Re: [Freesurfer] SIENAX

[Hassan bakhshi]

We have some cases which we want to process , I searched about SIENAX and
as you are more expert in this area, I wanted to know Freesurfer
preferences on SIENAX ???
The other thing is process time in these two software.

Kind Regards,
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[Freesurfer] SIENAX

[Hassan bakhshi]

Hi,

I lately heard about SIENAX and when I looked into it it seems like
Freesurfer,
using the same brain extraction process and etc.

I wanted to ask if it is more complete than Freesurfer or not? and why
researcher are going after it?

It is for Oxford University I think.

Kind Regards,
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Re: [Freesurfer] white surf area

[Hassan bakhshi]

Hello Bruce,
Sorry I'm in a hurry and its 3rd time I emailed.
What is exactly the feature white surface area and how can I visualize it?
Kind regards,
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[Freesurfer] lh-WhiteSurfArea

[Hassan bakhshi]

Hello,

In Freesurfer stats there is a feature named lh-WhiteSurfArea.

where is exactly this WhiteSurfArea and how can I show it in freeview on
surface or image?

Kind Regards,
Hassan
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[Freesurfer] .Img format

[Hassan bakhshi]

Hello ,

I have an image with .img format and an image with .hdr format.

Freesurfer cant run them. What im suppose to di0o??? I just want to view
the image.
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Re: [Freesurfer] recon all erro

[Hassan bakhshi]

Hi emad,
I think if you change format type of images to nifti it will work as
allright.
I had a problem like this and it worked for me...
On Dec 24, 2015 8:30 PM,  wrote:

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> Today's Topics:
>
>1. Recon-all error (Emad Ahmadi)
>
>
> --
>
> Message: 1
> Date: Thu, 24 Dec 2015 09:50:52 -0500
> From: Emad Ahmadi 
> Subject: [Freesurfer] Recon-all error
> To: Freesurfer support list 
> Message-ID: 
> Content-Type: text/plain; charset="utf-8"
>
> Hi,
>
> I ran recon-all on the dicoms of a subject, obtained at Bay 4, and I
> received the following error:
>
> mris_calc -o lh.area.mid lh.area add lh.area.pial
> 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
>
> Trace/BPT trap
> Wed Dec 23 21:59:54 EST 2015
> ERROR: vertexvol
> mris_calc -o lh.area.mid lh.area add lh.area.pial
> Darwin MGH000844.local 15.2.0 Darwin Kernel Version 15.2.0: Fri Nov 13
> 19:56:56 PST 2015; root:xnu-3248.20.55~2/RELEASE_X86_64 x86_64
>
> recon-all -s 3Lt_002 exited with ERRORS at Wed Dec 23 21:59:54 EST 2015
>
> For more details, see the log file
> /Users/Emad/Projects/3LT/subjDir/3Lt_002/scripts/recon-all.log
> To report a problem, see
> http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>
> I have attached the log file. I?d truly appreciate your help.
>
> Thank you, and with best wishes for a wonderful holiday season for
> everyone,
> Emad
>
>
> Emad Ahmadi, MD
> ---
> Research Fellow in Radiology
> Massachusetts General Hospital
> Harvard Medical School
>
> 25 New Chardon Street, Suite 400
> Boston, MA 02114
> Tel: 617 726 5237
> Email: e...@nmr.mgh.harvard.edu
>
> -- next part --
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[Freesurfer] Supratentorial Volume

[Hassan bakhshi]

Dear all,

I have 3 features which i want to display and visualize.

-Supratentorial Volume
-TotalGrayVol
-rh-superiorTemporal Volume

how can i do that???
Another thing how can i get the characteristic of these areas like which
parts they have in brain and etc.
Kind Regrds,
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[Freesurfer] BA lable Error

[Hassan bakhshi]

Hi,

Recon-all has error at BA Labels stage.
how can i run it from this stage again.
I need cortical thickness,  Do i need to run it?
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[Freesurfer] Recon-all balabels

[Hassan bakhshi]

Hi,

I found out how to creat BA labels with command below:

recon-all -s subjid -ba-labels

and it ran and finished without error, but it didnt create the Ex-Vivo
Entorhinal stats.

I ran it twice but it just made the BA lables.

Kind Regards,
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[Freesurfer] recon-all complete in 10 hours!!!!

[Hassan bakhshi]

Hi all,

Recon-all  complete in 10 hours,should i be concerned?

I asked this question before, and Bruce said depend on your computer it is
acceptable. i checked the hardware, I use virtual box which has 5 cores of
cpu and 4GB of RAM. i ran 2 instance of recon-all and both finished within
10 hours. I have 4 pc like this which i'm running freesurfer on them and
they finished within 10 hours for most of subjects and for some of them in
20 hours.

I'm really concerned about the quality. If it is ok just make me relief.
Kind Regards,
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[Freesurfer] Dev Version

[Hassan bakhshi]

Hi
I downloaded the centos 6 freeview.bin and replaced it into
$freesurferhome/bin/freeview.bin

but now i cant open freeview, it says that it is not a executable file and
it is binary.

i wanted to test hippocampal subfields.

Kind regards
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[Freesurfer] Recon-all Error

[Hassan bakhshi]

Hello,

I had the problem which was the recon-all error at Fix Topology lh stage
for 6 of 12 subjects i ran freesurfer.
Bruce then told me to check the lh.orig.nofix and lh.inflated.nofix to see
if there is part of skull or cerebellum.

But when i want to open them with this command:
tkmedit lh.orig.nofix

it says that it cant open file . How can i check these files to see where
is the problem for these 6 subjects.
Kind Regards
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[Freesurfer] Diffrence Between stat files and mris

[Hassan bakhshi]

Hi,

I wanted to ask what is the difference between stat files result and the
mris_anatomical_stats?

can we get the same result using both?

i want to get the anatomical thickness of temporal gyruses such as superior
temporal gyrus thickness, and non neocortex volumes like hippocamp and
amygdala volume!
Kind regards
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[Freesurfer] Hippocamp subfields

[Hassan bakhshi]

Hi,

I am using freesurfer v5.3, can I have hippocamp subfields in this version??

Kind regards
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[Freesurfer] Dialogs go behind freeview

[Hassan bakhshi]

Dear all,
Hi,

When i open freeview the images at the center of the screen dont let me see
an opne dialog,
for example when i want to add surface, the opening dialog go behind them
and i cant access the dialog.

Kind Regards
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[Freesurfer] Successfull Recon-all

[Hassan bakhshi]

Hi,

Finally I could run recon-all with nifti files, dicom couldnt run 

it showed that recon-all done without errors, but how can i be sure about
the quality of the resultws.

I ran the tkmedit and tksurfer as the website said!

I got the stats too, how can i be sure that stats are correct and trusty???

Kind Regards,
Hassan
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[Freesurfer] Parallel

[Hassan bakhshi]

Hi,

Is it possible to run recon-all in parallel for fastening the speed ???
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Re: [Freesurfer] recon-all

[Hassan bakhshi]

Hi Bruce,

As you wanted i attached the log file.

and by the way /usr/local/139942/I000 is a image file which is in dicom
format and high res T1-Weighted 1*1*1.  It is sagital series in the folder
139942 which contains about 165 images.

If you need i can send files too

Kind Regards


Hi Hassan

first, you need to send us the screen output and the recon-all.log. The
info you sent is not sufficient for us to help you.

Second, is  /usr/local/139942/I000 a directory or a file? It needs to
be a file, and should be a  single slice in the correct (i.e. high res
T1-weighted) series. Is it in dicom format?

cheers
Bruce

On Sat,
7 Mar 2015, Hassan bakhshi wrote:

 Hi?
 I'm still stopped at the recon-all stage.?
 I use the command correctly and there it is:

 recon-all -i /usr/local/139942/I000 -subject test -all


 the data is a sagital series. I think the command cant be execute at the
 mri_convert step, because i dont have .mgz files in the test directory.?


 The error is segfault !!!

 What can I do to solve it???




recon-all.error
Description: Binary data
‫یکشنبه ۰۸ مارس ۱۵، ساعت ۰۹:۳۷:۳۲ (IRST)‬
/usr/local/freesurfer/subjects/test
/usr/local/freesurfer/bin/recon-all
-i /usr/local/139942/I000 -subject test -all
subjid test
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 circle-Ubuntu 3.13.0-32-generic #57-Ubuntu SMP Tue Jul 15 03:51:08 UTC 2014 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  47440 
maxlocks unlimited
maxsignal47440 
maxmessage   819200 
maxnice  0 
maxrtprio0 
maxrttimeunlimited

 total   used   free sharedbuffers cached
Mem:   609403221171763976856  30228  836361075816
-/+ buffers/cache: 9577245136308
Swap:   102396  0 102396


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: 2015/03/08-06:07:32-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: root  Machine: circle-Ubuntu  Platform: Linux  PlatformVersion: 3.13.0-32-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: 2015/03/08-06:07:32-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: root  Machine: circle-Ubuntu  Platform: Linux  PlatformVersion: 3.13.0-32-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: 2015/03/08-06:07:32-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: root  Machine: circle-Ubuntu  Platform: Linux  PlatformVersion: 3.13.0-32-generic  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_normalize  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2015/03/08-06:07:32-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: root  Machine: circle-Ubuntu  Platform: Linux  PlatformVersion: 3.13.0-32-generic  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_watershed  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2015/03/08-06:07:32-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: root  Machine: circle-Ubuntu  Platform: Linux  PlatformVersion: 3.13.0-32-generic  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_gcut  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2015/03/08-06:07:32-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: root  Machine: circle-Ubuntu  Platform: Linux  PlatformVersion: 3.13.0-32-generic  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_segment  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2015

[Freesurfer] Recon-all (Data for test )

[Hassan bakhshi]

Hi

Where can i find data to test freesurfer

I want to test recon-all command and then get volume of hippocamp!!

Thanks alot
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[Freesurfer] Fwd: Recon-all Error

[Hassan bakhshi]

HI,

Im using freesurfer newly, i have a folder of a subject's MRI's named
139942

I tried to run recon-all of a File named I000 The point is to get
Superior temporal gyrus thickness.

but it show an error and stop working. i looked up archive of FAQ's but i
didnt anything usefull.

There is the recon-all log attached!

Please Help!


By the way I'm using Ubuntu 14.04 LTS!!
‫چهارشنبه ۰۴ مارس ۱۵، ساعت ۰۹:۴۷:۱۵ (IRST)‬
/usr/local/freesurfer/subjects/139942
/usr/local/freesurfer/bin/recon-all
-s 139942 -i /usr/local/139942/I000
subjid 139942
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 circle-Ubuntu 3.13.0-32-generic #57-Ubuntu SMP Tue Jul 15 03:51:08 UTC 2014 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  47440 
maxlocks unlimited
maxsignal47440 
maxmessage   819200 
maxnice  0 
maxrtprio0 
maxrttimeunlimited

 total   used   free sharedbuffers cached
Mem:   609403227211923372840  24664 1398361525816
-/+ buffers/cache:10555405038492
Swap:   102396  0 102396


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: 2015/03/04-06:17:15-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: root  Machine: circle-Ubuntu  Platform: Linux  PlatformVersion: 3.13.0-32-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: 2015/03/04-06:17:15-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: root  Machine: circle-Ubuntu  Platform: Linux  PlatformVersion: 3.13.0-32-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: 2015/03/04-06:17:16-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: root  Machine: circle-Ubuntu  Platform: Linux  PlatformVersion: 3.13.0-32-generic  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_normalize  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2015/03/04-06:17:16-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: root  Machine: circle-Ubuntu  Platform: Linux  PlatformVersion: 3.13.0-32-generic  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_watershed  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2015/03/04-06:17:16-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: root  Machine: circle-Ubuntu  Platform: Linux  PlatformVersion: 3.13.0-32-generic  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_gcut  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2015/03/04-06:17:16-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: root  Machine: circle-Ubuntu  Platform: Linux  PlatformVersion: 3.13.0-32-generic  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_segment  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2015/03/04-06:17:16-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: root  Machine: circle-Ubuntu  Platform: Linux  PlatformVersion: 3.13.0-32-generic  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_label2label  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2015/03/04-06:17:16-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: root  Machine: circle-Ubuntu  Platform: Linux  PlatformVersion: 3.13.0-32-generic  CompilerName: GCC  CompilerVersion: 40400 


 === NUMBER OF OPENMP THREADS = 1 === 
ProgramName: mri_em_register  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: