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
>
>
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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
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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

[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

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Re: [Freesurfer] Tracula Question, step 2

[Anastasia Yendiki]

Hi Shannon - Which version of FSL do you have? Older versions didn't use 
to save the mean_dsamples.nii.gz, but that was a while ago.


How quickly it runs depends on the size of the brain mask, so I'd check 
that that's ok too.


a.y

On Wed, 9 Nov 2011, Shannon Buckley wrote:


Hi Anastasia,

It turns out that I was NOT able to run the original bedpostx on our 
cluster, so thank you for pointing me in the right direction! In case other 
users experience a similar problem, this is what we did to get the ball rolling 
on our grid:

We found the "fsl_sub_seychelles" and "fsl_sub" scripts where the 
default q-names were identified. We modified the files (changing long and short.q to reflect the 
naming convention used here) and ran the original bedpostx. The preproc and datacheck functions 
worked perfectly. The bedpostx function SEEMED to have launched fine, but we hit another snag...

The program finished far too quickly for it to have worked properly (an hour, 
tops), and when I try to run the next "-prep" step I get the following error, 
which confirms that suspicion:

_+_+_+_+_+_+_+_+_+_+_
"Loading BEDPOST parameter samples from 
/cind/07/PPMI/Freesurfer/Tracula/PPMI_088_S_3551m00/dmri.bedpostX
niiRead(): error opening file 
/cind/07/PPMI/Freesurfer/Tracula/PPMI_088_S_3551m00/dmri.bedpostX/mean_dsamples.nii.gz
ERROR: Could not read 
/cind/07/PPMI/Freesurfer/Tracula/PPMI_088_S_3551m00/dmri.bedpostX/mean_dsamples.nii.gz
Linux paris 2.6.18-194.11.1.el5 #1 SMP Tue Aug 10 19:05:06 EDT 2010 x86_64 
x86_64 x86_64 GNU/Linux

trac-paths exited with ERRORS at Wed Nov  9 16:18:53 PST 2011

Word too long."
+_+_+_+_+_+_+_+_+_+_+_


I have to confess I'm not familiar with the "word too long" error. In any case, 
bedpostx seems to fail to produce the requisite files for -prep (mean_dsamples.nii.gz). Since I'm 
not sure what the inputs would be for creating such a file, I'm including my "ls" output 
for our dmri.bedpostX path.

_+_+_+_+_+_+_+_+_+_+_+

"[vhasfcbuckls@paris dmri.bedpostX]$ ls
bvals dyads2.nii.gz   mean_ph2samples.nii.gz
merged_ph2samples.nii.gz
bvecs error.log   mean_th1samples.nii.gz
merged_th1samples.nii.gz
cancellogsmean_th2samples.nii.gz
merged_th2samples.nii.gz
commands.txt  mean_f1samples.nii.gz   merged_f1samples.nii.gz   monitor
dmri.bedpostX.nii.gz  mean_f2samples.nii.gz   merged_f2samples.nii.gz   
nodif_brain_mask.nii.gz
dyads1.nii.gz mean_ph1samples.nii.gz  merged_ph1samples.nii.gz  xfms
[vhasfcbuckls@paris dmri.bedpostX]$"
+_+_+_+_+_+_+_+_+_+_


Do you have any advice for getting passed this step? We are fairly in 
the dark with this function over here, so any help / hints you can provide 
would be wonderful. Please let me know if you need more information.

Thanks again for your help and patience,

~Shannon B.
-Original Message-
From: Anastasia Yendiki [mailto:ayend...@nmr.mgh.harvard.edu]
Sent: Thursday, November 03, 2011 7:39 AM
To: shannon.buck...@radiology.ucsf.edu
Cc: freesurfer@nmr.mgh.harvard.edu; Mensch, Henry
Subject: Re: [Freesurfer] Tracula Question, step 2


Hi Shannon - Does the original bedpostx run fine on your cluster? You'd
probably have to edit that to get it to work, it's not made to work on
every possible cluster. Bedpostx_seychelles is the modified version that
tracula calls that I've modified from the original FSL version so that it
runs on our clusters.

In either case, trac-all is meant to always be run from the command line,
whether you're on a personal computer (where is runs jobs serially) or a
cluster (where it submits them as jobs using qsub). But probably some
editing will be needed as I said.

Hope this helps,
a.y

On Wed, 2 Nov 2011, Shannon Buckley wrote:



Hi Anastasia,



I am trying to run Tracula for the first time in our lab and
I’m getting errors during step 2 that seem to involve how the program wants
to be launched via grid. I’ve attached the configuration file I’m using and
the error message is below...





$trac-all -bedp -c /cind/01/users/vhasfcbuckls/PPMI/Tracula.sh

Using Freesurfer version 5.1.



  Subjects Directory is /cind/00/PPMI/Freesurfer/Tracula/

  Sessions Directory is /home/vhasfcbuckls/sessions



INFO: SUBJECTS_DIR is /cind/07/PPMI/Freesurfer/subjects

INFO: Diffusion root is /cind/00/PPMI/Freesurfer/Tracula

Actual FREESURFER_HOME /cind/01/apps/freesurfer/64bit/freesurfer5.1

ln 
-sf/cind/00/PPMI/Freesurfer/Tracula/PPMI_088_S_3551m00/dlabel/diff/anat_brain_
mask.bbr.nii.gz/cind/00/PPMI/Freesurfer/Tracula/PPMI_088_S_3551m00/dmri/nodif_brain_mask.n
ii.gz

ln -sf /cind/00/PPMI/Freesurfer/Tracula/PPMI_088_S_3551m00/dmri/dwi.nii.gz
/cind/00/PPMI/Freesurfer/Tracula/PPMI_088_S_3551m00/dmri/data.nii.gz

WARN: Running FSL's bedbost locally - this might take a while

WARN: It is recomm

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.
>
>
___
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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] Tracula Question, step 2

[Shannon Buckley]

Hi Anastasia, 

It turns out that I was NOT able to run the original bedpostx on our 
cluster, so thank you for pointing me in the right direction! In case other 
users experience a similar problem, this is what we did to get the ball rolling 
on our grid: 

We found the "fsl_sub_seychelles" and "fsl_sub" scripts where the 
default q-names were identified. We modified the files (changing long and 
short.q to reflect the naming convention used here) and ran the original 
bedpostx. The preproc and datacheck functions worked perfectly. The bedpostx 
function SEEMED to have launched fine, but we hit another snag...  

The program finished far too quickly for it to have worked properly (an 
hour, tops), and when I try to run the next "-prep" step I get the following 
error, which confirms that suspicion: 

_+_+_+_+_+_+_+_+_+_+_
"Loading BEDPOST parameter samples from 
/cind/07/PPMI/Freesurfer/Tracula/PPMI_088_S_3551m00/dmri.bedpostX
niiRead(): error opening file 
/cind/07/PPMI/Freesurfer/Tracula/PPMI_088_S_3551m00/dmri.bedpostX/mean_dsamples.nii.gz
ERROR: Could not read 
/cind/07/PPMI/Freesurfer/Tracula/PPMI_088_S_3551m00/dmri.bedpostX/mean_dsamples.nii.gz
Linux paris 2.6.18-194.11.1.el5 #1 SMP Tue Aug 10 19:05:06 EDT 2010 x86_64 
x86_64 x86_64 GNU/Linux

trac-paths exited with ERRORS at Wed Nov  9 16:18:53 PST 2011

Word too long."
+_+_+_+_+_+_+_+_+_+_+_


I have to confess I'm not familiar with the "word too long" error. In 
any case, bedpostx seems to fail to produce the requisite files for -prep 
(mean_dsamples.nii.gz). Since I'm not sure what the inputs would be for 
creating such a file, I'm including my "ls" output for our dmri.bedpostX path. 

_+_+_+_+_+_+_+_+_+_+_+

"[vhasfcbuckls@paris dmri.bedpostX]$ ls
bvals dyads2.nii.gz   mean_ph2samples.nii.gz
merged_ph2samples.nii.gz
bvecs error.log   mean_th1samples.nii.gz
merged_th1samples.nii.gz
cancellogsmean_th2samples.nii.gz
merged_th2samples.nii.gz
commands.txt  mean_f1samples.nii.gz   merged_f1samples.nii.gz   monitor
dmri.bedpostX.nii.gz  mean_f2samples.nii.gz   merged_f2samples.nii.gz   
nodif_brain_mask.nii.gz
dyads1.nii.gz mean_ph1samples.nii.gz  merged_ph1samples.nii.gz  xfms
[vhasfcbuckls@paris dmri.bedpostX]$"
+_+_+_+_+_+_+_+_+_+_


Do you have any advice for getting passed this step? We are fairly in 
the dark with this function over here, so any help / hints you can provide 
would be wonderful. Please let me know if you need more information. 

Thanks again for your help and patience, 

~Shannon B.
-Original Message-
From: Anastasia Yendiki [mailto:ayend...@nmr.mgh.harvard.edu] 
Sent: Thursday, November 03, 2011 7:39 AM
To: shannon.buck...@radiology.ucsf.edu
Cc: freesurfer@nmr.mgh.harvard.edu; Mensch, Henry
Subject: Re: [Freesurfer] Tracula Question, step 2


Hi Shannon - Does the original bedpostx run fine on your cluster? You'd 
probably have to edit that to get it to work, it's not made to work on 
every possible cluster. Bedpostx_seychelles is the modified version that 
tracula calls that I've modified from the original FSL version so that it 
runs on our clusters.

In either case, trac-all is meant to always be run from the command line, 
whether you're on a personal computer (where is runs jobs serially) or a 
cluster (where it submits them as jobs using qsub). But probably some 
editing will be needed as I said.

Hope this helps,
a.y

On Wed, 2 Nov 2011, Shannon Buckley wrote:

> 
> Hi Anastasia,
> 
>  
> 
> I am trying to run Tracula for the first time in our lab and
> I’m getting errors during step 2 that seem to involve how the program wants
> to be launched via grid. I’ve attached the configuration file I’m using and
> the error message is below...
> 
> 
> 
> 
> 
> $trac-all -bedp -c /cind/01/users/vhasfcbuckls/PPMI/Tracula.sh
> 
> Using Freesurfer version 5.1.
> 
>  
> 
>   Subjects Directory is /cind/00/PPMI/Freesurfer/Tracula/
> 
>   Sessions Directory is /home/vhasfcbuckls/sessions
> 
>  
> 
> INFO: SUBJECTS_DIR is /cind/07/PPMI/Freesurfer/subjects
> 
> INFO: Diffusion root is /cind/00/PPMI/Freesurfer/Tracula
> 
> Actual FREESURFER_HOME /cind/01/apps/freesurfer/64bit/freesurfer5.1
> 
> ln 
> -sf/cind/00/PPMI/Freesurfer/Tracula/PPMI_088_S_3551m00/dlabel/diff/anat_brain_
> mask.bbr.nii.gz/cind/00/PPMI/Freesurfer/Tracula/PPMI_088_S_3551m00/dmri/nodif_brain_mask.n
> ii.gz
> 
> ln -sf /cind/00/PPMI/Freesurfer/Tracula/PPMI_088_S_3551m00/dmri/dwi.nii.gz
> /cind/00/PPMI/Freesurfer/Tracula/PPMI_088_S_3551m00/dmri/data.nii.gz
> 
> WARN: Running FSL's bedbost locally - this might take a while
> 
> WARN: It is recommended to run this step on a cluster
> 
> bedpostx_seychelles /cind/00/PPMI/Freesurfer/Tracula/PPMI_088_S_3551m00/dmri
> 
> subjectdir is /cind/00/PPMI/Freesurfer/Tracula/PPMI_088

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

[Satrajit Ghosh]

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.
>
>
___
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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] Sub-cortical structure

[Douglas N Greve]

yes, that has the subcortical segmentation based on the automatic 
algorithm and any changes that you might have made manually. The "auto" 
is only the result from the automatic method.
doug

Jie Shi wrote:
> Thanks a lot. Will try. Basically, is aseg.mgz the resulting file 
> which contains the results of FreeSurfer subcortical segmentation? 
> What role is the aseg.auto.mgz?
>
> Jie
>
>
> On Wed, Nov 9, 2011 at 5:15 PM, Douglas N Greve 
> mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>
> cd $SUBJECTS_DIR/subject/surf
> mri_tesselate ../mri/aseg.mgz 17 lh.hippocampus; # this generates
> a surface with jagged edges
> mris_smooth -nw -n 10 lh.hippocampus lh.hippocampus.sm10; #
> smooths surface 10 smoothing steps is just a guess
>
> # Visusalize the surface
> tksurfer subject lh hippocampus.sm10
> # See the surface overlaid on the volume
> tkmedit subject orig.mgz lh.hippocampus.sm10 -aseg
>
> Not that when you run the tkmedit/tksurfer commands, they will
> complain that the surface does not match. This is not a problem
> for this application.
>
> doug
>
>
> Jie Shi wrote:
>
> Hi, thank you very much. Actually we do want to know how to
> get the surfaces in order to compare with ours.
>
> Jie
>
>
> On Wed, Nov 9, 2011 at 4:59 PM, Douglas N Greve
> mailto:gr...@nmr.mgh.harvard.edu>
>  >> wrote:
>
>You can extract a binary mask for any structure with
>mri_binarize --i aseg.mgz --match XX --o yourmask.mgh
>where XX is a number from
> $FREESURFER_HOME/FreeSurferColorLUT.txt
>(eg, 17 = left hippo)
>It is possible to generate hippo surfaces, but we cannot
> guarantee
>accuracy. Let me know if you want to know how.
>doug
>
>Jie Shi wrote:
>
>Hi, experts. We need to use FreeSurfer to process some
> analyze
>image data. More specifically, we want to extract the
>hippocampus surfaces. We know that FreeSurfer has done
>subcortical segmentation during -autorecon2 stage in
>recon-all. We have checked the resulting aseg.mgz file and
>found that it contains all substructures. So we wonder if
>there is a way to get the separated .mgz files for each
>substructure or could FreeSurfer generate the subcortical
>surfaces? Thanks a lot.
>
>Best,
>Jie
>  
>  
> 
>
>___
>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
> 
>
>
>
>
>
>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.
>
>
>
> -- 
> 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
> 
>
>

-- 
Douglas 

Re: [Freesurfer] Sub-cortical structure

[Douglas N Greve]

cd $SUBJECTS_DIR/subject/surf
mri_tesselate ../mri/aseg.mgz 17 lh.hippocampus; # this generates a 
surface with jagged edges
 mris_smooth -nw -n 10 lh.hippocampus lh.hippocampus.sm10; # smooths 
surface 10 smoothing steps is just a guess

# Visusalize the surface
tksurfer subject lh hippocampus.sm10
# See the surface overlaid on the volume
tkmedit subject orig.mgz lh.hippocampus.sm10 -aseg

Not that when you run the tkmedit/tksurfer commands, they will complain 
that the surface does not match. This is not a problem for this application.

doug


Jie Shi wrote:
> Hi, thank you very much. Actually we do want to know how to get the 
> surfaces in order to compare with ours.
>
> Jie
>
>
> On Wed, Nov 9, 2011 at 4:59 PM, Douglas N Greve 
> mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>
> You can extract a binary mask for any structure with
> mri_binarize --i aseg.mgz --match XX --o yourmask.mgh
> where XX is a number from $FREESURFER_HOME/FreeSurferColorLUT.txt
> (eg, 17 = left hippo)
> It is possible to generate hippo surfaces, but we cannot guarantee
> accuracy. Let me know if you want to know how.
> doug
>
> Jie Shi wrote:
>
> Hi, experts. We need to use FreeSurfer to process some analyze
> image data. More specifically, we want to extract the
> hippocampus surfaces. We know that FreeSurfer has done
> subcortical segmentation during -autorecon2 stage in
> recon-all. We have checked the resulting aseg.mgz file and
> found that it contains all substructures. So we wonder if
> there is a way to get the separated .mgz files for each
> substructure or could FreeSurfer generate the subcortical
> surfaces? Thanks a lot.
>
> Best,
> Jie
> 
> 
>
> ___
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> 
> 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
> 
>
>
>
> 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.
>
>

-- 
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
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[Freesurfer] Mean curvature analysis

[Alexander Lebedev]

