[Freesurfer] FreeSurfer 6

[Pedro Paulo de Magalhães Oliveira Junior]

Hey Guys,

Sorry if this is a frequently asked question.

Do we have an updated ETA for version 6 of Freesurfer? We are planning on
upgrading our 1024-node cluster and version 6 is a big deal for us.

Best

Pedro Paulo Jr.
-
Pedro Paulo de Magalhães Oliveira Junior
Netfilter & SpeedComm Telecom
-- www.netfilter.com.br
-- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441
___
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.

Re: [Freesurfer] Amazon EC2 for FreeSurfer 5.3

[Pedro Paulo de Magalhães Oliveira Junior]

Yes. CerebralVol.com does it

-
Pedro Paulo de Magalhães Oliveira Junior
Netfilter & SpeedComm Telecom
-- www.netfilter.com.br
-- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441


On Wed, Apr 15, 2015 at 9:47 PM, Pedro Rosa - GMail <
pedrogomesr...@gmail.com> wrote:

> Dear FreeSurfer users,
> Has anyone succeeded in running FreeSurfer 5.3 in a cloud processing
> system, such as Amazon EC2?
> I have seen prior posts in regard of FreeSurfer 5.1 (
> https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-November/021181.html),
> but not for 5.3.
> Regards,
> Pedro Rosa.
> ___
> 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.
>
>
___
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.

[Freesurfer] Head motion during MRI acquisition reduces gray matter volume and thickness estimates

[Pedro Paulo de Magalhães Oliveira Junior]

The paper Martin Reuter and the FS group wrote was featured in an article
of Discover Magazine by Neuroskeptic.

http://blogs.discovermagazine.com/neuroskeptic/2014/12/19/head-motion-structural-scans/#.VJhYkBSACk

Reuter M, Tisdall MD, Qureshi A, Buckner RL, van der Kouwe AJ, & Fischl B
(2014). Head motion during MRI acquisition reduces gray matter volume and
thickness estimates. NeuroImage, 107C, 107-115 PMID: 25498430

___
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.

Re: [Freesurfer] Generating T1 + Aseg views without Tkmedit and Freeview

[Pedro Paulo de Magalhães Oliveira Junior]

Hi Bruce.

I believe Tksurfer, even with renderoffscreen, requires X11.

I suppose I could export one slice of T1 data and the same Slice of Aseg
data and make a script to superimpose both. Not sure which of the cmd line
tools to use for this slice export.

-
Pedro Paulo de Magalhães Oliveira Junior
Netfilter & SpeedComm Telecom
-- www.netfilter.com.br
-- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441


On Wed, Nov 5, 2014 at 8:03 PM, Bruce Fischl 
wrote:

> Hi PPJ
>
> I'm not sure it is. Tksurfer has an offscreen rendering option :
> setenv renderoffscreen 1
>
> used to work, and maybe still does, but I don't think we ever implemented
> it in tkmedit, and I'm not sure about freeview. Ruopeng can answer that part
>
> On Wed, 5 Nov 2014, Pedro Paulo de Magalhães Oliveira Junior wrote:
>
>  I'm sorry if this has been answered before, I have browsed the mailing and
>> found nothing answering this.
>> I need to generate three views of the T1 data superimposed with Aseg data
>> automatically for Quality Control without using FreeView or Tkmedit (the
>> server generating this has no X11)
>>
>> Is it possible to do it with the command line tools?
>>
>> Thanks
>> -----
>> Pedro Paulo de Magalhães Oliveira Junior
>> Netfilter & SpeedComm Telecom-- www.netfilter.com.br
>> -- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441
>>
>>
>>
> ___
> 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.
>
>
___
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.

Re: [Freesurfer] Generating T1 + Aseg views without Tkmedit and Freeview

[Pedro Paulo de Magalhães Oliveira Junior]

This server cannot run any X11 for security reasons.

-
Pedro Paulo de Magalhães Oliveira Junior
Netfilter & SpeedComm Telecom
-- www.netfilter.com.br
-- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441


On Wed, Nov 5, 2014 at 8:11 PM, Chris Watson <
christopher.wat...@childrens.harvard.edu> wrote:

>  Have you tried installing 'xauth' on the server and connecting via 'ssh
> -X'? That should show all graphical output on the local machine.
>
>
>  On 11/05/2014 05:03 PM, Bruce Fischl wrote:
>
> Hi PPJ
>
> I'm not sure it is. Tksurfer has an offscreen rendering option :
> setenv renderoffscreen 1
>
> used to work, and maybe still does, but I don't think we ever implemented
> it in tkmedit, and I'm not sure about freeview. Ruopeng can answer that
> part
>
> On Wed, 5 Nov 2014, Pedro Paulo de Magalhães Oliveira Junior wrote:
>
> I'm sorry if this has been answered before, I have browsed the mailing and
> found nothing answering this.
> I need to generate three views of the T1 data superimposed with Aseg data
> automatically for Quality Control without using FreeView or Tkmedit (the
> server generating this has no X11)
>
> Is it possible to do it with the command line tools?
>
> Thanks
> -
> Pedro Paulo de Magalhães Oliveira Junior
> Netfilter & SpeedComm Telecom-- www.netfilter.com.br
> -- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441
>
>
>
>
>
> ___
> Freesurfer mailing 
> listfreesur...@nmr.mgh.harvard.eduhttps://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 
> athttp://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.
>
>
>
> ___
> 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.
>
>
___
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.

[Freesurfer] Generating T1 + Aseg views without Tkmedit and Freeview

[Pedro Paulo de Magalhães Oliveira Junior]

I'm sorry if this has been answered before, I have browsed the mailing and
found nothing answering this.

I need to generate three views of the T1 data superimposed with Aseg data
automatically for Quality Control without using FreeView or Tkmedit (the
server generating this has no X11)

Is it possible to do it with the command line tools?

Thanks
-
Pedro Paulo de Magalhães Oliveira Junior
Netfilter & SpeedComm Telecom
-- www.netfilter.com.br
-- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441
___
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.

Re: [Freesurfer] Freesurfer course 2015 Brazil

[Pedro Paulo de Magalhães Oliveira Junior]

We don't have a date yet. An estimate would be March/April

-
Pedro Paulo de Magalhães Oliveira Junior
Netfilter & SpeedComm Telecom
-- www.netfilter.com.br
-- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441


On Fri, Oct 24, 2014 at 3:00 PM, Andrea Horváth 
wrote:

> Dear Freesurfers,
>
> Does anyone know the exact date of the upcoming Freesurfer course in Sao
> Paolo, Brazil? I know that it is too early, but we need the date for a
> travel grant application. Thank you for your help in advance!
> Cheers,
>Andrea
>
>
>
> --
> *Andrea Horvath M.D.*
> PhD Fellow
> Diagnostic Centre of Pécs
> horvath.andr...@pte.hu
>
> ___
> 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.
>
>
___
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.

Re: [Freesurfer] recon-all subject folder size

[Pedro Paulo de Magalhães Oliveira Junior]

300mb is fine.

-
Pedro Paulo de Magalhães Oliveira Junior
Netfilter & SpeedComm Telecom
-- www.netfilter.com.br
-- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441



On Mon, Feb 24, 2014 at 3:01 PM, Durai Arasan  wrote:

> Hi Freesurfer experts,
>
> I am successfully running recon-all on my cluster. However I find that the
> subject folders have sizes ranging from 300mb to 900mb.
>
> I grepped all recon-all.log files for "finished without error" and that
> seemed fine for all subjects.
>
> But I would like to know what is the expected subject folder size when you
> run recon-all (with -all option) starting from a standard MPRAGE T1 image.
> This might be useful since I have limited control over the cluster nodes
> where the processing takes place.
>
> Thank you
> Durai
>
>
> On Mon, Feb 17, 2014 at 2:55 AM, Durai Arasan  wrote:
>
>> Hi Freesurfer experts,
>>
>> so I got this error when I ran recon-all on my cluster. I am really
>> hoping this is just a case of missing GCC libraries and nothing is wrong
>> with the Freesurfer installation on the nodes. Kindly confirm this.
>>
>> Thank you
>>
>>
>> **
>>
>> Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
>> Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
>> INFO: SUBJECTS_DIR is /**
>> Actual FREESURFER_HOME /**
>> Linux *  SMP Fri Mar 22 05:41:51 EDT 2013
>> x86_64 x86_64 x86_64 GNU/Linux
>> mri_convert: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not
>> found (required by mri_convert)
>> mri_convert: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found
>> (required by mri_convert)
>> mri_convert: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by
>> mri_convert)
>> mri_convert: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not
>> found (required by mri_convert)
>> mri_convert: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found
>> (required by mri_convert)
>> mri_convert: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by
>> mri_convert)
>> tkregister2_cmdl: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not
>> found (required by tkregister2_cmdl)
>> tkregister2_cmdl: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not
>> found (required by tkregister2_cmdl)
>> tkregister2_cmdl: /lib64/libc.so.6: version `GLIBC_2.7' not found
>> (required by tkregister2_cmdl)
>> mri_make_uchar: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not
>> found (required by mri_make_uchar)
>> mri_make_uchar: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not
>> found (required by mri_make_uchar)
>> mri_make_uchar: /lib64/libc.so.6: version `GLIBC_2.7' not found (required
>> by mri_make_uchar)
>> mri_normalize: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not
>> found (required by mri_normalize)
>> mri_normalize: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not
>> found (required by mri_normalize)
>> mri_normalize: /lib64/libc.so.6: version `GLIBC_2.7' not found (required
>> by mri_normalize)
>> mri_watershed: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not
>> found (required by mri_watershed)
>> mri_watershed: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not
>> found (required by mri_watershed)
>> mri_watershed: /lib64/libc.so.6: version `GLIBC_2.7' not found (required
>> by mri_watershed)
>> mri_gcut: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found
>> (required by mri_gcut)
>> mri_gcut: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found
>> (required by mri_gcut)
>> mri_gcut: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by
>> mri_gcut)
>> mri_segment: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not
>> found (required by mri_segment)
>> mri_segment: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found
>> (required by mri_segment)
>> mri_segment: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by
>> mri_segment)
>> mri_label2label: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not
>> found (required by mri_label2label)
>> mri_label2label: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not
>

Re: [Freesurfer] longer run time on 5.3 versus 5.2 ?

[Pedro Paulo de Magalhães Oliveira Junior]

I saw this issue too.

The total running time went from an average of 16.3h to 20.4h

-
Pedro Paulo de Magalhães Oliveira Junior
Netfilter & SpeedComm Telecom
-- www.netfilter.com.br
-- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441



On Tue, Jun 4, 2013 at 2:54 PM, Mehul Sampat  wrote:

> Hi Bruce,
>
> Okay. It went from ~4 hours in 5.2 to ~9 hours in 5.3; we thought it was a
> big change to
> and are trying to isolate the root cause
>
> We are running  75 cases run with 5.3 that have been run with 5.2 before;
> once they are done, will let you all know if this issue is seen in other
> cases too.
> Mehul
> ps: the cases were run on different machines but the specs of the two
> machines are quite similar;
> we are also trying to see if it is hard-ware related..
>
>
>
>
> On Tue, Jun 4, 2013 at 10:37 AM, Bruce Fischl 
> wrote:
>
>> Hi Mehul
>>
>> no, that's definitely not expected for it to go from 20 min to almost 5
>> hours! We'll investigate as that shouldn't be the case.
>> Bruce
>>
>>
>>
>> On Tue, 4 Jun 2013, Mehul Sampat wrote:
>>
>>  In some cases, we are seeing that, for the same subject, the run time is
>>> slower for 5.3 versus 5.2;
>>> A quick check on recon-all-status.log shows that the CA Reg Inv step is
>>> taking longer with 5.3.
>>>
>>> recon-all-status.log from data processed with 5.2:
>>>
>>> #@# CA Reg Thu Jan 17 16:03:53 PST 2013
>>> #@# CA Reg Inv Thu Jan 17 20:17:32 PST 2013
>>>
>>> recon-all-status.log from data processed with 5.3
>>>
>>> #@# CA Reg Mon Jun  3 19:46:37 PDT 2013
>>> #@# CA Reg Inv Tue Jun  4 04:52:57 PDT 2013
>>>
>>>  Is this expected ? Or in your own testing are the recon-all processing
>>> times similar for 5.2 versus 5.3 ? The recon-all.log
>>> file for both cases are attached;
>>> Thanks
>>> Mehul
>>>
>>>
>>>
>>>
>>
>> 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<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.
>>
>
>
> ___
> 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.
>
>
___
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.

[Freesurfer] [Release] - iSurf BrainView 4.1.0

[Pedro Paulo de Magalhães Oliveira Junior]

Today it was released the version 4.1.0 of iSurf BrainView for iPad, iPhone
and iPod Touch.

Major changes:
- Color scheme has been changed to match Windows 8 Version.
- Icon has been redesigned as suggested by many users.
- Now it supports the new resolution. 1136x640
- 3D engine has been redesigned to take advantage of new iOS device GPU
- Aseg from FreeSurfer 5.2

As usual suggestions and feedback are welcome.

The link for download is:

http://itunes.apple.com/us/app/isurf-brainview/id381072423?mt=8

-
Pedro Paulo de Magalhães Oliveira Junior
Netfilter & SpeedComm Telecom
-- www.netfilter.com.br
-- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441
___
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.

Re: [Freesurfer] Very different results between 5.1.0 and 5.2.0

[Pedro Paulo de Magalhães Oliveira Junior]

Daniel,

Unfortunately, since I run all the individuals again with FreeSurfer 5.2, I
just saved from the 5.1 the info I was using for comparison between version
- the aseg stats.

I don't have cortical thickness information for 5.1 unless we run all the
cases again in 5.1



-
Pedro Paulo de Magalhães Oliveira Junior
Netfilter & SpeedComm Telecom
-- www.netfilter.com.br
-- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441



On Thu, Apr 11, 2013 at 2:47 PM, Yang, Daniel wrote:

>  Hi PPJ and all,
>
>  I found that the 5.2 – 5.1 difference is primarily seen in the cortical
> thickness, and much less so in the aseg.volume.
>
>  Here, I picked right-amygdala volume as an example of aseg.volume and
> rh_bankssts_thickness as an example of rh.aparc.thickness.
>
>  While the correlation between the two versions of right-amygdala is r =
> .92 (n = 161), that of the rh_bankssts_thickness is r = .45.
>
>  Presumably I believe the correlation should be > .90 for a strong
> continuity between the two versions?
>
>  Do you have anything in the cortical thickness?
>
>  Daniel
>
>  --
>  Yung-Jui "Daniel" Yang, PhD
> Postdoctoral Researcher
> Yale Child Study Center
> New Haven, CT
> (203) 737-5454
>
>   From: Pedro Paulo de Magalhães Oliveira Junior 
> Date: Wednesday, April 10, 2013 11:07 AM
> To: Daniel Yang 
> Cc: Bruce Fischl , "
> freesurfer@nmr.mgh.harvard.edu" 
>
> Subject: Re: [Freesurfer] Very different results between 5.1.0 and 5.2.0
>
>   Ok, I'll try to put together a stat from aparc too.
>
> -
> Pedro Paulo de Magalhães Oliveira Junior
> Netfilter & SpeedComm Telecom
> -- www.netfilter.com.br
> -- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441
>
>
>
> On Wed, Apr 10, 2013 at 12:04 PM, Yang, Daniel wrote:
>
>>  Hi PPJ,
>>
>>  Thanks! It looks interesting. I also found FS 5.2 is faster. Is there
>> any chance you could also provide the cortical thickness of the 2009 atlas
>> (e.g., rh)?
>>
>>  I will take a look into the aseg.volume in my data too.
>>
>>  Best,
>>  Daniel
>>
>>
>>  --
>>  Yung-Jui "Daniel" Yang, PhD
>> Postdoctoral Researcher
>> Yale Child Study Center
>> New Haven, CT
>> (203) 737-5454
>>
>>   From: Pedro Paulo de Magalhães Oliveira Junior 
>> Date: Wednesday, April 10, 2013 10:49 AM
>> To: Bruce Fischl 
>> Cc: Daniel Yang , "freesurfer@nmr.mgh.harvard.edu"
>> 
>> Subject: Re: [Freesurfer] Very different results between 5.1.0 and 5.2.0
>>
>>   You'll find attached some preliminary data of the comparison we did
>> among versions.
>>
>> -
>> Pedro Paulo de Magalhães Oliveira Junior
>> Netfilter & SpeedComm Telecom
>> -- www.netfilter.com.br
>> -- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441
>>
>>
>>
>> On Wed, Apr 10, 2013 at 10:42 AM, Bruce Fischl <
>> fis...@nmr.mgh.harvard.edu> wrote:
>>
>>>  Hi PPJ
>>> That's exactly what we are doing. Good to hear its stable for you
>>>  Bruce
>>>
>>>
>>>
>>> On Apr 10, 2013, at 8:38 AM, Pedro Paulo de Magalhães Oliveira Junior<
>>> p...@netfilter.com.br> wrote:
>>>
>>>   I have processed more that 600 brains with both versions in the last
>>> weeks and the only difference I'm seeing between version 5.2.0 and 5.1,
>>> besides the obvious new features, is processing time.
>>>
>>>  Version 5.2 is 10% faster than 5.1 in an Amazon EC2 instance.
>>>
>>>  Besides that there's no visible difference in terms of cortical
>>> thickness, volumes, etc.
>>>
>>>  If you have access to computer resources to spare you can run
>>> recon-all of both versions in some well known database of images and do a
>>> more formal test.
>>>
>>>
>>>
>>>
>>>
>>>
>>> -
>>> Pedro Paulo de Magalhães Oliveira Junior
>>> Netfilter & SpeedComm Telecom
>>> -- www.netfilter.com.br
>>> -- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441
>>>
>>>
>>>
>>> On Wed, Apr 10, 2013 at 8:11 AM, Yang, Daniel wrote:
>>>
>>>> Dear FreeSurfer Expert

Re: [Freesurfer] Very different results between 5.1.0 and 5.2.0

[Pedro Paulo de Magalhães Oliveira Junior]

Ok, I'll try to put together a stat from aparc too.

-
Pedro Paulo de Magalhães Oliveira Junior
Netfilter & SpeedComm Telecom
-- www.netfilter.com.br
-- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441



On Wed, Apr 10, 2013 at 12:04 PM, Yang, Daniel wrote:

>  Hi PPJ,
>
>  Thanks! It looks interesting. I also found FS 5.2 is faster. Is there
> any chance you could also provide the cortical thickness of the 2009 atlas
> (e.g., rh)?
>
>  I will take a look into the aseg.volume in my data too.
>
>  Best,
> Daniel
>
>
>  --
>  Yung-Jui "Daniel" Yang, PhD
> Postdoctoral Researcher
> Yale Child Study Center
> New Haven, CT
> (203) 737-5454
>
>   From: Pedro Paulo de Magalhães Oliveira Junior 
> Date: Wednesday, April 10, 2013 10:49 AM
> To: Bruce Fischl 
> Cc: Daniel Yang , "freesurfer@nmr.mgh.harvard.edu"
> 
> Subject: Re: [Freesurfer] Very different results between 5.1.0 and 5.2.0
>
>   You'll find attached some preliminary data of the comparison we did
> among versions.
>
> -
> Pedro Paulo de Magalhães Oliveira Junior
> Netfilter & SpeedComm Telecom
> -- www.netfilter.com.br
> -- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441
>
>
>
> On Wed, Apr 10, 2013 at 10:42 AM, Bruce Fischl  > wrote:
>
>>  Hi PPJ
>> That's exactly what we are doing. Good to hear its stable for you
>>  Bruce
>>
>>
>>
>> On Apr 10, 2013, at 8:38 AM, Pedro Paulo de Magalhães Oliveira Junior<
>> p...@netfilter.com.br> wrote:
>>
>>   I have processed more that 600 brains with both versions in the last
>> weeks and the only difference I'm seeing between version 5.2.0 and 5.1,
>> besides the obvious new features, is processing time.
>>
>>  Version 5.2 is 10% faster than 5.1 in an Amazon EC2 instance.
>>
>>  Besides that there's no visible difference in terms of cortical
>> thickness, volumes, etc.
>>
>>  If you have access to computer resources to spare you can run recon-all
>> of both versions in some well known database of images and do a more formal
>> test.
>>
>>
>>
>>
>>
>>
>> -
>> Pedro Paulo de Magalhães Oliveira Junior
>> Netfilter & SpeedComm Telecom
>> -- www.netfilter.com.br
>> -- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441
>>
>>
>>
>> On Wed, Apr 10, 2013 at 8:11 AM, Yang, Daniel wrote:
>>
>>> Dear FreeSurfer Experts and Users,
>>>
>>> Did anyone find similar things using FS 5.2 (please see my previous post
>>> below)? That is, FS 5.2 is including more non-cortical "black spaces"
>>> within pial surfaces, compared to FS 5.1?
>>>
>>> I'm not interested in nitpicking but I feel this is a rather serious
>>> issue, so I would like to raise it again before it's completely
>>> forgotten.
>>>
>>> At the meantime I keep receiving Emails from people asking me this issue.
>>>
>>> Thanks!
>>> Daniel
>>>
>>> --
>>> Yung-Jui "Daniel" Yang, PhD
>>> Postdoctoral Researcher
>>> Yale Child Study Center
>>> New Haven, CT
>>> (203) 737-5454
>>>
>>>
>>>
>>>
>>>
>>>
>>>  On 3/19/13 7:07 AM, "Yang, Daniel"  wrote:
>>>
>>> >
>>> >Posting one of the brains.
>>> >
>>> >https://yalesurvey.qualtrics.com/SE/?SID=SV_ddwW7I9yMQuCtPn
>>> >
>>> >
>>> >It seems to me that neither version is perfect; however, 5.2.0 is
>>> >capturing more "black spaces" in the region I'm looking at.
>>> >
>>> >It's in the right hemisphere, TAL coordinate about ~ (44, -46, 20).
>>> >
>>> >Given that the correlation between 5.1.0 and 5.2.0 is r = .33 in the
>>> >region I examined with my samples, it's not a systematic "predictable"
>>> >bias.
>>> >
>>> >Any solution?
>>> >
>>> >--
>>> >Yung-Jui "Daniel" Yang, PhD
>>> >Postdoctoral Researcher
>>> >Yale Child Study Center
>>> >New Haven, CT
>>> >(203) 737-5454
>>> >
>>> >
>>> >
>>> >
>>> >
>>>

Re: [Freesurfer] Very different results between 5.1.0 and 5.2.0

[Pedro Paulo de Magalhães Oliveira Junior]

I have processed more that 600 brains with both versions in the last weeks
and the only difference I'm seeing between version 5.2.0 and 5.1, besides
the obvious new features, is processing time.

