Re: [Freesurfer] Failed to download Freesurfer from ftp, server seems empty

[Bruce Fischl]

Hi Minos

we are having major hardware issues that we hope to have resolved 
tonight. Try again tomorrow

cheers
Bruce
On Wed, 29 Jun 2016, C. Minos Niu wrote:

> Hello,
> 
> I tried to have my new students download and install Freesurfer from
> https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall, but all
> download links gave "550 Failed to change directory" error. I logged into
> the FTP anonymously only to find it empty under "pub/".
> 
> Any idea how to proceed with the downloading? Thanks!
> 
> -Minos
> 
>
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[Freesurfer] Problem while using the -localGI

[Hari Guragain]

Dear Freesurfer experts,

I am having trouble using the -localGI option to smoothen the pial surface.
When I use the command like:

recon-all -s ABC -localGI

I got the following error:

INFO: FreeSurfer build stamps do not match

Subject Stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0

Current Stamp: freesurfer-Darwin-OSX-dev-20160611-876a0e6

cp: /Applications/freesurfer/subjects/ABC/scripts/lastcall.build-stamp.txt:
Permission denied

INFO: SUBJECTS_DIR is /Applications/freesurfer/subjects

Actual FREESURFER_HOME /Applications/freesurfer

/Applications/freesurfer/subjects/ABC/scripts/recon-all.cmd: Permission
denied.

But when I tried to do the same reconstruction via  the super user(su), it
says something about the library linking like below. I am wondering if it
is a problem related to Matlab or freesurfer? I am currently using the
development version of freesurfer.

Any help will be greatly appreciated.

reading surface from lh.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

Thank you all.

Hari
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Re: [Freesurfer] Question about FreeSurfer

[Bruce Fischl]

Hi Dorsa

as I said, if you rerun don't include the -i. And please include the full 
command and output pasted into the email


thanks
Bruce


On Tue, 28 Jun 2016, Dorsa Haji Ghaffari wrote:


Hi,

Thanks for the help. I ran the following code and I got errors. I have
attached the log.

recon-all -i LT7616_3TS_Copy_0001.dcm -subjid test6 -all


On Tue, Jun 28, 2016 at 4:23 PM, Bruce Fischl 
wrote:
  Hi Dorsa

  can you just copy and paste the text into the email? It's much
  easier than trying to look at images of text.

  Your recon-all command finished successfully. Essentially you
  didn't tell it to do anything except import the data and create
  the subject dir. Typically you want to give the -all directive.
  I'm not sure what the warnings are, but you can look at the
  subject's mri/orig/001.mgz volume in freeview to see if it
  worked. Next time you give recon-all do it without the -i (since
  it already imported the data) or it will complain

  cheers
  Bruce


   On Tue, 28 Jun 2016, Dorsa Haji Ghaffari wrote:

sure, following is the code I run:
source $FREESURFER_HOME/SetUpFreeSurfer.sh
export SUBJECTS_DIR=/usr/local/freesurfer/subjects
recon-all -i LT7616_3TS_Copy_0001.dcm -subjid test3

And I have attached two screenshots of what I get
after running the code.



On Tue, Jun 28, 2016 at 4:06 PM, Bruce Fischl

wrote:
      Hi Dorsa

      you need to give us more information that that
if you want us to
      help you. Send us the full command line you
ran and the full
      screen output and log files for starters.

      cheers
      Bruce
       On Tue, 28 Jun 2016, Dorsa Haji Ghaffari
wrote:

            Thank you! When I recon-all my files, I
get the
            following error:files are
            not found to be different and cannot be
sorted

            Do you have any suggestions?

            Thank you

            Dorsa


            On Tue, Jun 28, 2016 at 12:57 PM, Bruce
Fischl
            
            wrote:
                  just give recon-all a single slice
from the
            series with -i
                  .  It will figure out

                  the rest of them

                  On Tue, 28 Jun 2016, Dorsa Haji
Ghaffari
            wrote:

                  > Hi,
                  > I am a little confused about how
should I
            save my files to
                  execute recon-all on
                  > them. I have 240 slices of dicom
format and
            I put them in a
                  folder in my
                  > subjects_dir. but I get errors
when using
            recon-all on the
                  folder containing the
                  > MRIs. Can you help me with that?
I really
            appreciate your help
                  >
                  > Thank you
                  >
                  > Dorsa
                  >
                  > On Mon, Jun 27, 2016 at 3:13 PM,
Bruce
            Fischl
                  
wrote:
                  >       Hi Dorsa
                  >
                  >       what specific models do
you need? The
            10-20 hours is to
                  process the
                  >       data
                  >       from a single subject at a
single
            timepoint. If you
                  check out our
                  >       wiki
                  >     
           
 (http://surfer.nmr.mgh.harvard.edu/fswiki) there
            are
                  lots of
                  >       tutorials and
                  >       sample datasets and such
                  >
                  >       cheers
                  >       Bruce
                  >
                  >       On Mon, 27 Jun 2016, Dorsa
Haji
                  >       Ghaffari wrote:
      

Re: [Freesurfer] Question about FreeSurfer

[Bruce Fischl]

Hi Dorsa

can you just copy and paste the text into the email? It's much easier 
than trying to look at images of text.


