Re: [Freesurfer] Operating System

2020-03-19 Thread fsbuild 
External Email - Use Caution

Hello Stephanie,
I already had 6.0.0 installed and did an incremental upgrade from 10.13 to 
10.15, and did not run into any serious issues other than having to grant some 
permissions.  
However, other older software already in /Applications may fail to run after 
the upgrade (which was the case after I did one upgrade).

If you must upgrade, I suggest using Disk Utility to make a disk image backup 
of your entire boot or Macintosh HD partition so you can try to revert back 
using its restore function if necessary.  I've only put the upgrade on one 
machine because it is new Apple hardware that cannot run 10.13 or 10.14.. 
 My advice generally is to always stay one revision behind the latest 
version of Mac OS - which right now would be 10.14 Mojave.  I don’t have 
or know of any software that only runs on 10.15 but does not run on 
10.14.  So all my other machines that can still run 10.14 have not been 
upgraded.

- R.

On Mar 19, 2020, at 16:11, Rellick, Stephanie  
wrote:External Email - Use 
CautionI am needing to upgrade 
my operating system to Catalina on my Mac, and I am running Freesurfer version 
6.0.0.  Is this version compatible with 
CatalinaOS?Thanks,Stephanie___Freesurfer
 mailing 
listfreesur...@nmr.mgh.harvard.eduhttps://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] Operating System

2020-03-19 Thread Rellick, Stephanie 
External Email - Use Caution

I am needing to upgrade my operating system to Catalina on my Mac, and I am 
running Freesurfer version 6.0.0.  Is this version compatible with CatalinaOS?

Thanks,

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

[Freesurfer] Is it possible to "fill in" the region delimited by an ROI label?

2020-03-19 Thread Mohammad Rashid 
External Email - Use Caution

Hi all,

I'm able to load in a yellow outline for the entorhinal region by loading a 
file named ?h.entorhinal_exvivo.label as a volume. (I first load in a brain 
image such as brain.mgz, and then display the outline on top of it.) Is it 
possible to get a solid highlight of the entorhinal region in this manner, as 
opposed to just an outline of the region?

(Strangely enough, if I load ?h.entorhinal_exvivo.label as a label on an 
surface file, such as ?h.inflated, then the entorhinal region is seen filled in 
with a yellow color on the 3D surface. This is the effect I want, except on a 
2D volume.)

Any help is greatly appreciated,
Mohammad
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] Flip left-right orientation command

2020-03-19 Thread Miguel Ángel Rivas Fernández 
External Email - Use Caution

Dear Douglas,

In these emails I asked to you how to flip the left-right orientation of an
image in PIL orientation and you recommend to me this command

mri_convert --in_orientation PIR t1_flip.nii t1_flip_flip.nii


All have worked fine but now I am in the same situation with an image in
RAS orientation. *Which command should I use to flip the left/right
orientation of an image in RAS orientation?*. As I explained in my previous
emails, the orientation is fine. The reason is that am using a software to
detect brain lesions that only works in left hemisphere and my subject have
the lesion in the right hemisphere. After the lesion estimation I need to
flip the left-right orientation.

Thank you very much for your time and attention.

Best regards,

El vie., 14 feb. 2020 a las 17:34, Miguel Ángel Rivas Fernández (<
miguelrivasf...@gmail.com>) escribió:

> Yes, it works!.
>
> Thank you so much.
>
> El vie., 14 feb. 2020 a las 17:22, Douglas N. Greve (<
> dgr...@mgh.harvard.edu>) escribió:
>
>> You can try,
>> mri_convert --in_orientation PIR t1_flip.nii t1_flip_flip.nii
>> but I'm not promising anything
>>
>> On 2/14/2020 11:03 AM, Miguel Ángel Rivas Fernández wrote:
>>
>> External Email - Use Caution
>> Dear Douglas,
>>
>> My image is in the correct orientation. The reason is that am using a
>> software to detect brain lesions that only works in left hemisphere and my
>> subject have the lesion in the right hemisphere. I tried it with the
>> following command and it works
>>
>> mri_convert --in_orientation PIL t1.nii t1_flip.nii
>>
>> Now I would like to come back to the original orientation, which command
>> should I use?
>>
>> Thanks in advance.
>>
>> Best regards,
>>
>> El vie., 14 feb. 2020 a las 16:01, Douglas N. Greve (<
>> dgr...@mgh.harvard.edu>) escribió:
>>
>>> Is the image in the wrong orientation (ie, is it not truly in PIR) or do
>>> you want to change the orientation? doing a left-right swap is more than
>>> changing the orientation
>>>
>>> On 2/11/2020 4:06 PM, Miguel Ángel Rivas Fernández wrote:
>>>
>>> External Email - Use Caution
>>> Dear Freesurfer experts,
>>>
>>> Which command should I use to flip the left-right orientation of a T1
>>> image?. Actually my image is in PIR orientation, I used the following
>>> command
>>>
>>> mri_info --orientation '/home/rmn/Desktop/study/E03/3d/coanat_E03.nii'
>>>
>>> *PIR*
>>>
>>>
>>> Thanks in advance,
>>>
>>> Best regards,
>>>
>>> --
>>> *Miguel Ángel Rivas Fernández*
>>>
>>> ___
>>> Freesurfer mailing 
>>> listfreesur...@nmr.mgh.harvard.eduhttps://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
>>
>>
>>
>> --
>> *Miguel Ángel Rivas Fernández*
>>
>> ___
>> Freesurfer mailing 
>> listfreesur...@nmr.mgh.harvard.eduhttps://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
>
>
>
> --
> *Miguel Ángel Rivas Fernández*
>


-- 
*Miguel Ángel Rivas Fernández*
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] recon-all error

2020-03-19 Thread Mason Wells 
External Email - Use Caution

Hello FreeSurfer Developers,


I'm attempting to run the recon-all command on a Linux machine but it appears 
to be falling at one of the first hurdles.

INFO: extension is mgz
#
#@# Talairach Wed Mar 18 15:30:51 GMT 2020
/home/masontwells/Documents/Data/freesurfer/subjects/LM/mri

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

Linux masontwells-VIG800S 5.3.0-40-generic #32~18.04.1-Ubuntu SMP Mon Feb 3 
14:05:59 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s LM exited with ERRORS at Wed Mar 18 15:30:53 GMT 2020

For more details, see the log file 
/home/masontwells/Documents/Data/freesurfer/subjects/LM/scripts/recon-all.log
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

masontwells@masontwells-VIG800S:

Does anyone have any thoughts on how to trouble-shoot this one? Also, Ive 
attached the recon-all.log in case it's of any use. I am running 
freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0

Thanks in advance,
Mason

Mason T Wells, MSc

PhD student

School of Optometry and Vision Sciences

& Cardiff University Brain Research

Imaging Centre (CUBRIC), School of Psychology

Cardiff University

Cardiff

CF24 4HQ

UK



Email: wells...@cardiff.ac.uk

Tel: 02920 879628

Web: Cardiff University 
webpage

Mason T Wells, MSc

Myfyriwr PhD

Yr Ysgol Optometreg a Gwyddorau’r Golwg

& Canolfan Ymchwil Delweddu’r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr Ysgol 
Seicoleg

Prifysgol Caerdydd

Heol Maindy

Caerdydd

CF24 4HQ

DU



E-bost: wells...@caerdydd.ac.uk

Ffôn: 02920 879628

Wed Mar 18 15:30:36 GMT 2020
/home/masontwells/Documents/Data/freesurfer/subjects/LM
/usr/local/freesurfer/bin/recon-all
-i T1.nii.gz -s LM -all
subjid LM
setenv SUBJECTS_DIR /home/masontwells/Documents/Data/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 masontwells-VIG800S 5.3.0-40-generic #32~18.04.1-Ubuntu SMP Mon Feb 3 14:05:59 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 16384 kbytes
maxproc  31280 
maxlocks unlimited
maxsignal31280 
maxmessage   819200 
maxnice  0 
maxrtprio0 
maxrttimeunlimited

  totalusedfree  shared  buff/cache   available
Mem:8056648 2680684  202376  278332 5173588 4793908
Swap:   2097148   36864 2060284


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: 2020/03/18-15:30:36-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: masontwells  Machine: masontwells-VIG800S  Platform: Linux  PlatformVersion: 5.3.0-40-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: 2020/03/18-15:30:37-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: masontwells  Machine: masontwells-VIG800S  Platform: Linux  PlatformVersion: 5.3.0-40-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: 2020/03/18-15:30:37-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: masontwells  Machine: masontwells-VIG800S  Platform: Linux  PlatformVersion: 5.3.0-40-generic  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_normalize  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2020/03/18-15:30:37-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: masontwells  Machine: masontwells-VIG800S  Platform: Linux  PlatformVersion: 5.3.0-40-generic  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_watershed  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeSta