[Freesurfer] About FreeSurfer source code

2018-09-07 Thread Renew Andrade 
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Dear community:
I was curious about how the software is made and I decided to write an email to 
Dr. Bruce Fischl who answered all of the questions I asked, but he gave me the 
input to ask these questions also in FreeSurfer Community. I first asked the 
programming language of the software(I didn’t know that it was even open 
source). He says its mostly C but also some Matlab and C++. I am concerned with 
the long preprocessing time of raw T1 data so if anyone has some insights about 
which is the longest part and how faster it can get with nowadays hardware of 
course share with us. I think perhaps if some of the code of C were translated 
to C++ may be it could be faster. Although I don’t know how faster in fact but 
it could be a start. It should be easier if there were someone with clear head 
picture of time processing in different parts of the program in different 
hardware specifics. I know there is an entry in FreeSurfer wiki but I’m talking 
of an exchange of experiences with different machines with the same version of 
the software. May be I am going too far on my expectations. It would be nice to 
have a thread where we all shared our knowledge about how to improve 
performance. May be programming language translation is a bit of a lazy start 
and a change in some of the algorithms is the what we should  encourage. 

Sincerely, 
Andrade. 

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Re: [Freesurfer] Freeview: Load multiples overlays for one surface

2018-09-07 Thread Emanuel Alvaredo 
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It's works! Thanks a lot!
El vie., 7 sept. 2018 a las 16:46, Ruopeng Wang ()
escribió:

> Yes, it is possible. But you should use ':' as separator like this:
>
> -f
> surf/lh.inflated:overlay=surf/lh.sulc:overlay=surf/lh.thickness:overlay_threshold=1,5
>
> Ruopeng
>
> On 09/07/2018 03:11 PM, Emanuel Alvaredo wrote:
>
> External Email - Use Caution
>
> Hi! I would like from command line to open one surface with multiple
> ovelays. For example, intead of this
>
> ..-f surf/lh.inflated:overlay=surf/lh.sulc
> surf/lh.inflated:overlay=surf/lh.thickness:overlay_threshold=1,5
>
> I would like to do something like that
>
> -f
> surf/lh.inflated:overlay=surf/lh.sulc,overlay=surf/lh.thickness:overlay_threshold=1,5
>
>
> is this possible?
>
> Thanks!
>
>
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Re: [Freesurfer] Freeview: Load multiples overlays for one surface

2018-09-07 Thread Ruopeng Wang 

Yes, it is possible. But you should use ':' as separator like this:

-f 
surf/lh.inflated:overlay=surf/lh.sulc:overlay=surf/lh.thickness:overlay_threshold=1,5


Ruopeng


On 09/07/2018 03:11 PM, Emanuel Alvaredo wrote:


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Hi! I would like from command line to open one surface with multiple 
ovelays. For example, intead of this


..-f surf/lh.inflated:overlay=surf/lh.sulc 
surf/lh.inflated:overlay=surf/lh.thickness:overlay_threshold=1,5


I would like to do something like that

-f 
surf/lh.inflated:overlay=surf/lh.sulc,overlay=surf/lh.thickness:overlay_threshold=1,5



is this possible?

Thanks!


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[Freesurfer] Freeview: Load multiples overlays for one surface

2018-09-07 Thread Emanuel Alvaredo 
External Email - Use Caution

Hi! I would like from command line to open one surface with multiple
ovelays. For example, intead of this

..-f surf/lh.inflated:overlay=surf/lh.sulc
surf/lh.inflated:overlay=surf/lh.thickness:overlay_threshold=1,5

I would like to do something like that

-f
surf/lh.inflated:overlay=surf/lh.sulc,overlay=surf/lh.thickness:overlay_threshold=1,5


is this possible?

Thanks!
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[Freesurfer] longitudinal hippocampal aseg editing

2018-09-07 Thread Rebecca Ray 
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Martin,

That is the point.  I have edited the hippocampus in the -long 2 times
and the recon does not maintain my edits.

I would love any help to changes I should be making to my recon
statement to maintain my edits.


Rebecca



Hi Rebecca,

aseg edits to subcortical structures need to be done in the -long
stage.
(see here: https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalEdits
)
Best, Martin



On Thu, 2018-09-06 at 14:37 -0700, Rebecca Ray wrote:
>* External Email - Use Caution
*>* HELP
*>* -- Forwarded message --
*>* From: Rebecca Ray https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>
*>* Date: Thu, Sep 6, 2018 at 12:05 PM
*>* Subject: longitudinal hippocampal aseg editing
*>* To: freesurfer at nmr.mgh.harvard.edu

*> > >* I have 2 time points on 60 subjects with most being in some form of
*>* AD.  There are considerable differences in hippocampal volume between
*>* time points.  I edited the raw images before making the template. I
*>* then had to edit the aseg template image and there were still
*>* problems on the -long images.  I tried to edit and rerun autorecon2-
*>* noaseg and autorecon3 and it does not appear to be keeping my edits.
*> >* What am I doing wrong?
*> >* Rebecca
*> >* ___*
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Re: [Freesurfer] recon-all error

2018-09-07 Thread Douglas Greve 
The terminal output is evrything that gets printed to the screen. The 
analysis in the recon-all.log file looks  like it did not finish right 
away (and there is no error msg in it)


On 9/7/18 11:51 AM, Song, Da-Yea wrote:


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I have attached the recon-all.log on this email. I’m not so sure what 
you mean by the terminal output file?


Thanks,

Da-Yea

*From:*freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] *On Behalf Of *Douglas 
Greve

*Sent:* Friday, September 07, 2018 11:36 AM
*To:* freesurfer@nmr.mgh.harvard.edu
*Subject:* Re: [Freesurfer] recon-all error

can you send the terminal output and recon-all.log?
thanks

On 9/7/18 9:58 AM, Song, Da-Yea wrote:

*External Email - Use Caution *

Hello,

I’m running some subjects through recon-all but have noticed that
some error out (terminate the job) within seconds of starting. Any
suggestions would be really appreciated. Here is the recon-all.cmd
error message:

#-

# New invocation of recon-all Fri Sep  7 09:34:58 EDT 2018

mri_convert /g5/dcn/freesurfer/MPRAGE/PS070/001
/g5/dcn/freesurfer/subjects/PS070/mri/orig/001.mgz

#

#@# MotionCor Fri Sep  7 09:35:30 EDT 2018

cp /g5/dcn/freesurfer/subjects/PS070/mri/orig/001.mgz
/g5/dcn/freesurfer /subjects/PS070/mri/rawavg.mgz

mri_convert /g5/dcn/freesurfer/subjects/PS070/mri/rawavg.mgz
/g5/dcn/freesurfer /subjects/PS070/mri/orig.mgz --conform

mri_add_xform_to_header -c /g5/dcn/freesurfer
/subjects/PS070/mri/transforms/talairach.xfm /g5/dcn/freesurfer
/subjects/PS070/mri/orig.mgz /g5/dcn/freesurfer
/subjects/PS070/mri/orig.mgz

#

#@# Talairach Fri Sep  7 09:35:44 EDT 2018

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

#-

# New invocation of recon-all Fri Sep  7 09:36:58 EDT 2018

#-

# New invocation of recon-all Fri Sep  7 09:37:03 EDT 2018

#-

# New invocation of recon-all Fri Sep  7 09:39:43 EDT 2018

#-

# New invocation of recon-all Fri Sep  7 09:39:47 EDT 2018

#-

# New invocation of recon-all Fri Sep  7 09:42:58 EDT 2018

#-

# New invocation of recon-all Fri Sep  7 09:43:02 EDT 2018

Best,

Da-yea



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Re: [Freesurfer] FsPalm patch

2018-09-07 Thread Douglas Greve 
Actually, I figured it out. Everything is there now, just follow the 
instructions in the README.

On 9/7/18 11:48 AM, Douglas Greve wrote:
> I have recreated the patch. The only problem is that I don't quite
> remember what should be in it. The wiki says that there are 3 files to
> install, but I can only remember two. Tom, can you install those two
> files and run it and see what fails? That will tell me what the 3rd file is.
> thanks
> doug
>
>
> On 9/7/18 11:30 AM, ts...@rcmd.org wrote:
>>   External Email - Use Caution
>>
>> Hi Tom and Zahra,
>>
 From: freesurfer-boun...@nmr.mgh.harvard.edu 
  on behalf of Tom Parker
 I am attempting to download the FsPalm patch 
 (https://surfer.nmr.mgh.harvard.edu/fswiki/FsPalm)
>>> On September 7, 2018 at 4:10 PM "Nasiriavanaki, Zahra" 
>>>  wrote:
>>> I downloaded it from this link.
>>> https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/PALM/UserGuide
>> I think you are talking about 2 different things: PALM and FsPalm.
>>
>> @Tom: On the problem with the FsPalm download: the FreeSurfer FTP server is 
>> currently unavailable due to a hard disk failure, see this recent message on 
>> this list:
>>
>> https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg59312.html
>>
>> Just wait a bit.
>>
>>
>> Best,
>>
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Re: [Freesurfer] FsPalm patch

2018-09-07 Thread Douglas Greve 
I have recreated the patch. The only problem is that I don't quite 
remember what should be in it. The wiki says that there are 3 files to 
install, but I can only remember two. Tom, can you install those two 
files and run it and see what fails? That will tell me what the 3rd file is.
thanks
doug


On 9/7/18 11:30 AM, ts...@rcmd.org wrote:
>  External Email - Use Caution
>
> Hi Tom and Zahra,
>
>>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>>>  on behalf of Tom Parker
>>> I am attempting to download the FsPalm patch 
>>> (https://surfer.nmr.mgh.harvard.edu/fswiki/FsPalm)
>> On September 7, 2018 at 4:10 PM "Nasiriavanaki, Zahra" 
>>  wrote:
>> I downloaded it from this link.
>> https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/PALM/UserGuide
> I think you are talking about 2 different things: PALM and FsPalm.
>
> @Tom: On the problem with the FsPalm download: the FreeSurfer FTP server is 
> currently unavailable due to a hard disk failure, see this recent message on 
> this list:
>
>https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg59312.html
>
> Just wait a bit.
>
>
> Best,
>

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Re: [Freesurfer] recon-all error

2018-09-07 Thread Douglas Greve 

can you send the terminal output and recon-all.log?
thanks

On 9/7/18 9:58 AM, Song, Da-Yea wrote:


External Email - Use Caution

Hello,

I’m running some subjects through recon-all but have noticed that some 
error out (terminate the job) within seconds of starting. Any 
suggestions would be really appreciated. Here is the recon-all.cmd 
error message:


#-

# New invocation of recon-all Fri Sep  7 09:34:58 EDT 2018

mri_convert /g5/dcn/freesurfer/MPRAGE/PS070/001 
/g5/dcn/freesurfer/subjects/PS070/mri/orig/001.mgz


#

#@# MotionCor Fri Sep  7 09:35:30 EDT 2018

cp /g5/dcn/freesurfer/subjects/PS070/mri/orig/001.mgz 
/g5/dcn/freesurfer /subjects/PS070/mri/rawavg.mgz


mri_convert /g5/dcn/freesurfer/subjects/PS070/mri/rawavg.mgz 
/g5/dcn/freesurfer /subjects/PS070/mri/orig.mgz --conform


mri_add_xform_to_header -c /g5/dcn/freesurfer 
/subjects/PS070/mri/transforms/talairach.xfm /g5/dcn/freesurfer 
/subjects/PS070/mri/orig.mgz /g5/dcn/freesurfer 
/subjects/PS070/mri/orig.mgz


#

#@# Talairach Fri Sep  7 09:35:44 EDT 2018

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


#-

# New invocation of recon-all Fri Sep  7 09:36:58 EDT 2018

#-

# New invocation of recon-all Fri Sep  7 09:37:03 EDT 2018

#-

# New invocation of recon-all Fri Sep  7 09:39:43 EDT 2018

#-

# New invocation of recon-all Fri Sep  7 09:39:47 EDT 2018

#-

# New invocation of recon-all Fri Sep  7 09:42:58 EDT 2018

#-

# New invocation of recon-all Fri Sep  7 09:43:02 EDT 2018

Best,

Da-yea


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Re: [Freesurfer] FsPalm patch

2018-09-07 Thread ts+ml 
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Hi Tom and Zahra,

>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>>  on behalf of Tom Parker
>> I am attempting to download the FsPalm patch 
>> (https://surfer.nmr.mgh.harvard.edu/fswiki/FsPalm)
> On September 7, 2018 at 4:10 PM "Nasiriavanaki, Zahra" 
>  wrote:
> I downloaded it from this link.
> https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/PALM/UserGuide

I think you are talking about 2 different things: PALM and FsPalm.

@Tom: On the problem with the FsPalm download: the FreeSurfer FTP server is 
currently unavailable due to a hard disk failure, see this recent message on 
this list:

  https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg59312.html

Just wait a bit.


Best,

-- 
Tim Schäfer

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Re: [Freesurfer] FsPalm patch

2018-09-07 Thread Nasiriavanaki, Zahra 
Hi


I downloaded it from this link.


https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/PALM/UserGuide

PALM/UserGuide - FslWiki - University of 
Oxford
fsl.fmrib.ox.ac.uk
Downloading and installing PALM. To download latest packaged version, please 
click here.. Alternatively, visit the repository on GitHub.. PALM can run as a 
standalone command (i.e., executed directly from the command line/terminal), or 
inside Octave or Matlab.



Good luck

Mona



Zahra (Mona) Nasiriavanaki

Postdoctoral Research Fellow

Martinos Center for Biomedical Imaging

Massachusetts General Hospital

149 13th Street, 149-2615

Charlestown, MA, USA, 02129




From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Tom Parker 

Sent: Friday, September 7, 2018 5:01:37 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] FsPalm patch


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Dear Freesurfer developers,

I am attempting to download the FsPalm patch 
(https://surfer.nmr.mgh.harvard.edu/fswiki/FsPalm) using: the link described in 
the wiki - ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-patch/PALM

However, there appears to be no directory at that location.

Please can you inform me how to install the FsPalm patch?

Many thanks
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[Freesurfer] recon-all error

2018-09-07 Thread Song, Da-Yea 
External Email - Use Caution

Hello,

I'm running some subjects through recon-all but have noticed that some error 
out (terminate the job) within seconds of starting. Any suggestions would be 
really appreciated. Here is the recon-all.cmd error message:

#-
# New invocation of recon-all Fri Sep  7 09:34:58 EDT 2018

mri_convert /g5/dcn/freesurfer/MPRAGE/PS070/001 
/g5/dcn/freesurfer/subjects/PS070/mri/orig/001.mgz

#
#@# MotionCor Fri Sep  7 09:35:30 EDT 2018

cp /g5/dcn/freesurfer/subjects/PS070/mri/orig/001.mgz /g5/dcn/freesurfer 
/subjects/PS070/mri/rawavg.mgz


mri_convert /g5/dcn/freesurfer/subjects/PS070/mri/rawavg.mgz /g5/dcn/freesurfer 
/subjects/PS070/mri/orig.mgz --conform


mri_add_xform_to_header -c /g5/dcn/freesurfer 
/subjects/PS070/mri/transforms/talairach.xfm /g5/dcn/freesurfer 
/subjects/PS070/mri/orig.mgz /g5/dcn/freesurfer /subjects/PS070/mri/orig.mgz

#
#@# Talairach Fri Sep  7 09:35:44 EDT 2018

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



#-
# New invocation of recon-all Fri Sep  7 09:36:58 EDT 2018


#-
# New invocation of recon-all Fri Sep  7 09:37:03 EDT 2018


#-
# New invocation of recon-all Fri Sep  7 09:39:43 EDT 2018


#-
# New invocation of recon-all Fri Sep  7 09:39:47 EDT 2018


#-
# New invocation of recon-all Fri Sep  7 09:42:58 EDT 2018


#-
# New invocation of recon-all Fri Sep  7 09:43:02 EDT 2018

Best,
Da-yea


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Re: [Freesurfer] FS6.0-dev (Jun27, 2018) Hippocampal subfield Matlab runtime Java error

2018-09-07 Thread Niels Bergsland 
External Email - Use Caution

Hi all,
Not sure if this was resolved off-list or not, but I just ran into it
myself and it turned out to be a permissions-related error in that the user
didn't have read access to some of the required files in the Matlab
runtime. Setting them appropriately resolved the issue.

Best,
Niels

On Thu, Jul 5, 2018 at 9:37 PM Sean Ma  wrote:

> External Email - Use Caution
>
> Hi Eugenio,
>
> Thanks for the tip.
>
> I've deleted the /MCR* folder in /tmp and made sure I had enough space in
> /tmp - 9GB.
>
> Unfortunately, the same error message still exists.
>
> Let me know if I could further send any debugging logs to help isolate
> this issue.
>
> Thanks for your help!
>
>
> Best,
>
> Sean
> University of Michigan
>
>
>
> On Tue, Jul 3, 2018 at 5:59 AM, Iglesias Gonzalez, Eugenio <
> e.igles...@ucl.ac.uk> wrote:
>
>> External Email - Use Caution
>>
>> I was thinking it could be a corrupt MCR cache. Could you please:
>>
>> a) Delete /tmp/MCR* directories
>>
>> b) Make sure you've got enough space in /tmp/
>>
>> Cheers,
>>
>> /Eugenio
>>
>>
>> Juan Eugenio Iglesias
>>
>> Centre for Medical Image Computing (CMIC)
>>
>> University College London
>>
>> http://www.jeiglesias.com
>>
>> http://cmictig.cs.ucl.ac.uk/
>>
>>
>> --
>> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
>> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Sean Ma <
>> tehsh...@umich.edu>
>> *Sent:* Tuesday, July 3, 2018 1:43:18 AM
>> *To:* Freesurfer support list
>> *Cc:* Hoopes, Andrew
>> *Subject:* Re: [Freesurfer] FS6.0-dev (Jun27, 2018) Hippocampal subfield
>> Matlab runtime Java error
>>
>>
>> External Email - Use Caution
>>
>> Hi Eugenio,
>>
>> I’ve followed the wiki and installed it based on the instructions. My
>> server runs on RHEL7.
>>
>> Best,
>>
>> Sean
>>
>>
>>
>> On Mon, Jul 2, 2018 at 3:47 PM Iglesias Gonzalez, Eugenio <
>> e.igles...@ucl.ac.uk> wrote:
>>
>> External Email - Use Caution
>>
>> That’s rather ugly.
>>
>> Sean: did you install the runtime from the Mathworks website, or did you
>> download / uncompress following the instrucitons in the wiki?
>>
>> Andrew:  any ideas?
>>
>> Cheers,
>>
>> /Eugenio
>>
>>
>>
>> --
>>
>> Juan Eugenio Iglesias
>>
>> ERC Senior Research Fellow
>>
>> Centre for Medical Image Computing (CMIC)
>>
>> University College London
>>
>> http://www.jeiglesias.com
>>
>> http://cmictig.cs.ucl.ac.uk/
>>
>>
>>
>>
>>
>> *From: * on behalf of Sean Ma <
>> tehsh...@umich.edu>
>> *Reply-To: *Freesurfer support list 
>> *Date: *Monday, 2 July 2018 at 20:33
>> *To: *"freesurfer@nmr.mgh.harvard.edu" 
>> *Subject: *[Freesurfer] FS6.0-dev (Jun27, 2018) Hippocampal subfield
>> Matlab runtime Java error
>>
>>
>>
>> *External Email - Use Caution*
>>
>> Hi Eugenio,
>>
>>
>>
>> I'd like to report a Matlab runtime Java error when running the
>> Hippocampal subfield on FS6.0-dev (Jun 27, 2018) after a successful
>> completion of `recon-all`. Matlab 2014b runtime has been successfully
>> expanded at /MCRv84.
>>
>>
>>
>> The error I've encountered follows. Any suggestions on how I can overcome
>> this error?
>>
>>
>>
>> Thanks for your pointers!
>>
>>
>>
>> Best,
>>
>>
>>
>> Sean Ma
>>
>> University of Michigan
>>
>>
>>
>> ==
>>
>>
>>
>> [tehsheng@b-fmri FS6results]$ segmentHA_T1.sh b30002_02712
>>
>> #
>>
>> #@# Hippocampal Subfields processing (T1) left Mon Jul  2 15:16:41 EDT
>> 2018
>>
>> --
>>
>> Setting up environment variables
>>
>> ---
>>
>> LD_LIBRARY_PATH is
>> .:/opt/freesurfer6/MCRv84//runtime/glnxa64:/opt/freesurfer6/MCRv84//bin/glnxa64:/opt/freesurfer6/MCRv84//sys/os/glnxa64::/opt/freesurfer6/MCRv84//sys/opengl/lib/glnxa64:
>>
>> Error using checkRequiredMCRProducts (line 25)
>>
>> Java exception occurred:
>>
>> java.lang.NullPointerException
>>
>> at
>> com.mathworks.install.InstalledProductFactory$1.execute(InstalledProductFactory.java:56)
>>
>> at
>> com.mathworks.install.InstalledProductFactory$1.execute(InstalledProductFactory.java:49)
>>
>> at
>> com.mathworks.install.InstalledProductFactory$InstallerWorkSpace.executeTask(InstalledProductFactory.java:193)
>>
>> at
>> com.mathworks.install.InstalledProductFactory$InstallerWorkSpace.access$200(InstalledProductFactory.java:108)
>>
>> at
>> com.mathworks.install.InstalledProductFactory.getInstalledProducts(InstalledProductFactory.java:67)
>>
>>
>>
>> Error in deployrc (line 9)
>>
>>
>>
>> Error in matlabrc (line 238)
>>
>>
>>
>>
>>
>> @#@FSTIME  2018:07:02:15:16:41
>> run_segmentSubjectT1_autoEstimateAlveusML.sh N 13 e 32.59 S 0.39 U 5.00 P
>> 16% M 205368 F 82 R 43627 W 0 c 54 w 1963 I 24008 O 82888 L 0.00 0.07 0.89
>>
>> @#@FSLOADPOST 2018:07:02:15:17:13
>> run_segmentSubjectT1_autoEstimateAlveusML.sh N 13 0.15 0.11 0.87
>>
>> Linux b-fmri.edu 2.6.32-696.28.1.el6.x86_64 #1 SMP

[Freesurfer] FsPalm patch

2018-09-07 Thread Tom Parker 
External Email - Use Caution

Dear Freesurfer developers,

I am attempting to download the FsPalm patch 
(https://surfer.nmr.mgh.harvard.edu/fswiki/FsPalm 
) using: the link described 
in the wiki - 
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-patch/PALM 


However, there appears to be no directory at that location. 

Please can you inform me how to install the FsPalm patch?

Many thanks___
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Re: [Freesurfer] Fwd: longitudinal hippocampal aseg editing

2018-09-07 Thread Martin Reuter 
Hi Rebecca,

aseg edits to subcortical structures need to be done in the -long
stage.
(see here: https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalEdits
)
Best, Martin



On Thu, 2018-09-06 at 14:37 -0700, Rebecca Ray wrote:
> External Email - Use Caution
> HELP
> -- Forwarded message --
> From: Rebecca Ray 
> Date: Thu, Sep 6, 2018 at 12:05 PM
> Subject: longitudinal hippocampal aseg editing
> To: freesurfer@nmr.mgh.harvard.edu
> 
> 
> I have 2 time points on 60 subjects with most being in some form of
> AD.  There are considerable differences in hippocampal volume between
> time points.  I edited the raw images before making the template. I
> then had to edit the aseg template image and there were still
> problems on the -long images.  I tried to edit and rerun autorecon2-
> noaseg and autorecon3 and it does not appear to be keeping my edits.
> 
> What am I doing wrong?
> 
> Rebecca
> 
> ___
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Re: [Freesurfer] Did not find any volume info. Warning: MatrixInverse failed

2018-09-07 Thread Sofia Rodriguez Penuela 
External Email - Use Caution

Thanks for your quick answer Ruopeng. 

They are loaded with the same command and we check that the freeview's
build time is the same in both computers: 

_Version 2.0_ 

_Build Jan 18 2017 16:48:55_ 

_Copyright (c) 2016_ 

Do you know what else can happen? 

Thanks

---
Sofía Rodríguez Peñuela, Técnico de Laboratorio.
Laboratorio de Neurociencia Funcional
Departamento de Fisiología, Anatomía y Biología Celular. 
Universidad Pablo de Olavide
Ctra. de Utrera, Km.1
41013 - Sevilla
- España -
Movil: 627273085
Email: srod...@upo.es
http://www.upo.es/neuroaging/es/ 

El 2018-09-06 18:00, freesurfer-requ...@nmr.mgh.harvard.edu escribió:

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> 
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of Freesurfer digest..."
> 
> Today's Topics:
> 
> 1. Data Analyst Position - Child Mind Institute (New York)
> (Suk Jun Hong)
> 2. Re: Did not find any volume info. Warning: MatrixInverse
> failed (Ruopeng Wang)
> 3. Using the new Thalamus tool (Erik O'Hanlon)
> 4. Parcellations (e.g.,labels for Brodmann Areas) for
> Connectome Workbench? (Dinicola, Lauren)
> 
> --
> 
> Message: 1
> Date: Thu, 6 Sep 2018 14:52:13 +
> From: Suk Jun Hong 
> Subject: [Freesurfer] Data Analyst Position - Child Mind Institute
> (New York)
> To: "freesurfer@nmr.mgh.harvard.edu" 
> Message-ID: 
> Content-Type: text/plain; charset="utf-8"
> 
> External Email - Use Caution
> 
> The Child Mind Institute is seeking a Data Analyst to support a collaborative 
> study with Dr. Amy Roy at Fordham University. The Data Analyst?s role is to 
> assist with the analysis of functional MRI data, as well as reporting 
> results. In particular, the work includes: 1) preprocessing of a large fMRI 
> dataset and implementing quality assurance protocols, 2) maintaining the 
> database and imaging processing pipeline; 3) supporting post-doctoral 
> researchers by implementing novel analytic methods; and 4) training graduate 
> and undergraduate students in how to preprocess and analyze resting state and 
> task-based functional MRI data.
> 
> Reporting to Dr. Suk Jun Hong and the Director of the Center for the 
> Developing Brain, this is a full-time position, primarily located at the CMI 
> headquarters (101 E 56th St, New York, NY 10022).
> 
> Responsibilities:
> Implementation, execution, and maintenance of fMRI imaging analysis pipelines
> Conduct neuroanatomical profile analyses as well as analyses of resting-state 
> functional MRI data using novel software packages and neuroinformatic 
> platforms
> Develop graphs, reports, and presentations of project results
> Training undergraduate and graduate students in data analysis theory and 
> implementation
> Perform basic statistical analyses for projects and reports
> 
> Qualifications:
> Master?s degree in neuroscience, computer science, mathematics, statistics or 
> related areas is preferred
> Extensive neuroimaging experience in fMRI analysis and proficiency with one 
> or more packages (e.g. FreeSurfer, AFNI, FSL, Workbench or SPM)
> Programming experience in one or more languages (e.g., Python, Matlab, R or 
> similar platforms is required)
> Significant prior neuroimaging experience with more imaging and/or simulation 
> modalities (e.g., DTI, EEG, MEG, TMS etc.) is a plus, but not required
> A passion for the applying computational methods to understand clinical 
> conditions.
> 
> If you are interested in the positions, please apply to
> https://workforcenow.adp.com/mascsr/default/mdf/recruitment/recruitment.html?cid=1b50a554-ed4a-4219-a358-aa3cbeea1e70=259986=en_US=CC3=19000101_01
> 
> Thank you!
> 
> --
> Suk-Jun Hong, PhD
> Postdoc, Center for the Developing Brain
> Child Mind Institute
> -- next part --
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> 
> --
> 
> Message: 2
> Date: Thu, 6 Sep 2018 11:29:32 -0400
> From: Ruopeng Wang 
> Subject: Re: [Freesurfer] Did not find any volume info. Warning:
> MatrixInverse failed
> To: freesurfer@nmr.mgh.harvard.edu
> Message-ID: <57736545-c834-b94f-8fe1-289f6a6d0...@nmr.mgh.harvard.edu>
> Content-Type: text/plain; charset="utf-8"
> 
> Were they loaded with the same command? Can you check freeview's build 
> time to make sure they are the same build? You can check it from menu 
> Help->About.
> 
> Ruopeng
> 
> On