Re: [Freesurfer] extracting mean thickness values across subjects from qdec clusters

[Tudor Popescu]

Thanks Doug, I've FileDropped you the zip. Running FS 5.3.0 on Virtualbox
4.2.12 (Ubuntu guest, Windows host)
T


On 4 April 2014 22:09, Douglas N Greve  wrote:

>
> Can you upload the y.mgh file and fsgd file so that I can try to replicate
> it? What platform are you running on and what version of FS?
> doug
>
>
> On 04/02/2014 06:34 PM, Tudor Popescu wrote:
>
>> Hi Doug
>> Sorry, again I wasn't sure whether you'd noticed my reply amonst the
>> latest list messages. Hopefully there is a fix for this error.
>> Thanks
>> Tudor
>>
>>
>> On 2 April 2014 12:33, Tudor Popescu > tud...@gmail.com>> wrote:
>>
>>
>>
>> Your mri_glmfit-sim command line is not correct and
>> does not match
>> examples in the help. Basically you need to spec
>> "--cache 1.3 abs"
>> not "--cache 1.3 --sim-sign abs"
>>
>> Thanks Doug, now it worked, however I'm getting this
>> error, which several other people seem to get: "Computing
>> spatial average of each frame
>>   0  1  2*** glibc detected *** mri_segstats: malloc():
>> memory corruption: 0x2e8df328 ***". I am running FS 5.3.0
>> through VirtualBox, 2GB ram allocated.
>>
>> What is your full command line? Sometimes this happens when
>> setting the cwp to 1 (or close to 1).
>>
>>
>> My command was
>>  mri_glmfit-sim --glmdir
>> /media/math/all38subj/qdec/A2SepGroup_C_DODS_lgi_lh --cache 1.3 abs
>> therefore I did not change the --cwpvalthresh input argument,
>> meaning cwp presumably stayed at its default of .05.
>> Terminal output is attached.
>> What else can I try to make this command work?
>>
>>
>>
> --
> 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: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
>
>
> 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
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> contains patient information, please contact the Partners Compliance
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Re: [Freesurfer] Create a label from a binary mask

[Douglas N Greve]

Try this first
mri_cor2label --c aseg.mgz --id 17 --l lh.hippo.label
Then load lh.hippo.label

If wramygdala.R.001.nii is not in the conformed space, your command will 
not work

On 04/04/2014 05:17 PM, Cherisse Onuigbo wrote:
> mri_cor2label --c wramygdala.R.001.nii --id 1 --l wramygdala.R.001.label
> tkmedit Subjects_for_Cherisse/S001 T1.mgz -aux brainmask.mgz -seg aseg.mgz
>
> And then I added the label using the drop down menu.
> On Friday, April 4, 2014 3:45 PM, Douglas N Greve 
>  wrote:
>
> What were your mri_cor2label and tkmedit command lines? SPM will never
> work properly for what you are trying to do.
>
> On 04/04/2014 04:42 PM, Cherisse Onuigbo wrote:
> > I first checked it in tkmedit, but I didn't see the region in green as
> > I went through the slices. I also put another label in there just to
> > check if I was displaying labels correctly and others showed up. Then
> > I used the display function in spm and input the coordinates there,
> > but it showed that the coordinates were outside the region. Also I was
> > wondering why in the label file, all of the vertex id's are -1 instead
> > of what I specify in the command.
> > On Friday, April 4, 2014 3:08 PM, Douglas N Greve
> > mailto:gr...@nmr.mgh.harvard.edu>> wrote:
> >
> > How are you checking the vertex coordinates? You can't use SPM, you'll
> > have to use tkmedit or freeview
> >
> > On 04/04/2014 04:04 PM, Cherisse Onuigbo wrote:
> > > My mask is a volume mask. When I run the function normally, the
> > > vertices that are in the text file do not fall in the region of my 
> mask.
> > > On Friday, April 4, 2014 2:28 PM, Douglas N Greve
> > > mailto:gr...@nmr.mgh.harvard.edu> 
> >> 
> wrote:
> > >
> > > Hi Cherisse, i don't understand what you have done. Is the mask a 
> volume
> > > mask or surface mask? In mri_cor2label, you can specify a surface 
> to get
> > > surface vertex numbers.
> > >
> > > doug
> > >
> > > On 04/02/2014 07:03 PM, Cherisse Onuigbo wrote:
> > > > Hello
> > > >
> > > > I was wondering how to create a label from a binary mask. I 
> created a
> > > > mask and then normalized it to the template space. When I tried 
> to use
> > > > mri_cor2vol, all the vertex numbers come out as -1. I understand 
> that
> > > > the vertex numbers should come out as -1, but when I entered the
> > > > coordinates in the display function in spm, it was not in the 
> region.
> > > >
> > > > Thank you,
> > > > Cherisse
> > >
> > > >
> > > >
> > > > ___
> > > > 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: https://gate.nmr.mgh.harvard.edu/filedrop2
> > > www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> > > Outgoing: 
> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
> > >
> > > ___
> > > 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://

Re: [Freesurfer] Create a label from a binary mask

[Cherisse Onuigbo]

mri_cor2label --c wramygdala.R.001.nii --id 1 --l wramygdala.R.001.label
tkmedit Subjects_for_Cherisse/S001 T1.mgz -aux brainmask.mgz -seg aseg.mgz

And then I added the label using the drop down menu.
On Friday, April 4, 2014 3:45 PM, Douglas N Greve  
wrote:
 

What were your mri_cor2label and tkmedit command lines? SPM will never 
work properly for what you are trying to do.

On 04/04/2014 04:42 PM, Cherisse Onuigbo wrote:
> I first checked it in tkmedit, but I didn't see the region in green as 
> I went through the slices. I also put another label in there just to 
> check if I was displaying labels correctly and others showed up. Then 
> I used the display function in spm and input the coordinates there, 
> but it showed that the coordinates were outside the region. Also I was 
> wondering why in the label file, all of the vertex id's are -1 instead 
> of what I specify in the command.
> On Friday, April 4, 2014 3:08 PM, Douglas N Greve 
>  wrote:
>
> How are you checking the vertex coordinates? You can't use SPM, you'll
> have to use tkmedit or freeview
>
> On 04/04/2014 04:04 PM, Cherisse Onuigbo wrote:
> > My mask is a volume mask. When I run the function normally, the
> > vertices that are in the text file do not fall in the region of my mask.
> > On Friday, April 4, 2014 2:28 PM, Douglas N Greve
> > mailto:gr...@nmr.mgh.harvard.edu>> wrote:
> >
> > Hi Cherisse, i don't understand what you have done. Is the mask a volume
> > mask or surface mask? In mri_cor2label, you can specify a surface to get
> > surface vertex numbers.
> >
> > doug
> >
> > On 04/02/2014 07:03 PM, Cherisse Onuigbo wrote:
> > > Hello
> > >
> > > I was wondering how to create a label from a binary mask. I created a
> > > mask and then normalized it to the template space. When I tried to use
> > > mri_cor2vol, all the vertex numbers come out as -1. I understand that
> > > the vertex numbers should come out as -1, but when I entered the
> > > coordinates in the display function in spm, it was not in the region.
> > >
> > > Thank you,
> > > Cherisse
> >
> > >
> > >
> > > ___
> > > 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: https://gate.nmr.mgh.harvard.edu/filedrop2
> > www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
> >
> > ___
> > 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
>
> -- 
> 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: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
> ___
> 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

-- 
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: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html

Re: [Freesurfer] Create a label from a binary mask

[Douglas N Greve]

What were your mri_cor2label and tkmedit command lines? SPM will never 
work properly for what you are trying to do.

