[Freesurfer] Freeview segmentation fault on Mac OS X High Sierra

[Mikael Novén]

External Email - Use Caution

Dear experts,

I recently updated to FreeSurfer 7.1.1 but this caused Freeview to stop 
working. I can neither use the terminal command ”freeview” or open it through 
the .app in Finder. I get a ”Segmentation fault: 11”. I attach the crash report 
below. XQuartz works (I can run ”xclock” and similar programs).
Any help with getting Freeview to work is much appreciated.

Kind regards,
Mikael Novén

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

[Freesurfer] QDEC error Two Groups three covariates

[Mikael Novén]

External Email - Use Caution

Dear FreeSurfer Developers,

I’m attempting to run a cortical thickness correlation analysis regressing out 
the effect of brain size, age and gender. However, when attempting to run this 
analysis in qdec (or trying to use mri_glmfit separately) I get the following 
error:
"MatrixMultiplyD(): m2 is null
 break matrix.c:415

No such file or directory”

Full output from the mri_glmfit call is last in this mail.

The first lines of my fsgd files look like this:
"GroupDescriptorFile 1
Title RTfMRI
Class M
Class F
Variables RT eICV Age
Input 101 M 36.767 1046505.93 25
Input 102 F -58.589 955597.34 30
Input 103 M 68.883 1107660.32 22”

My contrast matrix looks like this:
"+0.0 +0.0 +1.0 +1.0 +0.0 +0.0 +0.0 +0.0”

Any help is much appreciated.

Kind regards,
Mikael

mri_glmfit --y lh.thickness.fMRIRT_revision.10.mgh --fsgd 
fMRIRT_age_gender_eICV.fsgd --C RT_covNI_cp.mat --surf fsaverage lh --cortex 
--glmdir fMRIRT_revision_test2
gdfRead(): reading fMRIRT_age_gender_eICV.fsgd
INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done.
Continuous Variable Means (all subjects)
0 RT 82.6508 76.4669
1 eICV 980394 122148
2 Age 24.5294 3.23797
Class Means of each Continuous Variable
1 M  97.4687 1037828.2188  25.
2 F  74.5684 949066.0966  24.2727
INFO: gd2mtx_method is dods
Reading source surface /Applications/freesurfer/subjects/fsaverage/surf/lh.white
Number of vertices 163842
Number of faces327680
Total area 65416.984375
AvgVtxArea   0.399269
AvgVtxDist   0.721953
StdVtxDist   0.195470

$Id: mri_glmfit.c,v 1.241.2.4 2016/12/08 22:02:40 zkaufman Exp $
cwd /Applications/freesurfer/subjects
cmdline mri_glmfit.bin --y lh.thickness.fMRIRT_revision.10.mgh --fsgd 
fMRIRT_age_gender_eICV.fsgd --C RT_covNI_cp.mat --surf fsaverage lh --cortex 
--glmdir fMRIRT_revision_test2
sysname  Darwin
hostname LUMAC1089
machine  x86_64
user root
FixVertexAreaFlag = 1
UseMaskWithSmoothing 1
OneSampleGroupMean 0
y/Applications/freesurfer/subjects/lh.thickness.fMRIRT_revision.10.mgh
logyflag 0
usedti  0
FSGD fMRIRT_age_gender_eICV.fsgd
labelmask  /Applications/freesurfer/subjects/fsaverage/label/lh.cortex.label
maskinv 0
glmdir fMRIRT_revision_test2
IllCondOK 0
ReScaleX 1
DoFFx 0
Creating output directory fMRIRT_revision_test2
Loading y from 
/Applications/freesurfer/subjects/lh.thickness.fMRIRT_revision.10.mgh
   ... done reading.
INFO: gd2mtx_method is dods
Saving design matrix to fMRIRT_revision_test2/Xg.dat
Computing normalized matrix
Normalized matrix condition is 3815.6
Matrix condition is 1e+08
Found 149955 points in label.
Pruning voxels by thr: 1.175494e-38
Found 149078 voxels in mask
Saving mask to fMRIRT_revision_test2/mask.mgh
Reshaping mriglm->mask...
search space = 74130.630564
DOF = 9
Starting fit and test
Fit completed in 0.0511667 minutes
Computing spatial AR1 on surface
Residual: ar1mn=0.995881, ar1std=0.003426, gstd=6.299149, fwhm=14.833361
Writing results
  RT_covNI_cp
maxvox sig=-4.61019  F=62.3686  at  index 156731 0 0seed=1590285961
MatrixMultiplyD(): m2 is null
 break matrix.c:415

No such file or directory


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

Re: [Freesurfer] GLM_Fit Question

[Mikael Novén]

Dear Freesurfer experts,

I also have this problem and can't seem to find the script. Would it be 
possible to get access to it?