Version 5.2 is 10% faster than 5.1 in an Amazon EC2 instance.

Besides that there's no visible difference in terms of cortical thickness,
volumes, etc.

If you have access to computer resources to spare you can run recon-all of
both versions in some well known database of images and do a more formal
test.






-----
Pedro Paulo de Magalhães Oliveira Junior
Netfilter & SpeedComm Telecom
-- www.netfilter.com.br
-- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441



On Wed, Apr 10, 2013 at 8:11 AM, Yang, Daniel wrote:

> Dear FreeSurfer Experts and Users,
>
> Did anyone find similar things using FS 5.2 (please see my previous post
> below)? That is, FS 5.2 is including more non-cortical "black spaces"
> within pial surfaces, compared to FS 5.1?
>
> I'm not interested in nitpicking but I feel this is a rather serious
> issue, so I would like to raise it again before it's completely forgotten.
>
> At the meantime I keep receiving Emails from people asking me this issue.
>
> Thanks!
> Daniel
>
> --
> Yung-Jui "Daniel" Yang, PhD
> Postdoctoral Researcher
> Yale Child Study Center
> New Haven, CT
> (203) 737-5454
>
>
>
>
>
>
> On 3/19/13 7:07 AM, "Yang, Daniel"  wrote:
>
> >
> >Posting one of the brains.
> >
> >https://yalesurvey.qualtrics.com/SE/?SID=SV_ddwW7I9yMQuCtPn
> >
> >
> >It seems to me that neither version is perfect; however, 5.2.0 is
> >capturing more "black spaces" in the region I'm looking at.
> >
> >It's in the right hemisphere, TAL coordinate about ~ (44, -46, 20).
> >
> >Given that the correlation between 5.1.0 and 5.2.0 is r = .33 in the
> >region I examined with my samples, it's not a systematic "predictable"
> >bias.
> >
> >Any solution?
> >
> >--
> >Yung-Jui "Daniel" Yang, PhD
> >Postdoctoral Researcher
> >Yale Child Study Center
> >New Haven, CT
> >(203) 737-5454
> >
> >
> >
> >
> >
> >
> >On 3/18/13 6:27 PM, "Matt Glasser"  wrote:
> >
> >>Do the surfaces look correct in these regions?  You might post some
> >>screenshots of subjects who have a big difference between 5.1 and 5.2
> >>with
> >>the 5.1 and 5.2 white and pial surfaces on volume slices that highlight
> >>the difference.  Without this kind of info, its hard to know which was
> >>more correct, 5.1 or 5.2.
> >>
> >>Peace,
> >>
> >>Matt.
> >>
> >>On 3/18/13 5:13 PM, "Ritobrato Datta" 
> wrote:
> >>
> >>>I concur. I have seen similar results in primary visual cortex from ~40
> >>>subjects. While fs 5.1 estimated mean thickness in the range of 1.5 to
> >>>1.9 in V1, fs 5.2 is giving me V1 thickness in the range of 2 to 2.3.
> >>>
> >>>Ritobrato Datta, Ph.D.
> >>>Post Doctoral Researcher
> >>>Department of Neurology
> >>>University of Pennsylvania School of Medicine
> >>>3rd Floor, Room 312
> >>>3710 Hamilton Walk (Goddard Laboratories)
> >>>Philadelphia, PA 19104-6241
> >>>email - rida...@mail.med.upenn.edu
> >>>
> >>>
> >>>- Original Message -
> >>>From: Daniel Yang 
> >>>To: freesurfer@nmr.mgh.harvard.edu
> >>>Sent: Mon, 18 Mar 2013 17:44:44 -0400 (EDT)
> >>>Subject: [Freesurfer] Very different results between 5.1.0 and 5.2.0
> >>>
> >>>Dear FreeSurfer Experts,
> >>>
> >>>I ran FreeSurfer 5.1.0 and FreeSurfer 5.2.0 on identical set of 161
> >>>subjects, and I'm interested in rh_superior_temporal_sulcus_thickness in
> >>>particular.
> >>>
> >>>Previously, the mean thickness is 2.24 mm in 5.1.0; now it is 3.28 mm in
> >>>5.2.0. They are significantly different, t(160) = 56.71.
> >>>
> >>>The correlation between the two versions is r = .33
> >>>
> >>>Is this something possible?? I can't see what went wrong in my
> >>>procedures.
> >>>
> >>>Thanks!
> >>>Daniel
> >>>
> >>>--
> >>>Yung-Jui "Daniel" Yang, PhD
> >>>Postdoctoral Researcher
> >>>Yale Chil

[Freesurfer] iSurf BrainView now available for Windows 8 {Disarmed}

[Pedro Paulo de Magalhães Oliveira Junior]

Today Microsoft approved iSurf BrainView version for Windows 8 Tablets and
computers. It's a free App.

http://apps.microsoft.com/windows/en-us/app/brainview/be2623f5-c5e3-4295-a28e-d3f64dc19266

BrainView is a Brain MRI tutor based on the MRI automatic segmentation
produced by FreeSurfer.

FreeSurfer is a software package developed by investigators at the
Athinoula A. Martinos Center for Biomedical Imaging.

This App uses its automatic segmentation to produce an automatic atlas of
neuroimaging based on T1 MRI Images. It also displays 3D accurate models of
brain cortex with automatic structure labeling.

A great tool for teaching brain MRI and for learning neuroanatomy.

For more reference on the educational use of iSurf BrainView:
Oliveira Jr, PPM; Fischl, Bruce; Amaro, Edson "Teaching neuroanatomy using
Iphone and IPad. In: Human Brain Mapping, 2011, Quebec, CA. Proc. Human
Brain Mapping 2011, 2011."

---------
Pedro Paulo de Magalhães Oliveira Junior
Netfilter & SpeedComm Telecom
-- www.netfilter.com <http://www.netfilter.com.br>
___
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.

[Freesurfer] Error in Talairach transform version 5.2

[Pedro Paulo de Magalhães Oliveira Junior]

I'm having some recon-all errors like this:

mritotal -verbose -debug -clobber -modeldir
/usr/local/freesurfer/mni/bin/../share/mni_autoreg -protocol icbm
transforms/tmp.talairach.3505/src.mnc transforms/talairach.auto.xfm
Use of uninitialized value $path in join or string at
/usr/local/freesurfer/mni/bin/mritotal line 462.
mritotal: Couldn't find configuration file mritotal.cfg anywhere in
:/usr/local/freesurfer/mni/bin/../etc/mni_autoreg
ERROR: mritotal failed, see transforms/talairach.log
Linux ip-10-147-137-177 3.2.39-6.88.amzn1.i686 #1 SMP Sat Mar 2 05:13:38
UTC 2013 i686 i686 i386 GNU/Linux

recon-all -s caso765 exited with ERRORS at Mon Mar 25 19:24:29 UTC 2013

To report a problem, see
http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting



Is this file /usr/local/freesurfer/mni/bin/../etc/mni_autoreg really
missing in the distribution?
___
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.

Re: [Freesurfer] Freesurfer problem on Amazon EC2

[Pedro Paulo de Magalhães Oliveira Junior]

The micro instance won't work. You'll need at least one m1.medium instance.

I don't want to advertise it again but have you considered using
http://cerebralvol.com that runs EC2 instances



---------
Pedro Paulo de Magalhães Oliveira Junior
Netfilter & SpeedComm Telecom
-- www.netfilter.com.br
-- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441



On Tue, Feb 26, 2013 at 12:07 AM, Tawfik Moher Alsady
wrote:

>  Dear Freesurfers,
>
>
> I tried to install freesurfer on amazon EC2 as instructed on the wiki page.
>
> Everything went well except that mri_* tools like mri_convert doesn't work.
>
> When calling it, it returns nothing.\
>
> I also tried to make another Centos instance and install freesurfer manuall, 
> but the same problem existed.
>
> I am trying to use it via ssh (ssh to the server and then enter the 
> freesurfer commands).
>
> Any suggestions?
>
> And is it fast enough to use FS on Amazon micro instance? On my PC freesurfer 
> takes around 35-40 hours for the whole process.
>
>
> Grazie,
> Tawfik
>
> --
>
> Sent with Sparrow <http://www.sparrowmailapp.com/?sig>
>
>
> ___
> 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.
>
>
___
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.

Re: [Freesurfer] FS 5.2-beta run-times on Amazon Web services (AWS)

[Pedro Paulo de Magalhães Oliveira Junior]

In the http://cerebralvol.com service we are having 23.5 hours average with
5.1 and 23.8 hours average with 5.2-Beta

Notice that in order to minimize the cost to the user we are running it in
m1.medium

We have achieved a full recon-all in less than 4 hours (3.83 hours) with
cg1.4xlarge

But for a large amount of data I believe our 1024-core m1.medium is the
best cost benefit.

-
Pedro Paulo de Magalhães Oliveira Junior
Netfilter & SpeedComm Telecom
-- www.netfilter.com.br
-- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441



On Sat, Feb 2, 2013 at 2:11 AM, Mehul Sampat  wrote:

> Hi Bruce,
> No I did not specify the # of open mp threads on the recon-all cmd line.
> These run times were obtained by  running one subject per core. for example
>  cc2.8xlarge has 8 cores and so we ran 8 subjects at once;
> Thanks for the info about the # of open mp threads options; I will look
> into it.
>
> One other note: Bruce, Nick did you improve the memory management in 5.2 ?
> On our local machine we noticed we can run 6 subjects simultaneously even
> though we only have 12gb of ram.
> I thought some of the them might crash since we only have 2gb per subject
> but no crashes so far over 30 subjects..
> Mehul
>
>
> On Fri, Feb 1, 2013 at 7:12 PM, Bruce Fischl 
> wrote:
>
>> Hi Mehul
>>
>> did you specify the # of open mp threads on the recon-all cmd line?
>> cheers
>> Bruce
>>
>> On Fri, 1 Feb 2013, Mehul Sampat wrote:
>>
>>  Hi Folks,
>>> Just wanted to share our experience with running FS 5.2-beta on Amazon
>>> Web
>>> Services (AWS).
>>> Basically, AWS has multiple instance types
>>> (http://aws.amazon.com/ec2/**instance-types/<http://aws.amazon.com/ec2/instance-types/>)
>>> and we were trying to figure out
>>> the most cost-effective approach.
>>>
>>> We ran two subjects through FS 5.2-beta on M1 Large Instance (m1.large)
>>> and Cluster Compute Eight Extra Large Instance (cc2.8xlarge). (same
>>> subjects
>>> run on both instance). We expected cc2.8xlarge to be faster (but it is
>>> also
>>> more expensive: $2.4 per hour; 8 cores); The run-times we got:
>>>
>>> instance-type subject start-time end-time run-time
>>> m1.large subject-1 01:05:44 UTC 2013 15:40:45 UTC 2013 ~14hr-35mins
>>> m1.large subject-2 01:06:06 UTC 2013 15:08:45 UTC 2013 ~14hr-02mins
>>> cc2.8xlarge subject-1 01:26:38 UTC 2013 12:30:23 UTC 2013 ~11hr-04mins
>>> cc2.8xlarge subject-2 01:27:28 UTC 2013 12:19:08 UTC 2013 ~10hr-52mins
>>>
>>> Although m1.large is a few hours slower, it seems to be the more cost
>>> effective option since it is $0.24 per hour (2 cores). If you have run
>>> Freesurfer on AWS, do you have a similar experience ? Any suggestions to
>>> speed up the run-times on AWS would be very helpful.
>>>
>>> Thanks
>>> Mehul
>>>
>>>
>>>
>>>
>>
>> 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<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.
>>
>
>
> ___
> 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.
>
>
___
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.

Re: [Freesurfer] FreeSurfer problem on VirtualBox Linux

[Pedro Paulo de Magalhães Oliveira Junior]

Unfortunately Windows XP SP3 is no longer Tier-1 supported for VirtualBox.

I suggest you to try it on Windows 7 or Windows 8.

cheers

PPJ

-
Pedro Paulo de Magalhães Oliveira Junior
Netfilter & SpeedComm Telecom
-- www.netfilter.com.br
-- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441



On Wed, Jan 9, 2013 at 7:49 PM, Nick Schmansky wrote:

> Carissa,
>
> Unfortunately I dont think we can help with this problem, as we
> currently do not have the resources to support the Windows VM instance.
> However, an alternative that has worked for others is to do the
> following: install the FSL Windows VM, described here:
>
> http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FslInstallation/Windows
>
> once that is up-and-running, then within that linux instance, just
> download and install our linux centos 4 freesurfer build.  this also
> means you can update to v5.2 when that is released in a couple weeks.
>
> Nick
>
>
> On Wed, 2013-01-09 at 08:34 +, Carissa Nadia Kuswanto (IMH) wrote:
> > Hi there,
> >
> >
> >
> > My operating system is Windows XP SP3 and it has been loaded with
> > VirtualBox 4.2.6 for Windows hosts and we would like to run
> > freesurfer-Virtualbox-linux-x86-stable-pub-v5.1.0-full.vdi. But when
> > we attempt to launch FreeSurfer, the terminal seems to hang with the
> > following message:
> >
> >
> >
> > GRUB loading stage 1.5
> >
> > GRUB loading, please wait...
> >
> >
> >
> > Would you kindly help us on how to overcome this problem? I thank you
> > in advance for your kind attention.
> >
> >
> >
> > Best regards,
> >
> > Carissa
> >
> >
> >
> > __
> > The information contained in this e-mail and the attachments (if any)
> > may be privileged and confidential and is intended solely for the
> > named addressee. If you are not the intended recipient, please do not
> > print, retain copy, disseminate, distribute, or use this e-mail or any
> > part thereof. Please notify the sender immediately by replying to this
> > e-mail and delete all copies of this e-mail and the attachments.
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> 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.
>
>
___
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.

Re: [Freesurfer] mri_cc segfault

[Pedro Paulo de Magalhães Oliveira Junior]

Bruce found that the data had the direction cosine wrong.

I have fixed the direction and I'm running it again.

I've put the data in the ftp

-----
Pedro Paulo de Magalhães Oliveira Junior
Netfilter & SpeedComm Telecom
-- www.netfilter.com.br
-- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441




On Tue, Dec 18, 2012 at 8:41 PM, Nick Schmansky
wrote:

> PPJ,
>
> Hi, if you want, you can send me the input files (the two aseg's and the
> lta) and i can try to replicate the segfault in a debugger.
>
> also, if you want, there is a beta of the upcoming v5.2 which is posted
> here:
> ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.2.0-BETA/
> which you could try.  hopefully that mri_cc doesnt segfault.
>
> Nick
>
>
>
> On Tue, 2012-12-18 at 12:46 -0200, Pedro Paulo de Magalhães Oliveira
> Junior wrote:
> > I'm having a segfault with mri_cc it's happening sometimes using
> > FreeSurfer 5.1
> >
> >
> > Searching the mailing list I saw a similar problem in 2008 but with no
> > answers.
> >
> >
> > The relevant portion of recon-all.log:
> >
> >
> >  mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz
> > -lta
> /usr/local/freesurfer/subjects/c70eb728-c505-46c2-a2a1-1ed409c36ea1/mri/transforms/cc_up.lta
> c70eb728-c505-46c2-a2a1-1ed409c36ea1
> >
> >
> > will read input aseg from aseg.auto_noCCseg.mgz
> > writing aseg with cc labels to aseg.auto.mgz
> > will write lta
> > as
> /usr/local/freesurfer/subjects/c70eb728-c505-46c2-a2a1-1ed409c36ea1/mri/transforms/cc_up.lta
> > reading aseg
> > from
> /usr/local/freesurfer/subjects/c70eb728-c505-46c2-a2a1-1ed409c36ea1/mri/aseg.auto_noCCseg.mgz
> > reading norm
> > from
> /usr/local/freesurfer/subjects/c70eb728-c505-46c2-a2a1-1ed409c36ea1/mri/norm.mgz
> > 2358 voxels in left wm, 13846 in right wm, xrange [122, 136]
> > searching rotation angles z=[-10  4], y=[-31 -17]
> > ^Msearching scale 1 Z rot -9.8  ^Msearching scale 1 Z rot -9.5
> >  ^Msearching scale 1 Z rot -9.3  ^Msearching scale 1 Z rot -9.0
> >  ^Msearching scale 1 Z rot -8.8  ^Msearching scale 1 Z rot -8.5
> >  ^Msearching scale 1 Z rot -8.3  ^Msearching scale 1 Z rot -8.0
> >  ^Msearching scale 1 Z rot -7.8  ^Msearching scale 1 Z rot -7.5
> >  ^Msearching scale 1 Z rot -7.3  ^Msearching scale 1 Z rot -7.0
> >  ^Msearching scale 1 Z rot -6.8  ^Msearching scale 1 Z rot -6.5
> >  ^Msearching scale 1 Z rot -6.3  ^Msearching scale 1 Z rot -6.0
> >  ^Msearching scale 1 Z rot -5.8  ^Msearching scale 1 Z rot -5.5
> >  ^Msearching scale 1 Z rot -5.3  ^Msearching scale 1 Z rot -5.0
> >  ^Msearching scale 1 Z rot -4.8  ^Msearching scale 1 Z rot -4.5
> >  ^Msearching scale 1 Z rot -4.3  ^Msearching scale 1 Z rot -4.0
> >  ^Msearching scale 1 Z rot -3.8  ^Msearching scale 1 Z rot -3.5
> >  ^Msearching scale 1 Z rot -3.3  ^Msearching scale 1 Z rot -3.0
> >  ^Msearching scale 1 Z rot -2.8  ^Msearching scale 1 Z rot -2.5
> >  ^Msearching scale 1 Z rot -2.3  ^Msearching scale 1 Z rot -2.0
> >  ^Msearching scale 1 Z rot -1.8
> > ^Msearching scale 1 Z rot -1.5  ^Msearching scale 1 Z rot -1.3
> >  ^Msearching scale 1 Z rot -1.0  ^Msearching scale 1 Z rot -0.8
> >  ^Msearching scale 1 Z rot -0.5  ^Msearching scale 1 Z rot -0.3
> >  ^Msearching scale 1 Z rot -0.0  ^Msearching scale 1 Z rot 0.2
> >  ^Msearching scale 1 Z rot 0.5  ^Msearching scale 1 Z rot 0.7
> >  ^Msearching scale 1 Z rot 1.0  ^Msearching scale 1 Z rot 1.2
> >  ^Msearching scale 1 Z rot 1.5  ^Msearching scale 1 Z rot 1.7
> >  ^Msearching scale 1 Z rot 2.0  ^Msearching scale 1 Z rot 2.2
> >  ^Msearching scale 1 Z rot 2.5  ^Msearching scale 1 Z rot 2.7
> >  ^Msearching scale 1 Z rot 3.0  ^Msearching scale 1 Z rot 3.2
> >  ^Msearching scale 1 Z rot 3.5  ^Msearching scale 1 Z rot 3.7  global
> > minimum found at slice 129.0, rotations (-2.52, -3.27)
> > final transformation (x=129.0, yr=-2.521, zr=-3.273):
> >  0.997   0.057  -0.044  -2.975;
> > -0.057   0.998   0.003  -6.742;
> >  0.044  -0.000   0.999  -9.547;
> >  0.000   0.000   0.000   1.000;
> > Segmentation fault
> >
> >
> > Thanks
> >
> >
> > PPJ
> > -
> > Pedro Paulo de Magalhães Oliveira Junior
> > Netfilter & SpeedComm Telecom
> > -- www.netfilter.com.br
> > -- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441
> >
> >
> >
> >
> > ___
> > Fre

[Freesurfer] mri_cc segfault

[Pedro Paulo de Magalhães Oliveira Junior]

I'm having a segfault with mri_cc it's happening sometimes using FreeSurfer
5.1

Searching the mailing list I saw a similar problem in 2008 but with no
answers.

The relevant portion of recon-all.log:

 mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta
/usr/local/freesurfer/subjects/c70eb728-c505-46c2-a2a1-1ed409c36ea1/mri/transforms/cc_up.lta
c70eb728-c505-46c2-a2a1-1ed409c36ea1

will read input aseg from aseg.auto_noCCseg.mgz
writing aseg with cc labels to aseg.auto.mgz
will write lta as
/usr/local/freesurfer/subjects/c70eb728-c505-46c2-a2a1-1ed409c36ea1/mri/transforms/cc_up.lta
reading aseg from
/usr/local/freesurfer/subjects/c70eb728-c505-46c2-a2a1-1ed409c36ea1/mri/aseg.auto_noCCseg.mgz
reading norm from
/usr/local/freesurfer/subjects/c70eb728-c505-46c2-a2a1-1ed409c36ea1/mri/norm.mgz
2358 voxels in left wm, 13846 in right wm, xrange [122, 136]
searching rotation angles z=[-10  4], y=[-31 -17]
^Msearching scale 1 Z rot -9.8  ^Msearching scale 1 Z rot -9.5  ^Msearching
scale 1 Z rot -9.3  ^Msearching scale 1 Z rot -9.0  ^Msearching scale 1 Z
rot -8.8  ^Msearching scale 1 Z rot -8.5  ^Msearching scale 1 Z rot -8.3
 ^Msearching scale 1 Z rot -8.0  ^Msearching scale 1 Z rot -7.8
 ^Msearching scale 1 Z rot -7.5  ^Msearching scale 1 Z rot -7.3
 ^Msearching scale 1 Z rot -7.0  ^Msearching scale 1 Z rot -6.8
 ^Msearching scale 1 Z rot -6.5  ^Msearching scale 1 Z rot -6.3
 ^Msearching scale 1 Z rot -6.0  ^Msearching scale 1 Z rot -5.8
 ^Msearching scale 1 Z rot -5.5  ^Msearching scale 1 Z rot -5.3
 ^Msearching scale 1 Z rot -5.0  ^Msearching scale 1 Z rot -4.8
 ^Msearching scale 1 Z rot -4.5  ^Msearching scale 1 Z rot -4.3
 ^Msearching scale 1 Z rot -4.0  ^Msearching scale 1 Z rot -3.8
 ^Msearching scale 1 Z rot -3.5  ^Msearching scale 1 Z rot -3.3
 ^Msearching scale 1 Z rot -3.0  ^Msearching scale 1 Z rot -2.8
 ^Msearching scale 1 Z rot -2.5  ^Msearching scale 1 Z rot -2.3
 ^Msearching scale 1 Z rot -2.0  ^Msearching scale 1 Z rot -1.8
^Msearching scale 1 Z rot -1.5  ^Msearching scale 1 Z rot -1.3  ^Msearching
scale 1 Z rot -1.0  ^Msearching scale 1 Z rot -0.8  ^Msearching scale 1 Z
rot -0.5  ^Msearching scale 1 Z rot -0.3  ^Msearching scale 1 Z rot -0.0
 ^Msearching scale 1 Z rot 0.2  ^Msearching scale 1 Z rot 0.5  ^Msearching
scale 1 Z rot 0.7  ^Msearching scale 1 Z rot 1.0  ^Msearching scale 1 Z rot
1.2  ^Msearching scale 1 Z rot 1.5  ^Msearching scale 1 Z rot 1.7
 ^Msearching scale 1 Z rot 2.0  ^Msearching scale 1 Z rot 2.2  ^Msearching
scale 1 Z rot 2.5  ^Msearching scale 1 Z rot 2.7  ^Msearching scale 1 Z rot
3.0  ^Msearching scale 1 Z rot 3.2  ^Msearching scale 1 Z rot 3.5
 ^Msearching scale 1 Z rot 3.7  global minimum found at slice 129.0,
rotations (-2.52, -3.27)
final transformation (x=129.0, yr=-2.521, zr=-3.273):
 0.997   0.057  -0.044  -2.975;
-0.057   0.998   0.003  -6.742;
 0.044  -0.000   0.999  -9.547;
 0.000   0.000   0.000   1.000;
Segmentation fault

Thanks

PPJ
-----
Pedro Paulo de Magalhães Oliveira Junior
Netfilter & SpeedComm Telecom
-- www.netfilter.com.br
-- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441
___
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.

[Freesurfer] Public Supercomputing service to process FreeSurfer data

[Pedro Paulo de Magalhães Oliveira Junior]

We are announcing today the release of the Public Beta of
CerebralVol.com<http://cerebralvol.com/>,
a public cloud based supercomputer service to process FreeSurfer data.

CerebralVol.com users can process large amount of data using recon-all in a
single day without the hassle of dealing with Unix commands, scripts, etc.
Users can upload input data (NifTI and MGZ) through the web and download
the results of the recon-all from the web interface.

It's also possible to separate your cases in Groups and have Studies
associated with the Groups.

This week we are shipping the service with 20 CPUs and we are growing it to
1024 CPUs by the end of next week. The system will be fully operational by
January with 4096 nodes available to process more than 4000 recon-all per
day.

Those of you who want to know more about the technical details of the
project can find more information at
https://www.cerebralvol.com/about.html also
you can find information regarding HIPAA at
https://www.cerebralvol.com/hipaa.html

Signup for free at: https://www.cerebralvol.com

We strongly appreciate any suggestions and feedback.

Pedro Paulo Oliveira Jr.

-----
Pedro Paulo de Magalhães Oliveira Junior
Netfilter & SpeedComm Telecom
-- www.netfilter.com.br
-- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441
___
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.

Re: [Freesurfer] Freesurfer on Mac Os X 10.8

[Pedro Paulo de Magalhães Oliveira Junior]

Yes it works.

But for the X11 stuff you need to download X11 (ML doesn't include X11
anymore)

http://support.apple.com/kb/HT5293?viewlocale=en_US&locale=en_US
-----
Pedro Paulo de Magalhães Oliveira Junior
Netfilter & SpeedComm Telecom
-- www.netfilter.com.br
-- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441




On Sat, Sep 8, 2012 at 5:44 PM, Melissa Lancaster <
melissa.lancas...@my.rfums.org> wrote:

> Hi,
>
> Is Freesurfer able to run on Mountain Lion?
>
> Thanks!!!
>
>
>
>
> ___
> 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.
>
>
___
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.

Re: [Freesurfer] slanted

[Pedro Paulo de Magalhães Oliveira Junior]

No! Do you have a dropbox account? Copy there and send the link to them.

-
Pedro Paulo de Magalhães Oliveira Junior
Netfilter & SpeedComm Telecom
-- www.netfilter.com.br
-- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441


On Wed, Jul 11, 2012 at 3:39 PM, Borzello, Mia wrote:

> can i just send it to freesurfer@nmr.mgh.harvard.edu?
>
> thanks
> 
> From: Bruce Fischl [fis...@nmr.mgh.harvard.edu]
> Sent: Wednesday, July 11, 2012 1:58 PM
> To: Borzello, Mia
> Cc: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] slanted
>
> when you say ftp doesn't work, what do you mean? It works for me:
>
> ftp surfer.nmr.mgh.harvard.edu
> Connected to surfer.nmr.mgh.harvard.edu (132.183.202.158).
> 220-This is the Martinos Center Anonymous FTP service. Use of this site
> 220-shows implicit consent to our Acceptable Use Policy outlined at
> 220-http://www.nmr.mgh.harvard.edu/martinos/userInfo/computer/nmr-aup.php
> 220-
> 220-OPERATIONAL NOTE:  If, when doing a GET or PUT, you encounter either
> 220-
> 220-229 Entering Extended Passive Mode
> 220-
> 220-   and nothing happens OR
> 220-
> 220-229 Entering Extended Passive Mode
> 220-500 Bad EPRT protocol.
> 220-
> 220-  try issuing the EPSV command prior to GET or PUT.
> 220-
> 220
> Name (surfer.nmr.mgh.harvard.edu:fischl): anonymous
> 331 Please specify the password.
> Password:
> 230 Login successful.
> Remote system type is UNIX.
> Using binary mode to transfer files.
> ftp> cd /space/incoming
> 250 Directory successfully changed.
> ftp> ls
> 227 Entering Passive Mode (132,183,202,158,147,239)
> 150 Here comes the directory listing.
> 226 Transfer done (but failed to open directory).
> ftp> put test.mgz
> local: test.mgz remote: test.mgz
> 227 Entering Passive Mode (132,183,202,158,147,226)
> 150 Ok to send data.
> 226 File receive OK.
> 1696595 bytes sent in 0.209 secs (7.9e+03 Kbytes/sec)
>
>
> On Wed, 11 Jul 2012, Borzello, Mia wrote:
>
> > i saw the instructions, but it doesn't give an e-mail specifically for
> that and ftp surfer.nmr.mgh.harvard.edu doesn't work.
> > 
> > From: freesurfer-boun...@nmr.mgh.harvard.edu [
> freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [
> fis...@nmr.mgh.harvard.edu]
> > Sent: Wednesday, July 11, 2012 1:24 PM
> > To: Borzello, Mia
> > Cc: freesurfer@nmr.mgh.harvard.edu
> > Subject: Re: [Freesurfer] slanted
> >
> > Hi Mia,
> >
> > no, there are instructions on the wiki for uploading your data using
> > either ftp or the filedrop. And no, I think it will be another couple of
> > days
> > Bruce
> > On Wed, 11 Jul 2012, Borzello, Mia wrote:
> >
> >> Will he be back today? Upload it in an e-mail?
> >>
> >> Thanks,
> >> m
> >> 
> >> From: Bruce Fischl [fis...@nmr.mgh.harvard.edu]
> >> Sent: Wednesday, July 11, 2012 12:21 PM
> >> To: Borzello, Mia
> >> Cc: freesurfer@nmr.mgh.harvard.edu
> >> Subject: Re: [Freesurfer] slanted
> >>
> >> Hi Mia,
> >>
> >> you'll probably have to wait until Doug is back to get an answer. In the
> >> meantime, feel free to upload your data so we can take a look
> >>
> >> cheers
> >> Bruce
> >> On Wed, 11 Jul
> >> 2012, Borzello, Mia wrote:
> >>
> >>> Hi,
> >>>
> >>> I'm not exactly sure what the problem is, but for some reason, this
> brain is kind of sheered. I'm not sure if it's because of the CT, but on
> the right side of the picture i attached, it kind of wider on one side.
> It's alignment isn't right, and using "rotate" does help. How should I
> correct this?
> >>>
> >>> Thanks,
> >>> Mia
> >>>
> >>
> >>
> >>
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> >
> >
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailma

Re: [Freesurfer] TkSurfer and new color table. Mislabelling

[Pedro Paulo de Magalhães Oliveira Junior]

Thanks Douglas.

It did work using the color table with just the included labels (I had to
renumber the labels in the table)

For left:
1 ctx-lh-bankssts 255 42 0 0
2 ctx-lh-caudalmiddlefrontal 255 14 0 0
3 ctx-lh-entorhinal 255 17 0 0
4 ctx-lh-paracentral 255 43 0 0
5 ctx-lh-parstriangularis 255 15 0 0
6 ctx-lh-postcentral 255 14 0 0
7 ctx-lh-superiorfrontal 255 79 0 0
8 ctx-lh-frontalpole 255 17 0 0
9 ctx-lh-temporalpole 255 14 0 0

For right:
1 ctx-rh-bankssts 255 18 0 0
2 ctx-rh-isthmuscingulate 255 39 0 0
3 ctx-rh-medialorbitofrontal 255 60 0 0
4 ctx-rh-parstriangularis 255 13 0 0
5 ctx-rh-rostralanteriorcingulate 255 40 0 0
6 ctx-rh-superiorparietal 255 48 0 0
7 ctx-rh-frontalpole 255 106 0 0


On Thu, Jul 5, 2012 at 7:14 PM, Douglas N Greve
wrote:

> Hi Pedro Paulo, it is not quite the right procedure, but I'm surprised
> that it gave unknown for all labels. Try
> modifying the colortable.txt such that the first entry is the name and
> color for your first label, etc.
> doug
>
>
> On 07/05/2012 03:44 PM, Pedro Paulo de Magalhães Oliveira Junior wrote:
>
>> Doug,
>>
>> I did
>>
>> mri_annotation2label --subject bert --hemi lh --outdir
>> $SUBJECTS_DIR/bert/label
>> mri_annotation2label --subject bert --hemi rh --outdir
>> $SUBJECTS_DIR/bert/label
>>
>> And then
>>
>> mris_label2annot --s bert --hemi lh --ctab 
>> $FREESURFER_HOME/**FreeSurferColorLUT.txt
>> --l lh.bankssts.label --l lh.caudalmiddlefrontal.label --l
>> lh.entorhinal.label --l lh.paracentral.label --l lh.parstriangularis.label
>> --l lh.postcentral.label --l lh.superiorfrontal.label --l
>> lh.frontalpole.label --l lh.temporalpole.label --a myannot
>>
>> and
>>
>> mris_label2annot --s bert --hemi rh --ctab 
>> $FREESURFER_HOME/**FreeSurferColorLUT.txt
>> --l rh.bankssts.label --l rh.isthmuscingulate.label --l
>> rh.medialorbitofrontal.label --l rh.parstriangularis.label --l
>> rh.rostralanteriorcingulate.**label --l rh.superiorparietal.label --l
>> rh.frontalpole.label --a myannot
>>
>> If this is the right procedure I guess I'll have to modify the existing
>> annot in matlab because all the surface is being labelled as Unknown.
>>
>> Thanks
>>
>> PPJ
>>
>>
>> On Thu, Jul 5, 2012 at 4:01 PM, Douglas N Greve <
>> gr...@nmr.mgh.harvard.edu 
>> <mailto:gr...@nmr.mgh.harvard.**edu>>
>> wrote:
>>
>> You can also break up the annot into labels (
>> mri_annotation2label) then
>> recombine them with a new color table with mris_label2annot.
>> doug
>>
>> On 07/05/2012 02:57 PM, Bruce Fischl wrote:
>> > Hi PPJ,
>> >
>> > I think the color lut is embedded in the aparc.annot. If you want to
>> > change it you have to change the one that's in the .annot. I
>> would do
>> > it in matlab.
>> >
>> > cheers
>> > Bruce
>> >
>> > On Thu, 5 Jul 2012, Pedro Paulo de Magalhães Oliveira Junior wrote:
>> >
>> >> I'm trying to generate an image to a paper and I have to colorize
>> >> some areas of the cortex with specific
>> >> colors.
>> >> I have edited the FreeSurferColorLUT.txt changing the following
>> lines:
>> >> 1001 ctx-lh-bankssts 255 42 0 0
>> >> 1003 ctx-lh-caudalmiddlefrontal 255 14 0 0
>> >> 1006 ctx-lh-entorhinal 255 17 0 0
>> >> 1017 ctx-lh-paracentral 255 43 0 0
>> >> 1020 ctx-lh-parstriangularis 255 15 0 0
>> >> 1022 ctx-lh-postcentral 255 14 0 0
>> >> 1028 ctx-lh-superiorfrontal 255 79 0 0
>> >> 1032 ctx-lh-frontalpole 255 17 0 0
>> >> 1033 ctx-lh-temporalpole 255 14 0 0
>> >> 2001 ctx-rh-bankssts 255 18 0 0
>> >> 2010 ctx-rh-isthmuscingulate 255 39 0 0
>> >> 2014 ctx-rh-medialorbitofrontal 255 60 0 0
>> >> 2020 ctx-rh-parstriangularis 255 13 0 0
>> >> 2026 ctx-rh-**rostralanteriorcingulate 255 40 0 0
>> >> 2029 ctx-rh-superiorparietal 255 48 0 0
>> >> 2032 ctx-rh-frontalpole 255 106 0 0
>> >>
>> >> all other regions are 127 127 127 0
>> >>
>>     >> When I load the surface for some case with:
>> >> tksurfer bert lh pial -annot aparc -ctab FreeSurferColorLUT.txt
>> >>
>> >> I get the usual coloring scheme with the labels correct. TkSurfer
>> >> seems to be ignoring

Re: [Freesurfer] TkSurfer and new color table. Mislabelling

[Pedro Paulo de Magalhães Oliveira Junior]

Doug,

I did

mri_annotation2label --subject bert --hemi lh --outdir
$SUBJECTS_DIR/bert/label
mri_annotation2label --subject bert --hemi rh --outdir $SUBJECTS_DIR
/bert/label

And then

mris_label2annot --s bert --hemi lh --ctab
$FREESURFER_HOME/FreeSurferColorLUT.txt --l lh.bankssts.label --l
lh.caudalmiddlefrontal.label --l lh.entorhinal.label --l
lh.paracentral.label --l lh.parstriangularis.label --l lh.postcentral.label
--l lh.superiorfrontal.label --l lh.frontalpole.label --l
lh.temporalpole.label --a myannot

and

mris_label2annot --s bert --hemi rh
--ctab $FREESURFER_HOME/FreeSurferColorLUT.txt --l rh.bankssts.label --l
rh.isthmuscingulate.label --l rh.medialorbitofrontal.label --l
rh.parstriangularis.label --l rh.rostralanteriorcingulate.label --l
rh.superiorparietal.label --l rh.frontalpole.label --a myannot

If this is the right procedure I guess I'll have to modify the existing
annot in matlab because all the surface is being labelled as Unknown.

Thanks

PPJ


On Thu, Jul 5, 2012 at 4:01 PM, Douglas N Greve
wrote:

> You can also break up the annot into labels ( mri_annotation2label) then
> recombine them with a new color table with mris_label2annot.
> doug
>
> On 07/05/2012 02:57 PM, Bruce Fischl wrote:
> > Hi PPJ,
> >
> > I think the color lut is embedded in the aparc.annot. If you want to
> > change it you have to change the one that's in the .annot. I would do
> > it in matlab.
> >
> > cheers
> > Bruce
> >
> > On Thu, 5 Jul 2012, Pedro Paulo de Magalhães Oliveira Junior wrote:
> >
> >> I'm trying to generate an image to a paper and I have to colorize
> >> some areas of the cortex with specific
> >> colors.
> >> I have edited the FreeSurferColorLUT.txt changing the following lines:
> >> 1001 ctx-lh-bankssts 255 42 0 0
> >> 1003 ctx-lh-caudalmiddlefrontal 255 14 0 0
> >> 1006 ctx-lh-entorhinal 255 17 0 0
> >> 1017 ctx-lh-paracentral 255 43 0 0
> >> 1020 ctx-lh-parstriangularis 255 15 0 0
> >> 1022 ctx-lh-postcentral 255 14 0 0
> >> 1028 ctx-lh-superiorfrontal 255 79 0 0
> >> 1032 ctx-lh-frontalpole 255 17 0 0
> >> 1033 ctx-lh-temporalpole 255 14 0 0
> >> 2001 ctx-rh-bankssts 255 18 0 0
> >> 2010 ctx-rh-isthmuscingulate 255 39 0 0
> >> 2014 ctx-rh-medialorbitofrontal 255 60 0 0
> >> 2020 ctx-rh-parstriangularis 255 13 0 0
> >> 2026 ctx-rh-rostralanteriorcingulate 255 40 0 0
> >> 2029 ctx-rh-superiorparietal 255 48 0 0
> >> 2032 ctx-rh-frontalpole 255 106 0 0
> >>
> >> all other regions are 127 127 127 0
> >>
> >> When I load the surface for some case with:
> >> tksurfer bert lh pial -annot aparc -ctab FreeSurferColorLUT.txt
> >>
> >> I get the usual coloring scheme with the labels correct. TkSurfer
> >> seems to be ignoring
> >> FreeSurferColorLUT.txt, but the labels are placed in the right spots.
> >>
> >> When I try to manually force the FreeSurferColorLUT.txt I'm
> >> visualizing an all grey image. And the surface is
> >> completely mislabeled, there is a 4th ventricle in the surface,
> >> putamen in the surface, etc.
> >>
> >> What am I doing wrong?
> >> -
> >> Pedro Paulo de Magalhães Oliveira Junior
> >> Netfilter & SpeedComm Telecom-- www.netfilter.com.br
> >> -- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441
> >>
> >>
> >>
> >>
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>
> ___
> 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.
>
>
___
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.

[Freesurfer] TkSurfer and new color table. Mislabelling

[Pedro Paulo de Magalhães Oliveira Junior]

I'm trying to generate an image to a paper and I have to colorize some
areas of the cortex with specific colors.