On 04/04/2014 04:42 PM, Cherisse Onuigbo wrote:
> I first checked it in tkmedit, but I didn't see the region in green as 
> I went through the slices. I also put another label in there just to 
> check if I was displaying labels correctly and others showed up. Then 
> I used the display function in spm and input the coordinates there, 
> but it showed that the coordinates were outside the region. Also I was 
> wondering why in the label file, all of the vertex id's are -1 instead 
> of what I specify in the command.
> On Friday, April 4, 2014 3:08 PM, Douglas N Greve 
>  wrote:
>
> How are you checking the vertex coordinates? You can't use SPM, you'll
> have to use tkmedit or freeview
>
> On 04/04/2014 04:04 PM, Cherisse Onuigbo wrote:
> > My mask is a volume mask. When I run the function normally, the
> > vertices that are in the text file do not fall in the region of my mask.
> > On Friday, April 4, 2014 2:28 PM, Douglas N Greve
> > mailto:gr...@nmr.mgh.harvard.edu>> wrote:
> >
> > Hi Cherisse, i don't understand what you have done. Is the mask a volume
> > mask or surface mask? In mri_cor2label, you can specify a surface to get
> > surface vertex numbers.
> >
> > doug
> >
> > On 04/02/2014 07:03 PM, Cherisse Onuigbo wrote:
> > > Hello
> > >
> > > I was wondering how to create a label from a binary mask. I created a
> > > mask and then normalized it to the template space. When I tried to use
> > > mri_cor2vol, all the vertex numbers come out as -1. I understand that
> > > the vertex numbers should come out as -1, but when I entered the
> > > coordinates in the display function in spm, it was not in the region.
> > >
> > > Thank you,
> > > Cherisse
> >
> > >
> > >
> > > ___
> > > 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: https://gate.nmr.mgh.harvard.edu/filedrop2
> > www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
> >
> > ___
> > 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
>
> -- 
> 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: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
> ___
> 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

-- 
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: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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Re: [Freesurfer] Create a label from a binary mask

[Cherisse Onuigbo]

I first checked it in tkmedit, but I didn't see the region in green as I went 
through the slices. I also put another label in there just to check if I was 
displaying labels correctly and others showed up. Then I used the display 
function in spm and input the coordinates there, but it showed that the 
coordinates were outside the region. Also I was wondering why in the label 
file, all of the vertex id's are -1 instead of what I specify in the command.
On Friday, April 4, 2014 3:08 PM, Douglas N Greve  
wrote:
 

How are you checking the vertex coordinates? You can't use SPM, you'll 
have to use tkmedit or freeview

On 04/04/2014 04:04 PM, Cherisse Onuigbo wrote:
> My mask is a volume mask. When I run the function normally, the 
> vertices that are in the text file do not fall in the region of my mask.
> On Friday, April 4, 2014 2:28 PM, Douglas N Greve 
>  wrote:
>
> Hi Cherisse, i don't understand what you have done. Is the mask a volume
> mask or surface mask? In mri_cor2label, you can specify a surface to get
> surface vertex numbers.
>
> doug
>
> On 04/02/2014 07:03 PM, Cherisse Onuigbo wrote:
> > Hello
> >
> > I was wondering how to create a label from a binary mask. I created a
> > mask and then normalized it to the template space. When I tried to use
> > mri_cor2vol, all the vertex numbers come out as -1. I understand that
> > the vertex numbers should come out as -1, but when I entered the
> > coordinates in the display function in spm, it was not in the region.
> >
> > Thank you,
> > Cherisse
>
> >
> >
> > ___
> > 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: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
> ___
> 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

-- 
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: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

___
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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] Mac OSX installations incomplete? What to do?

[Markus Gschwind]

Thank you Zeke,

What about these?

/usr/local/freesurfer/bin/bet.fsl
/usr/local/freesurfer/bin/flirt.fsl
/usr/local/freesurfer/bin/slicetimer.fsl

They are not there neither compared to the ubuntu install.

Best,
Markus




2014-04-04 19:05 GMT+02:00 Z K :

> There are 3 missing fsl files from the OSX snow leopard installation.
> They can be downloaded from here:
>
> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/fsdev/zkaufman/fsl
>
> Copy them into your "$FREESURFER_HOME/bin" directory.
>
> -Zeke
>
>
>
> On 04/04/2014 12:32 PM, Markus Gschwind wrote:
> > Dear Freesurfers,
> >
> > As discovered here,
> >
> > http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg35160.html
> >
> > it seams that some Mac OSX installations suffered from incomplete files.
> >
> > I just veryfied that I had downloaded the complete image and wget says
> yes:
> >
> > Logging in as anonymous ... Logged in!
> > ==> SYST ... done.==> PWD ... done.
> > ==> TYPE I ... done.  ==> CWD (1) /pub/dist/freesurfer/5.3.0 ...
> done.
> > ==> SIZE freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0.dmg
> > ... 3394499614
> > File has already been retrieved.
> > 2014-04-04 18:24:26 (0.00 B/s) -
> > 'freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0.dmg' saved
> > [3394499614]
> >
> >
> > So this is what I installed recently and it seems that there are some
> > files missing (at least some of the fsl-functions in bin).
> >
> > Doug, you said that you suspected that it could be a problem of the
> > installer script?
> >
> > What should we do (also Eiran) in order to complete the installation?
> >
> > Thanks for you work!
> > Markus
> >
> >
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Re: [Freesurfer] TRACULA longitudinal stream - length of Center variable

[Anastasia Yendiki]

Hi Vincent - Overall measures for the whole tract would not be affected 
by this type of error.

a.y

On Fri, 4 Apr 2014, Vincent Brunsch wrote:

