-25 Thread Bruce Fischl 

Hi Vin

are you sure you have space on that disk? Can you run:

mri_info /home/Downloads/reorient/test.nii
mri_info  /media/results/mri/orig/001.mgz 
ls -l /media/results/mri/orig/001.mgz /media/results/mri/rawavg.mgz


and send us the results?

cheers
Bruce

On Thu, 25 Jul 2019, 
vin rasa wrote:




External Email - Use Caution

Please also find recon-all.log file.

Thanks!

On Thu, Jul 25, 2019 at 6:50 AM vin rasa  wrote:
  Dear Freesurfer experts,
Greetings!


In the first minute of recon-all, we are getting following error:

mghRead(/media/results/mri/rawavg.mgz): could not read 262144 bytes at
slice 0



T1 data type is int16, data type 4 (looked using fslinfo) 

Looking forward to have your input!

Thank you so much,
Kind regards


___
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[Freesurfer] convert stl to .surf.gii

2019-07-25 Thread Hanad Sharmarke 
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Hello,

I am attempting to convert a .stl file to a .surf.gii. I tried using
mris_convert but that did not work.

This is the command.

mris_convert cb4mesh-dec250k_fixnMf6_Euler-448_scale001.stl
cb4mesh-dec250k_fixnMf6_Euler-448_scale001.surf.gii

This is the error I get.

MRISreadSTLfile: error reading file
cb4mesh-dec250k_fixnMf6_Euler-448_scale001.stl
No such file or directory
mris_convert: could not read surface file
cb4mesh-dec250k_fixnMf6_Euler-448_scale001.stl
No such file or directory

I’m definitely in the right directory so I’m not sure why this error is
occurring.

Thank you,
Hanad
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Re: [Freesurfer] Error running recon-all

2019-07-25 Thread vin rasa 
External Email - Use Caution

Please also find recon-all.log file.

Thanks!

On Thu, Jul 25, 2019 at 6:50 AM vin rasa  wrote:

> Dear Freesurfer experts,
> Greetings!
>
>
> In the first minute of recon-all, we are getting following error:
>
> mghRead(/media/results/mri/rawavg.mgz): could not read 262144 bytes at
> slice 0
>
>
> T1 data type is int16, data type 4 (looked using fslinfo)
>
> Looking forward to have your input!
>
> Thank you so much,
> Kind regards
>
>
Mi 24. Jul 17:45:53 CEST 2019
/media/results/test
/usr/local/freesurfer/bin/recon-all
-i /home/Downloads/reorient/test.nii -all -sd /media/results/Oasis -s test
subjid test
setenv SUBJECTS_DIR /media/results/Oasis
FREESURFER_HOME /usr/local/freesurfer
Actual FREESURFER_HOME /usr/local/freesurfer
build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
Linux tuffan 4.15.0-46-generic #49~16.04.1-Ubuntu SMP Tue Feb 12 17:45:24 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux
cputime  unlimited
filesize unlimited
datasize unlimited
stacksize8192 kbytes
coredumpsize 0 kbytes
memoryuseunlimited
vmemoryuse   unlimited
descriptors  1024 
memorylocked 64 kbytes
maxproc  257062 
maxlocks unlimited
maxsignal257062 
maxmessage   819200 
maxnice  0 
maxrtprio0 
maxrttimeunlimited

  totalusedfree  shared  buff/cache   available
Mem:   6587885662267900  613692 1379984 2997264 1411128
Swap:  62606332 727946855326864