I have edited the FreeSurferColorLUT.txt changing the following lines:
1001 ctx-lh-bankssts 255 42 0 0
1003 ctx-lh-caudalmiddlefrontal 255 14 0 0
1006 ctx-lh-entorhinal 255 17 0 0
1017 ctx-lh-paracentral 255 43 0 0
1020 ctx-lh-parstriangularis 255 15 0 0
1022 ctx-lh-postcentral 255 14 0 0
1028 ctx-lh-superiorfrontal 255 79 0 0
1032 ctx-lh-frontalpole 255 17 0 0
1033 ctx-lh-temporalpole 255 14 0 0
2001 ctx-rh-bankssts 255 18 0 0
2010 ctx-rh-isthmuscingulate 255 39 0 0
2014 ctx-rh-medialorbitofrontal 255 60 0 0
2020 ctx-rh-parstriangularis 255 13 0 0
2026 ctx-rh-rostralanteriorcingulate 255 40 0 0
2029 ctx-rh-superiorparietal 255 48 0 0
2032 ctx-rh-frontalpole 255 106 0 0

all other regions are 127 127 127 0

When I load the surface for some case with:
tksurfer bert lh pial -annot aparc -ctab FreeSurferColorLUT.txt

I get the usual coloring scheme with the labels correct. TkSurfer seems to
be ignoring FreeSurferColorLUT.txt, but the labels are placed in the right
spots.

When I try to manually force the FreeSurferColorLUT.txt I'm visualizing an
all grey image. And the surface is completely mislabeled, there is a 4th
ventricle in the surface, putamen in the surface, etc.

What am I doing wrong?
-----
Pedro Paulo de Magalhães Oliveira Junior
Netfilter & SpeedComm Telecom
-- www.netfilter.com.br
-- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441
___
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.

Re: [Freesurfer] .license file

[Pedro Paulo de Magalhães Oliveira Junior]

If FreeSurfer on Mac has been installed on /Applications you may need to
type

sudo cat > $FREESURFER_HOME/.license

and enter your account password when asked
-----
Pedro Paulo de Magalhães Oliveira Junior
Netfilter & SpeedComm Telecom
-- www.netfilter.com.br
-- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441




On Mon, Jun 18, 2012 at 10:57 AM, Paul Raines wrote:

>
> I am assuming you are on a OSX box which has that stupid protection.
>
> Just open a Terminal and run
>
>   cat > $FREESURFER_HOME/.license
>
> then type in the 3 lines and Enter and then do a Control-D to exit
>
> -- Paul Raines 
> (http://help.nmr.mgh.harvard.**edu<http://help.nmr.mgh.harvard.edu>
> )
>
>
>
> On Sun, 17 Jun 2012 1:45am, Monica Giraldo wrote:
>
>  Hello, I created a file with this data, but when I'm going to save it as
>> .license doesnt let me because a message appears and says that files
>> starting with . are of the system and that i have to choose another name.
>> What can I do? Thanks.
>>
>> Mónica Giraldo Chica
>> PhD. Candidate Biomedicine
>> Sherman Health Science Research Centre
>> www.monicagiraldochica.com
>> __**_
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
>>
>>
>>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> 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.
>
>
___
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.

[Freesurfer] [Release] - iSurf BrainView 4.0.5

[Pedro Paulo de Magalhães Oliveira Junior]

Today it was released the version 4.0.5 of iSurf Brainview, it's a
major redesign version
release for IPad, IPhone and IPod Touch.

The UI has been redesigned to be more compliant to the Apple Human
Interface Guidelines.

 As usual suggestions and feedback are welcome.

The link for download is:
http://itunes.apple.com/WebObjects/MZStore.woa/wa/viewSoftware?id=381072423&mt=8

Note: A version for Windows Phone 7.5 (Nokia Lumia 900, 800, 710, etc) is
under development.
-----
Pedro Paulo de Magalhães Oliveira Junior
Netfilter & SpeedComm Telecom
-- www.netfilter.com.br
-- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441
___
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.

Re: [Freesurfer] OBJ conversion

[Pedro Paulo de Magalhães Oliveira Junior]

There's a how-to in the FreeSurfer website:
http://surfer.nmr.mgh.harvard.edu/fswiki/HowTo/HowTo

Pedro Paulo Jr.

On Mon, Feb 20, 2012 at 23:32, Manfred G Kitzbichler <
manfr...@nmr.mgh.harvard.edu> wrote:

>  Hi Darshan,
>
> as Bruce suggested, you can use mris_convert to get an STL file which you
> can import into Blender or MeshLab. Both write Wavefront OBJ files.
>
> - Manfred
>
>
>
> On 02/20/2012 07:24 PM, Darshan P wrote:
>
>  Hello all,
>
>  I was wondering if I can convert the surface outputs to an OBJ mesh file
> format .
> Since most of the applications are in windows I was hoping if there is
> conversion tool to do this .
>
>  Regards
> Darshan
>
>
> ___
> Freesurfer mailing 
> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
> --
> Manfred G. 
> Kitzbichler,
> Research Fellow
> Harvard Medical School & Mass General Hospital
> Martinos Center for Biomedical Imaging
> 149 Thirteenth Street, Rm 10.018
> Charlestown, MA 02129, USA
>
> ___
> 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.
>
>
___
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.

Re: [Freesurfer] Performance questions

[Pedro Paulo de Magalhães Oliveira Junior]

I think IBM has a better compiler. Better than gcc and slightly slower
than intel compiler

Sent from my iPad

On Jan 18, 2012, at 16:09, Nick Schmansky  wrote:

> Malcolm,
>
> actually, they (IBM) are looking at openmp (to allow multiple threads to
> process for-loops) and SSE3 instructions (better vectorization).
>
> recon-all --help contains some timings for an AMD processor.  centos4
> vs. centos5 itself should not account for any speed differences, but it
> is true that our centos5 build was built with gcc 4.1 while our centos4
> build uses gcc 3.4.7, so those compiler difference likely account for
> speed differences.
>
> another major factor that affects runtime is whether the Intel Nahalem
> architecture exists on your system.  this memory controller is much
> better at handling the wide memory layout of freesurfer structures
> (minimizing cache-line hits).
>
> Nick
>
>
> On Fri, 2012-01-13 at 09:13 -0500, Bruce Fischl wrote:
>> Hi Malcolm
>>
>> in collaboration with IBM we are also looking at MPI and pthreads.
>>
>> cheers
>> Bruce
>>
>> On Fri,
>> 13 Jan 2012, Malcolm Tobias wrote:
>>
>>>
>>> Is there a standard benchmark for FreeSurfer?
>>> I've been using the data under subjects (Bert?/Ernie?) and running a recon-
>>> all:
>>>
>>> recon-all -s ernie -i ./sample-001.mgz -i ./sample-002.mgz  -all
>>>
>>> On our hardware using the 5.1 distributed binary (freesurfer-Linux-
>>> centos4_x86_64-stable-pub-v5.1.0.tar.gz) it takes about 12 hours.
>>>
>>> I was surprised that 5.1 was running so much faster than 5.0.  With 5.0
>>> (freesurfer-Linux-centos5_x86_64-stable-pub-v5.0.0.tar.gz) it was taking 
>>> about
>>> 18 hours.  Did anyone else notice a big speed-up from 5.0 to 5.1?  Maybe 
>>> it's
>>> a difference between centos5 vs. centos4?  If so, wouldn't you expect the
>>> former to be faster?
>>>
>>> If I back-port the changes Nick made to configure.in for the dev branch to 
>>> the
>>> stable release of 5.1 and build from source on our systems, I'm able to run 
>>> in
>>> ~10 hours.  I'm guessing this is mostly due to the difference in the 
>>> versions
>>> of gcc used on our system (4.1.2) vs. those used for the centos4 distributed
>>> binary?
>>>
>>> For the dev release, it's taking about ~11 hours.  I'm guessing the dev 
>>> branch
>>> is mostly focused on features/bug-fixes and performance is only looked at
>>> before a release?
>>>
>>> Besides GPUs, what else are people doing to increase performance?
>>>
>>> Cheers,
>>> Malcolm
>>>
>>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> 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.
>
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] iSurf Brainview now ported to Mac

[Pedro Paulo de Magalhães Oliveira Junior]

Today Apple released in the Mac Store, for free, the version of iSurf
BrainView for Mac. It's yet not as complete as the iPad and iPhone version
but it has some nice features to help you or your students to learn
neuroanatomy using FreeSurfer automated parcellation and subcortical
segmentation.

You can download it at:
http://itunes.apple.com/us/app/isurf-brainview-desktop/id491367143?ls=1&mt=12

As usual, suggestions are welcome.

Happy 2012 for everyone.

PPJ
-----
Pedro Paulo de Magalhães Oliveira Junior
Netfilter & SpeedComm Telecom
-- www.netfilter.com.br
-- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441
___
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.

Re: [Freesurfer] Amazon EC2 Version of FreeSurfer 5.1 Available

[Pedro Paulo de Magalhães Oliveira Junior]

I have restored the image: 060244368407/FREESURFER51

I'll create a web service that can log the number of instances spawned. Is
that ok with you?
-
Pedro Paulo de Magalhães Oliveira Junior
Netfilter & SpeedComm Telecom
-- www.netfilter.com.br
-- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441




2011/11/18 Bruce Fischl 

> Hi PPJ,
>
> I would rather people use FS without licenses than find themselves unable
> to use it, so why not leave it for now. Can you put a request that they
> first download a license or register on your website? Alternatively, can
> you just remove the .license file from the AMI forcing the users to get one?
>
> thanks for making this available
> Bruce
>
>
>
> On Fri, 18 Nov 2011, Pedro Paulo de Magalhães Oliveira Junior wrote:
>
>  As requested I removed the AMI image because that image contains a
>> .license file.
>> I can republish the image when we find a solution for the licensing issue.
>>
>> ----------**------**-
>> Pedro Paulo de Magalhães Oliveira Junior
>> Netfilter & SpeedComm Telecom-- www.netfilter.com.br
>>
>> -- For mobile: http://itunes.apple.**com/br/artist/netfilter/**
>> id365306441 <http://itunes.apple.com/br/artist/netfilter/id365306441>
>>
>>
>>
>>
>> 2011/11/15 Joshua Lee 
>>  It would be great if Freesurfer maintained an official AMI. One
>> important reason to do so is security. If the
>>  AMI is maintained by the organization, then people can feel
>> reassured that their data is not being downloaded to
>>  a compromised instance, not that any on this board would have such
>> malicious intent. Moreover, it could contain
>>  such scripts as makes the analysis process easier.
>>
>>      -
>> Joshua Lee
>> Graduate Student
>> Center for Mind and Brain &
>> Department of Psychology
>> University of California, Davis
>> 530.747.3805
>>
>>
>> 2011/11/14 Pedro Paulo de Magalhães Oliveira Junior > >
>>  Ok. I'll label as private this AMI that has .license file.
>> Maybe we can make a tutorial on how to create an AMI instead.
>> --**--**-
>> Pedro Paulo de Magalhães Oliveira Junior
>> Netfilter & SpeedComm Telecom-- www.netfilter.com.br
>>
>> -- For mobile: http://itunes.apple.**com/br/artist/netfilter/**
>> id365306441 <http://itunes.apple.com/br/artist/netfilter/id365306441>
>>
>>
>>
>>
>> On Mon, Nov 14, 2011 at 21:07, Nick Schmansky 
>> wrote:
>>  Glad to hear it works well.  To revisit the issue of the license (in
>> the
>>  form of the .license file which needs to be in the $FREESURFER_HOME
>>  directory and the request of which is used for usage tracking), I
>> think
>>  the convention to follow for any publicly available AMI freesurfer
>>  instances should be to not include a .license file with it, so as to
>>  force the download of this file (so that freesurfer usage will be
>>  tracked).  A user need only do this once for however many times they
>> use
>>  the cloud instance.
>>
>>  N.
>>
>>
>>
>>
>>
>
> 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<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.
>
___
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.

Re: [Freesurfer] Amazon EC2 Version of FreeSurfer 5.1 Available

[Pedro Paulo de Magalhães Oliveira Junior]

As requested I removed the AMI image because that image contains a .license
file.

I can republish the image when we find a solution for the licensing issue.

-
Pedro Paulo de Magalhães Oliveira Junior
Netfilter & SpeedComm Telecom
-- www.netfilter.com.br
-- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441




2011/11/15 Joshua Lee 

> It would be great if Freesurfer maintained an official AMI. One important
> reason to do so is security. If the AMI is maintained by the organization,
> then people can feel reassured that their data is not being downloaded to a
> compromised instance, not that any on this board would have such malicious
> intent. Moreover, it could contain such scripts as makes the analysis
> process easier.
>
>
> -
> Joshua Lee
> Graduate Student
> Center for Mind and Brain &
> Department of Psychology
> University of California, Davis
> 530.747.3805
>
>
> 2011/11/14 Pedro Paulo de Magalhães Oliveira Junior 
>
>> Ok. I'll label as private this AMI that has .license file.
>>
>> Maybe we can make a tutorial on how to create an AMI instead.
>>
>> -----
>> Pedro Paulo de Magalhães Oliveira Junior
>> Netfilter & SpeedComm Telecom
>> -- www.netfilter.com.br
>> -- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441
>>
>>
>>
>>
>> On Mon, Nov 14, 2011 at 21:07, Nick Schmansky 
>> wrote:
>>
>>> Glad to hear it works well.  To revisit the issue of the license (in the
>>> form of the .license file which needs to be in the $FREESURFER_HOME
>>> directory and the request of which is used for usage tracking), I think
>>> the convention to follow for any publicly available AMI freesurfer
>>> instances should be to not include a .license file with it, so as to
>>> force the download of this file (so that freesurfer usage will be
>>> tracked).  A user need only do this once for however many times they use
>>> the cloud instance.
>>>
>>> N.
>>>
>>>
___
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.

Re: [Freesurfer] Amazon EC2 Version of FreeSurfer 5.1 Available

[Pedro Paulo de Magalhães Oliveira Junior]

Ok. I'll label as private this AMI that has .license file.

Maybe we can make a tutorial on how to create an AMI instead.
-
Pedro Paulo de Magalhães Oliveira Junior
Netfilter & SpeedComm Telecom
-- www.netfilter.com.br
-- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441




On Mon, Nov 14, 2011 at 21:07, Nick Schmansky wrote:

> Glad to hear it works well.  To revisit the issue of the license (in the
> form of the .license file which needs to be in the $FREESURFER_HOME
> directory and the request of which is used for usage tracking), I think
> the convention to follow for any publicly available AMI freesurfer
> instances should be to not include a .license file with it, so as to
> force the download of this file (so that freesurfer usage will be
> tracked).  A user need only do this once for however many times they use
> the cloud instance.
>
> N.
>
> On Mon, 2011-11-14 at 17:16 -0500, Joshua Lee wrote:
> > Thanks again Pedro. I just ran 220 brains through in day or two using
> > the cloud. Fantastic.
> > The script people have been talking about would have been useful.
> > One thing I didn't realize was that I should have moved the freesurfer
> > subject directory from /usr/local/freesurfer/subjects to the larger
> > disk that comes with the instance. I had disk-write errors because the
> > the main partition ran out of space.
> >
> > Anyway, ec2 rocks with Freesurfer.
> > -
> >
> > Joshua Lee
> >
> > Graduate Student
> > Center for Mind and Brain &
> >
> > Department of Psychology
> >
> > University of California, Davis
> > 530.747.3805
> >
> >
> > 2011/11/12 Nolan Nichols 
> > If only running a small number of instances, I think it is
> > reasonable
> > to leave the ami w/o a .license file since it is easy enough
> > to scp it
> > up to the cloud. For running a cluster it would be nice to
> > have a
> > script, perhaps using Fabric, to upload a .license file to
> > each
> > instance in a cluster. As it stands, the starcluster FS AMI
> > does not
> > have a .license file and requires one to be uploaded manually.
> >
> > Nolan
> >
> > 2011/11/12 Thomas Ballinger :
> >
> >     > Perhaps the AMI image could be without a licence file and
> > uploading one
> > > (acquired though normal means) would be required?  (I
> > suppose that's the
> > > basic solution we're looking for a clean way around)
> > >
> > > 2011/11/12 Pedro Paulo de Magalhães Oliveira Junior
> > 
> > >>
> > >> Maybe we can set up a web server in the Martinos center and
> > the AMI Image
> > >> can authenticate in it.
> > >>
> >
> -
> > >> Pedro Paulo de Magalhães Oliveira Junior
> > >> Netfilter & SpeedComm Telecom
> > >> -- www.netfilter.com.br
> > >> -- For
> > mobile: http://itunes.apple.com/br/artist/netfilter/id365306441
> > >>
> > >>
> > >>
> > >>
> > >> On Sat, Nov 12, 2011 at 15:28, Nick Schmansky
> > 
> > >> wrote:
> > >>>
> > >>> I'm happy to see the work getting the cloud to be
> > feasible. I still need
> > >>> to catch up on this thread but one issue that I'd like to
> > sort out is
> > >>> tracking the license count.  Its fine for a new user to
> > use an existing
> > >>> image, but I think there will need to be a way to remind
> > people to request
> > >>> our .license file even if they don't actually use the file
> > so that cloud
> > >>> usages get counted (license count is critical for us for
> > grant renewal
> > >>> purposes). Ideas on a clean way to do this?
> > >>> N.
> > >>>
> > >>> On Nov 12, 2011, at 11:10 AM, Thomas Ballinger
> > >>>  wrote:
> > >>>
> > >>> Satra, the ipython example looks grea

Re: [Freesurfer] Amazon EC2 Version of FreeSurfer 5.1 Available

[Pedro Paulo de Magalhães Oliveira Junior]

Maybe we can set up a web server in the Martinos center and the AMI Image
can authenticate in it.
-
Pedro Paulo de Magalhães Oliveira Junior
Netfilter & SpeedComm Telecom
-- www.netfilter.com.br
-- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441




On Sat, Nov 12, 2011 at 15:28, Nick Schmansky wrote:

> I'm happy to see the work getting the cloud to be feasible. I still need
> to catch up on this thread but one issue that I'd like to sort out is
> tracking the license count.  Its fine for a new user to use an existing
> image, but I think there will need to be a way to remind people to request
> our .license file even if they don't actually use the file so that cloud
> usages get counted (license count is critical for us for grant renewal
> purposes). Ideas on a clean way to do this?
>
> N.
>
>
> On Nov 12, 2011, at 11:10 AM, Thomas Ballinger 
> wrote:
>
> Satra, the ipython example looks great. The scripts I posted also use
> fabric for running Freesurfer, but don't download Freesurfer due to it
> already being installed on Pedro's image. I agree with Satra that
> individually administered instances might work better for those wishing to
> run a few cases with Freesurfer, particularly due to the predictable long
> running time (lessening the benefits of job distribution) and ability of a
> recon-all job to efficiently use all of a ec2 small instance's cpu. I think
> starcluster is pretty awesome, and I would love to push people in that
> direction, but it won't be quite as push-button, and the benefits may be
> minimal for small use cases.  That's not to say there aren't plenty of
> folks who would rather use Nolan's solution (me for one :))
>
> Tom
>
>
> On Sat, Nov 12, 2011 at 9:14 AM, Nolan Nichols  wrote:
>
>> Hi Satra,
>>
>> Fabric does look nice, thanks for pointing it out and for a link to the
>> ipython_in_a_box example.
>>
>> That framework might work for what I had in mind for freesurfer and
>> starcluster, which uses the same idea to keep the initial AMI footprint
>> smaller/flexible.
>>
>> Cheers,
>>
>> Nolan
>> On Nov 12, 2011 7:32 AM, "Satrajit Ghosh"  wrote:
>>
>>> hi nolan,
>>>
>>> i think starcluster is a great way to create a cluster on aws. but for
>>> those wanting to create a single instance and install things on an ami
>>> without actually having a large ami, fabric might be a good option.
>>>
>>> fabric:
>>> http://docs.fabfile.org/en/1.3.2/index.html
>>>
>>> example: (another neurodebian ami)
>>> https://github.com/wholeslide/ipython_in_a_box/blob/master/fabfile.py
>>>
>>> cheers,
>>>
>>> satra
>>>
>>> On Sat, Nov 12, 2011 at 6:11 AM, Nolan Nichols  wrote:
>>>
>>>> Thanks, Pedro!
>>>>
>>>> I am glad to see that you posted a public AMI for freesurfer. And
>>>> thanks to Thomas for producin documentation on how to use it.
>>>>
>>>> This thread inspired me share a StarCluster AMI (ami-27f1384e in the
>>>> us-east-1 region) that I built for batch FS jobs, which includes the
>>>> initial setup for installing tools from the NeuroDebian repository.
>>>> I've also been playing around with using s3fs, which allows Amazon's
>>>> S3 to be mounted as a drive and accessed directly as the
>>>> "subjects_dir".
>>>>
>>>> The AMI can be launched here:
>>>>
>>>> https://console.aws.amazon.com/ec2/home?region=us-east-1#launchAmi=ami-27f1384e
>>>>
>>>> I did not include the .license for FS as I wasn't sure about licensing
>>>> issues, but I would be happy to publish an AMI with a built-in license
>>>> if I get the go ahead. For now you will need to start a cluster and
>>>> your license to each instance.
>>>>
>>>> A few details:
>>>>
>>>> Ubuntu 10.04 x86
>>>> built from StarClusters ami-8cf913e5
>>>> us-east-1 region
>>>> See the StarCluster details at http://web.mit.edu/stardev/cluster/
>>>> Customizing StarCluster
>>>> (
>>>> http://web.mit.edu/stardev/cluster/docs/latest/manual/create_new_ami.html
>>>> )
>>>> s3fs (http://code.google.com/p/s3fs/)
>>>> Freesurfer 5.1 32-bit
>>>> NeuroDebian ready (so you can apt-get install mricron, fsl, nipype,
>>>> etc.)
>>>>
>&

Re: [Freesurfer] Amazon EC2 Version of FreeSurfer 5.1 Available

[Pedro Paulo de Magalhães Oliveira Junior]

I've put together the basic tutorial on getting started using Amazon AWS
system:

It's in the same place Nick pointed out:
https://surfer.nmr.mgh.harvard.edu/fswiki/AmazonCloud


-----
Pedro Paulo de Magalhães Oliveira Junior
Netfilter & SpeedComm Telecom
-- www.netfilter.com.br
-- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441




2011/11/9 Nick Schmansky 

> Pedro Paulo,
>
> thanks for posting the info.  i've added this to the Download wiki page,
> and created a stub page for the Amazon Cloud:
>
> https://surfer.nmr.mgh.harvard.edu/fswiki/AmazonCloud
>
> i've never set one up so i have no idea how to do it.  maybe someone can
> flesh-out this page as using the ec2 seems like a great alternative to a
> cluster.
>
> n.
>
>
> On Wed, 2011-11-09 at 22:44 -0200, Pedro Paulo de Magalhães Oliveira
> Junior wrote:
> > No. This is for non GPU instances
> >
> > -- iOS 5.0
> >
> > Em 09/11/2011, às 22:28, Satrajit Ghosh  escreveu:
> >
> >
> >
> > > hi pedro,
> > >
> > >
> > > will this work with gpu instances as well?
> > >
> > > cheers,
> > >
> > > satra
> > >
> > > 2011/11/9 Pedro Paulo de Magalhães Oliveira Junior
> > > 
> > > Some weeks ago I was asked about a public image (AMI) to run
> > > in the Amazon EC2 infrastructure
> > >
> > >
> > > If you want to use FreeSurfer in the EC2 infrastructure you
> > > can use this public AMI: 060244368407/FREESURFER51
> > >
> > >
> > > Just for your information this AMI can run a recon-all in 23
> > > hours in an Amazon AWS Small Instance. So with the current
> > > Amazon cost per Small Instance/Hour you'll have a recon-all
> > >     for USD 2.04
> > >
> > >
> > > Amazon request a credit card in order to create an account
> > > in http://aws.amazon.com
> > >
> > >
> > > Hope it helps,
> > >
> > >
> > > Pedro Paulo Jr.
> > >
> -
> > > Pedro Paulo de Magalhães Oliveira Junior
> > > Netfilter & SpeedComm Telecom
> > > -- www.netfilter.com.br
> > > -- For
> > > mobile:
> http://itunes.apple.com/br/artist/netfilter/id365306441
> > >
> > >
> > >
> > >
> > >
> > > ___
> > > 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.
> > >
> > >
> > >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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.