> Great, thank you!
>
> Do you maybe know if these changes will only affect the "center
> variables"? I have almost completed my soon-due report about the
> longitudinal analysis of "weighted average variables" (overall not
> byvoxel along the MAP) and now I fear that results are maybe not correct
> because after all the MAP is a part of all sampled paths.
>
> Best, Vincent
>
> Am 4/4/2014 11:49 AM, schrieb Anastasia Yendiki:
>> Hi Vincent - I suspect that this problem would be fixed by some recent
>> changes that I've implemented for the longitudinal stream of tracula, and
>> that I'm in the process of testing. As soon as we can get a new dev
>> version built, I'll let you know so you can test it.
>>
>> Thank you for your patience!
>>
>> a.y
>>
>> On Fri, 4 Apr 2014, Vincent Brunsch wrote:
>>
>>> Dear TRACULA experts,
>>>
>>> I have used the longitudinal version and find that for some subjects'
>>> tracts Len_Min is larger than Len_Center. How is this possible? (An
>>> extreme example is Len_Min: 36, Len_Max: 75, Len_Center: 4.)
>>>
>>> Best, Vincent
>>>
>>> ---
>>> This email is free from viruses and malware because avast! Antivirus 
>>> protection is active.
>>> http://www.avast.com
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>>>
>>>
>>>
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>>
>
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Re: [Freesurfer] extracting mean thickness values across subjects from qdec clusters

[Douglas N Greve]

Can you upload the y.mgh file and fsgd file so that I can try to 
replicate it? What platform are you running on and what version of FS?
doug

On 04/02/2014 06:34 PM, Tudor Popescu wrote:
> Hi Doug
> Sorry, again I wasn't sure whether you'd noticed my reply amonst the 
> latest list messages. Hopefully there is a fix for this error.
> Thanks
> Tudor
>
>
> On 2 April 2014 12:33, Tudor Popescu  > wrote:
>
>
>
> Your mri_glmfit-sim command line is not correct and
> does not match
> examples in the help. Basically you need to spec
> "--cache 1.3 abs"
> not "--cache 1.3 --sim-sign abs"
>
> Thanks Doug, now it worked, however I'm getting this
> error, which several other people seem to get: "Computing
> spatial average of each frame
>   0  1  2*** glibc detected *** mri_segstats: malloc():
> memory corruption: 0x2e8df328 ***". I am running FS 5.3.0
> through VirtualBox, 2GB ram allocated.
>
> What is your full command line? Sometimes this happens when
> setting the cwp to 1 (or close to 1).
>
>
> My command was
>  mri_glmfit-sim --glmdir
> /media/math/all38subj/qdec/A2SepGroup_C_DODS_lgi_lh --cache 1.3 abs
> therefore I did not change the --cwpvalthresh input argument,
> meaning cwp presumably stayed at its default of .05.
> Terminal output is attached.
> What else can I try to make this command work?
>
>

-- 
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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

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Re: [Freesurfer] TRACULA longitudinal stream - length of Center variable

[Vincent Brunsch]

Great, thank you!

Do you maybe know if these changes will only affect the "center 
variables"? I have almost completed my soon-due report about the 
longitudinal analysis of "weighted average variables" (overall not 
byvoxel along the MAP) and now I fear that results are maybe not correct 
because after all the MAP is a part of all sampled paths.

Best, Vincent

Am 4/4/2014 11:49 AM, schrieb Anastasia Yendiki:
> Hi Vincent - I suspect that this problem would be fixed by some recent
> changes that I've implemented for the longitudinal stream of tracula, and
> that I'm in the process of testing. As soon as we can get a new dev
> version built, I'll let you know so you can test it.
>
> Thank you for your patience!
>
> a.y
>
> On Fri, 4 Apr 2014, Vincent Brunsch wrote:
>
>> Dear TRACULA experts,
>>
>> I have used the longitudinal version and find that for some subjects'
>> tracts Len_Min is larger than Len_Center. How is this possible? (An
>> extreme example is Len_Min: 36, Len_Max: 75, Len_Center: 4.)
>>
>> Best, Vincent
>>
>> ---
>> This email is free from viruses and malware because avast! Antivirus 
>> protection is active.
>> http://www.avast.com
>>
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>>
>>
>>
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Re: [Freesurfer] Create a label from a binary mask

[Douglas N Greve]

How are you checking the vertex coordinates? You can't use SPM, you'll 
have to use tkmedit or freeview

On 04/04/2014 04:04 PM, Cherisse Onuigbo wrote:
> My mask is a volume mask. When I run the function normally, the 
> vertices that are in the text file do not fall in the region of my mask.
> On Friday, April 4, 2014 2:28 PM, Douglas N Greve 
>  wrote:
>
> Hi Cherisse, i don't understand what you have done. Is the mask a volume
> mask or surface mask? In mri_cor2label, you can specify a surface to get
> surface vertex numbers.
>
> doug
>
> On 04/02/2014 07:03 PM, Cherisse Onuigbo wrote:
> > Hello
> >
> > I was wondering how to create a label from a binary mask. I created a
> > mask and then normalized it to the template space. When I tried to use
> > mri_cor2vol, all the vertex numbers come out as -1. I understand that
> > the vertex numbers should come out as -1, but when I entered the
> > coordinates in the display function in spm, it was not in the region.
> >
> > Thank you,
> > Cherisse
>
> >
> >
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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
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>
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> addressed. If you believe this e-mail was sent to you in error and the 
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Re: [Freesurfer] Create a label from a binary mask

[Cherisse Onuigbo]

My mask is a volume mask. When I run the function normally, the vertices that 
are in the text file do not fall in the region of my mask.
On Friday, April 4, 2014 2:28 PM, Douglas N Greve  
wrote:
 

Hi Cherisse, i don't understand what you have done. Is the mask a volume 
mask or surface mask? In mri_cor2label, you can specify a surface to get 
surface vertex numbers.

doug


On 04/02/2014 07:03 PM, Cherisse Onuigbo wrote:
> Hello
>
> I was wondering how to create a label from a binary mask. I created a 
> mask and then normalized it to the template space. When I tried to use 
> mri_cor2vol, all the vertex numbers come out as -1. I understand that 
> the vertex numbers should come out as -1, but when I entered the 
> coordinates in the display function in spm, it was not in the region.
>
> Thank you,
> Cherisse
>
>
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> Freesurfer@nmr.mgh.harvard.edu
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-- 
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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

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Re: [Freesurfer] Converting a volume from MNI152 to subject space

[Douglas N Greve]

Hi Omar, there is a bug in that version off mni152reg. Use the version 
in dev instead
doug

On 04/03/2014 03:50 PM, Omar Singleton wrote:
> Hi Freesurfers,
>
> I am trying to convert a volume from MNI152 to subject space. I tried to
> do what this previous question suggested:
>
> https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2013-December/034722.html
>
> I tried to create a registration matrix from subject space to MNI152:
>
> mni152reg --s AL15
>
> However, this error appeared:
>
> ...
> mkdir: cannot create directory
> `/usr/pubsw/packages/fsl/current/data/standard/tmp.fslregister.28345':
> Permission denied
> ...
> writing to
> /usr/pubsw/packages/fsl/current/data/standard/tmp.fslregister.28345/refvol.fslregister.nii...
> ERROR: failure writing
> /usr/pubsw/packages/fsl/current/data/standard/tmp.fslregister.28345/refvol.fslregister.nii
>
>
> I would then have used this command:
>
> mri_label2vol --seg lh.AItou.nii.gz --reg
> AL15/mri/transforms/reg.mni152.2mm.dat --invertmtx --o
> lh.aitou.AL15.nii.gz --temp AL15/mri/orig.mgz
>
> How can I make the mni152reg command work? Is this the correct way to do
> this?
>
> Thanks!
>
> Best,
> Omar
>
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Re: [Freesurfer] Displaying parcellated ROI in color but remainder of brain in grey

[Douglas N Greve]

This is a question for Ruopeng (who is the author of freeview, and 
cc'ed). Can you upload the subject and the annot file so that he can 
replicate the problem?
doug

On 04/03/2014 06:55 PM, Laura Taylor wrote:
> Hi Again Doug,
>
> I was able to get what I was looking for after I modified my ctab file 
> slightly and used tksurfer instead of freeview to display the images.  
> I am hoping, however, that it is still possible to get things to work 
> in freeview.
>
> For the ctab file, I put my 6 parcellated ROI's at the start of the 
> ctab file and numbered them 1 to 6.  I numbered the remaining regions 
> 7-75.
>
> In freeview the ROI's were in color but the remainder of the brain was 
> black (not what I wanted).  However in tksurfer, everything looked 
> good (brain in grey and ROI's in different colors).
>
> Do you think it would be possible to display these images properly in 
> freeview as well?
>
> Thank you very much for your time,
>
> Laura
>
>
> On Wed, Apr 2, 2014 at 10:05 AM, Laura Taylor 
> mailto:taylor.cnos@gmail.com>> wrote:
>
> Hi Doug,
>
> Thank you for your reply.
>
> This was my mris_label2annot command line:
>
> woodward@Bambi:~$ mris_label2annot --s TGT_N61AvgSubject --h rh
> --ctab
> 
> /Data/freesurfer/subjects/TGT_N61AvgSubject/label/aparc.annot.a2009s_comp2RH.ctab
> --a Comp2RH_TGTN61_properGreyRH --l
> 
> /Data/freesurfer/subjects/TGT_N61AvgSubject/mri_annotation2label/rh.S_collat_transv_ant.label
> --l
> 
> /Data/freesurfer/subjects/TGT_N61AvgSubject/mri_annotation2label/rh.S_oc-temp_med_and_Lingual.label
> --l
> 
> /Data/freesurfer/subjects/TGT_N61AvgSubject/mri_annotation2label/rh.G_oc-temp_med-Lingual.label
> --l
> 
> /Data/freesurfer/subjects/TGT_N61AvgSubject/mri_annotation2label/rh.G_oc-temp_lat-fusifor.label
> --l
> 
> /Data/freesurfer/subjects//TGT_N61AvgSubject/mri_annotation2label/rh.S_occipital_ant.label
> --l
> 
> /Data/freesurfer/subjects/TGT_N61AvgSubject/mri_annotation2label/rh.S_temporal_inf.label
>
>
>
>
> This is the terminal output:
>
> Reading ctab
> 
> /Data/freesurfer/subjects/TGT_N61AvgSubject/label/aparc.annot.a2009s_comp2RH.ctab
> Number of ctab entries 76
>
> $Id: mris_label2annot.c,v 1.17 2011/03/02 00:04:32 nicks Exp $
> cwd /home/woodward
> cmdline mris_label2annot --s TGT_N61AvgSubject --h rh --ctab
> 
> /Data/freesurfer/subjects/TGT_N61AvgSubject/label/aparc.annot.a2009s_comp2RH.ctab
> --a Comp2RH_TGTN61_properGreyRH --l
> 
> /Data/freesurfer/subjects/TGT_N61AvgSubject/mri_annotation2label/rh.S_collat_transv_ant.label
> --l
> 
> /Data/freesurfer/subjects/TGT_N61AvgSubject/mri_annotation2label/rh.S_oc-temp_med_and_Lingual.label
> --l
> 
> /Data/freesurfer/subjects/TGT_N61AvgSubject/mri_annotation2label/rh.G_oc-temp_med-Lingual.label
> --l
> 
> /Data/freesurfer/subjects/TGT_N61AvgSubject/mri_annotation2label/rh.G_oc-temp_lat-fusifor.label
> --l
> 
> /Data/freesurfer/subjects//TGT_N61AvgSubject/mri_annotation2label/rh.S_occipital_ant.label
> --l
> 
> /Data/freesurfer/subjects/TGT_N61AvgSubject/mri_annotation2label/rh.S_temporal_inf.label
>
> sysname  Linux
> hostname Bambi
> machine  x86_64
> user woodward
>
> subject TGT_N61AvgSubject
> hemirh
> SUBJECTS_DIR /Data/freesurfer/subjects
> ColorTable
> 
> /Data/freesurfer/subjects/TGT_N61AvgSubject/label/aparc.annot.a2009s_comp2RH.ctab
> AnnotName  Comp2RH_TGTN61_properGreyRH
> nlables 6
> LabelThresh 0 0.00
> Loading /Data/freesurfer/subjects/TGT_N61AvgSubject/surf/rh.orig
>  1 8355711 G_and_S_frontomargin
>  2 8355711 G_and_S_occipital_inf
>  3 8355711 G_and_S_paracentral
>  4 8355711 G_and_S_subcentral
>  5 8355711 G_and_S_transv_frontopol
>  6 8355711 G_and_S_cingul-Ant
> Mapping unhit to unknown
> Found 154540 unhit vertices
> Writing annot to
> 
> /Data/freesurfer/subjects/TGT_N61AvgSubject/label/rh.Comp2RH_TGTN61_properGreyRH.annot
>
>
>
>
> colortab file:
> 
> /Data/freesurfer/subjects/TGT_N61AvgSubject/label/aparc.annot.a2009s_comp2RH.ctab
>
>  0  Unknown   0   0   00
>   1  G_and_S_frontomargin 127 127 127   0
>   2  G_and_S_occipital_inf127 127 127   0
>   3  G_and_S_paracentral  127 127 127   0
>   4  G_and_S_subcentral   127 127 127   0
>   5  G_and_S_transv_frontopol 127 127 127   0
>   6  G_and_S_cingul-Ant   127 127 127   0
>   7  G_and_S_cingul-Mid-Ant   127 127 127   0
>   8  G_and_S_cingul-Mid-Post  127 127 127   0
>   9  G_cingul-Post-dorsal 127 127 127   0
>  10  G_cingul-Post-ventral127 127 127   0
>  11  G_cuneus 127 127 127   0
>  12  G_front_inf-Opercular127 127 127   0
>  13  G_front_inf-Orb

Re: [Freesurfer] reading colorized labels in tcl file to tksurfer...

[Douglas N Greve]

You can use mris_label2annot to create an annotation and then control 
the colors via the ctab
doug

On 04/03/2014 09:13 AM, Rudolph Pienaar wrote:
> Hi all --
>
> I have a process that generates a list of ROIs (from aparc.annot) based
> on some cost condition. I wanted to view these labeled ROIs in
> 'tksurfer'. I created the following rough tcl script:
>
> 'label_load.tcl'
>
> set label lh.bankssts.label ; read_and_color_labeled_vertices 255 255 0
> set label lh.caudalanteriorcingulate.label ;
> read_and_color_labeled_vertices 255 255 10
> set label lh.caudalmiddlefrontal.label ; read_and_color_labeled_vertices
> 255 255 20
> set label lh.cuneus.label ; read_and_color_labeled_vertices 255 255 30
> set label lh.inferiorparietal.label ; read_and_color_labeled_vertices
> 255 255 40
> set label lh.lateraloccipital.label ; read_and_color_labeled_vertices
> 255 255 50
>
> and then ran with
>
>   tksurfer-tcl label_load.tcl
>
> The labels all load, but they are all the same teal-like color. I'm
> guessing that I am using the wrong tksurfer internal command... I have
> looked through the wiki, but didn't immediately see a solution.
>
> Help?
>
> Best
> -=R
>

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

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Re: [Freesurfer] Display tkmedit image of surface after mri_vol2surf with projfrac or projdist

[Douglas N Greve]

They are not exactly the same. However, if you run mri_vol2surf with 
--surf white50 --projfrac 0 it will be identical (where white50 is the 
surface create with mris_expand)

doug

On 04/04/2014 05:34 AM, Righart, Ruthger wrote:
> Hi Markus,
> Thank you, excellent tool and gives exactly what I was searching for!
> Is the resulting surface the same for mris_expand taken at 50% as the
> one that is used in mri_vol2surf with flag projfrac 0.5? I wondered if
> something is done differently as processing time for mris_expand is much
> longer (at about 14 min.) as compared with mri_vol2surf (couple of
> minutes). Any ideas on this would be welcome!
> Ruthger
>
> Le 2014-04-03 16:39, Markus Gschwind a écrit :
>> Hi Ruthger!
>>
>> Use mris_expand to create a surf inside or outside of white
>>
>> e.g.
>>
>> mris_expand surf/lh.white -1 surf/lh.white_1mm_inside
>> # use positive values for outside ?h.white border
>>
>> mris_expand -thickness surf/lh.white -1
>> surf/lh.white_in100%_thickness
>> # this samples in % of GM thickness, use positive values for outside
>> white
>>
>> Cheers!
>> Markus
>>
>> 2014-04-03 16:24 GMT+02:00 Righart, Ruthger
>> :
>>
>>> Hi All,
>>>
>>> mri_vol2surf has the flags --projfrac and --projdist. If I
>>> understand
>>> these flags correctly, the volume is sampled inbetween the
>>> white-matter
>>> surface and the pial surface (for ex. --projfrac 0.5 is midway). Is
>>> there a possibility in tkmedit/Freeview to display with a colored
>>> line
>>> for ex. --projfrac 0.5 for a given subject? (actually similar to
>>> what
>>> was done by Salat et al., NeuroImage 2009, 48, p23, fig 1A,
>>> http://surfer.nmr.mgh.harvard.edu/pub/articles/salat_2009.pdf [1]).
>>>
>>> Thank you very much in advance for your help!
>>>
>>> All the best,
>>>
>>> Ruthger
>>> ___
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>>
>>
>> Links:
>> --
>> [1] http://surfer.nmr.mgh.harvard.edu/pub/articles/salat_2009.pdf
>> [2] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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-- 
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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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Re: [Freesurfer] CWP values

[Douglas N Greve]

The QDEC output does not quite report what you want to report. I would 
run mri_glmfit-sim using --glmdir /path/to/qdec/folder and the same 
parameters as you used for the monte carlo simulation. this will produce 
several files including a summary/table file with the MNI305 coordinates 
of most significant voxel in the cluster. If you want the centroid, add 
--centroid to the cmd line.

doug


On 04/03/2014 07:17 AM, Francesco Puccettone wrote:
> Dear FreeSurfer list,
>
> When reporting coordinates of significant clusters found with Qdec, 
> should one report
> 1) the Talairach coordinates displayed immediately after running the 
> MonteCarlo correction (which I imagine are the center of gravity (CoG) 
> coordinates?!)
> or
> 2) the max vertex Talairachcoordinates displayed after using the "Find 
> clusters and go to max" button?
>
> The two sets of coordinates are close for a given cluster, but never 
> quite the same, and I don;t know which one to report.
>
> Thank you!
> --Francesco
>
>
> On 31 March 2014 20:20, Francesco Puccettone 
>  > wrote:
>
> I see, makes sense! I had a second question, which I repeat below.
>
> When reporting significant clusters, should one refer to the
> cluster by
> 1) its annotation label, e.g. "sig differences were found in the
> precentral gyrus",
> 2) its max vertex as displayed after using the "Find clusters and
> go to max" button, e.g. "significant differences were found in a
> cluster whose maximum vertex was at (10,20,30)" , or
> 3) by its center of gravity coordinates as displayed (I think!)
> immediately after running the MonteCarlo correction, e.g.
> "significant differences were found in a cluster whose CoG was at
> (11,21,31)"?
>
>
> On 31 March 2014 17:43, Douglas N Greve  > wrote:
>
>
> This is just the way that the interface was programmed. It was
> fairly
> easy to add a button to run the correction, more difficult to
> pull that
> information back into the interface in a reasonable way. I
> agree that it
> makes using the interface less intuitive: once you get a button to
> press, you come to expect that everything else will be done
> for you.
> Unfortunately, we don't have the resources to be able to do
> that. You'll
> have to look at the text file generated by QDEC
> doug
>
>
> On 03/31/2014 09:05 AM, Francesco Puccettone wrote:
> > Hello,
> >
> > I see that after having qdec apply MonteCarlo correction to
> a certain
> > contrast, the CWP cluster-wise probability is displayed.
> Those values,
> > however, are not displayed when the "Find clusters and go to
> max"
> > button is used, either before or after correction. WHy is
> that, when
> > it seems that the CWP statistic makes sense for all 3 "stages"
> > (max-vertex pre-correction, mean-cluster post-correction,
> max-vertex
> > post-correction)?
> >
> > Thank you!
> >
> > --Francesco
> >
> >
> > ___
> > 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: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> 
> Outgoing:
> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
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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
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>
>
>
>
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Re: [Freesurfer] FW: registration difficulty

[Douglas N Greve]

First run this
tkregister2 --mov hipposubfield.mgz --reg hsf.reg.dat --s subject 
--regheader --fstarg

It will bring up the tkregister2 GUI and just double check that the 
subfields are where they need to be. Hit "Save Reg" and exit. In the 
future, you can run the tkregister2 command with --noedit and it will 
not bring the  GUI up (and will save the registration). 
hipposubfield.mgz is the HSF segmentation.