program versions used
$Id: recon-all,v 1.580.2.16 2017/01/18 14:11:24 zkaufman Exp $
$Id: mri_motion_correct.fsl,v 1.15 2016/02/16 17:17:20 zkaufman Exp $
mri_convert.bin -all-info 
ProgramName: mri_convert.bin  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2019/07/24-15:45:53-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $  User: vin  Machine: tuffan  Platform: Linux  PlatformVersion: 4.15.0-46-generic  CompilerName: GCC  CompilerVersion: 40400 
FLIRT version 5.5
$Id: talairach_avi,v 1.13 2015/12/23 04:25:17 greve Exp $
mri_convert.bin --version 
stable6
ProgramName: tkregister2_cmdl  ProgramArguments: --all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2019/07/24-15:45:53-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: tkregister2.c,v 1.132.2.1 2016/08/02 21:17:29 greve Exp $  User: vin  Machine: tuffan  Platform: Linux  PlatformVersion: 4.15.0-46-generic  CompilerName: GCC  CompilerVersion: 40400 
Program nu_correct, built from:
Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34
ProgramName: mri_make_uchar  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2019/07/24-15:45:53-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $  User: vin  Machine: tuffan  Platform: Linux  PlatformVersion: 4.15.0-46-generic  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_normalize  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2019/07/24-15:45:53-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_normalize.c,v 1.88.2.3 2016/12/27 16:47:13 zkaufman Exp $  User: vin  Machine: tuffan  Platform: Linux  PlatformVersion: 4.15.0-46-generic  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_watershed  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2019/07/24-15:45:53-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_watershed.cpp,v 1.103 2016/06/17 18:00:49 zkaufman Exp $  User: vin  Machine: tuffan  Platform: Linux  PlatformVersion: 4.15.0-46-generic  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_gcut  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2019/07/24-15:45:53-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $  User: vin  Machine: tuffan  Platform: Linux  PlatformVersion: 4.15.0-46-generic  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_segment  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2019/07/24-15:45:53-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_segment.c,v 1.43.2.1 2016/10/27 22:24:52 zkaufman Exp $  User: vin  Machine: tuffan  Platform: Linux  PlatformVersion: 4.15.0-46-generic  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_label2label.bin  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2019/07/24-15:45:53-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_label2label.c,v 1.48.2.2 2016/12/12 14:15:26 zkaufman Exp $  User: vin  Machine: tuffan  Platform: Linux  PlatformVersion: 4.15.0-46-generic  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_em_register  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2019/07/24-15:45:53-GMT  BuildTimeStamp: Jan 18

[Freesurfer] DPABISurf V1.1 Is Released

2019-07-25 Thread YAN Chao-Gan 
External Email - Use Caution

Dear Colleagues,

We are pleased to announce the release of DPABISurf V1.1!

DPABISurf is a surface-based resting-state fMRI data analysis toolbox
evolved from DPABI/DPARSF, as easy-to-use as DPABI/DPARSF. DPABISurf is
based on fMRIPprep 1.4.1 (Esteban et al., 2018)(RRID:SCR_016216), and based
on FreeSurfer 6.0.1 (Dale et al., 1999)(RRID:SCR_001847), ANTs 2.2.0
(Avants et al., 2008)(RRID:SCR_004757), FSL 5.0.9 (Jenkinson et al.,
2002)(RRID:SCR_002823), AFNI 20160207 (Cox, 1996)(RRID:SCR_005927), SPM12
(Ashburner, 2012)(RRID:SCR_007037), PALM alpha112 (Winkler et al., 2016),
GNU Parallel (Tange, 2011), MATLAB (The MathWorks Inc., Natick, MA, US)
(RRID:SCR_001622), Docker (https://docker.com) (RRID:SCR_016445), and DPABI
V4.1 (Yan et al., 2016)(RRID:SCR_010501). DPABISurf provides user-friendly
graphical user interface (GUI) for pipeline surface-based preprocessing,
statistical analyses and results viewing, while requires no
programming/scripting skills from the users.



