[Freesurfer] Freesurfer 5.3.0 recon-all error

2020-10-06 Thread Michele Valotti 
External Email - Use Caution

I am using freesurfer 5.3.0 (unfortunately this is the version I have to
use) and I am encountering an error in the process. I have attached the
recon-all.log file. Any pointers to identify the error would be very
helpful,

Thank you,
Michele
Tue Oct  6 09:27:22 UTC 2020
/home/michele/spd_processing/freesurfer2016
/usr/local/freesurfer/bin/recon-all
-all -subjid ./freesurfer2016
subjid freesurfer2016
setenv SUBJECTS_DIR /home/michele/spd_processing
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 ian-System-Product-Name 5.4.0-48-generic #52~18.04.1-Ubuntu SMP Thu Sep 10 12:50:22 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux
cputime  unlimited
filesize unlimited
datasize unlimited
stacksize8192 kbytes
coredumpsize 0 kbytes
memoryuseunlimited
vmemoryuse   unlimited
descriptors  8192 
memorylocked 16384 kbytes
maxproc  63499 
maxlocks unlimited
maxsignal63499 
maxmessage   819200 
maxnice  0 
maxrtprio0 
maxrttimeunlimited

  totalusedfree  shared  buff/cache   available
Mem:   16369620 5832876 1560240  520488 8976504 9739308
Swap:   20971489216 2087932


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: 2020/10/06-09:27:22-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: michele  Machine: ian-System-Product-Name  Platform: Linux  PlatformVersion: 5.4.0-48-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: 2020/10/06-09:27:22-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: michele  Machine: ian-System-Product-Name  Platform: Linux  PlatformVersion: 5.4.0-48-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: 2020/10/06-09:27:22-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: michele  Machine: ian-System-Product-Name  Platform: Linux  PlatformVersion: 5.4.0-48-generic  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_normalize  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2020/10/06-09:27:22-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: michele  Machine: ian-System-Product-Name  Platform: Linux  PlatformVersion: 5.4.0-48-generic  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_watershed  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2020/10/06-09:27:22-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: michele  Machine: ian-System-Product-Name  Platform: Linux  PlatformVersion: 5.4.0-48-generic  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_gcut  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2020/10/06-09:27:22-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $  User: michele  Machine: ian-System-Product-Name  Platform: Linux  PlatformVersion: 5.4.0-48-generic  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_segment  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2020/10/06-09:27:22-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mri_segment.c,v 1.40 2011/03/02 00:04:24 nicks Exp $  User: michele  Machine: ian-System-Product-Name  Platform: Linux  PlatformVersion: 5.4.0-48-generic  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_label2label  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2020/10/06-09:27:23-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mri_label2label.c,v 1.40.2.2 2013/04/02 16:26:15 greve Exp $  User: michele  Machine: ian-System-Product-Name  Platform: Linux  PlatformVersion: 5.4.0-48-generic  CompilerName: GCC  CompilerVersion: 40400 


 === NUMBER OF OPENMP THREADS = 1 === 
ProgramName: mri_em_register  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2020/10/06-09:27:23-GMT  BuildTimeStam

Re: [Freesurfer] Freesurfer 5.3.0 recon-all error

2020-10-07 Thread Michele Valotti 
External Email - Use Caution

Hi, thank you for getting back to me so quickly, I can confirm that it does
not run through on any scan and I have tried to run the command as you
suggested.
This is the error I am getting:

--n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o
orig_nu.mgz
nIters 1
$Id: mri_nu_correct.mni,v 1.18.2.1 2013/01/09 21:23:42 nicks Exp $
Linux ian-System-Product-Name 5.4.0-48-generic #52~18.04.1-Ubuntu SMP Thu
Sep 10 12:50:22 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux
Wed  7 Oct 16:46:17 BST 2020
nu_correct: Command not found.
tmpdir is ./tmp.mri_nu_correct.mni.1081
/home/michele/spd_processing/freesurfer2016/mri
mri_convert orig.mgz ./tmp.mri_nu_correct.mni.1081/nu0.mnc -odt float
mri_convert orig.mgz ./tmp.mri_nu_correct.mni.1081/nu0.mnc -odt float
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from orig.mgz...
TR=7.92, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, -1.22236e-09, 3.72529e-09)
j_ras = (-3.72529e-09, 4.65661e-10, -1)
k_ras = (7.82893e-09, 1, -4.65661e-10)
changing data type from uchar to float (noscale = 0)...
writing to ./tmp.mri_nu_correct.mni.1081/nu0.mnc...


Iteration 1 Wed  7 Oct 16:46:18 BST 2020
nu_correct -clobber ./tmp.mri_nu_correct.mni.1081/nu0.mnc
./tmp.mri_nu_correct.mni.1081/nu1.mnc -tmpdir
./tmp.mri_nu_correct.mni.1081/0/ -iterations 1000 -distance 50
nu_correct: Command not found.
ERROR: nu_correct

I am assuming I am missing the MNI tools, so I have tried to download them
from http://bic-mni.github.io/ but all the downloads failed, do you have a
recommended way to download and install what I need to run my script?