Now run

mri_matrix_multiple -im register.dof6.dat -iim hsf.reg.dat -om 
func2hsf.reg.dat

where register.dof6.dat is the registration between the functional and 
anatomical

Check that it looks ok

tkregister2 --mov func.nii.gz --targ hipposubfield.mgz --reg 
func2hsf.reg.dat

I'm not sure what your final plans are, but you can use func2hsf.reg.dat 
with mri_vol2vol (similar to the tkregister2 cmd above)

doug


On 04/03/2014 05:23 AM, Erik O'Hanlon wrote:
> Hi Doug,
>
> Thanks for that, I will give that a shot and see how it looks.
>
> As for my highres hippo images, I ran the recon-all with the -hippo-subfields 
> setting on my T1 highres whole brain anatomy file. This gave me the usual FS 
> outputs and the extra hippo subfield volumes. I can look at these with  
> Freeview and when I load the anatomy, the aseg and the hippo subfields, 
> everything is fine. I then want to transform these to my diffusion space for 
> tractography, and managed to get the anat and aseg images to align with my 
> diffusion space B0 image but just can't get the subfields to align. I think 
> this is due to the smaller fov of the subfields as they appear a small cubes 
> with the hippo structures inside in the Freeview screen.
>
> Thanks again for the direction, I haven't tried the tkregister2 tool so I'll 
> play with it and see
>
> Much appreciated.
>
> best regards
>
> Erik
>
> Dr. Erik O'Hanlon PhD MSc BScEng
> Post Doctoral Researcher
>
>
> RCSI Psychiatry
> Royal College of Surgeons in Ireland
> Beaumont Road, Beaumont, D9, Ireland
> T: 8093740
> E: erikohan...@rcsi.ie  W: www.rcsi.ie
>
> RCSI DEVELOPING HEALTHCARE LEADERS
> WHO MAKE A DIFFERENCE WORLDWIDE
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
> [gr...@nmr.mgh.harvard.edu]
> Sent: 02 April 2014 22:35
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] FW: registration difficulty
>
>>> should I now rerun the bbregsiter and create a new dat file for the subfield
>>> volume to orig.mgz image?
> I did not entirely follow this thread. It sound like you have 3 volumes: 
> orig.mgz, an EPI, and some highres hippo seg? How did you get the hires hippo 
> seg? If it shares a scanner space with the orig.mgz, then run tkregister2 
> --mov hireshippo --s subject --fstarg --reg hip2orig.reg.dat --regheader
>
> this will bring up the tkregister2 window and you can double check that it 
> looks ok; save the reg. In the future you can just add --noedit and it will 
> write the output reg without bringing up the interface.
>
> but I might not understand what is going on ...
> doug
>
> On 04/02/2014 03:03 PM, Erik O'Hanlon wrote:
>> Apologies.
>>
>> forwarded it on now
>>
>> Thanks a million
>>
>> Erik
>>
>> Dr. Erik O'Hanlon PhD MSc BScEng
>> Post Doctoral Researcher
>>
>>
>> RCSI Psychiatry
>> Royal College of Surgeons in Ireland
>> Beaumont Road, Beaumont, D9, Ireland
>> T: 8093740
>> E: erikohan...@rcsi.ie  W: www.rcsi.ie
>>
>> RCSI DEVELOPING HEALTHCARE LEADERS
>> WHO MAKE A DIFFERENCE WORLDWIDE
>> 
>> From: Bruce Fischl [fis...@nmr.mgh.harvard.edu]
>> Sent: 02 April 2014 19:58
>> To: Erik O'Hanlon
>> Subject: Re: [Freesurfer] FW: registration difficulty
>>
>> Hi Erik
>>
>> can you cc the list so that others (like Doug!) can respond?
>>
>> thanks
>> Bruce
>> On Wed, 2 Apr
>> 2014, Erik O'Hanlon wrote:
>>
>>> Hi Bruce,
>>>
>>> Thanks so much for your reply. As for the specifics of what I have tried, so
>>> rry if it was unclear.
>>>
>>> I have performed the usual T1 based FS cortical and subcortical analysis and
>>>included the -hip_subfields so I also get all the subdivision volumes. I 
>>> ha
>>> ve also run a DWI analysis in ExploreDTI and now want to use the subfield vo
>>> lumes as masks for the purpose of tractography. I created my diff-to-orig da
>>> t file using bbregister. I then used this in the mri_vol2vol and aligned my
>>> aseg.mgz to my nodif image. This worked really well and I then used fslmaths
>>>to extract out the hippocampus from the aseg2diff. This aligns nicely. I 
>>> th
>>> en tried to apply the same transformation to my subfield volumes but this di
>>> dn't work. As you suggested, and just to clarify,
>>>
>>> should I now rerun the bbregsiter and create a new dat file for the subfield
>>>volume to orig.mgz image? Do I then use this in the mri_vol2vol and 
>>> align m
>>> y subfield volume to the orig.mgz and then run a second mri_vol2vol but use
>>> the nodif2or

Re: [Freesurfer] mri_surcluster and centroid option

[Douglas N Greve]

I'm not sure, when I run it it results in different xyz. What version 
are you using?

I've put a copy of my version (for linux) here
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_surfcluster

doug

On 04/03/2014 03:56 AM, Joerg Pfannmoeller wrote:
> Hi,
>
> I am trying to compute centroid coordinates of maps for functional activation 
> obtained from fsfast with mri_surfcluster. The command is:
>
>
> mri_surfcluster --in /.../sig.nii.gz  --thmin 3 --thmax infinity--sign pos 
> --subject subjid --hemi rh --surf white --annot aparc --frame 0 --minarea 0 
> --sum ./tabular_surfcluster.txt -- centroid
>
> Unfortunately, the centroid option has no effect. Results in 
> tabular_surfcluster.txt with and without centroid option are identical. What 
> am I doing wrong?
>
> Respectfully yours
>
>   pfannmoe
> ___
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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
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Re: [Freesurfer] mri_vol2surf --projopt

[Douglas N Greve]