Thank you in advance,
Mikael Novén

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


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] recon-all sudden stop during Talairach

[Mikael Novén]

Dear Freesurfer Developers,

I'm attempting to process high resolution images on a new system and following 
https://surfer.nmr.mgh.harvard.edu/fswiki/HiResRecon I at first try to run 
downsampled (1x1x1 mm) images. recon-all suddenly stops during #@# Talairach 
with no error codes except for the "exited with ERRORS" message. I'm a bit 
clueless as to what could be wrong. The images are from a Philips 7T Achieva 
system and have been normalized using ANTS N4BiasFieldCorrectionImageFilter() 
before attempting recon-all (though uncorrected gives the same resulting 
error). I thought that there was a problem with the permissions so I changed 
the default using setfacl which seems to work but no change.

OUTPUT:
INFO: extension is mgz
#
#@# Talairach tis 28 jun 2016 12:52:35 CEST
/usr/local/freesurfer/subjects/106_1/mri

 mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i 
orig.mgz --o orig_nu.mgz

Linux mikael-Aspire-VN7-591G 4.4.0-24-generic #43-Ubuntu SMP Wed Jun 8 19:27:37 
UTC 2016 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s 106_1 exited with ERRORS at tis 28 jun 2016 12:52:36 CEST"

BUILD-STAMP:
freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0

OPERATING SYSTEM:
No LSB modules are available.
Distributor ID:Ubuntu
Description:Ubuntu 16.04 LTS
Release:16.04
Codename:xenial

UNAME -A OUTPUT:
Linux mikael-Aspire-VN7-591G 4.4.0-24-generic #43-Ubuntu SMP Wed Jun 8 19:27:37 
UTC 2016 x86_64 x86_64 x86_64 GNU/Linux

Log file included.

Thank you very much for your help.

All the best,
Mikael Novén
tis 28 jun 2016 12:48:09 CEST
/usr/local/freesurfer/subjects/106_1
/usr/local/freesurfer/bin/recon-all
-i 106_T1divPD_1mm.nii.gz -s 106_1 -all
subjid 106_1
setenv SUBJECTS_DIR /usr/local/freesurfer/subjects
FREESURFER_HOME /usr/local/freesurfer
Actual FREESURFER_HOME /usr/local/freesurfer
build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
Linux mikael-Aspire-VN7-591G 4.4.0-24-generic #43-Ubuntu SMP Wed Jun 8 19:27:37 UTC 2016 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  31200 
maxlocks unlimited
maxsignal31200 
maxmessage   819200 
maxnice  0 
maxrtprio0 
maxrttimeunlimited

  totalusedfree  shared  buff/cache   available
Mem:8096588 1317792 4794552  331444 1984244 6214276
Swap:   83097566940 8302816


program versions used
$Id: recon-all,v 1.379.2.73 2013/05/12 23:15:37 nicks Exp $
$Id: mri_motion_correct.fsl,v 1.14 2011/03/02 20:16:39 nicks Exp $
mri_convert -all-info 
ProgramName: mri_convert  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2016/06/28-10:48:09-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $  User: mikael  Machine: mikael-Aspire-VN7-591G  Platform: Linux  PlatformVersion: 4.4.0-24-generic  CompilerName: GCC  CompilerVersion: 40400 
FLIRT version 5.5
$Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $
mri_convert --version 
stable5
ProgramName: tkregister2_cmdl  ProgramArguments: --all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2016/06/28-10:48:09-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $  User: mikael  Machine: mikael-Aspire-VN7-591G  Platform: Linux  PlatformVersion: 4.4.0-24-generic  CompilerName: GCC  CompilerVersion: 40400 
Program nu_correct, built from:
Package MNI N3, version 1.10, compiled by nicks@minerva (x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37
ProgramName: mri_make_uchar  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2016/06/28-10:48:09-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $  User: mikael  Machine: mikael-Aspire-VN7-591G  Platform: Linux  PlatformVersion: 4.4.0-24-generic  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_normalize  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2016/06/28-10:48:09-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mri_normalize.c,v 1.73.2.1 2012/10/17 19:11:32 nicks Exp $  User: mikael  Machine: mikael-Aspire-VN7-591G  Platform: Linux  PlatformVersion: 4.4.0-24-generic  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_watershed  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2016/06/28-10:48:09-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mri_watershed.cpp,v 1.96.2.1 2011/11/08 22:18:44 nicks Exp $  User: mikael  Machine: mikael-Aspire-VN7-591G  Platform: Linux  PlatformVersion: 4.4.0-24-generic  CompilerName: GCC  CompilerVersion: 40400 
Progra