Dear Freesurfer users and developers,

Yes, sorry... I should have specified this. I meant the mean curvature 
('curv' in qdec). And considering that this index is being calculated by 
formula: 1/radius - there must be an opposite interpretation (so, not a 
flattening actually, but folding?)... How come? Speaking about survivals 
after the correction for multiple comparison it is the parahippocampal 
area.
---
Kind Regards,
Alex


* Alexander Lebedev  [Tue, 08 Nov 2011 17:43:37 
+0400]:
> Dear Freesurfer Users!
> Is it wise to interpret the increased curvature index in
> neurodegenerative disorders as a more expressed atrophy (which 
manifests
> as a flattening)... I am just doubting because I have never worked 
with
> curvature analysis previously and its interpretations in different
> articles look quite controversal... The matter is that in our work the
> observed increase of the curvature index was found in the majority of
> the "thinned" areas...
> Thank you very much beforehand.
> ---
> Regards,
> Alex Lebedev
> Stavanger University Hospital
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Re: [Freesurfer] Sub-cortical structure

[Douglas N Greve]

You can extract a binary mask for any structure with
mri_binarize --i aseg.mgz --match XX --o yourmask.mgh
where XX is a number from $FREESURFER_HOME/FreeSurferColorLUT.txt (eg, 
17 = left hippo)
It is possible to generate hippo surfaces, but we cannot guarantee 
accuracy. Let me know if you want to know how.
doug

Jie Shi wrote:
> Hi, experts. We need to use FreeSurfer to process some analyze image 
> data. More specifically, we want to extract the hippocampus surfaces. 
> We know that FreeSurfer has done subcortical segmentation during 
> -autorecon2 stage in recon-all. We have checked the resulting aseg.mgz 
> file and found that it contains all substructures. So we wonder if 
> there is a way to get the separated .mgz files for each substructure 
> or could FreeSurfer generate the subcortical surfaces? Thanks a lot.
>
> Best,
> Jie
> 
>
> ___
> 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

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[Freesurfer] Sub-cortical structure

[Jie Shi]

Hi, experts. We need to use FreeSurfer to process some analyze image data.
More specifically, we want to extract the hippocampus surfaces. We know
that FreeSurfer has done subcortical segmentation during -autorecon2 stage
in recon-all. We have checked the resulting aseg.mgz file and found that it
contains all substructures. So we wonder if there is a way to get the
separated .mgz files for each substructure or could FreeSurfer generate the
subcortical surfaces? Thanks a lot.

Best,
Jie
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Re: [Freesurfer] MNI152 template regions

[Lilla Zollei]

The tool to use is: track_transform

It should be distributed with the DTK / TrackVis tools.

-Lilla

On Wed, 9 Nov 2011, Douglas N Greve wrote:

> Hi Paolo, I don't think we have have any tools to apply a matrix to a
> trk file. Or maybe I'm wrong?
> doug
>
> paolo wrote:
>> Bruce, Doug, Thomas, thank you so much, things are getting slowly
>> clearer now
>>
>> I can try to explain better what i want to do, so that perhaps
>> it will be easier for you too to tell what is the best way
>> to approach this problem
>>
>> essentially we have a number of subjects, with already extracted
>> white matter fiber tracts (in .trk format)
>> The idea was to transform these  fibers back to freesurfer space (is
>> it the talairach space? in any case, is this what happens by using the
>> talairach.xfm matrix?), and then compare them in this space, as, i would
>> guess, there is still some sort of deviation from the standard fiber
>> pathway.
>>
>> Is this unreasonable?
>>
>> also, just for visualization purposes, i was thinking of rendering
>> these fibers in their context, but the average brain is, as you point
>> out, a bit too blurry.
>> Would it make sense here to bring something like MNI152 into the
>> freesurfer space, and use this one (and its segmentation) instead of the
>> fsaverage as an illustrative atlas in freesurfer space?
>>
>> Paolo
>>
>>
>>
>> On Mon, 7 Nov 2011 11:41:46 -0500 (EST)
>> Bruce Fischl  wrote:
>>
>>
>>> Hi Paolo,
>>>
>>> Are you showing individual subject data in the MNI space, or group
>>> average data? In general showing template brains and average data is
>>> not a good idea. It misrepresents the spatial localization accuracy
>>> of the data. You should try to use averages of the anatomy for groups
>>> of tracts of average fmri data or other group stats/data.
>>>
>>> cheers
>>> Bruce
>>>
>>> On Mon, 7 Nov 2011, Paolo wrote:
>>>
>>>
 I think it is well possible.
 And in principle i just wanted to use it for presentation, but the
 fsaverage doesnt really look like a "template" brain, rather like
 an average

 that's why i was wondering whether there is a more realistic
 template available in freesurfer space, or how i can create one
 (the idea was to recon-all the MNI152, which to me resembles much
 more to a brain)

 would it be the correct approach, or do you have other suggestions?
 by the way is it normal that recon-all on mni152 takes just ages to
 complete? (>12 hours on an athlon64, dont know exactly how long, i
 always stopped it before it finished)

 Paolo


 On 07-Nov-11 16:03, Thomas Yeo wrote:

> I am probably wrong, but doesn't the volumetric part of fsaverage
> correspond to MNI305 space rather than MNI152 space?
>
> --Thomas
>
> On Mon, Nov 7, 2011 at 9:00 AM, Bruce
> Fischl  wrote:
>
>> Hi Paolo,
>>
>> I think fsaverage has this in the aseg.mgz.
>>
>> cheers
>> Bruce
>> On Mon, 7 Nov 2011, Paolo wrote:
>>
>>
>>> In the meanwhile i did some research, and it looks like
>>> freesurfer does not use MNI152 as default template, am i right?
>>> it seems that the default template is the fsaverage subject,
>>> which in fact does not look like very realistic.
>>>
>>>
>>> Is there any way to get a realistic brain&  segmentation that is
>>> "idealized" enough, and still in talairach space (freesurfer
>>> space)?
>>>
>>> maybe the MNI152 after recon-all and mri_transform to apply back
>>> the transformation?
>>>
>>> i am sorry if these questions look unreasonable, i am new of
>>> freesurfer, and still have problem orienting myself in the
>>> documentation :)
>>>
>>> best,
>>> Paolo
>>>
>>> On 05-Nov-11 00:57, Paolo wrote:
>>>
 Hello

 I am a new user of freesurfer.
 I was wondering whether the brain regions for the MNI152
 dataset are available anywhere (i mean the template brain
 regions for the default MNI152 template).


 I have also another question: i have the dti fiber tracts
 extracted and computed and already in .trk format.
 I was wondering: to bring them back into the template MNI152
 space, is it sufficient to apply the talairach.xfm
 transformation matrix to the vertex data, or do i also need to
 use the m3z files (which look like a nonlinear deformation
 field)?

 thanks in advance!
 Paolo

>>
>>
>>
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>>
>>
>>
>
>
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Re: [Freesurfer] convert nifti to surface file

[Douglas N Greve]

yes, use mri_vol2surf. You will need a proper registration file. If the 
zstat space is the native functional subject space, then you should use 
bbregister and specify the example_func as the template.
doug

kelsi wrote:
> Hi all,
>
> I would like to convert a nifti zstat file from post-processing 
> analysis to a surface to plot/view in freeview on the fsaverage or 
> MNI152 brain.  I think I would use mri_vol2surf, but I am not sure 
> about the registration file.  Would i need to run tkregister first?
>
> thank you!
> kelsi
> 
>
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-- 
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

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Re: [Freesurfer] MNI152 template regions

[Douglas N Greve]

Hi Paolo, I don't think we have have any tools to apply a matrix to a 
trk file. Or maybe I'm wrong?
doug

paolo wrote:
> Bruce, Doug, Thomas, thank you so much, things are getting slowly
> clearer now 
>
> I can try to explain better what i want to do, so that perhaps
> it will be easier for you too to tell what is the best way
> to approach this problem
>
> essentially we have a number of subjects, with already extracted
> white matter fiber tracts (in .trk format)
> The idea was to transform these  fibers back to freesurfer space (is
> it the talairach space? in any case, is this what happens by using the
> talairach.xfm matrix?), and then compare them in this space, as, i would
> guess, there is still some sort of deviation from the standard fiber
> pathway.
>
> Is this unreasonable?
>
> also, just for visualization purposes, i was thinking of rendering
> these fibers in their context, but the average brain is, as you point
> out, a bit too blurry.
> Would it make sense here to bring something like MNI152 into the
> freesurfer space, and use this one (and its segmentation) instead of the
> fsaverage as an illustrative atlas in freesurfer space?
>
> Paolo
>
>
>
> On Mon, 7 Nov 2011 11:41:46 -0500 (EST)
> Bruce Fischl  wrote:
>
>   
>> Hi Paolo,
>>
>> Are you showing individual subject data in the MNI space, or group
>> average data? In general showing template brains and average data is
>> not a good idea. It misrepresents the spatial localization accuracy
>> of the data. You should try to use averages of the anatomy for groups
>> of tracts of average fmri data or other group stats/data.
>>
>> cheers
>> Bruce
>>
>> On Mon, 7 Nov 2011, Paolo wrote:
>>
>> 
>>> I think it is well possible.
>>> And in principle i just wanted to use it for presentation, but the
>>> fsaverage doesnt really look like a "template" brain, rather like
>>> an average
>>>
>>> that's why i was wondering whether there is a more realistic
>>> template available in freesurfer space, or how i can create one
>>> (the idea was to recon-all the MNI152, which to me resembles much
>>> more to a brain)
>>>
>>> would it be the correct approach, or do you have other suggestions?
>>> by the way is it normal that recon-all on mni152 takes just ages to
>>> complete? (>12 hours on an athlon64, dont know exactly how long, i
>>> always stopped it before it finished)
>>>
>>> Paolo
>>>
>>>
>>> On 07-Nov-11 16:03, Thomas Yeo wrote:
>>>   
 I am probably wrong, but doesn't the volumetric part of fsaverage
 correspond to MNI305 space rather than MNI152 space?

 --Thomas

 On Mon, Nov 7, 2011 at 9:00 AM, Bruce
 Fischl  wrote:
 
> Hi Paolo,
>
> I think fsaverage has this in the aseg.mgz.
>
> cheers
> Bruce
> On Mon, 7 Nov 2011, Paolo wrote:
>
>   
>> In the meanwhile i did some research, and it looks like
>> freesurfer does not use MNI152 as default template, am i right?
>> it seems that the default template is the fsaverage subject,
>> which in fact does not look like very realistic.
>>
>>
>> Is there any way to get a realistic brain&  segmentation that is
>> "idealized" enough, and still in talairach space (freesurfer
>> space)?
>>
>> maybe the MNI152 after recon-all and mri_transform to apply back
>> the transformation?
>>
>> i am sorry if these questions look unreasonable, i am new of
>> freesurfer, and still have problem orienting myself in the
>> documentation :)
>>
>> best,
>> Paolo
>>
>> On 05-Nov-11 00:57, Paolo wrote:
>> 
>>> Hello
>>>
>>> I am a new user of freesurfer.
>>> I was wondering whether the brain regions for the MNI152
>>> dataset are available anywhere (i mean the template brain
>>> regions for the default MNI152 template).
>>>
>>>
>>> I have also another question: i have the dti fiber tracts
>>> extracted and computed and already in .trk format.
>>> I was wondering: to bring them back into the template MNI152
>>> space, is it sufficient to apply the talairach.xfm
>>> transformation matrix to the vertex data, or do i also need to
>>> use the m3z files (which look like a nonlinear deformation
>>> field)?
>>>
>>> thanks in advance!
>>> Paolo
>>>   
>
>
>
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> 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