Re: [Freesurfer] Amazon EC2 Version of FreeSurfer 5.1 Available

[Pedro Paulo de Magalhães Oliveira Junior]

Tomorrow I'll post a tutorial.

It's quite simple
-----
Pedro Paulo de Magalhães Oliveira Junior
Netfilter & SpeedComm Telecom
-- www.netfilter.com.br
-- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441




2011/11/9 Nick Schmansky 

> Pedro Paulo,
>
> thanks for posting the info.  i've added this to the Download wiki page,
> and created a stub page for the Amazon Cloud:
>
> https://surfer.nmr.mgh.harvard.edu/fswiki/AmazonCloud
>
> i've never set one up so i have no idea how to do it.  maybe someone can
> flesh-out this page as using the ec2 seems like a great alternative to a
> cluster.
>
> n.
>
>
> On Wed, 2011-11-09 at 22:44 -0200, Pedro Paulo de Magalhães Oliveira
> Junior wrote:
> > No. This is for non GPU instances
> >
> > -- iOS 5.0
> >
> > Em 09/11/2011, às 22:28, Satrajit Ghosh  escreveu:
> >
> >
> >
> > > hi pedro,
> > >
> > >
> > > will this work with gpu instances as well?
> > >
> > > cheers,
> > >
> > > satra
> > >
> > > 2011/11/9 Pedro Paulo de Magalhães Oliveira Junior
> > > 
> > > Some weeks ago I was asked about a public image (AMI) to run
> > > in the Amazon EC2 infrastructure
> > >
> > >
> > > If you want to use FreeSurfer in the EC2 infrastructure you
> > > can use this public AMI: 060244368407/FREESURFER51
> > >
> > >
> > > Just for your information this AMI can run a recon-all in 23
> > > hours in an Amazon AWS Small Instance. So with the current
> > > Amazon cost per Small Instance/Hour you'll have a recon-all
> > >     for USD 2.04
> > >
> > >
> > > Amazon request a credit card in order to create an account
> > > in http://aws.amazon.com
> > >
> > >
> > > Hope it helps,
> > >
> > >
> > > Pedro Paulo Jr.
> > >
> -
> > > Pedro Paulo de Magalhães Oliveira Junior
> > > Netfilter & SpeedComm Telecom
> > > -- www.netfilter.com.br
> > > -- For
> > > mobile:
> http://itunes.apple.com/br/artist/netfilter/id365306441
> > >
> > >
> > >
> > >
> > >
> > > ___
> > > 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.
> > >
> > >
> > >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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.

Re: [Freesurfer] Amazon EC2 Version of FreeSurfer 5.1 Available

[Pedro Paulo de Magalhães Oliveira Junior]

No. This is for non GPU instances

-- iOS 5.0

Em 09/11/2011, às 22:28, Satrajit Ghosh  escreveu:

hi pedro,

will this work with gpu instances as well?

cheers,

satra

2011/11/9 Pedro Paulo de Magalhães Oliveira Junior 

> Some weeks ago I was asked about a public image (AMI) to run in the Amazon
> EC2 infrastructure
>
> If you want to use FreeSurfer in the EC2 infrastructure you can use this
> public AMI: *060244368407/FREESURFER51*
>
> Just for your information this AMI can run a recon-all in 23 hours in an
> Amazon AWS Small Instance. So with the current Amazon cost per Small
> Instance/Hour you'll have a recon-all for USD 2.04
>
> Amazon request a credit card in order to create an account in
> http://aws.amazon.com
>
> Hope it helps,
>
> Pedro Paulo Jr.
> -------------
> Pedro Paulo de Magalhães Oliveira Junior
> Netfilter & SpeedComm Telecom
> -- www.netfilter.com.br
> -- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441
>
>
>
> ___
> 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.
>
>
___
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.

[Freesurfer] Amazon EC2 Version of FreeSurfer 5.1 Available

[Pedro Paulo de Magalhães Oliveira Junior]

Some weeks ago I was asked about a public image (AMI) to run in the Amazon
EC2 infrastructure

If you want to use FreeSurfer in the EC2 infrastructure you can use this
public AMI: *060244368407/FREESURFER51*

Just for your information this AMI can run a recon-all in 23 hours in an
Amazon AWS Small Instance. So with the current Amazon cost per Small
Instance/Hour you'll have a recon-all for USD 2.04

Amazon request a credit card in order to create an account in
http://aws.amazon.com

Hope it helps,

Pedro Paulo Jr.
-
Pedro Paulo de Magalhães Oliveira Junior
Netfilter & SpeedComm Telecom
-- www.netfilter.com.br
-- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441
___
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.

[Freesurfer] Recon-all step estimate

[Pedro Paulo de Magalhães Oliveira Junior]

Is there any script that I can use to estimate which step recon-all are in?

My idea is to have a progress indicator for recon-all and this script would
be very useful.

thanks

Pedro Paulo Jr
___
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.

Re: [Freesurfer] Any Pre-exisiting Public Amazon EC2 AMI with Freesurfer out there?

[Pedro Paulo de Magalhães Oliveira Junior]

I have one. I'll give you the link

-- iOS 5.0

Em 28/10/2011, às 20:52, Joshua Lee  escreveu:

Are there any existing Amazon EC2 AMI registered publicly that can be used?
I want to analyze a lot of data fast.

Thanks,
-
Joshua Lee

___
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.
___
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.

Re: [Freesurfer] cortical thickness asymmetries

[Pedro Paulo de Magalhães Oliveira Junior]

We have mentioned this in:
"Use of SVM Methods with Surface-Based Cortical and Volumetric Subcortical
Measurements to Detect Alzheimer's Disease"

You can find the PDF in the FreeSurfer page:
http://surfer.nmr.mgh.harvard.edu/ftp/articles/Oliveira_JAD2010.pdf

I don't have a good explanation though.
---------
Pedro Paulo de Magalhães Oliveira Junior
Netfilter & SpeedComm Telecom
-- www.netfilter.com.br
-- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441




On Thu, Oct 27, 2011 at 10:03, Bruce Fischl wrote:

> not that I know of
>
> Bruce
> On Thu, 27 Oct 2011, Irene Altarelli wrote:
>
> > Dear Freesurfer experts,
> >
> > have cortical thickness asymmetries ever been looked at using Destrieux
> > parcellation scheme, either in adults or (even better) in children?
> >
> > Thanks!
> > Irene
> >
> >
> >
> ___
> 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.
>
>
___
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.

Re: [Freesurfer] implementation on Neurodebian

[Pedro Paulo de Magalhães Oliveira Junior]

No. Cuda only runs in NVidia hardware.

-
Pedro Paulo de Magalhães Oliveira Junior
Netfilter & SpeedComm Telecom
-- www.netfilter.com.br
-- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441




On Mon, Oct 24, 2011 at 13:01, Cartik Sharma wrote:

> Bruce,
>
> http://surfer.nmr.mgh.harvard.edu/fswiki/CUDADevelopersGuide#Benchmarks
> Found this link..clearly impressive, are these benchmarks for GPU enabled
> cards with CUDA or also with ATI Radeon GPU enabled cards?
>
> Best,
> Cartik
>
> On Oct 24, 2011, at 10:30 AM, Bruce Fischl wrote:
>
> > not yet, although it is something we are working on.
> >
> > cheers
> > Bruce
> > On Mon, 24 Oct 2011, Cartik Sharma wrote:
> >
> >> Hi Knut,
> >> Good to know we can speed things up with CUDA. I have a multicore CPU
> and was wondering if
> >> there is a parallelized version of Freesurfer on the CPU.
> >> Thanks for the speedup!
> >> Best regards,
> >> Cartik
> >> On Oct 24, 2011, at 4:41 AM, Knut J Bjuland wrote:
> >>
> >>  Hi Cartik
> >>
> >>  You use -use-gpu to offload rendering to the GPU using cuda.
> >>
> >>  Knut J
> >>
> >>  > From: cartik.sha...@childmind.org
> >>  > To: knut...@hotmail.com
> >>  > Subject: Re: [Freesurfer] implementation on Neurodebian
> >>  > Date: Thu, 20 Oct 2011 15:48:10 +
> >>  >
> >>  > Hi Knut:
> >>  >
> >>  > Cool..is this speeding up things by rendering on the GPU.
> >>  > Is there a way to offload computation to the GPU.
> >>  >
> >>  > Best regards,
> >>  > Cartik
> >>  >
> >>  > On Oct 20, 2011, at 10:57 AM, Knut J Bjuland wrote:
> >>  >
> >>  > > Hi Cartik
> >>  > >
> >>  > > If you enable cuda with -use-gpu the recon-all will run faster.
> >>  > >
> >>  > > Knut J
> >>  > >
> >>  > > Den 17.10.2011 16:41, skrev Cartik Sharma:
> >>  > >> Dear Freesurfer developer(s),
> >>  > >>
> >>  > >> Is there a way to get Freesurfer run faster on Neurodebian.
> While the package produces
> >>  > >> some truly out of the world segmentations and labels for the
> cortical surface, it seems
> >>  > >> to take time.
> >>  > >>
> >>  > >> For eg:
> >>  > >> Defect correction and retesellation takes an hour, other steps
> take longer..I'm not sure if
> >>  > >> it's the original dataset, the OS platform (i.e Virtual
> Machine, Neurodebian) or original
> >>  > >> computational engine itself.
> >>  > >>
> >>  > >> Would be happy in efforts and hints to make this run faster.
> >>  > >>
> >>  > >> Best regards,
> >>  > >> Cartik Sharma
> >>  > >>
> >>  > >>
> >>  > >> ___
> >>  > >> 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.
> >>  > >>
> >>  > >>
> >>  > >>
> >>  > >
> >>  >
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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.

[Freesurfer] [Major Upgrade] - iSurf Brainview 4.0.0

[Pedro Paulo de Magalhães Oliveira Junior]

Today it was released the version 4.0.0 of iSurf Brainview, it's a
majorversion release for IPad, IPhone and IPod Touch. It's also a
landmark
release.

Major New Features
- 3D Visualization of Cortical structure
- 3D Model is fully "touchable" and displays the name of touched structure
using aparc.annot

Minor Changes
- iOS5 compliance
- Memory usage improvement
- Versioning


As usual suggestions and feedbacks are welcome.

The link for download is:
http://itunes.apple.com/WebObjects/MZStore.woa/wa/viewSoftware?id=381072423&mt=8

A personal note: This App is being used in the Radiology course. All med
students in São Paulo University now have basic MRI neuroanatomy training
using iSurf

---------
Pedro Paulo de Magalhães Oliveira Junior
Netfilter & SpeedComm Telecom
-- www.netfilter.com.br
-- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441
___
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.

Re: [Freesurfer] mris_convert exporting parcellation per vertex

[Pedro Paulo de Magalhães Oliveira Junior]

Michael,

Thanks for the hint.

Here's a program that converts the surface + annotation in a Stanford PLY
Object file

# Create ply
# Stanford Object format
from surfer import io as io_

surface = io_.read_geometry
('/Applications/freesurfer/subjects/bert/surf/lh.pial')
labels = io_.read_annot
('/Applications/freesurfer/subjects/bert/label/lh.aparc.annot')

facenum = len(surface[1])
vertnum = len(surface[0])

print "ply"
print "format ascii 1.0"
print "comment VCGLIB generated"
print "element vertex %d"%vertnum
print "property float x"
print "property float y"
print "property float z"
#print "property int flags"
print "property uchar red"
print "property uchar green"
print "property uchar blue"
print "property uchar alpha"
print "element face %d"%facenum
print "property list uchar int vertex_indices"
print "end_header"
for i in xrange(vertnum):
vert = surface[0][i];
color = labels[1][labels[0][i]]
print "%f %f %f %d %d %d
%d"%(vert[0],vert[1],vert[2],color[0],color[1],color[2],color[3])

for i in xrange(facenum):
face = surface[1][i]
print "3 %d %d %d"%(face[0],face[1],face[2])




2011/10/9 Michael Waskom 

> If you know Python, you can likely do this pretty easily with tools from
> the PySurfer package:  http://pysurfer.github.com/
>
> (Check out surfer.io.read_annotation).
>
> If you're just using the io routines, you won't need the somewhat heavy
> Mayavi visualization dependencies.  You should be able to read in and
> manipulate surfaces/annotations just with numpy.
>
> Best,
> Michael
>
>
> 2011/10/8 Bruce Fischl 
>
>> it wouldn't be that hard to put something together if you want to avoid
>> matlab. Spec out what you need and send me a sample, maybe on Bert
>>
>> Bruce
>>
>> On Sat, 8 Oct 2011, Pedro Paulo de Magalhães Oliveira Junior wrote:
>>
>>  Thanks.
>>>
>>> I suppose I can't do this without matlab. Right?
>>>
>>> -- iOS 5.0
>>>
>>> Em 08/10/2011, às 19:29, Bruce Fischl 
>>> escreveu:
>>>
>>>  there is a write_annotation.m file you can use
>>>> On Sat, 8 Oct 2011, Anderson Winkler wrote:
>>>>
>>>>  ops, it seems the comments inside the dpxwrite.m no longer reflect what
>>>>> it does. You probably don't need this, but anyway, the version attached is
>>>>> more up-to-date.
>>>>> Anderson
>>>>> On 08/10/11 17:28, Anderson Winkler wrote:
>>>>> Hi Pedro,
>>>>>
>>>>> There is probably a way to do that using FS tools from the command
>>>>> line, but the attached script should do the same. The result is a
>>>>> "data-per-vertex" file, which
>>>>> is the same as the .asc files from mris_convert. There is no
>>>>> geometry input, hence the vertex coordinates are all set to (0,0,0).
>>>>>
>>>>> Hope it helps!
>>>>>
>>>>> All the best,
>>>>>
>>>>> Anderson
>>>>>
>>>>> On 08/10/11 17:17, Pedro Paulo de Magalh�es Oliveira Junior
>>>>> wrote:
>>>>>   I need to create a file where I have the parcellation value
>>>>> (structure name) per vertex.
>>>>> I've tried�mris_convert --annot /Applications/freesurfer/**
>>>>> subjects/bert/label/lh.aparc.**annot 
>>>>> /Applications/freesurfer/**subjects/bert/surf/lh.pial
>>>>> parc.asc
>>>>> But I get the error:�ERROR: unknown file annot file type specified
>>>>> for output: saida.asc
>>>>> Has someone done this before?
>>>>> Thanks
>>>>> --**--**
>>>>> -
>>>>> Pedro Paulo de Magalh�es Oliveira Junior
>>>>> Netfilter & SpeedComm Telecom -- www.netfilter.com.br
>>>>> -- For mobile:�http://itunes.apple.**com/br/artist/netfilter/**
>>>>> id365306441 <http://itunes.apple.com/br/artist/netfilter/id365306441>
>>>>> __**_
>>>>> Freesurfer mailing list
>>>>> Freesurfer@nmr.mgh.harvard.edu
>>>>> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
>>>>> The information in this e

Re: [Freesurfer] mris_convert exporting parcellation per vertex

[Pedro Paulo de Magalhães Oliveira Junior]

Yes, but --seg in mri_annotation2label --subject bert --hemi lh --seg
saida.mgz produces a volume and not a surface.
-
Pedro Paulo de Magalhães Oliveira Junior
Netfilter & SpeedComm Telecom
-- www.netfilter.com.br
-- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441




On Tue, Oct 11, 2011 at 13:12, Douglas N Greve wrote:

> Have you tried using mri_annotation2label with the --seg output option?
> doug
>
> Michael Waskom wrote:
>
>> If you know Python, you can likely do this pretty easily with tools from
>> the PySurfer package:  http://pysurfer.github.com/
>>
>> (Check out surfer.io.read_annotation).
>>
>> If you're just using the io routines, you won't need the somewhat heavy
>> Mayavi visualization dependencies.  You should be able to read in and
>> manipulate surfaces/annotations just with numpy.
>> Best,
>> Michael
>>
>> 2011/10/8 Bruce Fischl > fis...@nmr.mgh.**harvard.edu >>
>>
>>
>>it wouldn't be that hard to put something together if you want to
>>    avoid matlab. Spec out what you need and send me a sample, maybe
>>on Bert
>>
>>Bruce
>>
>>On Sat, 8 Oct 2011, Pedro Paulo de Magalhães Oliveira Junior wrote:
>>
>>Thanks.
>>
>>I suppose I can't do this without matlab. Right?
>>
>>-- iOS 5.0
>>
>>Em 08/10/2011, às 19:29, Bruce Fischl
>>><mailto:fis...@nmr.mgh.**harvard.edu >>
>> escreveu:
>>
>>
>>there is a write_annotation.m file you can use
>>On Sat, 8 Oct 2011, Anderson Winkler wrote:
>>
>>ops, it seems the comments inside the dpxwrite.m no
>>longer reflect what it does. You probably don't need
>>this, but anyway, the version attached is more up-to-date.
>>Anderson
>>On 08/10/11 17:28, Anderson Winkler wrote:
>>Hi Pedro,
>>
>>There is probably a way to do that using FS tools
>>from the command line, but the attached script should
>>do the same. The result is a "data-per-vertex" file, which
>>is the same as the .asc files from mris_convert.
>>There is no geometry input, hence the vertex
>>coordinates are all set to (0,0,0).
>>
>>Hope it helps!
>>
>>All the best,
>>
>>Anderson
>>
>>On 08/10/11 17:17, Pedro Paulo de Magalh�es
>>Oliveira Junior wrote:
>>  I need to create a file where I have the
>>parcellation value (structure name) per vertex.
>>I've tried�mris_convert --annot
>>/Applications/freesurfer/
>>subjects/bert/label/lh.aparc. annot
>>/Applications/freesurfer/ subjects/bert/surf/lh.pial
>>parc.asc
>>But I get the error:�ERROR: unknown file annot file
>>type specified for output: saida.asc
>>Has someone done this before?
>>Thanks
>>--
>>-- -
>>Pedro Paulo de Magalh�es Oliveira Junior
>>Netfilter & SpeedComm Telecom -- www.netfilter.com.br
>><http://www.netfilter.com.br>
>>
>>-- For mobile:�http://itunes.apple.
>>com/br/artist/netfilter/ id365306441
>>
>> <http://itunes.apple.com/br/**artist/netfilter/id365306441<http://itunes.apple.com/br/artist/netfilter/id365306441>
>> >
>>__ _
>>Freesurfer mailing list
>>Freesurfer@nmr.mgh.harvard.edu
>>
>> <mailto:freesur...@nmr.mgh.**harvard.edu
>> >
>>https://mail.nmr.mgh.harvard. edu/mailman/listinfo/
>>freesurfer
>>
>><https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**
>> freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
>> >
>>The information in this e-mai

Re: [Freesurfer] mris_convert exporting parcellation per vertex

[Pedro Paulo de Magalhães Oliveira Junior]

Thanks.