Don't use --projopt and it won't segfault

On 04/03/2014 02:08 AM, Joerg Pfannmoeller wrote:
> The command is:
>
> mri_vol2surf --mov /.../f001.nii --reg /.../register.f1.dof6.dat --trgsubject 
> subjid --interp nearest --projopt /.../map001 --hemi rh --o 
> /.../f001_surf.nii --noreshape --cortex
>
> The output is the follwoing:
>
>
> srcvol = /.../f001.nii
> srcreg = /.../register.f001.dof6.dat
> srcregold = 0
> srcwarp unspecified
> surf = white
> hemi = rh
> trgsubject = subjid
> surfreg = sphere.reg
> reshape = 0
> interp = nearest
> float2int = round
> GetProjMax = 0
> INFO: float2int code = 0
> INFO: changing type to float
> Done loading volume
> Loading label /.../label/rh.cortex.label
> Reading surface /.../surf/rh.white
> Done reading source surface
> Reading thickness /.../surf/rh.thickness
> Done
> Mapping Source Volume onto Source Subject Surface
> reading gm volume fraction from /.../map001.gm.mgz
> reading wm volume fraction from /.../map001.wm.mgz
> reading csf volume fraction from /.../map001.csf.mgz
> mri_vol2surf --mov /.../f001.nii --reg /.../register.f1.dof6.dat --trgsubject 
> subjid --interp nearest --projopt /.../map001 --hemi rh --o 
> /.../f001_surf.nii --noreshape --cortex: Segmentation fault
>   
> Do you have an idea about the cause of the error?
>
>
>
>
>
> On Wed, 02 Apr 2014 17:28:14 -0400
> Douglas N Greve  wrote:
>
>> what is your command line that is seg faulting? What is the terminal output?
>>
>> On 04/02/2014 05:17 PM, pfannmo...@uni-greifswald.de wrote:
>>> Please help me with this issue:
>>>
>>> If I apply mri_surf2vol to a single volume of unprocessed epi-data, it
>>> results in a segmentation fault. It works if I apply mri_vol2vol for
>>> registration of epi and anatomy, but than an interpolation is
>>> involved. I would like to avoid the interpolation and apply
>>> mri_surf2vol directly to the unprocessed data in order to minimize the
>>> number of interpolations.
>>>
>>>
>>> At Wednesday, 02-04-2014 on 21:08 Douglas N Greve wrote:
>>>
>>>  This is something BF added Sept 1 2009:
>>>
>>>  added --projopt  switch to do optimal linear estimation of gray matter
>>>  values given a set of precomputed gray matter densities.
>>>
>>>  I don't know what it would mean beyond that
>>>
>>>  doug
>>>
>>>
>>>  On 04/02/2014 10:49 AM, Joerg Pfannmoeller wrote:
>>>  > Hello,
>>>  >
>>>  > I found an option in mri_vol2surf for which I could not find a
>>>  documentation. The option is called:
>>>  >
>>>  > --projopt
>>>  >
>>>  > It would be nice if somebody could give a description of this
>>>  option.
>>>  >
>>>  > Respectfully yours
>>>  >
>>>  > pfannmoe
>>>  >
>>>  >
>>>  > ___
>>>  > 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: https://gate.nmr.mgh.harvard.edu/filedrop2
>>>  www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>>>  Outgoing:
>>>  ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>>>
>>>  ___
>>>  Freesurfer mailing list
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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.
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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
>>
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Re: [Freesurfer] Displaying parcellated ROI in color but remainder of brain in grey

[Douglas N Greve]

Try excluding the following line from your ctab

0  Unknown   0   0   00

The list in the ctab should match that of the labels you are passing on 
the command line (it is ok to have more in the ctab than on the command 
line)

doug


On 04/02/2014 01:05 PM, Laura Taylor wrote:
> Hi Doug,
>
> Thank you for your reply.
>
> This was my mris_label2annot command line:
>
> woodward@Bambi:~$ mris_label2annot --s TGT_N61AvgSubject --h rh --ctab 
> /Data/freesurfer/subjects/TGT_N61AvgSubject/label/aparc.annot.a2009s_comp2RH.ctab
>  
> --a Comp2RH_TGTN61_properGreyRH --l 
> /Data/freesurfer/subjects/TGT_N61AvgSubject/mri_annotation2label/rh.S_collat_transv_ant.label
>  
> --l 
> /Data/freesurfer/subjects/TGT_N61AvgSubject/mri_annotation2label/rh.S_oc-temp_med_and_Lingual.label
>  
> --l 
> /Data/freesurfer/subjects/TGT_N61AvgSubject/mri_annotation2label/rh.G_oc-temp_med-Lingual.label
>  
> --l 
> /Data/freesurfer/subjects/TGT_N61AvgSubject/mri_annotation2label/rh.G_oc-temp_lat-fusifor.label
>  
> --l 
> /Data/freesurfer/subjects//TGT_N61AvgSubject/mri_annotation2label/rh.S_occipital_ant.label
>  
> --l 
> /Data/freesurfer/subjects/TGT_N61AvgSubject/mri_annotation2label/rh.S_temporal_inf.label
>  
>
>
>
>
> This is the terminal output:
>
> Reading ctab 
> /Data/freesurfer/subjects/TGT_N61AvgSubject/label/aparc.annot.a2009s_comp2RH.ctab
> Number of ctab entries 76
>
> $Id: mris_label2annot.c,v 1.17 2011/03/02 00:04:32 nicks Exp $
> cwd /home/woodward
> cmdline mris_label2annot --s TGT_N61AvgSubject --h rh --ctab 
> /Data/freesurfer/subjects/TGT_N61AvgSubject/label/aparc.annot.a2009s_comp2RH.ctab
>  
> --a Comp2RH_TGTN61_properGreyRH --l 
> /Data/freesurfer/subjects/TGT_N61AvgSubject/mri_annotation2label/rh.S_collat_transv_ant.label
>  
> --l 
> /Data/freesurfer/subjects/TGT_N61AvgSubject/mri_annotation2label/rh.S_oc-temp_med_and_Lingual.label
>  
> --l 
> /Data/freesurfer/subjects/TGT_N61AvgSubject/mri_annotation2label/rh.G_oc-temp_med-Lingual.label
>  
> --l 
> /Data/freesurfer/subjects/TGT_N61AvgSubject/mri_annotation2label/rh.G_oc-temp_lat-fusifor.label
>  
> --l 
> /Data/freesurfer/subjects//TGT_N61AvgSubject/mri_annotation2label/rh.S_occipital_ant.label
>  
> --l 
> /Data/freesurfer/subjects/TGT_N61AvgSubject/mri_annotation2label/rh.S_temporal_inf.label
>  
>
> sysname  Linux
> hostname Bambi
> machine  x86_64
> user woodward
>
> subject TGT_N61AvgSubject
> hemirh
> SUBJECTS_DIR /Data/freesurfer/subjects
> ColorTable 
> /Data/freesurfer/subjects/TGT_N61AvgSubject/label/aparc.annot.a2009s_comp2RH.ctab
> AnnotName  Comp2RH_TGTN61_properGreyRH
> nlables 6
> LabelThresh 0 0.00
> Loading /Data/freesurfer/subjects/TGT_N61AvgSubject/surf/rh.orig
>  1 8355711 G_and_S_frontomargin
>  2 8355711 G_and_S_occipital_inf
>  3 8355711 G_and_S_paracentral
>  4 8355711 G_and_S_subcentral
>  5 8355711 G_and_S_transv_frontopol
>  6 8355711 G_and_S_cingul-Ant
> Mapping unhit to unknown
> Found 154540 unhit vertices
> Writing annot to 
> /Data/freesurfer/subjects/TGT_N61AvgSubject/label/rh.Comp2RH_TGTN61_properGreyRH.annot
>
>
>
>
> colortab file: 
> /Data/freesurfer/subjects/TGT_N61AvgSubject/label/aparc.annot.a2009s_comp2RH.ctab
>
>  0  Unknown   0   0   00
>   1  G_and_S_frontomargin 127 127 127   0
>   2  G_and_S_occipital_inf127 127 127   0
>   3  G_and_S_paracentral  127 127 127   0
>   4  G_and_S_subcentral   127 127 127   0
>   5  G_and_S_transv_frontopol 127 127 127   0
>   6  G_and_S_cingul-Ant   127 127 127   0
>   7  G_and_S_cingul-Mid-Ant   127 127 127   0
>   8  G_and_S_cingul-Mid-Post  127 127 127   0
>   9  G_cingul-Post-dorsal 127 127 127   0
>  10  G_cingul-Post-ventral127 127 127   0
>  11  G_cuneus 127 127 127   0
>  12  G_front_inf-Opercular127 127 127   0
>  13  G_front_inf-Orbital  127 127 127   0
>  14  G_front_inf-Triangul 127 127 127   0
>  15  G_front_middle   127 127 127   0
>  16  G_front_sup  127 127 127   0
>  17  G_Ins_lg_and_S_cent_ins  127 127 127   0
>  18  G_insular_short  127 127 127   0
>  19  G_occipital_middle   127 127 127   0
>  20  G_occipital_sup  127 127 127   0
>  21  G_oc-temp_lat-fusifor60  20 1400
>  22  G_oc-temp_med-Lingual   220 180 1400
>  23  G_oc-temp_med-Parahip127 127 127   0
>  24  G_orbital127 127 127   0
>  25  G_pariet_inf-Angular 127 127 127   0
>  26  G_pariet_inf-Supramar127 127 127   0
>  27  G_parietal_sup   127 127 127   0
>  28  G_postcentral127 127 127   0
>  29  G_precentral 127 127 127   0
>  30  G_precuneus  127 127 127   0
>  31  G_rectus 127 127 127   0
>  32