Your recon-all command finished successfully. Essentially you didn't tell 
it to do anything except import the data and create the subject dir. 
Typically you want to give the -all directive. I'm not sure what the 
warnings are, but you can look at the subject's mri/orig/001.mgz volume in 
freeview to see if it worked. Next time you give recon-all do it without 
the -i (since it already imported the data) or it will complain


cheers
Bruce


 On Tue, 28 Jun 2016, Dorsa Haji 
Ghaffari wrote:



sure, following is the code I run:
source $FREESURFER_HOME/SetUpFreeSurfer.sh
export SUBJECTS_DIR=/usr/local/freesurfer/subjects
recon-all -i LT7616_3TS_Copy_0001.dcm -subjid test3

And I have attached two screenshots of what I get after running the code.



On Tue, Jun 28, 2016 at 4:06 PM, Bruce Fischl 
wrote:
  Hi Dorsa

  you need to give us more information that that if you want us to
  help you. Send us the full command line you ran and the full
  screen output and log files for starters.

  cheers
  Bruce
   On Tue, 28 Jun 2016, Dorsa Haji Ghaffari wrote:

Thank you! When I recon-all my files, I get the
following error:files are
not found to be different and cannot be sorted

Do you have any suggestions?

Thank you

Dorsa


On Tue, Jun 28, 2016 at 12:57 PM, Bruce Fischl

wrote:
      just give recon-all a single slice from the
series with -i
      .  It will figure out

      the rest of them

      On Tue, 28 Jun 2016, Dorsa Haji Ghaffari
wrote:

      > Hi,
      > I am a little confused about how should I
save my files to
      execute recon-all on
      > them. I have 240 slices of dicom format and
I put them in a
      folder in my
      > subjects_dir. but I get errors when using
recon-all on the
      folder containing the
      > MRIs. Can you help me with that? I really
appreciate your help
      >
      > Thank you
      >
      > Dorsa
      >
      > On Mon, Jun 27, 2016 at 3:13 PM, Bruce
Fischl
       wrote:
      >       Hi Dorsa
      >
      >       what specific models do you need? The
10-20 hours is to
      process the
      >       data
      >       from a single subject at a single
timepoint. If you
      check out our
      >       wiki
      >     
 (http://surfer.nmr.mgh.harvard.edu/fswiki) there
are
      lots of
      >       tutorials and
      >       sample datasets and such
      >
      >       cheers
      >       Bruce
      >
      >       On Mon, 27 Jun 2016, Dorsa Haji
      >       Ghaffari wrote:
      >
      >       > Hi,
      >       > I am graduate student at the
University of Michigan
      and I am
      >       performing
      >       > research on deep brain stimulation.
I want to warp an
      anatomical
      >       brain atlas
      >       > to individual patient MRIs to get
the patient specific
      brain models
      >       out of
      >       > it. I chose FreeSurfer to do this
and I have installed
      it on my
      >       computer. I
      >       > realized that it takes 10-20 hrs to
reconstruct the
      image. I wanted
      >       to ask
      >       > if that is the time for one image?
or the whole series
      of images?
      >       > I also wanted to ask if there is a
step by step
      tutorial on how to
      >       do this.
      >       >
      >       > Thank you
      >       >
      >       > Dorsa Ghaffari
      >       >
      >       >
      >       >
      >       >
      >
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      >

Re: [Freesurfer] freeview display problem

[Ruopeng Wang]

Ok, you should try updating your graphics card driver. There is also chance 
that your graphics card is broken. Unfortunately we are not able to diagnose 
that for you. Sorry.

Best,
Ruopeng

> On Jun 28, 2016, at 4:17 PM, Ramtilak Gattu  wrote:
> 
> Attached is the screen shot comparison side by side.
> 
> I downloaded 3d slicer and even it dispalys images similar to what freeview 
> does. 
> 
> Thanks
> 
> Regards
> Tilak
> From: Ramtilak Gattu
> Sent: Tuesday, June 28, 2016 3:46:34 PM
> To: freesurfer@nmr.mgh.harvard.edu 
> Subject: Re: freeview display problem
>  
> glxgears shows up a screen with three gear wheels in blue, pink and green and 
> frame information rate being printed out on the command window.
> From: Ramtilak Gattu
> Sent: Tuesday, June 28, 2016 2:55:32 PM
> To: freesurfer@nmr.mgh.harvard.edu 
> Subject: Re: freeview display problem
>  
> Nope they dont look normal they are being displayed in some other colors like 
> heat is showing up as blue , jet as green etc. Even when the surfaces are 
> loaded up the color of the surfaces doesnt look right. when the surface 
> yellow is chosen are red it is being displayed as blue.
> 
> Thanks
> 
> Regards
> Tilak
> From: Ramtilak Gattu
> Sent: Tuesday, June 28, 2016 2:01:00 PM
> To: freesurfer@nmr.mgh.harvard.edu 
> Subject: Re: freeview display problem
>  
> Hey Ruopeng,
> 
> I still couldnt figure out whats going on the freeview display. I updated the 
> Nvidia drivers but still its not displaying in gray scale.
> 
> please help.
> 
> thanks
> 
> Regards
> Tilak
> From: Ramtilak Gattu
> Sent: Friday, June 24, 2016 12:25:50 PM
> To: freesurfer@nmr.mgh.harvard.edu 
> Subject: Re: freeview display problem
>  
> That is all . No error messages at all.
> From: Ramtilak Gattu
> Sent: Friday, June 24, 2016 10:25:42 AM
> To: freesurfer@nmr.mgh.harvard.edu 
> Subject: Re: freeview display problem
>  
> I tried updating my Nvidia drivers. but now whenever I try to open freeview 
> it says " aborted ( core dumped).
> 
> please help.
> 
> Thanks
> 
> Regards
> Tilak
> From: Ramtilak Gattu
> Sent: Thursday, June 23, 2016 5:27:12 PM
> To: freesurfer@nmr.mgh.harvard.edu 
> Subject: Re: freeview display problem
>  
> May be thats the problem. I'll try to give it a shot to see if it fixes the 
> problem.
> 
> Thanks.
> From: Ramtilak Gattu
> Sent: Thursday, June 23, 2016 4:10:28 PM
> To: freesurfer@nmr.mgh.harvard.edu 
> Subject: Re: freeview display problem
>  
> This issue is only with freesurfer , images on fslview doesnt have this 
> problem.
> 
> 
> From: Ramtilak Gattu
> Sent: Thursday, June 23, 2016 3:31:41 PM
> To: freesurfer@nmr.mgh.harvard.edu 
> Subject: Re: freeview display problem
>  
> That is just one layer the yellow contrast is from when we tune the contrast 
> up or down.
> From: Ramtilak Gattu
> Sent: Thursday, June 23, 2016 2:37:36 PM
> To: freesurfer@nmr.mgh.harvard.edu 
> Subject: freeview display problem
>  
> Hello ,
> 
> I am having strange freeview display problem. The images doesnt appear in 
> gray scale anymore. Please have a look at the attachment.  Is there a switch 
> that was  turned on that I am not aware of.
> 
> Could some one help.
> 
> Thanks
> 
> Regards
> Tilak
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> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 
> 
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Re: [Freesurfer] freeview display problem