It works as I wished.

from surfer import io as sIo
a = sIo.read_annot('label/lh.aparc.annot')
b = sIo.read_geometry('surf/lh.pial')

And now I can have each vertex labeled
---------
Pedro Paulo de Magalhães Oliveira Junior
Netfilter & SpeedComm Telecom
-- www.netfilter.com.br
-- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441




2011/10/9 Michael Waskom 

> If you know Python, you can likely do this pretty easily with tools from
> the PySurfer package:  http://pysurfer.github.com/
>
> (Check out surfer.io.read_annotation).
>
> If you're just using the io routines, you won't need the somewhat heavy
> Mayavi visualization dependencies.  You should be able to read in and
> manipulate surfaces/annotations just with numpy.
>
> Best,
> Michael
>
>
> 2011/10/8 Bruce Fischl 
>
>> it wouldn't be that hard to put something together if you want to avoid
>> matlab. Spec out what you need and send me a sample, maybe on Bert
>>
>> Bruce
>>
>> On Sat, 8 Oct 2011, Pedro Paulo de Magalhães Oliveira Junior wrote:
>>
>>  Thanks.
>>>
>>> I suppose I can't do this without matlab. Right?
>>>
>>> -- iOS 5.0
>>>
>>> Em 08/10/2011, às 19:29, Bruce Fischl 
>>> escreveu:
>>>
>>>  there is a write_annotation.m file you can use
>>>> On Sat, 8 Oct 2011, Anderson Winkler wrote:
>>>>
>>>>  ops, it seems the comments inside the dpxwrite.m no longer reflect what
>>>>> it does. You probably don't need this, but anyway, the version attached is
>>>>> more up-to-date.
>>>>> Anderson
>>>>> On 08/10/11 17:28, Anderson Winkler wrote:
>>>>> Hi Pedro,
>>>>>
>>>>> There is probably a way to do that using FS tools from the command
>>>>> line, but the attached script should do the same. The result is a
>>>>> "data-per-vertex" file, which
>>>>> is the same as the .asc files from mris_convert. There is no
>>>>> geometry input, hence the vertex coordinates are all set to (0,0,0).
>>>>>
>>>>> Hope it helps!
>>>>>
>>>>> All the best,
>>>>>
>>>>> Anderson
>>>>>
>>>>> On 08/10/11 17:17, Pedro Paulo de Magalh�es Oliveira Junior
>>>>> wrote:
>>>>>   I need to create a file where I have the parcellation value
>>>>> (structure name) per vertex.
>>>>> I've tried�mris_convert --annot /Applications/freesurfer/**
>>>>> subjects/bert/label/lh.aparc.**annot 
>>>>> /Applications/freesurfer/**subjects/bert/surf/lh.pial
>>>>> parc.asc
>>>>> But I get the error:�ERROR: unknown file annot file type specified
>>>>> for output: saida.asc
>>>>> Has someone done this before?
>>>>> Thanks
>>>>> --**--**
>>>>> -
>>>>> Pedro Paulo de Magalh�es Oliveira Junior
>>>>> Netfilter & SpeedComm Telecom -- www.netfilter.com.br
>>>>> -- For mobile:�http://itunes.apple.**com/br/artist/netfilter/**
>>>>> id365306441 <http://itunes.apple.com/br/artist/netfilter/id365306441>
>>>>> __**_
>>>>> Freesurfer mailing list
>>>>> Freesurfer@nmr.mgh.harvard.edu
>>>>> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer<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<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.
>>>>> __**_
>>>>> Freesurfer mailing list
>>>>> Freesurfer@nmr.mgh.harvard.edu
>>>>> https://mail.nmr.mgh.harva

Re: [Freesurfer] mris_convert exporting parcellation per vertex

[Pedro Paulo de Magalhães Oliveira Junior]

Thanks.

I suppose I can't do this without matlab. Right?

-- iOS 5.0

Em 08/10/2011, às 19:29, Bruce Fischl  escreveu:

> there is a write_annotation.m file you can use
> On Sat, 8 Oct 2011, Anderson Winkler wrote:
>
>> ops, it seems the comments inside the dpxwrite.m no longer reflect what it 
>> does. You probably don't need this, but anyway, the version attached is more 
>> up-to-date.
>> Anderson
>> On 08/10/11 17:28, Anderson Winkler wrote:
>>  Hi Pedro,
>>
>>  There is probably a way to do that using FS tools from the command 
>> line, but the attached script should do the same. The result is a 
>> "data-per-vertex" file, which
>>  is the same as the .asc files from mris_convert. There is no geometry 
>> input, hence the vertex coordinates are all set to (0,0,0).
>>
>>  Hope it helps!
>>
>>  All the best,
>>
>>  Anderson
>>
>>  On 08/10/11 17:17, Pedro Paulo de Magalh�es Oliveira Junior wrote:
>>I need to create a file where I have the parcellation value 
>> (structure name) per vertex.
>> I've tried�mris_convert --annot 
>> /Applications/freesurfer/subjects/bert/label/lh.aparc.annot 
>> /Applications/freesurfer/subjects/bert/surf/lh.pial parc.asc
>> But I get the error:�ERROR: unknown file annot file type specified for 
>> output: saida.asc
>> Has someone done this before?
>> Thanks
>> -
>> Pedro Paulo de Magalh�es Oliveira Junior
>> Netfilter & SpeedComm Telecom -- www.netfilter.com.br
>> -- For mobile:�http://itunes.apple.com/br/artist/netfilter/id365306441
>> ___
>> 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.
>> ___
>> 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.
> ___
> 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.

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

[Freesurfer] mris_convert exporting parcellation per vertex

[Pedro Paulo de Magalhães Oliveira Junior]

I need to create a file where I have the parcellation value (structure name)
per vertex.

I've tried mris_convert --annot
/Applications/freesurfer/subjects/bert/label/lh.aparc.annot
/Applications/freesurfer/subjects/bert/surf/lh.pial parc.asc

But I get the error: ERROR: unknown file annot file type specified for
output: saida.asc

Has someone done this before?

Thanks
-
Pedro Paulo de Magalhães Oliveira Junior
Netfilter & SpeedComm Telecom
-- www.netfilter.com.br
-- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441
___
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.

[Freesurfer] Process monkey data

[Pedro Paulo de Magalhães Oliveira Junior]

I have data from 100 monkeys and I need to compare cortical thickness
among two groups.

In the wiki page there is an entry MonkeyData that has a set of
scripts which break-down the steps needed, unfortunately I'm having
trouble with this scripts and FS 5.1

Are there an updated version of those procedures?

Thanks

PPJ

-- iOS 5.0
___
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.

Re: [Freesurfer] tksurfer display

[Pedro Paulo de Magalhães Oliveira Junior]

I have added this answer to the FAQ:
http://surfer.nmr.mgh.harvard.edu/fswiki/UserContributions/FAQ


-
Pedro Paulo de Magalhães Oliveira Junior
Netfilter & SpeedComm Telecom
-- www.netfilter.com.br
-- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441




On Thu, Sep 22, 2011 at 14:33, Alexopoulos, Dimitrios <
alexopoulo...@kids.wustl.edu> wrote:

>  I found this site for the type of problem we are having with tksurfer
>
> http://surfer.nmr.mgh.harvard.edu/fswiki/TksurferDisplayProblems
>
> Jim
>
> --
> *From:* Peter Glynn [mailto:pgl...@bu.edu]
> *Sent:* Thu 9/22/2011 11:21 AM
> *To:* Alexopoulos, Dimitrios
> *Cc:* freesurfer@nmr.mgh.harvard.edu
> *Subject:* Re: [Freesurfer] tksurfer display
>
> attached find the output image. It looks very similar to Jim's, just
> rotated 180 degrees.
>
> On Thu, Sep 22, 2011 at 11:37 AM, Alexopoulos, Dimitrios <
> alexopoulo...@kids.wustl.edu> wrote:
>
>>   Interesting. I've had this problem trying to view the data on my dual
>> boot Windows PC by remotely login with SSH to the linux server while
>> running Xming or Hummingbird Exceed on the PC side.
>> (Output image attached). Could it be some 3D rendering issue?
>>
>>  I have no problem viewing the surfaces from my local ubuntu linux
>> running freesurfer.
>> tkmedit displays volumes properly.
>>  Jim
>>
>> --
>> *From:* freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Peter Glynn
>> *Sent:* Thu 9/22/2011 10:12 AM
>> *To:* freesurfer@nmr.mgh.harvard.edu
>> *Subject:* [Freesurfer] tksurfer display
>>
>>  Hello,
>>
>> I'm new to freesurfer and just downloaded and installed it on my dual boot
>> windows/linux (centos release 5.5). I went through the instructions to check
>> if everything is properly installed. Everything seemed to be fine except for
>> tksurfer. When I enter the tksurfer bert rh pial command, tksurfer does
>> launch but it only displays a very small sliver of a brain surface. Is this
>> a common problem? Is something wrong with my installation? Any suggestions
>> would be great. Thanks!
>>
>> Peter Glynn
>>
>>
>> The materials in this email are private and may contain Protected Health
>> Information. If you are not the intended recipient, be advised that any
>> unauthorized use, disclosure, copying, distribution or the taking of any
>> action in reliance on the contents of this information is strictly
>> prohibited. If you have received this email in error, please immediately
>> notify the sender via telephone or return email.
>>
>
>
>
> The materials in this email are private and may contain Protected Health
> Information. If you are not the intended recipient, be advised that any
> unauthorized use, disclosure, copying, distribution or the taking of any
> action in reliance on the contents of this information is strictly
> prohibited. If you have received this email in error, please immediately
> notify the sender via telephone or return email.
>
> ___
> 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.
>
>
___
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.

Re: [Freesurfer] tksurfer display

[Pedro Paulo de Magalhães Oliveira Junior]

Can you describe the hardware / video card you are using?
-
Pedro Paulo de Magalhães Oliveira Junior
Netfilter & SpeedComm Telecom
-- www.netfilter.com.br
-- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441




On Thu, Sep 22, 2011 at 12:12, Peter Glynn  wrote:

> Hello,
>
> I'm new to freesurfer and just downloaded and installed it on my dual boot
> windows/linux (centos release 5.5). I went through the instructions to check
> if everything is properly installed. Everything seemed to be fine except for
> tksurfer. When I enter the tksurfer bert rh pial command, tksurfer does
> launch but it only displays a very small sliver of a brain surface. Is this
> a common problem? Is something wrong with my installation? Any suggestions
> would be great. Thanks!
>
> Peter Glynn
>
> ___
> 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.
>
>
___
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.

Re: [Freesurfer] Renaming a processed subject

[Pedro Paulo de Magalhães Oliveira Junior]

You can just rename the directory ABC1234 to Case1

*mv ABC1234 Case1*


On Thu, Sep 1, 2011 at 12:01, Irwin, William  wrote:

> Hi
>
> ** **
>
> For purposes of de-identification, is there an easy way to “rename” all the
> contents of data for a processed subject?
>
> ** **
>
> For example, If I want to do share data or do reliability training on an
> existing subject (e.g., “ABC1234”), I want to rename everything associated
> with this case to “Case1”.
>
> ** **
>
> Thanks
>
> Wil
>
> ** **
>
> 
> William Irwin | Imaging Core Supervisor
> UCSF | Memory and Aging Center
> 350 Parnassus Avenue, Suite 905
> San Francisco  CA  94143-1207
> wir...@memory.ucsf.edu | memory.ucsf.edu
> p: 415.476.1680 | f: 415.476.1816
>
> ** **
>
> ** **
>
> ___
> 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.
>
>
___
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.

Re: [Freesurfer] FreeSurfer on AWS

[Pedro Paulo de Magalhães Oliveira Junior]

I'll try to write a tutorial this weekend

-- iOS 5

Em 18/08/2011, às 20:01, Nolan Nichols  escreveu:

Hi Pedro,

I came across your post on the FreeSurfer mailing list and am trying to find
the AMI you created (
https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-May/018272.html).
I have tried a few times now to install FreeSurfer 5.1 on an AMI with EBS,
but it is not working. Is there any chance you could help me out?

Thanks!

Nolan
___
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.

Re: [Freesurfer] Nvidia upgrade considerations

[Pedro Paulo de Magalhães Oliveira Junior]

I would go for a complete new PC. You won't benefit much of a GTX590 in an
old PC

PPJ

-
Pedro Paulo de Magalhães Oliveira Junior
-- check our new iOS app:
Cargo<http://itunes.apple.com/app/cargo/id444529879?ls=1&mt=8>


2011/8/5 Andries R. Van Der Leij 

> Hi pedro and Richard,
>
> Thank you for the responses! The T7400 has just one gpu slot, so I'll
> probably just buy the single 590, which itself is a dual card. The
> 2050 doesn't seem to be worth it on these older systems (ddr2, etc).
>
> For my supervisor, what kind of performance increase should I expect
> if we buy a newer nehalem system?
>
> Regards,
>
> Andries van der leij
>
> Sent from my iPhone
>
> On Aug 5, 2011, at 20:21, R Edgar  wrote:
>
> > 2011/8/5 Pedro Paulo de Magalhães Oliveira Junior  > r>:
> >> In my experience you'll have the benefit of using two cards
> >> simultaneously.
> >> That means you can run two recon-all with gpu acceleration
> >> simultaneously.
> >> The SLI is more important for graphics (cad, gaming) than for CUDA.
> >> So, I'd
> >> go for 2 GTX580
> >
> > CUDA doesn't use SLI at all - you don't want it. So long as each card
> > has enough RAM to handle one recon job, having more cards and using
> > the environment variable to select the GPU is certainly the way to go.
> > I don't think that Freesurfer is particularly heavy on the PCIe bus,
> > so you should even be able to get one of the dual GPU cards and get
> > good performance. However, Nehalem does help the data reorganisation
> > required for the GPU.
> >
> > Richard
>
___
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.

Re: [Freesurfer] Nvidia upgrade considerations

[Pedro Paulo de Magalhães Oliveira Junior]

In my experience you'll have the benefit of using two cards simultaneously.
That means you can run two recon-all with gpu acceleration simultaneously.
The SLI is more important for graphics (cad, gaming) than for CUDA. So, I'd
go for 2 GTX580

PPJ

-----
Pedro Paulo de Magalhães Oliveira Junior
-- check our new iOS app:
Cargo<http://itunes.apple.com/app/cargo/id444529879?ls=1&mt=8>




On Fri, Aug 5, 2011 at 14:28, Andries R. Van Der Leij <
a.r.vanderl...@gmail.com> wrote:

> Dear freesurfer team
>
> I'm currently investigating how to tweak 2 2 year old Dell 7400 Xeon
> machine's to run a large batch of fs jobs. Upgrading to Nehalem won't
> work, since it will require a new motherboard as well. However, we can
> replace our old non-fermi quadro card with a C2050.
>
> As an alternative, I was thinking about buying two GTX590 (two times 580
> and 1.5 GB ram) or two palit GTX580 (1 times 580 with 3GB ram) and running
> them in SLI. This will save quite some money, and intuitively, it feels that
> more separate cards will work better if you start batching more recon
> scripts at the same time (1 per CPU). You'll end up with 6 gb of vram in
> both cases compared to the 3 for the C2050, with 4 processors for the 590
> and 2 for the 580. As I don't understand cuda and sli well, I may very well
> be completely wrong. I'm not sure fi that running jobs under sli will work
> well. Do you have any ideas on this solution compared to a single c2050?
>
> thank you very much in advance,
>
> Andries van der Leij
>
> ___
> 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.
>
>
___
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.

Re: [Freesurfer] Re : Book with FreeSurfer chapter

[Pedro Paulo de Magalhães Oliveira Junior]

Sorry Andrew. I didn't know.

-- iOS 4.3

Em 16/07/2011, às 14:28, "Simmons, Andy"  escreveu:

There are also several other chapters of the same book using Freesurfer in
AD, including



Magnetic Resonance Imaging and Magnetic Resonance Spectroscopy for Detection
of Early Alzheimer's

Disease / Eric Westman, Lars-Olof Wahlund, Catherine Foy, Michaela Poppe,
Allison Cooper, Declan Murphy,

Christian Spenger, Simon Lovestone and Andrew Simmons



Combinatorial Markers of Mild Cognitive Impairment Conversion to Alzheimer's
Disease - Cytokines and MRI

Measures Together Predict Disease Progression / Simon J. Furney, Deborah
Kronenberg, Andrew Simmons,

Andreas Güntert, Richard J. Dobson, Petroula Proitsi, Lars-Olof Wahlund,
Iwona Kloszewska, Patrizia Mecocci,

Hilkka Soininen, Magda Tsolaki, Bruno Vellas, Christian Spenger and Simon
Lovestone



Best wishes,



Andy Simmons



-



Date: Fri, 15 Jul 2011 20:36:01 -0300

From: Pedro Paulo de Magalh?es Oliveira Junior 

Subject: [Freesurfer] Book with FreeSurfer chapter

To: Freesurfer Mailing List 

Message-ID:

  

Content-Type: text/plain; charset="iso-8859-1"



Just for information:



*Handbook of Imaging the Alzheimer Brain*

*

Editors: J.W. Ashford, A. Rosen, M. Adamson, P. Bayley,

O. Sabri, A. Furst, S.E. Black and M. Weiner

July 2011, 824 pp., hardcover

ISBN 978-1-60750-792-5 (print)

**



The chapter that describes the usage of FreeSurfer in AD is "Automated

Volumetric Methods to Detect Alzheimer's Disease" / Pedro Paulo de Magalh?es

Oliveira Jr. et al.

*









Dr Andy Simmons

Reader in Neuroimaging & Consultant Clinical Scientist

Centre for Neuroimaging Sciences and NIHR Biomedical Research Centre

Institute of Psychiatry, Box P089

Kings College London

De Crespigny Park

London, SE5 8AF, UK



Email - andy.simm...@kcl.ac.uk

Webpage  - http://www.iop.kcl.ac.uk/staff/profile/default.aspx?go=10338

Directions -
http://www.iop.kcl.ac.uk/virtual/?path=/about/how-to-find-the-institute-of-psychiatry/

ResearcherID - http://www.researcherid.com/rid/B-8848-2008

Fax +44 (0)203 228 2116



 



___
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.
___
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.

[Freesurfer] Book with FreeSurfer chapter

[Pedro Paulo de Magalhães Oliveira Junior]

Just for information:

*Handbook of Imaging the Alzheimer Brain*
*
Editors: J.W. Ashford, A. Rosen, M. Adamson, P. Bayley,
O. Sabri, A. Furst, S.E. Black and M. Weiner
July 2011, 824 pp., hardcover
ISBN 978-1-60750-792-5 (print)
**

The chapter that describes the usage of FreeSurfer in AD is "Automated
Volumetric Methods to Detect Alzheimer's Disease" / Pedro Paulo de Magalhães
Oliveira Jr. et al.
*
___
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.

Re: [Freesurfer] muliple fressurfer instance and cuda

[Pedro Paulo de Magalhães Oliveira Junior]

Try running only one GPU-assisted recon-all


On Fri, Jul 8, 2011 at 10:02, Knut J Bjuland  wrote:

> Hi
>
> When I have ran two or more Freesurfer instance in pc with one geforce
> gtx 460. I usually get a abort or memory corruption when running two or
> more Freesurfer instance. I usually get trouble when two ore more
> Freesurfer instance is in autocon3 phase of the recon-all protocol.
>
>
> Cheers
> Knut J
>
>
> ___
> 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.
>
>
___
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.

Re: [Freesurfer] cortical dysplasia

[Pedro Paulo de Magalhães Oliveira Junior]

Carolina,

We have worked with several cases of MCD (including cortical dysplasia). We
have published this paper:
https://surfer.nmr.mgh.harvard.edu/pub/articles/jon_372_LR.pdf

It may help.

But in most cases of cortical dysplasia (not Gray matter heterotopia cases)
you'll find a ticker cortex not a thinner one. But maybe you could post one
image illustrate this problem.

PPJ




On Thu, Jul 7, 2011 at 10:39, Carolina Valencia wrote:

> Hello FSexperts
>
> I have a MPRAGE image of cortical dysplasia, I have some regions of grey 
> matter within the white matter, and I measured the cortical thickness in the 
> projections of those regions and I expected to find a thinnercortex instead I 
> found a cortical thickening. FS takes into account the embedded region of the 
> grey matter to measure the cortical thickness?
>
> Best regards,
>
> Carolina
>
> ___
> 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.
>
>
___
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.

Re: [Freesurfer] measuring cortical thickness using FreeSurfer

[Pedro Paulo de Magalhães Oliveira Junior]

I usually can run one instance of FreeSurfer with 1GB if I use the -no-gut
flag

I have a benchmark of 4 recon-all running in a 4 Core AMD with 4GB RAM that
took only 10% more time than one recon-all alone.

2011/7/6 John Jan Drozd 

> Hi Bruce,
>
> Thanks for pointing this out to me about the RAM.
>
> I have 8 Gb of RAM. So I guess I can safely run 3 or 4 subjects
> simultaneously if each subject requires 2 to 3 Gb of RAM.
>
> Thanks,
> John
>
> Sent from my iPhone
>
> On 2011-07-05, at 6:08 PM, Bruce Fischl 
> wrote:
>
> > how much ram do you have? You'll need at least 2G/subject if not 3
> > On Tue, 5 Jul 2011, John Drozd wrote:
> >
> >> Hi Bruce,
> >> Thanks for the suggestion, Bruce. I'll run 8 different subjects at once.
> >> Take care,
> >> John
> >> 2011/7/5 Bruce Fischl 
> >> Sorry, that won't help a single subject much, although there are
> >> options to run the hemis in parallel. You can run multiple
> >> subjects at the same time, which is what we usually do. Or you
> >> can use cuss
> >> On Jul 5, 2011, at 5:11 PM, John Drozd  wrote:
> >>
> >> Hi Bruce,
> >>
> >> Okay, thank you. I understand and can see that to do an
> >> accurate job, the pipeline must be complicated.
> >> I have eight processors on my linux desktop computer.
> >> Maybe some parts of recon-all are multi-threaded which
> >> could speed things up for me :-)
> >>
> >> Thank you,
> >> John
> >>
> >> 2011/7/5 Bruce Fischl 
> >> sorry, but the majority of the time is
> >> required. We're working to speed things up,
> >> but it is complicated software with multiple
> >> nonlinear warps, segmentation procedures,
> >> etc
> >> Bruce
> >> On Tue, 5 Jul 2011, John Drozd wrote:
> >>
> >> Hi Bruce and Pedro,
> >>
> >> Thank you both for sending me your
> >> suggestions.
> >> Just to let you know, because my .dcm (dicom)
> >> files had a space and two dots
> >> in the filenames:
> >> (e.g. "2008_12_08.ek -0035-0001-1.dcm" )
> >> (and using quotes around the file name or "\ "
> >> within the filename without
> >> the quotes did not work with recon-all),
> >> recon-all truncated the filename
> >> before the space as "2008_12_08.ek" feeding it
> >> to an mri_convert command and
> >> gave an error message.
> >>
> >> So I worked around this problem as follows: I
> >> converted the .dcm series to a
> >> nifti .nii volume using 3D Slicer, and then
> >> used mri_convert to convert the
> >> .nii format to .mgz format. Then I ran
> >> recon-all on the .mgz formatted file
> >> and it is now running successfully.
> >>
> >> I see on the online tutorials and slides, that
> >> this process takes about 20
> >> hours. Is there a way to only run partial
> >> steps pertaining only to the
> >> cortical thickness?
> >>
> >> Pedro also suggested that I go through the
> >> FreeSurferBeginnersGuide wiki
> >> which I am doing now.
> >>
> >> Also, reading some mailing lists emails, I
> >> noticed that matlab can be used
> >> to analyze the cortical thickness statistiics,
> >> and also freesurfer comes
> >> with matlab scripts. I will try these tools
> >> out as well.
> >>
> >> Thank you for your time,
> >> John
> >>
> >> On Tue, Jul 5, 2011 at 1:18 PM, Bruce Fischl
> >> 
> >> wrote:
> >> recon-all \
> >> -i  >> dicom series> \
> >> -s  \
> >> -sd  >> folder in> \
> >> -all
> >>
> >> cheers
> >> Bruce
> >>
> >> On Tue, 5 Jul 2011, John Drozd wrote:
> >>
> >> Hi,
> >>
> >> I am running freesurfer on 64 bit Fedora
> >> 10 linux.
> >> I am using version:
> >>
> >> freesurfer-Linux-centos4_x86_64-stable-pub-v4.3.0.
> >> Can anyone point me to a reference web
> >> page listing what
> >> steps I need to
> >> type to process
> >> a series of MRI dicom slices and use
> >> FreeSurfer to measure
> >> cortical
> >> thickness for this dicom series?
> >>
> >> Thank you,
> >> John
> >>
> >> --
> >> John Drozd
> >> Post-Doctoral Fellow, Robarts Research
> >> Institute
> >> The University of Western Ontario
> >> London, ON, Canada
> >> http://publish.uwo.ca/~jdrozd2/index.htm
> >>
> >>
> >> ___
> >> 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.
> >>
> >> --
> >> John Drozd
> >> Post-Doctoral Fellow, Robarts Research
> >> Institute
> >> The University of Western Ontario
> >> London, ON, Canada
> >> http://publish.uwo.ca/~jdrozd2/index.htm
> >>
> >> --
> >> John Drozd
> >> Post-Doctoral Fellow, Robarts Research Institute
> >> The University of Western Ontari

Re: [Freesurfer] measuring cortical thickness using FreeSurfer

[Pedro Paulo de Magalhães Oliveira Junior]

http://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferBeginnersGuide

On Tue, Jul 5, 2011 at 13:14, John Drozd  wrote:

> Hi,
>
> I am running freesurfer on 64 bit Fedora 10 linux.
> I am using version:  freesurfer-Linux-centos4_x86_64-stable-pub-v4.3.0.
> Can anyone point me to a reference web page listing what steps I need to
> type to process
> a series of MRI dicom slices and use FreeSurfer to measure cortical
> thickness for this dicom series?
>
> Thank you,
> John
>
> --
> John Drozd
> Post-Doctoral Fellow, Robarts Research Institute
> The University of Western Ontario
> London, ON, Canada
> http://publish.uwo.ca/~jdrozd2/index.htm
>
>
>
> ___
> 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.
>
>
___
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.

Re: [Freesurfer] Fwd: freesurfer recon error

[Pedro Paulo de Magalhães Oliveira Junior]

Have you tried including the flag -cw256 with the recon-all command?


On Tue, Jul 5, 2011 at 10:18, Sarah Rappaport - UoB` wrote:

> Hi!,
>
> I am new to FreeSurfer and I am having some difficulty with the T1
> reconstruction. My MRI files were Par Rec and converted to nii. I
> successfully converted the nii file to mgz but had errors when running the
> recon -all command (see screen print attached). I have tried re-exporting
> the files in case there was an inital error at this stage but it returned
> the same error. I would appreciate any help with this.
>
> thanks
> Sarah
>
>
>
> ___
> 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.
>
>
___
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.

Re: [Freesurfer] Difference in hippocampal volume between scanners

[Pedro Paulo de Magalhães Oliveira Junior]

This is not normal. Maybe you should check the aseg volume for improper
segmentation.


On Thu, Jun 23, 2011 at 19:27, Jessica Liu  wrote:

> Hi everyone!
>
> I'm currently a summer student working at a lab which uses Freesurfer to
> measure hippocampal volumes.  I noticed that scanning the same patient first
> on a GE 3T (Multi-channel head coil) and then a GE 1.5T (single-channel head
> coil) 24 hours later resulted in a 30% increase in the left hippocampus
> volume and a 18% increase for the right hippocampus based on the values in
> aseg.stats.  Can anyone please comment on this and explain the large
> discrepancies?  Thanks!
>
> Jessica Liu
>
> ___
> 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.
>
>
___
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.

Re: [Freesurfer] How to obtain volume of specific structure

[Pedro Paulo de Magalhães Oliveira Junior]

Take a look in aseg.stats file

-- iOS 4.3

Em 22/06/2011, às 23:09, ZhiLiangLong  escreveu:

> Hi all:
>After all "recon-all -all" processing  has been completed for all subjects 
> ,I want to obtain volume of specific structure of each subject(e.g., the 
> volume of Caudate Nucleus). But i have no idea about it,Are there some tools 
> or commands that can help?
>   I hope you can give me some suggestions . Thanks!
>
>
> ___
> 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.

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

Re: [Freesurfer] recon-all -s exited with ERRORS

[Pedro Paulo de Magalhães Oliveira Junior]

recon-all -s bert -all -use-gpu

-- iOS 4.3

Em 13/06/2011, às 21:30, Leo Souza  escreveu:

/recon-all -use-gpu
___
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.

Re: [Freesurfer] choroid plexus

[Pedro Paulo de Magalhães Oliveira Junior]

The volume should be in aseg.stats

On Wed, Jun 8, 2011 at 16:45, Tracy Butler  wrote:

>  Is there a good method to segment choroid plexus and calculate volume?  I
> know it’s an aseg label.
>
> Thanks,
>
> Tracy
>
> ___
> 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.
>
>
___
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.

Re: [Freesurfer] FreeSurfer Tutorial and Workshop

[Pedro Paulo de Magalhães Oliveira Junior]

I think you should send an e-mail to Allison (astevens)


On Fri, May 27, 2011 at 13:34, Eisenstein, Sarah
wrote:

> Does anyone know how to register for the FreeSurfer Tutorial and Workshop
> scheduled for September, 2011?  I cannot find a link or a phone number to do
> this on the Course Description page (
> http://surfer.nmr.mgh.harvard.edu/fswiki/CourseDescription).
>
>
>
> Thanks!
>
>
>
> Sarah
>
>
>
> Sarah A. Eisenstein, Ph.D.
>
> Postdoctoral Scholar
>
> Hershey Lab
>
> Psychiatry/Neuroimaging Lab
>
> Washington University in St. Louis
>
> St. Louis, MO
>
> eisenste...@npg.wustl.edu
>
>
>
> ___
> 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.
>
>
___
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.

Re: [Freesurfer] FS5.1 for CentOS4 works for CentOS5-like OS?

[Pedro Paulo de Magalhães Oliveira Junior]

Yes. It works

-- iOS 4.3

Em 25/05/2011, às 10:14, Xinian Zuo  escreveu:

> Dear FS team, Only see new 5.1 version for CentOS4 in the website. Thanks, XN.
>
> --
> Xi-Nian Zuo, Ph.D of Applied Mathematics (http://lfcd.psych.ac.cn)
> ___
> 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.
>

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

Re: [Freesurfer] Error from cudadetect

[Pedro Paulo de Magalhães Oliveira Junior]

5.1 was released yesterday

-- iOS 4.3

Em 25/05/2011, às 09:42, R Edgar  escreveu:

> On Wed, May 25, 2011 at 7:59 AM, Howison, Mark  wrote:
>
>> We have installed Freesurfer 5.0.0 (CentOS x86_64) on our compute
>> cluster at Brown and are seeing the following error when running
>> 'cudadetect':
>>
>> ERROR: cuda driver does not appear to be installed!
>> Detecting CUDA... There are 2 devices supporting CUDA:
>> Device 0: "Tesla M2050"
>> CUDA Driver Version: 3.20
>> (etc.)
>
> Did you do a binary install, or compile from source? If the former,
> then it might be a problem with us using a different version of CUDA
> at the time of compilation. Things are supposed to work, but we've
> seen a lot of problems like this.
>
> I believe that 5.1 is about to be released, which should be compiled
> against the driver/library you're using. Otherwise, the best solution
> might be to get the source, and compile directly from that.
>
> Richard
> ___
> 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.
>

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

Re: [Freesurfer] Running FreeSurfer Remotely

[Pedro Paulo de Magalhães Oliveira Junior]

It will probably work. However the experience can be sluggish

On Mon, May 23, 2011 at 11:34,  wrote:

> Hi,
>
> Will FreeSurfer run remotely using NX Client for OSX or should I employ
> VNC only?
>
> Thanks,
>
> Gabriel
> ___
> 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.
>
>
___
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.

Re: [Freesurfer] ERROR: mpr2mni305 failed, see transforms/talairach_avi.log

[Pedro Paulo de Magalhães Oliveira Junior]

The images are:  0.5 x 0.5 x 1.0

Can mri_convert fix it or should I edit the Nifti header?

2011/5/16 Nick Schmansky 

> PPJ,
>
> Hi,
>
> mri_info /space/incoming/ga_2010.nii
>
> shows that the image is 0.5 x 0.5 x 0.5.  but when viewing in freeview
> or tkmedit, the brain seems 'squashed', as if there is a slice gap.  do
> you know the details of how this was acquired?
>
> N.
>
>
>
> On Mon, 2011-05-16 at 17:49 -0300, Pedro Paulo de Magalhães Oliveira
> Junior wrote:
> > I'm having this error in the recon-all
> >
> >
> > #
> > #@# Talairach Mon May 16 16:38:01 EDT 2011
> > /usr/local/freesurfer/subjects/GAGRICOLA/mri
> >
> >
> >  talairach_avi --i orig.mgz --xfm transforms/talairach.auto.xfm
> >
> >
> > ERROR: mpr2mni305 failed, see transforms/talairach_avi.log
> >
> >
> > I've uploaded to the ftp at surfer.nmr.mgh.harvard.edu the
> > talairach_avi.log, the orig.mgz (as ppj_orig.mgz) and the original
> > nifti image as ga_2010.nii
> >
> >
> > Any hints?
> >
> >
> >
> >
> > ___
> > 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.
>
___
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.

[Freesurfer] ERROR: mpr2mni305 failed, see transforms/talairach_avi.log

[Pedro Paulo de Magalhães Oliveira Junior]

I'm having this error in the recon-all

#
#@# Talairach Mon May 16 16:38:01 EDT 2011
/usr/local/freesurfer/subjects/GAGRICOLA/mri

 talairach_avi --i orig.mgz --xfm transforms/talairach.auto.xfm

ERROR: mpr2mni305 failed, see transforms/talairach_avi.log

I've uploaded to the ftp at surfer.nmr.mgh.harvard.edu the
talairach_avi.log, the orig.mgz (as ppj_orig.mgz) and the original nifti
image as ga_2010.nii

Any hints?
___
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.

[Freesurfer] [Major Upgrade] - iSurf Brainview 3.0.0

[Pedro Paulo de Magalhães Oliveira Junior]

Today it was released the version 3.0.0 of iSurf Brainview, it's a major
version release for IPad, IPhone and IPod Touch.

Major New Features
- Quiz for Brain structures (you can take a Quiz with 10 random questions
about structure locations. The current database has more than 40 questions)
- Select the brain structure by name - You have a list of available
structures.

Minor Changes
- Visual Improvements
- Memory usage improvement
- Paper of Destrieux, C.
- Versioning

 As usual suggestions and feedbacks are welcome.

The link for download is:
http://itunes.apple.com/WebObjects/MZStore.woa/wa/viewSoftware?id=381072423&mt=8

A personal note:
Some residents in Radiology of our med school found the quiz challenging. I
think it can be a very good tool to teach neuroanatomy in MRI

-----
Pedro Paulo de Magalhães Oliveira Junior
Diretor de Operações
Netfilter & SpeedComm Telecom
-- www.netfilter.com.br
-- For mobile: http://www.netfilter.com.br/mobile
___
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.

Re: [Freesurfer] Smaller Virtual Machine

[Pedro Paulo de Magalhães Oliveira Junior]

I have distributed another EC2 image. I think you can now start FreeSurfer
instances at Amazon EC2


On Tue, May 3, 2011 at 06:25, Fidel  wrote:

>  So... What about this?
>
> Cheers :)
>
> El 29/04/2011 16:43, Pedro Paulo de Magalhães Oliveira Junior escribió:
>
> I'll check if it's public
>
>
>
> On Fri, Apr 29, 2011 at 11:40, Fidel  wrote:
>
>>  Thanks PPJ,
>>
>> I have made a fast search in Amazon's page and via google and I did not
>> find it. Do i have to be registered to find it? Can anyone use a copy of
>> your virtual machine, or do we have to create our own and then, upload it to
>> Amazon?
>>
>> Thanks again.
>>
>> Fidel.
>>
>> El 29/04/2011 16:25, Pedro Paulo de Magalhães Oliveira Junior escribió:
>>
>> Yes. But that machine distributed by FreeSurfer is the one with full GUI
>> to run under Windows.
>>
>>  I have a machine for cloud processing in Amazon EC2 (you can look up for
>> FreeSurfer DMI in Amazon EC2)
>>
>>  PPJ
>>
>>
>> On Fri, Apr 29, 2011 at 11:15, Fidel  wrote:
>>
>>> Hi all,
>>>
>>> I have been trying the virtual disk image, and it works well.
>>> Nevertheless, I think that more than 7GB is a lot of space if somebody
>>> wants to use it as a Virtual Machine in a cloud environment, in which
>>> you are charged for used storage and maybe for used bandwidth in the
>>> data communication.
>>>
>>> Is anybody thinking about creating a lighter version of this virtual
>>> disk image?
>>>
>>> Thanks and best regards,
>>>
>>> Fidel.
>>>
>>> ___
>>> 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.
>>>
>>>
>>
>> ___
>> Freesurfer mailing 
>> listfreesur...@nmr.mgh.harvard.eduhttps://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 athttp://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.
>>
>>
>>
>> ___
>> 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.
>>
>>
>
> ___
> Freesurfer mailing 
> listfreesur...@nmr.mgh.harvard.eduhttps://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 
> athttp://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.
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
&g

[Freesurfer] [New release] - iSurf Brainview 2.1.1

[Pedro Paulo de Magalhães Oliveira Junior]

Today it was released a new upgrade of iSurf Brainview. (2.1.1)

*New features:
* Phone / IPod Touch
- IPhone now show webpage with structure description when you tap the name
of the structure

All iOS
- More structures with webpage description
- Cache webpages for speedup
As usual suggestions are welcome.

Upcoming features should include 3D visualization.

The link for download is:
http://itunes.apple.com/WebObjects/MZStore.woa/wa/viewSoftware?id=381072423&mt=8

Cheers

Pedro Paulo Jr.
___
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.

Re: [Freesurfer] Smaller Virtual Machine

[Pedro Paulo de Magalhães Oliveira Junior]

I'll check if it's public



On Fri, Apr 29, 2011 at 11:40, Fidel  wrote:

>  Thanks PPJ,
>
> I have made a fast search in Amazon's page and via google and I did not
> find it. Do i have to be registered to find it? Can anyone use a copy of
> your virtual machine, or do we have to create our own and then, upload it to
> Amazon?
>
> Thanks again.
>
> Fidel.
>
> El 29/04/2011 16:25, Pedro Paulo de Magalhães Oliveira Junior escribió:
>
> Yes. But that machine distributed by FreeSurfer is the one with full GUI to
> run under Windows.
>
>  I have a machine for cloud processing in Amazon EC2 (you can look up for
> FreeSurfer DMI in Amazon EC2)
>
>  PPJ
>
>
> On Fri, Apr 29, 2011 at 11:15, Fidel  wrote:
>
>> Hi all,
>>
>> I have been trying the virtual disk image, and it works well.
>> Nevertheless, I think that more than 7GB is a lot of space if somebody
>> wants to use it as a Virtual Machine in a cloud environment, in which
>> you are charged for used storage and maybe for used bandwidth in the
>> data communication.
>>
>> Is anybody thinking about creating a lighter version of this virtual
>> disk image?
>>
>> Thanks and best regards,
>>
>> Fidel.
>>
>> ___
>> 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.
>>
>>
>
> ___
> Freesurfer mailing 
> listfreesur...@nmr.mgh.harvard.eduhttps://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 
> athttp://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.
>
>
>
> ___
> 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.
>
>
___
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.

Re: [Freesurfer] Smaller Virtual Machine

[Pedro Paulo de Magalhães Oliveira Junior]

Yes. But that machine distributed by FreeSurfer is the one with full GUI to
run under Windows.

I have a machine for cloud processing in Amazon EC2 (you can look up for
FreeSurfer DMI in Amazon EC2)

PPJ


On Fri, Apr 29, 2011 at 11:15, Fidel  wrote:

> Hi all,
>
> I have been trying the virtual disk image, and it works well.
> Nevertheless, I think that more than 7GB is a lot of space if somebody
> wants to use it as a Virtual Machine in a cloud environment, in which
> you are charged for used storage and maybe for used bandwidth in the
> data communication.
>
> Is anybody thinking about creating a lighter version of this virtual
> disk image?
>
> Thanks and best regards,
>
> Fidel.
>
> ___
> 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.
>
>
___
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.

Re: [Freesurfer] FreeSurfer movie generation recipe

[Pedro Paulo de Magalhães Oliveira Junior]

easier.

Can you inflate until you get the sphere?

2011/4/28 Bruce Fischl 

> or you can save snapshots from mris_inflate with
>
> mris_inflate -w 1 -scale 1 ...
>
> then render each of the resulting surfaces.
> cheers,
> Bruce
>
>
> On Thu, 28 Apr 2011, Pedro Paulo de Magalhães Oliveira Junior wrote:
>
>  Some months ago it was asked in this list how to make a Movie of he
>> process
>> of the inflation of the brain.
>>
>> Some hints:
>>
>> Create this tcl script and name it as script.tcl:
>>
>> for {set x 0} {$x<120}  {incr x} {
>>  set r [expr (round(1.2*$x + 3))]
>>  shrink $r
>>  redraw
>>  save_tiff ${x}-img.tif
>> }
>> exit
>>
>> Then use the commands:
>> tksurfer bert lh pial -annotation aparc.annot -tcl script.tcl
>> ffmpeg -r 15 -b 2500 -sameq -i %d-img.tif videoOutput.mp4
>>
>>
>> You can check the results at:
>> http://www.youtube.com/watch?v=aj-d8PZMXt8
>>
>>
>
> 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.
>
___
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.

[Freesurfer] FreeSurfer movie generation recipe

[Pedro Paulo de Magalhães Oliveira Junior]

Some months ago it was asked in this list how to make a Movie of he process
of the inflation of the brain.

Some hints:

Create this tcl script and name it as script.tcl:

for {set x 0} {$x<120}  {incr x} {
   set r [expr (round(1.2*$x + 3))]
   shrink $r
   redraw
   save_tiff ${x}-img.tif
}
exit

Then use the commands:
tksurfer bert lh pial -annotation aparc.annot -tcl script.tcl
ffmpeg -r 15 -b 2500 -sameq -i %d-img.tif videoOutput.mp4


You can check the results at:
http://www.youtube.com/watch?v=aj-d8PZMXt8
___
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.

Re: [Freesurfer] Unknown label in Parcellation

[Pedro Paulo de Magalhães Oliveira Junior]

lh.aparc.stats

2011/4/27 Bruce Fischl 

> which parcellation are you using?
>
>
> On Wed, 27 Apr 2011, Pedro Paulo de Magalhães Oliveira Junior wrote:
>
>  In one study we are conducting we found significant difference in cortical
>> thickness between the two groups in some areas. One of those areas are
>> lh_unknown.
>>
>> Is this an error or it's a still unlabelled area?
>>
>> thanks
>>
>> Pedro Paulo Jr
>>
>>
>
> 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.
>
___
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.

[Freesurfer] Unknown label in Parcellation

[Pedro Paulo de Magalhães Oliveira Junior]

In one study we are conducting we found significant difference in cortical
thickness between the two groups in some areas. One of those areas are
lh_unknown.

Is this an error or it's a still unlabelled area?

thanks

Pedro Paulo Jr
___
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.

Re: [Freesurfer] qdec analysis different scanner

[Pedro Paulo de Magalhães Oliveira Junior]

Yes it does. However you can maybe use the scanner as a covariate.


On Wed, Apr 27, 2011 at 09:24, John Fredy  wrote:

> Hello all,
>
> In voxel based morphometry is not recommended use images from different
> scanners. This recommendation also apply in the qdec analysis?
>
> Thanks in advance
>
> John Ochoa
> Universidad de Antioquia
> Instituto Neurológico de Antioquia
>
> ___
> 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.
>
>
___
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.

Re: [Freesurfer] Fwd: display error

[Pedro Paulo de Magalhães Oliveira Junior]

in tcsh try:

setenv doublebufferflag 1

in bash it would be

export doublebufferflag=1

before running tksurfer

Refs:
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg11049.html
http://surfer.nmr.mgh.harvard.edu/fswiki/TksurferDisplayProblems


On Tue, Apr 26, 2011 at 10:35, Cris Lanting  wrote:

> In the hope that someone recognises the error as described in the
> attached email...
> (Sorry for the repost but I haven't found a solution yet and I'm quite
> sure someone will recognise it)
>
> Cris
>
> -- Forwarded message --
> From: Cris Lanting 
> Date: Mon, Apr 11, 2011 at 1:50 PM
> Subject: display error
> To: freesurfer@nmr.mgh.harvard.edu
>
>
> Dear Freesurfer community,
>
> I have a display problem that affects especially tkmedit and tksurfer.
> We run freesurfer ( freesurfer-Linux-centos4_x86_64-stable-pub-v5.0.0)
> on a remote unix server and use Exceed (v. 14.0.0.376) to port the
> display to a local (windows) computer. At first we got a openGL error
> stating that OpenGL was not supported when calling e.g. tksurfer. Now
> we have installed Exceed 3D to support OpenGL it seems to continue
> beyond the previous error message but comes up with a different one
> (see snippet)
>
> 
> subject is js
> hemiis rh
> surface is pial
> surfer: current subjects dir: /home/cris/freesurfer/subjects
> surfer: not in "scripts" dir ==> using cwd for session root
> surfer: session root data dir ($session) set to:
> surfer: /home/cris
> Reading image info (/home/cris/freesurfer/subjects/js)
> Reading /home/cris/freesurfer/subjects/js/mri/orig.mgz
> surfer: Reading header info from
> /home/cris/freesurfer/subjects/js/mri/orig.mgz
> fsurfer: vertices=156376, faces=312748
> surfer: single buffered window
> surfer: tkoInitWindow(js)
> Window type not found!
> surfer: failed, trying double buffered window
> Window type not found!
> surfer: failed, no suitable display found
> 
>
> Any ideas?
>
> Note that other programs that do not use OpenGL seem to run fine (i.e.
> fslview and gedit)
>
> Kind regards,
> Cris Lanting
>
> Career Development Fellow
> MRC Institute of Hearing Research
> Science Road, University Park
> Nottingham
> NG7 2RD
> c...@ihr.mrc.ac.uk
>
> ___
> 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.
>
>
___
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.

Re: [Freesurfer] Setup configuration error

[Pedro Paulo de Magalhães Oliveira Junior]

Freesurfer installation directory is the directory where you installed
FreeSurfer

In Mac it's usually /Applications/freesurfer

-- iOS 4.3

Em 21/04/2011, às 20:57, Jade  escreveu:

Hi,

After I installed FreeSurfer
( freesurfer-Darwin-leopard-i686-stable-pub-v5.0.0.dmg) in my Macbook (Snow
Leopard, Version 10.6.7),  I got the message saying " The software was
successfully installed" but while I tried to configure my shell,

after I typed

setenv FREESURFER_HOME /freesurfer
source $FREESURFER_HOME/SetUpFreeSurfer.csh

I got this message "freesurfer_installation_directory: No such file or
directory".

I tired it in both X11 and terminal.   Please help me to use Freesurfer.

Thank you.

Jade


___
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.
___
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.

Re: [Freesurfer] Could I run several freesurfers at the same time?

[Pedro Paulo de Magalhães Oliveira Junior]

the figure below show memory consumption for 3 running process (the OS
uses 400MB)


2011/4/21 Pedro Paulo de Magalhães Oliveira Junior :
> You can set up multicore in VirtualBox or VMWare
>
> In my experience ( without the gcut) 1GB is enough
>
> -- iOS 4.3
>
> Em 21/04/2011, às 13:53, "Richard G. Edgar"
>  escreveu:
>
>>
>> On Thu, 2011-04-21 at 09:48 -0700, Rongxiang Tang wrote:
>>>
>>> I was wondering if I can run several freesurfers in my virtualbox
>>> simultaneously by setting up several virtual machines...my computer
>>> has 16G RAM and it's Windows 7 64-bit.
>>> Would working multiple freesurfers at the same time slow down the
>>> calculations?
>>> Moreover, I was wondering if my computer could afford these loads...
>>>
>>
>> I can't speak for the virtualisation side, but it's certainly possible
>> (even advisable) to run more than one copy of Freesurfer on a machine. I
>> ran an experiment, running a recon-all instance on each of my box's four
>> cores, and they were all complete in about 110% of the time of a single
>> run - a big win.
>>
>> Now with virtualisation, you'd also be running extra copies of the guest
>> OS. Can you set up a single VM with multiple cores instead? If you have
>> a quad core machine, give the VM three cores, and run three Freesurfer
>> jobs on it. Trying it is the only way to be sure.
>>
>> Richard
>>
>> ___
>> 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.
>>
>
<>___
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.

Re: [Freesurfer] Could I run several freesurfers at the same time?

[Pedro Paulo de Magalhães Oliveira Junior]

You can set up multicore in VirtualBox or VMWare

In my experience ( without the gcut) 1GB is enough

-- iOS 4.3

Em 21/04/2011, às 13:53, "Richard G. Edgar"
 escreveu:

>
> On Thu, 2011-04-21 at 09:48 -0700, Rongxiang Tang wrote:
>>
>> I was wondering if I can run several freesurfers in my virtualbox
>> simultaneously by setting up several virtual machines...my computer
>> has 16G RAM and it's Windows 7 64-bit.
>> Would working multiple freesurfers at the same time slow down the
>> calculations?
>> Moreover, I was wondering if my computer could afford these loads...
>>
>
> I can't speak for the virtualisation side, but it's certainly possible
> (even advisable) to run more than one copy of Freesurfer on a machine. I
> ran an experiment, running a recon-all instance on each of my box's four
> cores, and they were all complete in about 110% of the time of a single
> run - a big win.
>
> Now with virtualisation, you'd also be running extra copies of the guest
> OS. Can you set up a single VM with multiple cores instead? If you have
> a quad core machine, give the VM three cores, and run three Freesurfer
> jobs on it. Trying it is the only way to be sure.
>
> Richard
>
> ___
> 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.
>

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

Re: [Freesurfer] Fedora 14

[Pedro Paulo de Magalhães Oliveira Junior]

Yes. It works.

-- iOS 4.3

Em 18/04/2011, às 21:13, "roger@yale.edu"  escreveu:

> Hi all,
> Quick question: will the latest Linux 32-bit install work with Fedora 14?
> Please let me know if there are known issues.
> Thanks,
> Roger
> ___
> 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.
>

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

[Freesurfer] Course FreeSurfer - São Paulo, Brazil

[Pedro Paulo de Magalhães Oliveira Junior]

Just to inform we still have two spots available for the course in São Paulo
next week

http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Brazil2011CourseSchedule

If there's anyone interested write me for more details.

cheers

Pedro Paulo Jr.
___
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.

Re: [Freesurfer] recommende pc and cuda

[Pedro Paulo de Magalhães Oliveira Junior]

Maybe a NVidia GTX590  (it's a dual GPU)


On Mon, Apr 4, 2011 at 08:13, Knut J Bjuland  wrote:
> Hi
>
> I am in the process of acquiring a new computer to run freesurfer on.  I am
> currently think about buying a PC with a geforce 4X0 and a Tesla card along
> with a two screen setup running either Ubuntu or Redhat Linux enterprise
> 6.0. I think the PC should be a core i7 with 6 core and above 12 gigs byte
> of ram. What kind of tesla card is recommend for using with Freesurfer? Will
> Freesurfer 5.1 also support cuda 4.0.
>
> Knut J
>
> ___
> 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.
>
>

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

Re: [Freesurfer] data preparation for SVM classification

[Pedro Paulo de Magalhães Oliveira Junior]

Sorry for the advertisement :)

I wrote a paper using this technique:

Use of SVM methods with surface-based cortical and volumetric subcortical
measurements to detect Alzheimer's
disease.

Oliveira PP Jr, Nitrini R, Busatto G, Buchpiguel C, Sato JR, Amaro E Jr.

J Alzheimers Dis. 2010;19(4):1263-72.
 PMID:  20061613  [PubMed - indexed for MEDLINE]



On Thu, Mar 24, 2011 at 09:10, Bruce Fischl wrote:

> what are you trying to classify and what is your hypothesis?
>
> cheers,
> Bruce
> On Thu, 24 Mar
> 2011, Alexander Ivanov wrote:
>
> > *Dear Freesurfers,*
> >
> > Could you please suggest me the best way to prepare structural data for
> SVM
> > classification? I googled, searched the archives - there're no examples
> of
> > such preparation using freesurfer algorithms (to my knowledge)...
> > Thank you beforehand.
> > ---
> > *Regards,*
> > *A. Hasfatin*
> >
> ___
> 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.
>
>
___
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.

Re: [Freesurfer] single subject versus a group map in qdec

[Pedro Paulo de Magalhães Oliveira Junior]

We have dono something like this in Cortical thickness reduction of normal
appearing cortex in patients with
polymicrogyria<https://surfer.nmr.mgh.harvard.edu/pub/articles/corticalPedroSep08.pdf>

<https://surfer.nmr.mgh.harvard.edu/pub/articles/corticalPedroSep08.pdf>
cheers,

PPJ
-----
Pedro Paulo de Magalhães Oliveira Junior
Diretor de Operações
Netfilter & SpeedComm Telecom
-- www.netfilter.com.br
-- For mobile: http://www.netfilter.com.br/mobile




On Wed, Mar 23, 2011 at 14:21, Emily Rogalski  wrote:

> Using q dec we have run a single patient versus a group of healthy control
> subjects (n=20ish) and found significant differences even after FDR
> correction.
>
> Could you describe the process qdec uses to compute these differences?
> Is it legitimate to report these single subject maps?
> Practically this is very useful for case reports but Im concerned about
> violating statistical rules.
>
> Thanks!
> --
> Emily J Rogalski, PhD
> Assistant Research Professor
> Northwestern University
> Cognitive Neurology and Alzheimer's Disease Center (CNADC)
> 320 E Superior Street
> Searle Building 11th Floor
> Chicago, IL 60611
> 312-503-1155 phone
> 312-908-8789 fax
> erogal...@gmail.com
>
> ___
> 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.
>
>
___
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.

[Freesurfer] [New release] - iSurf Brainview 2.1.0

[Pedro Paulo de Magalhães Oliveira Junior]

Today it was released a new major upgrade of iSurf Brainview. (2.1.0)

New features:
- New Atlas: Chistophe Destrieux 2009 Atlas

- Improved Interface
- Retina Display
- iOS 4.3

As usual suggestions are welcome.

Upcoming features will include 3D visualization.

The link for download is:
http://itunes.apple.com/WebObjects/MZStore.woa/wa/viewSoftware?id=381072423&mt=8

Cheers

Pedro Paulo Jr.
___
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.

Re: [Freesurfer] Mac Pro with 12cores

[Pedro Paulo de Magalhães Oliveira Junior]

That's without GPU?


On Thu, Mar 10, 2011 at 11:17, Richard G. Edgar
wrote:

>
> On Thu, 2011-03-10 at 08:27 -0500, Bruce Fischl wrote:
> > If you have enough memory! Maybe Richard can post current CPU recon
> > times with the latest hardware and optimizations. I think they are
> > much shorter than they used to be
>
> My workstation (3.2 GHz Nehalem) can do a recon-all ernie in about 8
> hours. Running four in parallel (one for each core) bumps the total
> walltime up to about eight and a half hours.
>
> Regards,
>
> Richard
>
> ___
> 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.
>
>
___
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.

Re: [Freesurfer] Mac Pro with 12cores

[Pedro Paulo de Magalhães Oliveira Junior]

You can run 12 recon-all in parallel.

You'll have 12 patients processed in each day approximately

-
Pedro Paulo de Magalhães Oliveira Junior
Diretor de Operações
Netfilter & SpeedComm Telecom
-- www.netfilter.com.br
-- For mobile: http://www.netfilter.com.br/mobile




2011/3/10 汪贵宏 

> Hi,all:
>As we have too many controls and patients to run the "recon-all",and
> it is really time-suming,so,how can I reduce the time of recon-all in a
> group of patients?
> After read the statistic info on the website
>   https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllRunTimes
> It seems the mac pro will take much more time than others,so ,can anybody
> give me a suggestion?Is it Mac Pro <http://www.apple.com/macpro/> with 12
> cores works?
> http://www.apple.com/macpro/
>
> Thanks a lot!
>
> Wang
>
>
>
> ___
> 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.
>
>
___
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.

Re: [Freesurfer] Newbie - problems compiling project tree

[Pedro Paulo de Magalhães Oliveira Junior]

libnetcdf-dev or netcdf-dev will do the trick


On Tue, Mar 8, 2011 at 19:42, Shay Ohayon  wrote:

> Hi All,
>
> I am having some problems compiling freesurfer .
> I checked out the recent development version from the CVS, ran
> "setup_configure" successfully, but upon "./configure", I end up with
> the following annoying message:
>
> checking for nccreate in -lnetcdf... no
> configure: error: FATAL: netcdf lib not found. Set LDFLAGS or
> --with-mni-dir.
>
> I attempted to install the netcdf-bin and libnetcdf6 packages using
> Synaptic, but this did not seem to help.
> How do I continue from here?
>
> -- Shay
> ___
> 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.
>
>
___
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.

Re: [Freesurfer] CUDA comparable to non-CUDA?

[Pedro Paulo de Magalhães Oliveira Junior]

We assume that.


On Tue, Mar 8, 2011 at 09:58, Marcus N Schmidt wrote:

> Hi FreeSurfer Experts,
>
> Just a quick question: Generally speaking, assuming everything else remains
> the same, are subjects run through a CUDA-enabled recon-all comparable to
> subjects run through recon-all without CUDA?
>
> Thanks,
> Marcus
>  *
> Marcus N Schmidt*
> Department of Child & Adolescent Psychiatry
> Erasmus MC
> Rotterdam, The Netherlands
>
>
>
>
> ___
> 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.
>
>
___
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.

[Freesurfer] Freesurfer Tutorial and Workshop April 16-18 in Sao Paulo, Brazil

[Pedro Paulo de Magalhães Oliveira Junior]

The Freesurfer group and the Hospital das Clinicas from São Paulo University
will be offering a three-day Freesurfer Tutorial and Workshop April 16-18 at
the Radiology Institute in Sao Paulo, SP, Brazil. A description of
the course and a list of the topics covered can be found soon at
http://www.neuroimagem.com but it's based on the description of
http://surfer.nmr.mgh.harvard.edu/fswiki/CourseDescription

The course will take three days this year and will be in English. The
registration fee is 400 BRL.

If you want to apply for a spot send an e-mail to ppj at
netfilter.com.brwith your details. We'll have a form in the website
soon.

There is room for only 40 participants and registration is on a first-come,
first-serve basis. If you are not one of the first 40, you will be put on a
waiting list and will be notified if a spot becomes available.

If you need any information about arranging payment for the course,
accommodations,course location, as well traveling issues please contact me
in the e-mail above.

Regards,

Pedro Paulo Oliveira Jr.
-----
Pedro Paulo de Magalhães Oliveira Junior
Diretor de Operações
Netfilter & SpeedComm Telecom
-- www.netfilter.com.br
-- For mobile: http://www.netfilter.com.br/mobile
___
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.

[Freesurfer] aparc+aseg.mgz and aparc.a2009s+aseg.mgz

[Pedro Paulo de Magalhães Oliveira Junior]

I was checking the values at both aparc.a2009s+aseg.mgz and aparc+aseg.mgz
and comparing it with the labels in FreeSurferColorLUT.txt

I have noticed some problems:
1) There are values out of the range specified in FreeSurferColorLUT.txt (in
bert dataset there are 353528 voxels with values above 14999)
2) There are many areas in FreeSurferColorLUT.txt that don't appear neither
in aparc+aseg nor in aparc.a2009s+aseg

My main concern is with the out of range values, which structure they map
to?

thanks
-
Pedro Paulo de Magalhães Oliveira Junior
Diretor de Operações
Netfilter & SpeedComm Telecom
-- www.netfilter.com.br
-- For mobile: http://www.netfilter.com.br/mobile
___
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.

Re: [Freesurfer] parellizing Freesurfer

[Pedro Paulo de Magalhães Oliveira Junior]

You'll find some answers here:
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg15728.html



2011/2/26 Pablo Polosecki 

> Hi Pedro and everyone,
>
> Thanks so much for pointing me there. I seems like the only way to
> parallelize is to run several recon-all simultanously intstead of wating for
> one to finshe and then run the following. I wonder if you (of someone else)
> managed to achieve some further decrease in running times, making a single
> recon-all run faster or something like that. Was it any different in the
> Amazon EC2?
>
> It would seem that the analysis fo functional data (at least parts of it)
> could run in parallel, since the analysis of one voxel is independent of the
> rest. I would love to know if this is something people do. An ugly
> implementation could be to split the volumes into several small volume files
> and run the analysis separately and then merge back the output volumes. Has
> anyone done something like that or nicer?
>
> Thanks!
>
> Pablo
>
> 2011/2/26 Pedro Paulo de Magalhães Oliveira Junior 
>
> Yes. Take a look at:
>> http://surfer.nmr.mgh.harvard.edu/fswiki/UserContributions/FAQ#Q.HowcanIreducethetimeofrecon-allinagroupofpatients.3F
>>
>> Also I have successfully executed it at Amazon EC2 instances.
>>
>> PPJ
>> -----
>> Pedro Paulo de Magalhães Oliveira Junior
>> Diretor de Operações
>> Netfilter & SpeedComm Telecom
>> -- www.netfilter.com.br
>> -- For mobile: http://www.netfilter.com.br/mobile
>>
>>
>>
>>
>> On Sat, Feb 26, 2011 at 19:59, Pablo Polosecki <
>> ppolose...@mail.rockefeller.edu> wrote:
>>
>>> Hi all,
>>>
>>> I was wondering if someone out there has any experience trying to
>>> parallelize their analysis streams in clusters or multiprocessor machines. I
>>> was thinking also about the cloud computing services offered by Google,
>>> Amazon or other. Has anyone tried or has any plans of implementing something
>>> along those lines?
>>>
>>> Best wishes,
>>>
>>> Pablo
>>>
>>>
>>>
>>>
>>> ___
>>> 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.
>>>
>>>
>>
>
___
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.