Thank you again,
Michele

On Tue, 6 Oct 2020 at 15:59, Douglas N. Greve 
wrote:

>
> My guess is it is a problem with the install of the MNI tools. Does it run
> all the way through on other subjects? What happens when you run this
> command?
>
> mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i
> orig.mgz --o orig_nu.mgz
>
>
> On 10/6/2020 9:16 AM, Michele Valotti wrote:
>
> External Email - Use Caution
> I am using freesurfer 5.3.0 (unfortunately this is the version I have to
> use) and I am encountering an error in the process. I have attached the
> recon-all.log file. Any pointers to identify the error would be very
> helpful,
>
> Thank you,
> Michele
>
> ___
> Freesurfer mailing 
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>
>
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[Freesurfer] Tracula error

2020-10-30 Thread Michele Valotti 
External Email - Use Caution

Hello all,
I am trying to run Tracula for one of my subjects and after creating the
configuration file I run trac-all -prep -c /path/to/config/file
but I am getting this error:
FSLDIR: Undefined variable.

I have run the SetUpFreeSurfer.sh script and echo $FSLDIR prints my fls
directory. Adding export FSLDIR=/my/fls/path also does not fix the error,

Any suggestions?

Thank you very much,
Michele
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Re: [Freesurfer] trac-all -bedp error after successful -prep

2020-11-10 Thread Michele Valotti 
External Email - Use Caution

solved it, turns out symlinks don't like relative paths (which I was using
in the config file for tracula), changing those to absolute paths tracula
finished with no errors

On Fri, 6 Nov 2020 at 11:38, Michele Valotti 
wrote:

> Hi all,
> I am trying to run tract segmentation on a scan and after running trac-all
> -prep without errors, trac-all -bedp can't run because it can't find
> dmri/data. Checking the dir I see a data.nii.gz but it looks like it's a
> broken link, even though the dwi.nii.gz image (which data.nii.gz should
> link to in my understanding) is in the folder. I have attached the log
> which I have skimmed through without seeing any obvious problems. Any help
> is greatly appreciated,
>
> Thank you,
> Michele
>
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[Freesurfer] mincRead error in recon-all

2021-01-04 Thread Michele Valotti 
External Email - Use Caution

Dear Freesurfer Team,
I am trying to run recon-all on a test scan, but I am getting this error:

Error opening ./tmp.mri_nu_correct.mni.6973/nu1.mnc
mincRead(): error reading volume from file
./tmp.mri_nu_correct.mni.6973/nu1.mnc

(logs attached)

I just reinstalled minc tools due to a nu_correct error I was getting, not
sure if this could be a problem. I read on the mailing list that it could
be a permission error but trying the suggested solutions did not solve the
problem

runningls -l tmp.mri_nu_correct.mni.3787/nu1.mnc

returns   -rw-rw-r-- 1 michele michele 22990022 Jan  4 15:01
tmp.mri_nu_correct.mni.3787/nu1.mnc

Any help is greatly appreciated
Thank you

Michele
Mon Jan  4 15:37:26 GMT 2021
/home/michele/Desktop/test_recon-all_adni_3b_027_S_6733/adni_3b_027_S_6733
/home/michele/freesurfer/bin/recon-all
-i /home/michele/Desktop/adni_3b_027_S_6733/T1_nifti.nii.gz -s adni_3b_027_S_6733 -sd /home/michele/Desktop/test_recon-all_adni_3b_027_S_6733 -autorecon1
subjid adni_3b_027_S_6733
setenv SUBJECTS_DIR /home/michele/Desktop/test_recon-all_adni_3b_027_S_6733
FREESURFER_HOME /home/michele/freesurfer
Actual FREESURFER_HOME /home/michele/freesurfer
build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
Linux michele-XPS-13-ubuntu 5.4.0-58-generic #64~18.04.1-Ubuntu SMP Wed Dec 9 17:11:11 UTC 2020 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 65536 kbytes
maxproc  62545 
maxlocks unlimited
maxsignal62545 
maxmessage   819200 
maxnice  0 
maxrtprio0 
maxrttimeunlimited

  totalusedfree  shared  buff/cache   available
Mem:   16060084 8193836  430564 2376724 7435684 5163036
Swap:  19530748   4992019480828