[Ruopeng Wang]

The color should be red, blue and green. It is your graphics card or graphics 
driver issue.

Best,
Ruopeng

> On Jun 28, 2016, at 3:46 PM, Ramtilak Gattu  wrote:
> 
> glxgears shows up a screen with three gear wheels in blue, pink and green and 
> frame information rate being printed out on the command window.
> From: Ramtilak Gattu
> Sent: Tuesday, June 28, 2016 2:55:32 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: freeview display problem
>  
> Nope they dont look normal they are being displayed in some other colors like 
> heat is showing up as blue , jet as green etc. Even when the surfaces are 
> loaded up the color of the surfaces doesnt look right. when the surface 
> yellow is chosen are red it is being displayed as blue.
> 
> Thanks
> 
> Regards
> Tilak
> From: Ramtilak Gattu
> Sent: Tuesday, June 28, 2016 2:01:00 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: freeview display problem
>  
> Hey Ruopeng,
> 
> I still couldnt figure out whats going on the freeview display. I updated the 
> Nvidia drivers but still its not displaying in gray scale.
> 
> please help.
> 
> thanks
> 
> Regards
> Tilak
> From: Ramtilak Gattu
> Sent: Friday, June 24, 2016 12:25:50 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: freeview display problem
>  
> That is all . No error messages at all.
> From: Ramtilak Gattu
> Sent: Friday, June 24, 2016 10:25:42 AM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: freeview display problem
>  
> I tried updating my Nvidia drivers. but now whenever I try to open freeview 
> it says " aborted ( core dumped).
> 
> please help.
> 
> Thanks
> 
> Regards
> Tilak
> From: Ramtilak Gattu
> Sent: Thursday, June 23, 2016 5:27:12 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: freeview display problem
>  
> May be thats the problem. I'll try to give it a shot to see if it fixes the 
> problem.
> 
> Thanks.
> From: Ramtilak Gattu
> Sent: Thursday, June 23, 2016 4:10:28 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: freeview display problem
>  
> This issue is only with freesurfer , images on fslview doesnt have this 
> problem.
> 
> 
> From: Ramtilak Gattu
> Sent: Thursday, June 23, 2016 3:31:41 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: freeview display problem
>  
> That is just one layer the yellow contrast is from when we tune the contrast 
> up or down.
> From: Ramtilak Gattu
> Sent: Thursday, June 23, 2016 2:37:36 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: freeview display problem
>  
> Hello ,
> 
> I am having strange freeview display problem. The images doesnt appear in 
> gray scale anymore. Please have a look at the attachment.  Is there a switch 
> that was  turned on that I am not aware of.
> 
> Could some one help.
> 
> Thanks
> 
> Regards
> Tilak
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] checking freesurfer output

[Bruce Fischl]

Hi Gabor,

it depends on what you are doing. What you describe is sufficient for 
maps/structure volumes, but for example if you wanted to measure thickness 
within parcels you would have to check the accuracy of the cortical 
parcellation


cheers
Bruce


On Tue, 28 Jun 2016, Gabor Perlaki wrote:


Sorry to repost my question. I would appreciate any reply.

Best Regards,
Gabor

2016-06-13 10:51 GMT+02:00 Gabor Perlaki :
  Dear all,

I've a lot of patients and we are looking for the fastest solution to
check the output of Freesurfer. On the troubleshooting page
(https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TroubleshootingData)
there are a lot of steps to check, but I think not all of that should
be done to find out whether there is error in the final segmentations.
I think, but I am not sure, that checking the surfaces (white and
pial) and checking the subcortical segmentations (aseg) is enough to
realize if something is wrong. After an error is detected based on the
checked outputs (surfaces and aseg), we can find out the exact nature
of the error and correct it based on the troubleshooting page. Is it a
good solution for verifying the performance of Freesurfer by checking
only these two things (surfaces and aseg) or I need to check all of
the steps listed on the troubleshooting page anyway?