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[Freesurfer] Question about tkmedit

[nooshin n.zade]

Dear Freesurfer Expers

I have installed FS on the new mini Mac today, it can open bert with
tkmedit and tksurfer.
Using tkmedit for seeing my subject in /Users/nzadeh/freesurfer/subjects,
it says
"cannot find subject N3237c in /Users/nzadeh/freesurfer/subjects or it is
not readable by you"
but when I get "ls", I see my subject in that directory, and with my old
Mac I can see that via tkmedit and tksurfer.
I think there are still problems for installation
Can you please advise me.
Thank you very much.

-- 

Best Regards
---
Nooshin N. Zadeh
Graduate Assistant

Departments of Electrical Engineering and Neurology
University of Miami
**
*
*
*
*
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[Freesurfer] Data Table

[Dusan Hirjak]

Dear Freesurfer experts,

I opened the table (qdec.table.dat) in a text editor and add a line at the end 
of the file. Then I tried to open the data table again. However, I received an 
automatic error message again: 
 
Number of columns: 286
fsid: column: 1
Number of factors: 285
Number of subjects: 0
ERROR: OdecDataTable::Load: number of subjects = 0
Error loading the data table. 

How should I solve this problem?

Thanks in advance!
 
 
Dusan
 

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Re: [Freesurfer] problem with skullstrip- shoulders and neck remaining

[Khoa Nguyen]

You can try running just recon-all -skullstrip first, if that doesn't fix 
the problem, you can try changing the wsthresh and removing the 
-no-wsgcaatlas flag (or add the flag if you didn't include it). Sometimes 
that makes a difference.

-Khoa

On Wed, 9 Nov 2011, Julia Hill wrote:

> Hi there,
>
> I am having difficulties with one of my images. On first inspection, 
> freesurfer had performed a bad skull strip, leaving the base of the skull 
> plus what looked to be the shoulders and neck. I decreased the watershed to 
> 5, and the shoulders/neck still appeared, so i decreased to 2 and now 
> sections of the brain have disappeared (see attached), do you know how i can 
> fix this?
>
> Many thanks ,
>
>
>
>
>
>
>
> Julia Hill
> Research Assistant
> School of Psychiatry
> University of New South Wales
>
>
>
>
>
> Previously Prince of Wales Medical Research Institute
> www.NeuRA.edu.au
> Barker Street Randwick Sydney NSW 2031 Australia
> PO Box 1165 Randwick Sydney NSW 2031 Australia
> T +61 2 9399 1268
>
>
>
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Re: [Freesurfer] Resize window using Tcl command

[Jonca, Jacek]

Jeff,

While resize window does not work when invoked through a tcl flag there is a 
manual way to bypass it. After you open tksurfer move back from the GUI to the 
tksurfer terminal window and paste your tcl script there. Not nearly as 
convenient as the tcl flag execution but it is the only solution I found to 
work.

Greetings,

Jacek Jońca-Jasiński


[cid:image001.png@01CC9ECF.8FA6E480]


Jacek Jońca-Jasiński, Ph.D.|The Graduate School|Texas Tech 
University
Holden Hall  Room 03   |Box 1030   |   Lubbock, TX 79409-1030
ph.: 806.742.2787|fax: 806.742.4038|
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From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Jeff Sadino
Sent: Monday, November 07, 2011 9:15 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Resize window using Tcl command

Hello,

I was wondering if there is a Tcl command to resize the window.  I saw this 
thread, but it would not work on my computer, and I don't see any documentation 
in the tkmedit tcl scripting guide.

http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg02600.html

Thank you,
Jeff Sadino
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[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
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Re: [Freesurfer] color scale interpretation retinotopy eccen maps

[Douglas N Greve]

Nothing that is easy to do. You can try it in matlab. Another thing you 
can do is to convert the label into a binary mask in a "volume" format 
(eg, mgh or nifti) with mri_label2labe (using the --outmask option). Do 
this for both of your labels, then use fscalc to compute an "and" of the 
masks. You can view this mask in tksurfer by loading it as an overlay 
with a threshold of 0.5 (-fthresh 0.5). This could also be converted 
back to an annotation with mris_seg2annot.

doug

Erhan Genc wrote:
> Hi Doug,
>
> thanks a lot it worked for the eccen maps. I have now my eccen of interest...
> Is there a command to make a intersection area between two labels? I
> just found the command mri_mergelabels which merge two labels into a
> bigger one.
>
> cheers,
>
> Erhan
>
> 2011/11/1 Douglas N Greve :
>   
>> If you run something like this:
>> tksurfer-sess -a rtopy.self.lh -s sessid -map angle
>> it will show you the angle in radians (I think). Thresholding this map is
>> going to be tricky in tksurfer (can't remove things above a value). An
>> alternative is to run mri_binarize on the angle file itself. mri_biniarize
>> allows you to set upper and lower thresholds. You can then run tksurfer on
>> the result.
>> doug
>>
>> Erhan Genc wrote:
>> 
>>> Hi Doug,
>>>
>>> I see. My eccen run has 8 cycles of an expanding ring and each cycle
>>> take about 64 sec. So in general the color "red" would show the
>>> average of the 8 cycles for the first let say 10 sec. I know from my
>>> protocol which eccen (1°-12° per hemisphere) was shown when, but how
>>> can I exactly find a area of a specific eccentricity on my surfce
>>> without using the color wheel?
>>>
>>> I just would like to draw a label consisting 1°-5° in the visual field.
>>>
>>> Can you recommend me another strategy?
>>>
>>> Best,
>>>
>>> Erhan
>>>
>>> 2011/11/1 Douglas N Greve :
>>>
>>>   
 Hi Erhan, the results are collapsed across all time points, so no color
 represents a particular time point. The colors in the color wheel are
 hard
 to interpret, which is why I recommend against using the color wheel. If
 you
 click on  a point, I believe the value (phase) will be displayed in the
 control panel.
 doug

 Erhan Genc wrote:

 
> Dear freessurfer experts,
>
> I created my polar und eccen maps using the retinotopy pipeline. I
> also visualize them using the the rtview command on the inflated
> surface. But how can I interpret the colors (red to blue in the RYGB
> Wheel) in my eccen map? Which color refers to which timepoint (volume)
> of my functional run?
>
> Best,
>
> Erhan
>
>
>
>   
 --
 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



 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.



 
>>>
>>>
>>>   
>> --
>> 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
>>
>>
>> 
>
>
>
>   

-- 
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

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Re: [Freesurfer] Fwhm from mgh file produced by mri_glmfit

[Douglas N Greve]

No, it is computed from the residuals.
doug

Knut J Bjuland wrote:
> Hi 
>
> Is there any way to get fwhm information from an mgh produced by 
> mri_glmfit? I have only the mgh file produce by mri_glmfit.
>
>
> Knut J 
> 
>
> ___
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-- 
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

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Re: [Freesurfer] End-of-line detection in text file

[Rudolph Pienaar]

On 11/9/11 09:49 , Rudolph Pienaar wrote:
>
> sed 's/0xd/xoa/' file1.txt > file2.txt
>
   sed 's/0xd/x0a/' file1.txt > file2.txt

Oops... critical typo.



-- 
Rudolph Pienaar, M.Eng, D.Eng / email: rudo...@nmr.mgh.harvard.edu
MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging
149 (2301) 13th Street, Charlestown, MA 02129 USA
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Re: [Freesurfer] End-of-line detection in text file

[Rudolph Pienaar]

On 11/9/11 09:36 , Ed Gronenschild wrote:
> Hi Rudolph,
>
> I used TextEdit. On a Mac with OS version earlier than OS10.6
> this problem didn't occur. With TextEdit it is not possible to save
> as UNIX format.
> Thanks for the trick to use sed.
>
> Ed
>

I'm not a great fan of the built in 'TextEdit'. That having been said, 
did you check under its preferences and make sure that it is setup as 
'plain text' and not 'rich text'? I just tested on my TextEdit (Lion, 
10.7.2) and it saved in  and not  convention.

You might try 'aquamacs' on the Mac... assuming you're an emacs-ish type 
person. It works reasonably well. Another editor is "TextWrangler" 
(available in the Mac OSX App Store for free).  If you look in its 
preferences, under "Text Files" there is an explicit option to save as 
"Classic Mac, UNIX, or Windows". The default is "UNIX".

Oh, and make sure that the 's/x0d/x0a/' are enclosed in single quotes. I 
see that my copy-paste in the earlier email somehow lost the quotes. If 
you have a file called "file1.txt" and want to do the / sub and 
save to "file2.txt", the exact command is

sed 's/0xd/xoa/' file1.txt > file2.txt

HTH


-- 
Rudolph Pienaar, M.Eng, D.Eng / email: rudo...@nmr.mgh.harvard.edu
MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging
149 (2301) 13th Street, Charlestown, MA 02129 USA
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Re: [Freesurfer] End-of-line detection in text file

[Ed Gronenschild]

Hi Rudolph,

I used TextEdit. On a Mac with OS version earlier than OS10.6
this problem didn't occur. With TextEdit it is not possible to save
as UNIX format.
Thanks for the trick to use sed.

Ed

On 9 Nov 2011, at 15:27, Rudolph Pienaar wrote:

> On 11/9/11 07:59 , Ed Gronenschild wrote:
>> 
>> After editing a text file holding the b vecs to be supplied
>> as input to dt_recon this tool did not interpret the text
>> file correctly. It turned out that dt_recon did not recognise
>> the end-of line character in this file: this was decimal
>> code 13 (called "CR"). It seems that dt_recon only
>> accepts decimal code 10 (called "LF").
>> Is it possible to change dt_recon?
>> 
>> 
> What did you use to edit the b-vec file? Different operating systems use 
> different end-of-line (EOL) conventions on text files:
> 
> Windows:  
> "Old"-style (and largely depreciated) Mac: 
> Unix (including Mac and Linux): 
> 
> My guess is that you might have used a (possibly old) Mac-based editor to 
> edit your file. Often such editors have the option to save as "UNIX" format. 
> Choose that.
> 
> It's not necessary to change 'dt_recon'. Simply convert your old-style Mac 
>  text file to a new style  file with:
> 
>sed s/x0d/x0a/ old-b-vec-file > new-b-vec-file
> This replaces the '0x0d' (10 in hex) characters in the file with '0x0a' (13 
> in hex). 
> 
> For more details, see: 
> http://www.peterbenjamin.com/seminars/crossplatform/texteol.html
> 
> 
> 
> -- 
> Rudolph Pienaar, M.Eng, D.Eng / email: rudo...@nmr.mgh.harvard.edu
> MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging
> 149 (2301) 13th Street, Charlestown, MA 02129 USA
> 
> 
> The information in this e-mail is intended only for the person to whom it is
> addressed. If you believe this e-mail was sent to you in error and the e-mail
> contains patient information, please contact the Partners Compliance HelpLine 
> at
> http://www.partners.org/complianceline . If the e-mail was sent to you in 
> error
> but does not contain patient information, please contact the sender and 
> properly
> dispose of the e-mail.

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Re: [Freesurfer] End-of-line detection in text file

[Rudolph Pienaar]

On 11/9/11 07:59 , Ed Gronenschild wrote:

After editing a text file holding the b vecs to be supplied
as input to dt_recon this tool did not interpret the text
file correctly. It turned out that dt_recon did not recognise
the end-of line character in this file: this was decimal
code 13 (called "CR"). It seems that dt_recon only
accepts decimal code 10 (called "LF").
Is it possible to change dt_recon?


What did you use to edit the b-vec file? Different operating systems use 
different end-of-line (EOL) conventions on text files:


Windows: 
"Old"-style (and largely depreciated) Mac: 
Unix (including Mac and Linux): 

My guess is that you might have used a (possibly old) Mac-based editor 
to edit your file. Often such editors have the option to save as "UNIX" 
format. Choose that.


It's not necessary to change 'dt_recon'. Simply convert your old-style 
Mac  text file to a new style  file with:


  sed s/x0d/x0a/ old-b-vec-file>  new-b-vec-file

This replaces the '0x0d' (10 in hex) characters in the file with '0x0a' 
(13 in hex).


For more details, see: 
http://www.peterbenjamin.com/seminars/crossplatform/texteol.html




--
Rudolph Pienaar, M.Eng, D.Eng / email: rudo...@nmr.mgh.harvard.edu
MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging
149 (2301) 13th Street, Charlestown, MA 02129 USA

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[Freesurfer] End-of-line detection in text file

[Ed Gronenschild]

Hi,

After editing a text file holding the b vecs to be supplied
as input to dt_recon this tool did not interpret the text
file correctly. It turned out that dt_recon did not recognise
the end-of line character in this file: this was decimal
code 13 (called "CR"). It seems that dt_recon only
accepts decimal code 10 (called "LF").
Is it possible to change dt_recon?

I'm on a Mac, OSX 10.6.8.

Cheers,
Ed
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[Freesurfer] Fwhm from mgh file produced by mri_glmfit

[Knut J Bjuland]

Hi 
Is there any way to get fwhm information from an mgh produced by mri_glmfit? I 
have only the mgh file produce by mri_glmfit.

Knut J___
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Re: [Freesurfer] color scale interpretation retinotopy eccen maps

[Erhan Genc]

Hi Doug,

thanks a lot it worked for the eccen maps. I have now my eccen of interest...
Is there a command to make a intersection area between two labels? I
just found the command mri_mergelabels which merge two labels into a
bigger one.

cheers,

Erhan

2011/11/1 Douglas N Greve :
> If you run something like this:
> tksurfer-sess -a rtopy.self.lh -s sessid -map angle
> it will show you the angle in radians (I think). Thresholding this map is
> going to be tricky in tksurfer (can't remove things above a value). An
> alternative is to run mri_binarize on the angle file itself. mri_biniarize
> allows you to set upper and lower thresholds. You can then run tksurfer on
> the result.
> doug
>
> Erhan Genc wrote:
>>
>> Hi Doug,
>>
>> I see. My eccen run has 8 cycles of an expanding ring and each cycle
>> take about 64 sec. So in general the color "red" would show the
>> average of the 8 cycles for the first let say 10 sec. I know from my
>> protocol which eccen (1°-12° per hemisphere) was shown when, but how
>> can I exactly find a area of a specific eccentricity on my surfce
>> without using the color wheel?
>>
>> I just would like to draw a label consisting 1°-5° in the visual field.
>>
>> Can you recommend me another strategy?
>>
>> Best,
>>
>> Erhan
>>
>> 2011/11/1 Douglas N Greve :
>>
>>>
>>> Hi Erhan, the results are collapsed across all time points, so no color
>>> represents a particular time point. The colors in the color wheel are
>>> hard
>>> to interpret, which is why I recommend against using the color wheel. If
>>> you
>>> click on  a point, I believe the value (phase) will be displayed in the
>>> control panel.
>>> doug
>>>
>>> Erhan Genc wrote:
>>>

 Dear freessurfer experts,

 I created my polar und eccen maps using the retinotopy pipeline. I
 also visualize them using the the rtview command on the inflated
 surface. But how can I interpret the colors (red to blue in the RYGB
 Wheel) in my eccen map? Which color refers to which timepoint (volume)
 of my functional run?

 Best,

 Erhan



>>>
>>> --
>>> 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
>>>
>>>
>>>
>>> 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.
>>>
>>>
>>>
>>
>>
>>
>>
>
> --
> 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
>
>



-- 
Dipl. Psych. Erhan Genc
Max Planck Institute for Brain Research
Department of Neurophysiology
Deutschordenstr. 46
60528 Frankfurt am Main
-GERMANY-
phone:  +49 (69) 96769-471
fax:    +49 (69) 96769-327
e-mail: g...@mpih-frankfurt.mpg.de

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