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: 2021/01/04-15:37:26-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: michele  Machine: michele-XPS-13-ubuntu  Platform: Linux  PlatformVersion: 5.4.0-58-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: 2021/01/04-15:37:26-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: michele  Machine: michele-XPS-13-ubuntu  Platform: Linux  PlatformVersion: 5.4.0-58-generic  CompilerName: GCC  CompilerVersion: 40400 
Program nu_correct, built from:
N3 1.12.00
ProgramName: mri_make_uchar  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2021/01/04-15:37:26-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: michele  Machine: michele-XPS-13-ubuntu  Platform: Linux  PlatformVersion: 5.4.0-58-generic  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_normalize  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2021/01/04-15:37:26-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: michele  Machine: michele-XPS-13-ubuntu  Platform: Linux  PlatformVersion: 5.4.0-58-generic  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_watershed  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2021/01/04-15:37:26-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: michele  Machine: michele-XPS-13-ubuntu  Platform: Linux  PlatformVersion: 5.4.0-58-generic  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_gcut  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2021/01/04-15:37:26-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: michele  Machine: michele-XPS-13-ubuntu  Platform: Linux  PlatformVersion: 5.4.0-58-generic  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_segment  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2021/01/04-15:37:26-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: michele  Machine: michele-XPS-13-ubuntu  Platform: Linux  PlatformVersion: 5.4.0-58-generic  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_label2label.bin

[Freesurfer] comparing long and cross FS aparc+aseg

2021-02-03 Thread Michele Valotti 
External Email - Use Caution

Hi all,
I am running a test of long FS on some subjects to see if I can improve the
segmentation accuracy compared to cross FS. The aparc+aseg.mgz output of
long FS, however, is not aligned with the original timepoint structural
scan, but rather to the T1 image in the "base" folder (which I believe is
an average of the original timepoints).

I was wondering if there was a way to directly compare the results of long
FS segmentation to those of cross FS segmentation, essentially having both
the original aparc+aseg image and the new one in the same space and
aligned, or if that does not make sense since we are doing the long FS
segmentation on an effectively new image.

Thank you,
Michele
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[Freesurfer] mincRead error

2021-02-05 Thread Michele Valotti 
External Email - Use Caution

Hi all,
I am running long FreeSurfer and after successfully testing it on my local
machine I tried to run it on a server (which should however have the same
FreeSurfer version and setup), but I am getting this error

mri_convert ./tmp.mri_nu_correct.mni.533/nu1.mnc orig_nu.mgz --like
orig.mgz --conform
mri_convert.bin ./tmp.mri_nu_correct.mni.533/nu1.mnc orig_nu.mgz --like
orig.mgz --conform
ncopen: filename "./tmp.mri_nu_correct.mni.533/nu1.mnc": Not a netCDF file
miopen: MINC package entry point
Error opening ./tmp.mri_nu_correct.mni.533/nu1.mnc
mincRead(): error reading volume from file
./tmp.mri_nu_correct.mni.533/nu1.mnc
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from ./tmp.mri_nu_correct.mni.533/nu1.mnc...
Linux 18e36413df0c 5.4.0-1030-aws #31~18.04.1-Ubuntu SMP Tue Nov 17
10:48:34 UTC 2020 x86_64 GNU/Linux

recon-all -s base_freesurfer exited with ERRORS at Fri Feb  5 17:45:34 UTC
2021


Any idea what the cause of this might be?
Thank you!
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Re: [Freesurfer] mincRead error

2021-02-08 Thread Michele Valotti 
External Email - Use Caution

attached is the log for the run, the version of mri_convert is the same
version on my local machine (where the command runs) and in the cloud
instance

On Fri, 5 Feb 2021 at 18:02, Michele Valotti 
wrote:

> Hi all,
> I am running long FreeSurfer and after successfully testing it on my local
> machine I tried to run it on a server (which should however have the same
> FreeSurfer version and setup), but I am getting this error
>
> mri_convert ./tmp.mri_nu_correct.mni.533/nu1.mnc orig_nu.mgz --like
> orig.mgz --conform
> mri_convert.bin ./tmp.mri_nu_correct.mni.533/nu1.mnc orig_nu.mgz --like
> orig.mgz --conform
> ncopen: filename "./tmp.mri_nu_correct.mni.533/nu1.mnc": Not a netCDF file
> miopen: MINC package entry point
> Error opening ./tmp.mri_nu_correct.mni.533/nu1.mnc
> mincRead(): error reading volume from file
> ./tmp.mri_nu_correct.mni.533/nu1.mnc
> $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
> reading from ./tmp.mri_nu_correct.mni.533/nu1.mnc...
> Linux 18e36413df0c 5.4.0-1030-aws #31~18.04.1-Ubuntu SMP Tue Nov 17
> 10:48:34 UTC 2020 x86_64 GNU/Linux
>
> recon-all -s base_freesurfer exited with ERRORS at Fri Feb  5 17:45:34 UTC
> 2021
>
>
> Any idea what the cause of this might be?
> Thank you!
>
Mon Feb  8 13:34:27 UTC 2021
/execute/base_freesurfer
/usr/local/freesurfer/bin/recon-all
-base base_freesurfer -tp freesurfer -tp freesurfer_TS3 -all
subjid base_freesurfer
setenv SUBJECTS_DIR /execute
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 92df0dd7a4e2 5.4.0-1030-aws #31~18.04.1-Ubuntu SMP Tue Nov 17 10:48:34 UTC 2020 x86_64 GNU/Linux
cputime  unlimited
filesize unlimited
datasize unlimited
stacksize8192 kbytes
coredumpsize unlimited
memoryuseunlimited
vmemoryuse   unlimited
descriptors  1048576 
memorylocked 16384 kbytes
maxproc  unlimited
maxlocks unlimited
maxsignal31330 
maxmessage   819200 
maxnice  0 
maxrtprio0 
maxrttimeunlimited

  totalusedfree  shared  buff/cache   available
Mem:8049168  644776  203552 944 7200840 7097976
Swap: 0   0   0


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: 2021/02/08-13:34:27-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: docker  Machine: 92df0dd7a4e2  Platform: Linux  PlatformVersion: 5.4.0-1030-aws  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: 2021/02/08-13:34:27-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: docker  Machine: 92df0dd7a4e2  Platform: Linux  PlatformVersion: 5.4.0-1030-aws  CompilerName: GCC  CompilerVersion: 40400 
Program nu_correct, built from:
N3 1.12.00
ProgramName: mri_make_uchar  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2021/02/08-13:34:27-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: docker  Machine: 92df0dd7a4e2  Platform: Linux  PlatformVersion: 5.4.0-1030-aws  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_normalize  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2021/02/08-13:34:27-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: docker  Machine: 92df0dd7a4e2  Platform: Linux  PlatformVersion: 5.4.0-1030-aws  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_watershed  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2021/02/08-13:34:27-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: docker  Machine: 92df0dd7a4e2  Platform: Linux  PlatformVersion: 5.4.0-1030-aws  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_gcut  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2021/02/08-13:34:28-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: docker  Machine: 92df0dd7a4e2  Platform: Linux  PlatformVersion: 5.4.0-1030-aws  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_segment  ProgramArguments:

Re: [Freesurfer] mincRead error

2021-02-11 Thread Michele Valotti 
External Email - Use Caution

Hi Trisanna,
thank you for your reply, I am using minc2 (version 1.9.16) but this is the
same version I use on my local machine and it does not give any errors
there, and SetUpFreesurfer is sourced before exporting MINC paths and
variables.

Michele

On Wed, 10 Feb 2021 at 14:57, Trisanna Sprung-Much <
trisanna.sprung-m...@mail.mcgill.ca> wrote:

> External Email - Use Caution
>
> Hi All
>
>
>
> As a frequent user of minctools, I know I’ve had problems in the past if I
> source minctools before sourcing freesurfer in the same terminal, because
> freesurfer uses an older version of minctools.
>
> Also, freesurfer uses minc1 format not minc2.
>
>
>
> Best,
>
>
>
> Trisanna Sprung-Much
>
> Research Associate
>
> McGill University
>
> MD Anderson Cancer Centre
>
> --
>
>
>
>
>
> *From: * on behalf of "Hoopes,
> Andrew" 
> *Reply-To: *Freesurfer support list 
> *Date: *Wednesday, February 10, 2021 at 9:54 AM
> *To: *Freesurfer support list 
> *Subject: *Re: [Freesurfer] mincRead error
>
>
>
> Can you send the `mri/mri_nu_correct.mni.log` file as well? Have you
> installed minc tools separately on your local machine and do you have any
> of these variables set in your default environment?
>
>
>
> MNI_DIR
>
> MINC_BIN_DIR
>
> MINC_LIB_DIR
>
>
>
> It’s possible there’s another install of MNI that’s interfering with the
> freesurfer one.
>
> Andrew
>
>
>
> *From: *freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Michele Valotti <
> michele.valo...@gmail.com>
> *Date: *Monday, February 8, 2021 at 9:53 AM
> *To: *Freesurfer support list 
> *Subject: *Re: [Freesurfer] mincRead error
>
> *External Email - Use Caution*
>
> attached is the log for the run, the version of mri_convert is the same
> version on my local machine (where the command runs) and in the cloud
> instance
>
>
>
> On Fri, 5 Feb 2021 at 18:02, Michele Valotti 
> wrote:
>
> Hi all,
>
> I am running long FreeSurfer and after successfully testing it on my local
> machine I tried to run it on a server (which should however have the same
> FreeSurfer version and setup), but I am getting this error
>
>
>
> mri_convert ./tmp.mri_nu_correct.mni.533/nu1.mnc orig_nu.mgz --like
> orig.mgz --conform
> mri_convert.bin ./tmp.mri_nu_correct.mni.533/nu1.mnc orig_nu.mgz --like
> orig.mgz --conform
> ncopen: filename "./tmp.mri_nu_correct.mni.533/nu1.mnc": Not a netCDF file
> miopen: MINC package entry point
> Error opening ./tmp.mri_nu_correct.mni.533/nu1.mnc
> mincRead(): error reading volume from file
> ./tmp.mri_nu_correct.mni.533/nu1.mnc
> $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
> reading from ./tmp.mri_nu_correct.mni.533/nu1.mnc...
> Linux 18e36413df0c 5.4.0-1030-aws #31~18.04.1-Ubuntu SMP Tue Nov 17
> 10:48:34 UTC 2020 x86_64 GNU/Linux
>
> recon-all -s base_freesurfer exited with ERRORS at Fri Feb  5 17:45:34 UTC
> 2021
>
>
>
>
>
> Any idea what the cause of this might be?
>
> Thank you!
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://secure-web.cisco.com/1JGrZCpBCSuPapkm_HHIatoVooBbQLB65QiBaa7gloZuDTas3F7Jm5NUb0Jh70_kAxkiyAieOo4vj5KWnmyBckkZfLu5nV0KX3Mgw7SIvo89FMuleCURamxNMyNKLld0AulzlbFQN38jsbEpwGx9wGmFPQS4gS9S-eUBjNstDxOMweGNSdRBNhB41QYIdh7qgt-XD01A9MibR5VGK_Izj3WoT1yzm6BsCYIFiFRg95tYg3xA3NqMoGwukf1F2NvrYpc-xnrg8KIrVPxavMFasuA/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
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Re: [Freesurfer] mincRead error