Best Regards,
Gabor




--
Gabor Perlaki
research associate
Diagnostic Center of Pécs
H-7623 Pécs, Rét str. 2.
Tel.: 0036-30-2084367
E-mail: petzinger.ga...@gmail.com

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Re: [Freesurfer] Question about FreeSurfer

[Dorsa Haji Ghaffari]

Thank you! When I recon-all my files, I get the following error:
files are not found to be different and cannot be sorted

Do you have any suggestions?

Thank you

Dorsa


On Tue, Jun 28, 2016 at 12:57 PM, Bruce Fischl 
wrote:

> just give recon-all a single slice from the series with -i  name>.  It will figure out
>
> the rest of them
>
> On Tue, 28 Jun 2016, Dorsa Haji Ghaffari wrote:
>
> > Hi,
> > I am a little confused about how should I save my files to execute
> recon-all on
> > them. I have 240 slices of dicom format and I put them in a folder in my
> > subjects_dir. but I get errors when using recon-all on the folder
> containing the
> > MRIs. Can you help me with that? I really appreciate your help
> >
> > Thank you
> >
> > Dorsa
> >
> > On Mon, Jun 27, 2016 at 3:13 PM, Bruce Fischl <
> fis...@nmr.mgh.harvard.edu> wrote:
> >   Hi Dorsa
> >
> >   what specific models do you need? The 10-20 hours is to process the
> >   data
> >   from a single subject at a single timepoint. If you check out our
> >   wiki
> >   (http://surfer.nmr.mgh.harvard.edu/fswiki) there are lots of
> >   tutorials and
> >   sample datasets and such
> >
> >   cheers
> >   Bruce
> >
> >   On Mon, 27 Jun 2016, Dorsa Haji
> >   Ghaffari wrote:
> >
> >   > Hi,
> >   > I am graduate student at the University of Michigan and I am
> >   performing
> >   > research on deep brain stimulation. I want to warp an anatomical
> >   brain atlas
> >   > to individual patient MRIs to get the patient specific brain
> models
> >   out of
> >   > it. I chose FreeSurfer to do this and I have installed it on my
> >   computer. I
> >   > realized that it takes 10-20 hrs to reconstruct the image. I
> wanted
> >   to ask
> >   > if that is the time for one image? or the whole series of images?
> >   > I also wanted to ask if there is a step by step tutorial on how
> to
> >   do this.
> >   >
> >   > Thank you
> >   >
> >   > Dorsa Ghaffari
> >   >
> >   >
> >   >
> >   >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> >
> > The information in this e-mail is intended only for the person to whom it
> > is
> > addressed. If you believe this e-mail was sent to you in error and the
> > e-mail
> > contains patient information, please contact the Partners Compliance
> > HelpLine at
> > http://www.partners.org/complianceline . If the e-mail was sent to you
> in
> > error
> > but does not contain patient information, please contact the sender and
> > properly
> > dispose of the e-mail.
> >
> >
> >
> >
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Re: [Freesurfer] freeview display problem

[Ruopeng Wang]

This sounds very likely a video card/driver issue. Would it be possible for you 
any other program that uses OpenGL/vtk, such as 3D slicer, Paraview? How does 
glxgears command show? 

> On Jun 28, 2016, at 2:55 PM, Ramtilak Gattu  wrote:
> 
> Nope they dont look normal they are being displayed in some other colors like 
> heat is showing up as blue , jet as green etc. Even when the surfaces are 
> loaded up the color of the surfaces doesnt look right. when the surface 
> yellow is chosen are red it is being displayed as blue.
> 
> Thanks
> 
> Regards
> Tilak
> From: Ramtilak Gattu
> Sent: Tuesday, June 28, 2016 2:01:00 PM
> To: freesurfer@nmr.mgh.harvard.edu 
> Subject: Re: freeview display problem
>  
> Hey Ruopeng,
> 
> I still couldnt figure out whats going on the freeview display. I updated the 
> Nvidia drivers but still its not displaying in gray scale.
> 
> please help.
> 
> thanks
> 
> Regards
> Tilak
> From: Ramtilak Gattu
> Sent: Friday, June 24, 2016 12:25:50 PM
> To: freesurfer@nmr.mgh.harvard.edu 
> Subject: Re: freeview display problem
>  
> That is all . No error messages at all.
> From: Ramtilak Gattu
> Sent: Friday, June 24, 2016 10:25:42 AM
> To: freesurfer@nmr.mgh.harvard.edu 
> Subject: Re: freeview display problem
>  
> I tried updating my Nvidia drivers. but now whenever I try to open freeview 
> it says " aborted ( core dumped).
> 
> please help.
> 
> Thanks
> 
> Regards
> Tilak
> From: Ramtilak Gattu
> Sent: Thursday, June 23, 2016 5:27:12 PM
> To: freesurfer@nmr.mgh.harvard.edu 
> Subject: Re: freeview display problem
>  
> May be thats the problem. I'll try to give it a shot to see if it fixes the 
> problem.
> 
> Thanks.
> From: Ramtilak Gattu
> Sent: Thursday, June 23, 2016 4:10:28 PM
> To: freesurfer@nmr.mgh.harvard.edu 
> Subject: Re: freeview display problem
>  
> This issue is only with freesurfer , images on fslview doesnt have this 
> problem.
> 
> 
> From: Ramtilak Gattu
> Sent: Thursday, June 23, 2016 3:31:41 PM
> To: freesurfer@nmr.mgh.harvard.edu 
> Subject: Re: freeview display problem
>  
> That is just one layer the yellow contrast is from when we tune the contrast 
> up or down.
> From: Ramtilak Gattu
> Sent: Thursday, June 23, 2016 2:37:36 PM
> To: freesurfer@nmr.mgh.harvard.edu 
> Subject: freeview display problem
>  
> Hello ,
> 
> I am having strange freeview display problem. The images doesnt appear in 
> gray scale anymore. Please have a look at the attachment.  Is there a switch 
> that was  turned on that I am not aware of.
> 
> Could some one help.
> 
> Thanks
> 
> Regards
> Tilak
> ___
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> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 
> 
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[Freesurfer] [TRACULA] ERROR: cannot unpack mosiacs without ASCII header

[Koubiyr, Ismail]

Hi everyone,

I have some problems trying to run TRACULA on some DWI data. It is a mosaic 
Siemens DWI. I first converted the DICOM files with dcm2nii to get the bvec and 
bval files.
Then I run the trac-all -prep -c command and I get the following error :

WARNING: file /My/path/to/dicom does not contain a Siemens ASCII header
has this file been anonymized?
ERROR: cannot unpack mosiacs without ASCII header

I tried to unpack the mosaics with gdcmtar, but I got the same error.

Thank you in advance for your help,

Ismail
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Re: [Freesurfer] freeview display problem

[Ramtilak Gattu]

Nope they dont look normal they are being displayed in some other colors like 
heat is showing up as blue , jet as green etc. Even when the surfaces are 
loaded up the color of the surfaces doesnt look right. when the surface yellow 
is chosen are red it is being displayed as blue.


Thanks

Regards

Tilak


From: Ramtilak Gattu
Sent: Tuesday, June 28, 2016 2:01:00 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: freeview display problem


Hey Ruopeng,


I still couldnt figure out whats going on the freeview display. I updated the 
Nvidia drivers but still its not displaying in gray scale.


please help.


thanks

Regards

Tilak


From: Ramtilak Gattu
Sent: Friday, June 24, 2016 12:25:50 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: freeview display problem


That is all . No error messages at all.


From: Ramtilak Gattu
Sent: Friday, June 24, 2016 10:25:42 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: freeview display problem


I tried updating my Nvidia drivers. but now whenever I try to open freeview it 
says " aborted ( core dumped).


please help.


Thanks


Regards

Tilak


From: Ramtilak Gattu
Sent: Thursday, June 23, 2016 5:27:12 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: freeview display problem


May be thats the problem. I'll try to give it a shot to see if it fixes the 
problem.


Thanks.


From: Ramtilak Gattu
Sent: Thursday, June 23, 2016 4:10:28 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: freeview display problem


This issue is only with freesurfer , images on fslview doesnt have this problem.




From: Ramtilak Gattu
Sent: Thursday, June 23, 2016 3:31:41 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: freeview display problem


That is just one layer the yellow contrast is from when we tune the contrast up 
or down.


From: Ramtilak Gattu
Sent: Thursday, June 23, 2016 2:37:36 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: freeview display problem


Hello ,


I am having strange freeview display problem. The images doesnt appear in gray 
scale anymore. Please have a look at the attachment.  Is there a switch that 
was  turned on that I am not aware of.


Could some one help.


Thanks


Regards
Tilak
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Re: [Freesurfer] Can't locate a good link to 5.3-dev builds (Linux/Ubuntu or Neuro-debian)

[Z K]

The Martinos Center is currently experiencing a system wide hardware
failure on our network file servers and hope to have the issues resolved 
in a soon, but it might be a day or more depending on the exact nature 
of the problem. Thanks for you patience.

-Zeke

On 06/28/2016 02:41 PM, Shannon Buckley wrote:
> Hiya,
>
>  I’m trying to download a copy of your latest dev build
> for Freesurfer 5.3 – I’m interested in getting the latest build for
> Freeview for Linux/Ubuntu or Neuro-Debian – but I seem to keep getting
> an “unreachable site” message?
>
> ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev
>
>  Is there another location I should be trying to use
> instead?
>
> Thank you very much for your time,
>
> Shannon T. Buckley
>
> Research Associate
>
> Fair Neuroimaging Lab
>
> Department of Behavioral Neuroscience and Psychiatry
>
> Oregon Health & Science University
> Mail code: L470
> 3181 SW Sam Jackson Park Road
> Portland, Oregon 97239-3098
>
>
>
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>
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[Freesurfer] Can't locate a good link to 5.3-dev builds (Linux/Ubuntu or Neuro-debian)

[Shannon Buckley]

Hiya,

I'm trying to download a copy of your latest dev build for 
Freesurfer 5.3 - I'm interested in getting the latest build for Freeview for 
Linux/Ubuntu or Neuro-Debian - but I seem to keep getting an "unreachable site" 
message?

ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev

Is there another location I should be trying to use instead?

Thank you very much for your time,

Shannon T. Buckley
Research Associate
Fair Neuroimaging Lab
Department of Behavioral Neuroscience and Psychiatry
Oregon Health & Science University
Mail code: L470
3181 SW Sam Jackson Park Road
Portland, Oregon 97239-3098

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Re: [Freesurfer] freeview display problem

[Ruopeng Wang]

Do other colormaps (heat scale, jets, etc) look normal? 