The DPABISurf pipeline first converts the user specified data into BIDS
format (Gorgolewski et al., 2016), and then calls fMRIPprep 1.4.1 docker to
preprocess the structural and functional MRI data, which integrates
FreeSurfer, ANTs, FSL and AFNI. With fMRIPprep, the data is processed into
FreeSurfer fsaverage5 surface space and MNI volume space. DPABISurf further
performs nuisance covariates regression (including ICA-AROMA) on the
surface-based data (volume-based data is processed as well), and then
calculate the commonly used R-fMRI metrics: amplitude of low frequency
fluctuation (ALFF) (Zang et al., 2007), fractional ALFF (Zou et al., 2008),
regional homogeneity (Zang et al., 2004), degree centrality (Zuo and Xing,
2014), and seed-based functional connectivity. DPABISurf also performs
surface-based smoothing by calling FreeSurfer’s mri_surf2surf command.
These processed metrics then enters surfaced-based statistical analyses
within DPABISurf, which could perform surfaced-based permutation test with
TFCE by integrating PALM. Finally, the corrected results could be viewed by
the convenient surface viewer DPABISurf_VIEW, which is derived from
spm_mesh_render.m.



DPABISurf is designed to make surface-based data analysis require minimum
manual operations and almost no programming/scripting experience. We
anticipate this open-source toolbox will assist novices and expert users
alike and continue to support advancing R-fMRI methodology and its
application to clinical translational studies.

DPABISurf is open-source and distributed under GNU/GPL, available with
DPABI at http://www.rfmri.org/dpabi. It supports Windows 10 Pro, MacOS and
Linux operating systems. You can run it with or without MATLAB.

1. With MATLAB.
1.1. Please go to http://www.rfmri.org/dpabi to download DPABI.
1.2. Add with subfolders for DPABI in MATLAB's path setting.
1.3. Input 'dpabi' and then follow the instructions of the "Install" Button
on DPABISurf.
2. Without MATLAB.
2.1. Install Docker.
2.2. Terminal: docker pull cgyan/dpabi
2.3. Terminal: docker run -d --rm -v
/My/FreeSurferLicense/Path/license.txt:/opt/freesurfer/license.txt
-v /My/Data/Path:/data -p 5925:5925 cgyan/dpabi x11vnc -forever -shared
-usepw -create -rfbport 5925
/My/FreeSurferLicense/Path/license.txt: Where you stored the
FreeSurferLicense got from
https://surfer.nmr.mgh.harvard.edu/registration.html.
/My/Data/Path: This is where you stored your data. In Docker, the path is
/data.
2.4. Open VNC Viewer, connect to localhost:5925, the password is 'dpabi'.
2.5. In the terminal within the VNC Viewer, input "bash", and then input:
/opt/DPABI/DPABI_StandAlone/run_DPABI_StandAlone.sh ${MCRPath}


Now please enjoy the StandAlone version of DPABISurf with GUI!


If you don't want to run with GUI, you can also call the compiled version
of DPABISurf_run. E.g.,
docker run -it --rm -v
/My/FreeSurferLicense/Path/license.txt:/opt/freesurfer/license.txt
-v /My/Data/Path:/data cgyan/dpabi /bin/bash
/opt/DPABI/DPABI_StandAlone/run_DPABISurf_run_StandAlone.sh ${MCRPath}
/data/DPABISurf_Cfg.mat

New features of DPABISurf_V1.1_190725  (download at http://rfmri.org/dpabi):
1. New module for Surface-Based Temporal Dynamic Analysis (DPABI_TDA_Surf)
was added. Dynamic regional indices (ALFF, fALFF, ReHo, Degree Centrality
and Global Signal Correlation) and dynamic functional connectivity could be
automatically calculated by one click through DPABI_TDA_Surf (with
DPABISurf preprocessed data). The statistics maps (CV, Mean and SD) of the
dynamic regional indices would also be generated by DPABI_TDA_Surf. A
neuroimaging index which measures the concordance of the dynamic regional
indices is incorporated into DPABI_TDA_Surf. Please see more details at:
Yan, C.-G., Yang, Z., Colcombe, S.J., Zuo, X.-N., Milham, M.P., 2017.
Concordance among indices of intrinsic brain function: insights from
inter-individual variation and temporal