2021-02-11 Thread Michele Valotti 
External Email - Use Caution

Hi Andrew,

on my machine those variables are all empty but in the container they return
in the container

echo $MNI_DIR returns:

echo $MINC_BIN_DIR returns:
/usr/local/freesurfer/mni/bin
echo $MINC_LIB_DIR returns:
/usr/local/freesurfer/mni/lib

I'll try and get the mri_nu_correct.mni.log file

On Wed, 10 Feb 2021 at 14:54, Hoopes, Andrew 
wrote:

> Can you send the `mri/mri_nu_correct.mni.log` file as well? Have you
> installed minc tools separately on your local machine and do you have any
> of these variables set in your default environment?
>
>
>
> MNI_DIR
>
> MINC_BIN_DIR
>
> MINC_LIB_DIR
>
>
>
> It’s possible there’s another install of MNI that’s interfering with the
> freesurfer one.
>
> Andrew
>
>
>
> *From: *freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Michele Valotti <
> michele.valo...@gmail.com>
> *Date: *Monday, February 8, 2021 at 9:53 AM
> *To: *Freesurfer support list 
> *Subject: *Re: [Freesurfer] mincRead error
>
> *External Email - Use Caution*
>
> attached is the log for the run, the version of mri_convert is the same
> version on my local machine (where the command runs) and in the cloud
> instance
>
>
>
> On Fri, 5 Feb 2021 at 18:02, Michele Valotti 
> wrote:
>
> Hi all,
>
> I am running long FreeSurfer and after successfully testing it on my local
> machine I tried to run it on a server (which should however have the same
> FreeSurfer version and setup), but I am getting this error
>
>
>
> mri_convert ./tmp.mri_nu_correct.mni.533/nu1.mnc orig_nu.mgz --like
> orig.mgz --conform
> mri_convert.bin ./tmp.mri_nu_correct.mni.533/nu1.mnc orig_nu.mgz --like
> orig.mgz --conform
> ncopen: filename "./tmp.mri_nu_correct.mni.533/nu1.mnc": Not a netCDF file
> miopen: MINC package entry point
> Error opening ./tmp.mri_nu_correct.mni.533/nu1.mnc
> mincRead(): error reading volume from file
> ./tmp.mri_nu_correct.mni.533/nu1.mnc
> $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
> reading from ./tmp.mri_nu_correct.mni.533/nu1.mnc...
> Linux 18e36413df0c 5.4.0-1030-aws #31~18.04.1-Ubuntu SMP Tue Nov 17
> 10:48:34 UTC 2020 x86_64 GNU/Linux
>
> recon-all -s base_freesurfer exited with ERRORS at Fri Feb  5 17:45:34 UTC
> 2021
>
>
>
>
>
> Any idea what the cause of this might be?
>
> Thank you!
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://secure-web.cisco.com/1rq_9xnopEr11nl-pGNGwGv1FjB1oDi6omQYXt2c9AMmisVc_P2mObQiWpRQC2On_j8b64m5dVU71ipDOxqcM4gJQ94JuzOCpTjKNVoTlO5d7Oel7zyWdfBoxsOAugIPSZJX_ay_DhNLVgRjTXSjiTyaBFw4OSbyp9IqL2iWkhknvEPxQ5m0G-I-QJjBTUW77dCjyfVfY5tzfw9BPYs2yKXHpW3vom5mPdm0Vn1CpVM_46d6CGOQu2GzhsWtWWfcBz94PUL8LPpZWmNmOkQOywA/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
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Freesurfer@nmr.mgh.harvard.edu
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Re: [Freesurfer] mincRead error

2021-02-11 Thread Michele Valotti 
External Email - Use Caution

Hi Andrew,
I do think the problem is in the MINC but the minc paths point to the
freesurfer installation, so I think it should be running using that

thank you,
Michele

On Thu, 11 Feb 2021 at 16:29, Hoopes, Andrew 
wrote:

> Hi Michele,
>
> I think that’s the problem then. The freesurfer code is written to work
> with the specific version of minc that we distribute with the release. If
> possible, you should run freesurfer without setting any MINC paths to your
> local install to see if that fixes things.
>
> Andrew
>
>
>
> *From: *freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Michele Valotti <
> michele.valo...@gmail.com>
> *Date: *Thursday, February 11, 2021 at 11:02 AM
> *To: *Freesurfer support list 
> *Subject: *Re: [Freesurfer] mincRead error
>
> *External Email - Use Caution*
>
> Hi Trisanna,
>
> thank you for your reply, I am using minc2 (version 1.9.16) but this is
> the same version I use on my local machine and it does not give any errors
> there, and SetUpFreesurfer is sourced before exporting MINC paths and
> variables.
>
>
>
> Michele
>
>
>
> On Wed, 10 Feb 2021 at 14:57, Trisanna Sprung-Much <
> trisanna.sprung-m...@mail.mcgill.ca> wrote:
>
> *External Email - Use Caution*
>
> Hi All
>
>
>
> As a frequent user of minctools, I know I’ve had problems in the past if I
> source minctools before sourcing freesurfer in the same terminal, because
> freesurfer uses an older version of minctools.
>
> Also, freesurfer uses minc1 format not minc2.
>
>
>
> Best,
>
>
>
> Trisanna Sprung-Much
>
> Research Associate
>
> McGill University
>
> MD Anderson Cancer Centre
>
> --
>
>
>
>
>
> *From: * on behalf of "Hoopes,
> Andrew" 
> *Reply-To: *Freesurfer support list 
> *Date: *Wednesday, February 10, 2021 at 9:54 AM
> *To: *Freesurfer support list 
> *Subject: *Re: [Freesurfer] mincRead error
>
>
>
> Can you send the `mri/mri_nu_correct.mni.log` file as well? Have you
> installed minc tools separately on your local machine and do you have any
> of these variables set in your default environment?
>
>
>
> MNI_DIR
>
> MINC_BIN_DIR
>
> MINC_LIB_DIR
>
>
>
> It’s possible there’s another install of MNI that’s interfering with the
> freesurfer one.
>
> Andrew
>
>
>
> *From: *freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Michele Valotti <
> michele.valo...@gmail.com>
> *Date: *Monday, February 8, 2021 at 9:53 AM
> *To: *Freesurfer support list 
> *Subject: *Re: [Freesurfer] mincRead error
>
> *External Email - Use Caution*
>
> attached is the log for the run, the version of mri_convert is the same
> version on my local machine (where the command runs) and in the cloud
> instance
>
>
>
> On Fri, 5 Feb 2021 at 18:02, Michele Valotti 
> wrote:
>
> Hi all,
>
> I am running long FreeSurfer and after successfully testing it on my local
> machine I tried to run it on a server (which should however have the same
> FreeSurfer version and setup), but I am getting this error
>
>
>
> mri_convert ./tmp.mri_nu_correct.mni.533/nu1.mnc orig_nu.mgz --like
> orig.mgz --conform
> mri_convert.bin ./tmp.mri_nu_correct.mni.533/nu1.mnc orig_nu.mgz --like
> orig.mgz --conform
> ncopen: filename "./tmp.mri_nu_correct.mni.533/nu1.mnc": Not a netCDF file
> miopen: MINC package entry point
> Error opening ./tmp.mri_nu_correct.mni.533/nu1.mnc
> mincRead(): error reading volume from file
> ./tmp.mri_nu_correct.mni.533/nu1.mnc
> $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
> reading from ./tmp.mri_nu_correct.mni.533/nu1.mnc...
> Linux 18e36413df0c 5.4.0-1030-aws #31~18.04.1-Ubuntu SMP Tue Nov 17
> 10:48:34 UTC 2020 x86_64 GNU/Linux
>
> recon-all -s base_freesurfer exited with ERRORS at Fri Feb  5 17:45:34 UTC
> 2021
>
>
>
>
>
> Any idea what the cause of this might be?
>
> Thank you!
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> *MailScanner has detected a possible fraud attempt from
> "secure-web.cisco.com" claiming to be*
> https://secure-web.cisco.com/1xs9PzPP9V2FuqxvdDUNBOJ4r4_8Psp1WNP2tVrDYnPLg4T1blP_wTgTNOvBQV4oNdMuIsD2N6iC5HUD1XgKtYuwymDzV_-gfo9Q1vPTy6x0DDdZWi1jfUJlMYtYb2mF1QNQlQZxa1_onIQnw9nrcvd4R2-Y7geTHa4C4IqiOSrQN9jkUXkvGupjRMcqImISZVGktvoiNSnuW8dj7Rn7G79C_d0NzthXmQwu62rTFU6fuQHd5ayefYvgAIPmiQ0PZ-QNRVjGeavlqRXeLvXks8Q/https%3A%2F%2Fmail.nmr.m

Re: [Freesurfer] mincRead error

2021-02-12 Thread Michele Valotti 
External Email - Use Caution

Hi Andrew,
thank you for your help, I have attached the mri_nu_correct log from the
base freesurfer directory, let me know if this helps

Michele

On Thu, 11 Feb 2021 at 17:16, Hoopes, Andrew 
wrote:

> If you send the mri_nu_correct.mni.log we can figure it out for sure.
>
> Andrew
>
>
>
> *From: *freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Michele Valotti <
> michele.valo...@gmail.com>
> *Date: *Thursday, February 11, 2021 at 12:07 PM
> *To: *Freesurfer support list 
> *Subject: *Re: [Freesurfer] mincRead error
>
> *External Email - Use Caution*
>
> Hi Andrew,
>
> I do think the problem is in the MINC but the minc paths point to the
> freesurfer installation, so I think it should be running using that
>
>
>
> thank you,
>
> Michele
>
>
>
> On Thu, 11 Feb 2021 at 16:29, Hoopes, Andrew 
> wrote:
>
> Hi Michele,
>
> I think that’s the problem then. The freesurfer code is written to work
> with the specific version of minc that we distribute with the release. If
> possible, you should run freesurfer without setting any MINC paths to your
> local install to see if that fixes things.
>
> Andrew
>
>
>
> *From: *freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Michele Valotti <
> michele.valo...@gmail.com>
> *Date: *Thursday, February 11, 2021 at 11:02 AM
> *To: *Freesurfer support list 
> *Subject: *Re: [Freesurfer] mincRead error
>
> *External Email - Use Caution*
>
> Hi Trisanna,
>
> thank you for your reply, I am using minc2 (version 1.9.16) but this is
> the same version I use on my local machine and it does not give any errors
> there, and SetUpFreesurfer is sourced before exporting MINC paths and
> variables.
>
>
>
> Michele
>
>
>
> On Wed, 10 Feb 2021 at 14:57, Trisanna Sprung-Much <
> trisanna.sprung-m...@mail.mcgill.ca> wrote:
>
> *External Email - Use Caution*
>
> Hi All
>
>
>
> As a frequent user of minctools, I know I’ve had problems in the past if I
> source minctools before sourcing freesurfer in the same terminal, because
> freesurfer uses an older version of minctools.
>
> Also, freesurfer uses minc1 format not minc2.
>
>
>
> Best,
>
>
>
> Trisanna Sprung-Much
>
> Research Associate
>
> McGill University
>
> MD Anderson Cancer Centre
>
> --
>
>
>
>
>
> *From: * on behalf of "Hoopes,
> Andrew" 
> *Reply-To: *Freesurfer support list 
> *Date: *Wednesday, February 10, 2021 at 9:54 AM
> *To: *Freesurfer support list 
> *Subject: *Re: [Freesurfer] mincRead error
>
>
>
> Can you send the `mri/mri_nu_correct.mni.log` file as well? Have you
> installed minc tools separately on your local machine and do you have any
> of these variables set in your default environment?
>
>
>
> MNI_DIR
>
> MINC_BIN_DIR
>
> MINC_LIB_DIR
>
>
>
> It’s possible there’s another install of MNI that’s interfering with the
> freesurfer one.
>
> Andrew
>
>
>
> *From: *freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Michele Valotti <
> michele.valo...@gmail.com>
> *Date: *Monday, February 8, 2021 at 9:53 AM
> *To: *Freesurfer support list 
> *Subject: *Re: [Freesurfer] mincRead error
>
> *External Email - Use Caution*
>
> attached is the log for the run, the version of mri_convert is the same
> version on my local machine (where the command runs) and in the cloud
> instance
>
>
>
> On Fri, 5 Feb 2021 at 18:02, Michele Valotti 
> wrote:
>
> Hi all,
>
> I am running long FreeSurfer and after successfully testing it on my local
> machine I tried to run it on a server (which should however have the same
> FreeSurfer version and setup), but I am getting this error
>
>
>
> mri_convert ./tmp.mri_nu_correct.mni.533/nu1.mnc orig_nu.mgz --like
> orig.mgz --conform
> mri_convert.bin ./tmp.mri_nu_correct.mni.533/nu1.mnc orig_nu.mgz --like
> orig.mgz --conform
> ncopen: filename "./tmp.mri_nu_correct.mni.533/nu1.mnc": Not a netCDF file
> miopen: MINC package entry point
> Error opening ./tmp.mri_nu_correct.mni.533/nu1.mnc
> mincRead(): error reading volume from file
> ./tmp.mri_nu_correct.mni.533/nu1.mnc
> $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
> reading from ./tmp.mri_nu_correct.mni.533/nu1.mnc...
> Linux 18e36413df0c 5.4.0-1030-aws #31~18.04.1-U

Re: [Freesurfer] mincRead error

2021-02-22 Thread Michele Valotti 
External Email - Use Caution

Hi all,
I was wondering if anyone had a chance to look at the log to shed some
light on this mystery error, or if more info or a different log are needed.

Thank you,
Michele

On Fri, 12 Feb 2021 at 10:05, Michele Valotti 
wrote:

> Hi Andrew,
> thank you for your help, I have attached the mri_nu_correct log from the
> base freesurfer directory, let me know if this helps
>
> Michele
>
> On Thu, 11 Feb 2021 at 17:16, Hoopes, Andrew 
> wrote:
>
>> If you send the mri_nu_correct.mni.log we can figure it out for sure.
>>
>> Andrew
>>
>>
>>
>> *From: *freesurfer-boun...@nmr.mgh.harvard.edu <
>> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Michele Valotti <
>> michele.valo...@gmail.com>
>> *Date: *Thursday, February 11, 2021 at 12:07 PM
>> *To: *Freesurfer support list 
>> *Subject: *Re: [Freesurfer] mincRead error
>>
>> *External Email - Use Caution*
>>
>> Hi Andrew,
>>
>> I do think the problem is in the MINC but the minc paths point to the
>> freesurfer installation, so I think it should be running using that
>>
>>
>>
>> thank you,
>>
>> Michele
>>
>>
>>
>> On Thu, 11 Feb 2021 at 16:29, Hoopes, Andrew 
>> wrote:
>>
>> Hi Michele,
>>
>> I think that’s the problem then. The freesurfer code is written to work
>> with the specific version of minc that we distribute with the release. If
>> possible, you should run freesurfer without setting any MINC paths to your
>> local install to see if that fixes things.
>>
>> Andrew
>>
>>
>>
>> *From: *freesurfer-boun...@nmr.mgh.harvard.edu <
>> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Michele Valotti <
>> michele.valo...@gmail.com>
>> *Date: *Thursday, February 11, 2021 at 11:02 AM
>> *To: *Freesurfer support list 
>> *Subject: *Re: [Freesurfer] mincRead error
>>
>> *External Email - Use Caution*
>>
>> Hi Trisanna,
>>
>> thank you for your reply, I am using minc2 (version 1.9.16) but this is
>> the same version I use on my local machine and it does not give any errors
>> there, and SetUpFreesurfer is sourced before exporting MINC paths and
>> variables.
>>
>>
>>
>> Michele
>>
>>
>>
>> On Wed, 10 Feb 2021 at 14:57, Trisanna Sprung-Much <
>> trisanna.sprung-m...@mail.mcgill.ca> wrote:
>>
>> *External Email - Use Caution*
>>
>> Hi All
>>
>>
>>
>> As a frequent user of minctools, I know I’ve had problems in the past if
>> I source minctools before sourcing freesurfer in the same terminal, because
>> freesurfer uses an older version of minctools.
>>
>> Also, freesurfer uses minc1 format not minc2.
>>
>>
>>
>> Best,
>>
>>
>>
>> Trisanna Sprung-Much
>>
>> Research Associate
>>
>> McGill University
>>
>> MD Anderson Cancer Centre
>>
>> --
>>
>>
>>
>>
>>
>> *From: * on behalf of "Hoopes,
>> Andrew" 
>> *Reply-To: *Freesurfer support list 
>> *Date: *Wednesday, February 10, 2021 at 9:54 AM
>> *To: *Freesurfer support list 
>> *Subject: *Re: [Freesurfer] mincRead error
>>
>>
>>
>> Can you send the `mri/mri_nu_correct.mni.log` file as well? Have you
>> installed minc tools separately on your local machine and do you have any
>> of these variables set in your default environment?
>>
>>
>>
>> MNI_DIR
>>
>> MINC_BIN_DIR
>>
>> MINC_LIB_DIR
>>
>>
>>
>> It’s possible there’s another install of MNI that’s interfering with the
>> freesurfer one.
>>
>> Andrew
>>
>>
>>
>> *From: *freesurfer-boun...@nmr.mgh.harvard.edu <
>> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Michele Valotti <
>> michele.valo...@gmail.com>
>> *Date: *Monday, February 8, 2021 at 9:53 AM
>> *To: *Freesurfer support list 
>> *Subject: *Re: [Freesurfer] mincRead error
>>
>> *External Email - Use Caution*
>>
>> attached is the log for the run, the version of mri_convert is the same
>> version on my local machine (where the command runs) and in the cloud
>> instance
>>
>>
>>
>> On Fri, 5 Feb 2021 at 18:02, Michele Valotti 
>> wrote:
>>
>> Hi all,
>>
>> I am running long FreeSurfer and after successfully testing it on my
>>

[Freesurfer] Freesurfer 7 Temporal lobe segmentation

2023-01-25 Thread Michele Valotti 
External Email - Use Caution

Dear Freesurfer experts,

Should I expect Freesurfer 7 to significantly improve segmentation of the
Temporal Lobe when compared to Freesurfer 6?  I often see sub-optimal
segmentation of this region in Freesurfer 6 and I am wondering if an
upgrade to 7 would be worth it or not.

Thank you!
Best,

Michele
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