> On Jun 28, 2016, at 2:01 PM, Ramtilak Gattu  wrote:
> 
> Hey Ruopeng,
> 
> I still couldnt figure out whats going on the freeview display. I updated the 
> Nvidia drivers but still its not displaying in gray scale.
> 
> please help.
> 
> thanks
> 
> Regards
> Tilak
> From: Ramtilak Gattu
> Sent: Friday, June 24, 2016 12:25:50 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: freeview display problem
>  
> That is all . No error messages at all.
> From: Ramtilak Gattu
> Sent: Friday, June 24, 2016 10:25:42 AM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: freeview display problem
>  
> I tried updating my Nvidia drivers. but now whenever I try to open freeview 
> it says " aborted ( core dumped).
> 
> please help.
> 
> Thanks
> 
> Regards
> Tilak
> From: Ramtilak Gattu
> Sent: Thursday, June 23, 2016 5:27:12 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: freeview display problem
>  
> May be thats the problem. I'll try to give it a shot to see if it fixes the 
> problem.
> 
> Thanks.
> From: Ramtilak Gattu
> Sent: Thursday, June 23, 2016 4:10:28 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: freeview display problem
>  
> This issue is only with freesurfer , images on fslview doesnt have this 
> problem.
> 
> 
> From: Ramtilak Gattu
> Sent: Thursday, June 23, 2016 3:31:41 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: freeview display problem
>  
> That is just one layer the yellow contrast is from when we tune the contrast 
> up or down.
> From: Ramtilak Gattu
> Sent: Thursday, June 23, 2016 2:37:36 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: freeview display problem
>  
> Hello ,
> 
> I am having strange freeview display problem. The images doesnt appear in 
> gray scale anymore. Please have a look at the attachment.  Is there a switch 
> that was  turned on that I am not aware of.
> 
> Could some one help.
> 
> Thanks
> 
> Regards
> Tilak
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] freeview display problem

[Ramtilak Gattu]

Hey Ruopeng,


I still couldnt figure out whats going on the freeview display. I updated the 
Nvidia drivers but still its not displaying in gray scale.


please help.


thanks

Regards

Tilak


From: Ramtilak Gattu
Sent: Friday, June 24, 2016 12:25:50 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: freeview display problem


That is all . No error messages at all.


From: Ramtilak Gattu
Sent: Friday, June 24, 2016 10:25:42 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: freeview display problem


I tried updating my Nvidia drivers. but now whenever I try to open freeview it 
says " aborted ( core dumped).


please help.


Thanks


Regards

Tilak


From: Ramtilak Gattu
Sent: Thursday, June 23, 2016 5:27:12 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: freeview display problem


May be thats the problem. I'll try to give it a shot to see if it fixes the 
problem.


Thanks.


From: Ramtilak Gattu
Sent: Thursday, June 23, 2016 4:10:28 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: freeview display problem


This issue is only with freesurfer , images on fslview doesnt have this problem.




From: Ramtilak Gattu
Sent: Thursday, June 23, 2016 3:31:41 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: freeview display problem


That is just one layer the yellow contrast is from when we tune the contrast up 
or down.


From: Ramtilak Gattu
Sent: Thursday, June 23, 2016 2:37:36 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: freeview display problem


Hello ,


I am having strange freeview display problem. The images doesnt appear in gray 
scale anymore. Please have a look at the attachment.  Is there a switch that 
was  turned on that I am not aware of.


Could some one help.


Thanks


Regards
Tilak
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Re: [Freesurfer] tutorial_data

[Z K]

The Martinos Center is currently experiencing a system wide hardware 
failure on our network file servers and hope to have the issues resolved 
in a soon. Thanks for you patience.


On 06/28/2016 01:32 PM, bruno fraccini pastorello wrote:
> Dear freesurfer support,
> I'm trying to download the freesurfer data to learn freesurfer, but i
> can't it. Do you know why? Could you help me?
>
> I tried use this
> link ftp://surfer.nmr.mgh.harvard.edu/pub/data/tutorial_data.tar.gz and
> I obtain this error: Safari cant open the page
> ftp://surfer.nmr.mgh.harvard.edu/pub/data/tutorial_data.tar.gz because
> Safari can't load any data from this location.
>
> Thanks in advance
> Bruno Pastorello
>
> PS: I tried use this link too
> :https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Data  using curl
> command on terminal and it has failed too
>
>
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[Freesurfer] Applying the lta transformation to PET image | mri_coreg | mri_segstats

[Pradeep]

Hello All,

I am trying to extract the SUV values a PET image

mri_segstats --seg wmparc.mgz --sum petsuv.segstats.dat --i rPET
--ctab-default

since rPET is supposed to be coregistered to MRI, I did the following

mri_coreg --s MRI --mov PET --lta mri_coreg.lta

which did not generate the coregistered image but just transformation.

Is there a way to generate this image or to just input the mri_coreg.lta as
a flag to mri_segstats?

Thanks,
Pradeep
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[Freesurfer] tutorial_data

[bruno fraccini pastorello]

Dear freesurfer support,I'm trying to download the freesurfer data to learn 
freesurfer, but i can't it. Do you know why? Could you help me?
I tried use this link 
ftp://surfer.nmr.mgh.harvard.edu/pub/data/tutorial_data.tar.gz and I obtain 
this error: Safari cant open the page 
ftp://surfer.nmr.mgh.harvard.edu/pub/data/tutorial_data.tar.gz because Safari 
can't load any data from this location.
Thanks in advanceBruno Pastorello
PS: I tried use this link too 
:https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Data  using curl command 
on terminal and it has failed too___
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Re: [Freesurfer] Question about FreeSurfer

[Bruce Fischl]

just give recon-all a single slice from the series with -i .  It will figure out

the rest of them

On Tue, 28 Jun 2016, Dorsa Haji Ghaffari wrote:

> Hi,
> I am a little confused about how should I save my files to execute recon-all 
> on
> them. I have 240 slices of dicom format and I put them in a folder in my
> subjects_dir. but I get errors when using recon-all on the folder containing 
> the
> MRIs. Can you help me with that? I really appreciate your help
> 
> Thank you
> 
> Dorsa
> 
> On Mon, Jun 27, 2016 at 3:13 PM, Bruce Fischl  
> wrote:
>   Hi Dorsa
>
>   what specific models do you need? The 10-20 hours is to process the
>   data
>   from a single subject at a single timepoint. If you check out our
>   wiki
>   (http://surfer.nmr.mgh.harvard.edu/fswiki) there are lots of
>   tutorials and
>   sample datasets and such
>
>   cheers
>   Bruce
>
>   On Mon, 27 Jun 2016, Dorsa Haji
>   Ghaffari wrote:
>
>   > Hi,
>   > I am graduate student at the University of Michigan and I am
>   performing
>   > research on deep brain stimulation. I want to warp an anatomical
>   brain atlas
>   > to individual patient MRIs to get the patient specific brain models
>   out of
>   > it. I chose FreeSurfer to do this and I have installed it on my
>   computer. I
>   > realized that it takes 10-20 hrs to reconstruct the image. I wanted
>   to ask
>   > if that is the time for one image? or the whole series of images?
>   > I also wanted to ask if there is a step by step tutorial on how to
>   do this.
>   >
>   > Thank you
>   >
>   > Dorsa Ghaffari
>   >
>   >
>   >
>   >
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> 
> 
> The information in this e-mail is intended only for the person to whom it
> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
> 
> 
> 
>
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Re: [Freesurfer] Question about FreeSurfer

[Dorsa Haji Ghaffari]

Hi,

I am a little confused about how should I save my files to execute
recon-all on them. I have 240 slices of dicom format and I put them in a
folder in my subjects_dir. but I get errors when using recon-all on the
folder containing the MRIs. Can you help me with that? I really appreciate
your help

Thank you

Dorsa

On Mon, Jun 27, 2016 at 3:13 PM, Bruce Fischl 
wrote:

> Hi Dorsa
>
> what specific models do you need? The 10-20 hours is to process the data
> from a single subject at a single timepoint. If you check out our wiki
> (http://surfer.nmr.mgh.harvard.edu/fswiki) there are lots of tutorials and
> sample datasets and such
>
> cheers
> Bruce
>
> On Mon, 27 Jun 2016, Dorsa Haji
> Ghaffari wrote:
>
> > Hi,
> > I am graduate student at the University of Michigan and I am performing
> > research on deep brain stimulation. I want to warp an anatomical brain
> atlas
> > to individual patient MRIs to get the patient specific brain models out
> of
> > it. I chose FreeSurfer to do this and I have installed it on my
> computer. I
> > realized that it takes 10-20 hrs to reconstruct the image. I wanted to
> ask
> > if that is the time for one image? or the whole series of images?
> > I also wanted to ask if there is a step by step tutorial on how to do
> this.
> >
> > Thank you
> >
> > Dorsa Ghaffari
> >
> >
> >
> >
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[Freesurfer] Research position, UCSF Department of Radiology and Biomedical Imaging

[Nick Schmansky, MGH]

posted on behalf of Dr. Rahul Desikan:
=


The UCSF Department of Radiology and Biomedical Imaging is looking for a 
researcher with strong interests in neuroimaging interested in a Specialist 
position at UCSF. We are a neurodevelopment and neuroimaging lab.

Specialists (research assistant) appointed at the junior rank must possess a 
baccalaureate degree (or equivalent degree) or four years of equivalent 
research experience (e.g., with instrumentation and research equipment, social 
science research methods, or creative activities). Specialists appointed at the 
Assistant or Associate rank must possess a master’s degree (or equivalent 
degree) or at least five years of experience demonstrating expertise in the 
relevant specialization. Specialists appointed at the full rank must possess a 
PhD degree or ten or more years of experience demonstrating expertise in the 
relevant specialization. The ideal candidate will have 1+ years of lab 
experience (beyond coursework lab experience) and familiarity with one or more 
of the following: Matlab, R, Linux/Unix, C+ or other statistical or MRI image 
analysis software such as Freesurfer or FSL. We are seeking candidates with a 
strong background in neurosciences or biomedical engineering who have the 
ability to perform independent research in addition to supporting the lab. 
Candidates interested in working in the lab for at least 2 years are preferred.

Combining neuroimaging, genetics and computational methods, we are primarily 
interested in elucidating mechanisms underlying neurodevelopment. Working in 
close collaboration with local collaborators at UCSF and investigators at UCSD, 
University of Oslo, and Harvard University/Martinos Center, the specialist will 
assist in a) developing a novel automated MRI atlas of the human brainstem and 
cerebellum, b) validating this hindbrain atlas on neuroimaging pediatric 
datasets with brain malformations, and c) organize and analyze our large 
database of pediatric neuroimaging and genetics datasets that we have in-house.

UC San Francisco seeks candidates whose experience, teaching, research, or 
community service has prepared them to contribute to our commitment to 
diversity and excellence. The University of California is an Equal 
Opportunity/Affirmative Action Employer. All qualified applicants will receive 
consideration for employment without regard to race, color, religion, sex, 
sexual orientation, gender identity, national origin, disability, age or 
protected veteran status.

To apply, please provide the following materials to Dr. Rahul Desikan 
(rahul.desi...@ucsf.edu):

1) CV (must contain previous research experience)
2) Cover Letter - Short statement on why you are interested in this position 
and how this position will help you achieve your career goals
3) Three references
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Re: [Freesurfer] QSM Hippocampal Segementation

[Bruce Fischl]

Hi Jessica

if we have T1/PD maps we typically run them through mri_synthesize to 
create a strongly T1-weighted image that is then passed to recon-all.  Can 
you tell us more about what data you have?


cheers
Bruce



On Tue, 28 Jun 2016, Jessica Sevick wrote:


Hello, 

I was wondering if it was possible to use the hippocampal subfield segmentation
function (for FreeSurfer V 6.0) on QSM images? We are working on quantitative
stratification of the hippocampus. If you could let me know any
thoughts/suggestions that would be great. 

Thanks,

Jessica Sevick
MRI Research Assistant
Seaman Family MR Research Centre

T: 403.944.8652
C: 587.576.
Jessica Sevick
T: 403.944.8652
C: 587.576.

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[Freesurfer] QSM Hippocampal Segementation

[Jessica Sevick]

Hello,

I was wondering if it was possible to use the hippocampal subfield segmentation 
function (for FreeSurfer V 6.0) on QSM images? We are working on quantitative 
stratification of the hippocampus. If you could let me know any 
thoughts/suggestions that would be great.

Thanks,

Jessica Sevick
MRI Research Assistant
Seaman Family MR Research Centre

T: 403.944.8652
C: 587.576.
Jessica Sevick
T: 403.944.8652
C: 587.576.
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[Freesurfer] Longitudinal Stream: Recon-all and Base template

[Tamara Tavares]

Hello All,

I am planning to run the longitudinal stream on my data set and I have a
few questions:

1) When I run the data cross sectionally using "recon-all -all" should I
specify all my subject's T1 volumes (using the -file1.nii -1file2.nii) or
can I run each of my subject's T1 volumes individually through recon-all?
My understanding is that some motion correction will occur if I specify
more than one T1 which may alter the results versus if I specify one T1?

2)  What input files should I use to create my base templates? Are the
input files the norm.mgz files from each subject?

Thank you in advance for your help!

Best,
Tamara
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Re: [Freesurfer] Download FreeSurfer

[Z K]

Unfortunately their is no alternate location. We are experiencing a 
system wide hardware failure on our network file servers and hope to 
have the issues resolved in a day or so. Thanks for you patience.

-Zeke



On 06/28/2016 05:02 AM, Damien Marie wrote:
> *This message contained a link to a web site whose IP address has
> recently been associated with malicious activity.  Due to that activity
> the site is not accessible from within the Partners Network.  The link
> has been modified in the message below.  If you feel this is an error
> please contact the IS Service Desk and open a ticket with the network
> security - phs assignment group.
>
>IS Service Desk numbers
> BWH 617-732-5927BWH-RICS 617-525-0848   DFCI 617-632-3399
> FALK 617-983-7454LCC 857-307-4150  MCL 781-416-8940
> MGH 617-726-5085NHP 617-643-2020   NSMC 978-354-2014
> NWH 617-243-6001PCHI 781-433-3757 PHH 617-726-0790
> PHS 617-726-5085 SRH 617-952-*
> *
>
> Hello everybody,
>
>
> Storage servers are offline for downloading FreeSurfer from the
> wikipage. Does anyone know an alternate location
> for the distribution please?
>
>
> Best,
>
> Damien
>
>
>
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Re: [Freesurfer] updated mri_convert file

[Bruce Fischl]

Hi Olivia and others


we are having major disk problems at Martinos and many of the links may 
not work for a few days


sorry
Bruce
On Tue, 28 Jun 2016, Olivia Cheung wrote:


Hi Freesurfer team,
I would like to download a copy of the updated mri_convert but the link on
the Release Notes webpage does not seem to work. Would you please fix that?

I need the updated mri_convert because I'm getting the following error: 
"nifti1Read(): unsupported slice timing pattern 5"

Thanks!
Olivia

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[Freesurfer] recon-all sudden stop during Talairach

[Mikael Novén]

Dear Freesurfer Developers,

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

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

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

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

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

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

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

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

Log file included.

Thank you very much for your help.

All the best,
Mikael Novén
tis 28 jun 2016 12:48:09 CEST
/usr/local/freesurfer/subjects/106_1
/usr/local/freesurfer/bin/recon-all
-i 106_T1divPD_1mm.nii.gz -s 106_1 -all
subjid 106_1
setenv SUBJECTS_DIR /usr/local/freesurfer/subjects
FREESURFER_HOME /usr/local/freesurfer
Actual FREESURFER_HOME /usr/local/freesurfer
build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
Linux mikael-Aspire-VN7-591G 4.4.0-24-generic #43-Ubuntu SMP Wed Jun 8 19:27:37 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux
cputime  unlimited
filesize unlimited
datasize unlimited
stacksize8192 kbytes
coredumpsize 0 kbytes
memoryuseunlimited
vmemoryuse   unlimited
descriptors  1024 
memorylocked 64 kbytes
maxproc  31200 
maxlocks unlimited
maxsignal31200 
maxmessage   819200 
maxnice  0 
maxrtprio0 
maxrttimeunlimited

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


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