Re: [Freesurfer] Create a label from a binary mask

[Douglas N Greve]

Hi Cherisse, i don't understand what you have done. Is the mask a volume 
mask or surface mask? In mri_cor2label, you can specify a surface to get 
surface vertex numbers.

doug

On 04/02/2014 07:03 PM, Cherisse Onuigbo wrote:
> Hello
>
> I was wondering how to create a label from a binary mask. I created a 
> mask and then normalized it to the template space. When I tried to use 
> mri_cor2vol, all the vertex numbers come out as -1. I understand that 
> the vertex numbers should come out as -1, but when I entered the 
> coordinates in the display function in spm, it was not in the region.
>
> Thank you,
> Cherisse
>
>
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-- 
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Re: [Freesurfer] Displaying parcellated ROI in color but remainder of brain in grey

[Laura Taylor]

Hi Shantanu,

Thanks for your reply.  My command line in tksurfer was:

 ~$ tksurfer TGT_N61AvgSubject rh inflated -annotation
/Data/freesurfer/subjects/TGT_N61AvgSubject/label/rh.Comp2RH_TGTN61_Apr3.annot

You can also do the same for the pial surface.

The original ctab file (r/lh.aparc.a2009s.ctab - or whichever one
corresponds to the parcellation scheme that you are using) is automatically
created in the labels folder for each subject (and it should be the same
for each subject).

I did indeed edit the ctab file using RGB color codes.  I used 127 127 127
for grey for the remainder of my brain.

Best wishes,

Laura








On Thu, Apr 3, 2014 at 5:53 PM, Shantanu Ghosh  wrote:

> Hi Laura,
> I am facing the same problem when using freeview. Can you tell me what was
> your commandline that solved the problem in tksurfer? How did you get the
> ctab file and did you edit it using the RGB color codes?
> Thanks in advance.
> Shantanu
>
>
> On Thu, April 3, 2014 6:55 pm, Laura Taylor wrote:
> > Hi Again Doug,
> >
> > I was able to get what I was looking for after I modified my ctab file
> slightly and used tksurfer instead of freeview to display the images.  I
> am
> > hoping, however, that it is still possible to get things to work in
> freeview.
> >
> > For the ctab file, I put my 6 parcellated ROI's at the start of the ctab
> file and numbered them 1 to 6.  I numbered the remaining regions 7-75.
> >
> > In freeview the ROI's were in color but the remainder of the brain was
> black (not what I wanted).  However in tksurfer, everything looked good
> (brain in grey and ROI's in different colors).
> >
> > Do you think it would be possible to display these images properly in
> freeview as well?
> >
> > Thank you very much for your time,
> >
> > Laura
> >
> >
> > On Wed, Apr 2, 2014 at 10:05 AM, Laura Taylor
> > wrote:
> >
> >> Hi Doug,
> >> Thank you for your reply.
> >> This was my mris_label2annot command line:
> >> woodward@Bambi:~$ mris_label2annot --s TGT_N61AvgSubject --h rh --ctab
>
> /Data/freesurfer/subjects/TGT_N61AvgSubject/label/aparc.annot.a2009s_comp2RH.ctab
> --a Comp2RH_TGTN61_properGreyRH --l
> >>
> /Data/freesurfer/subjects/TGT_N61AvgSubject/mri_annotation2label/rh.S_collat_transv_ant.label
> --l
> >>
> /Data/freesurfer/subjects/TGT_N61AvgSubject/mri_annotation2label/rh.S_oc-temp_med_and_Lingual.label
> --l
> >>
> /Data/freesurfer/subjects/TGT_N61AvgSubject/mri_annotation2label/rh.G_oc-temp_med-Lingual.label
> --l
> >>
> /Data/freesurfer/subjects/TGT_N61AvgSubject/mri_annotation2label/rh.G_oc-temp_lat-fusifor.label
> --l
> >>
> /Data/freesurfer/subjects//TGT_N61AvgSubject/mri_annotation2label/rh.S_occipital_ant.label
> --l
> >>
> /Data/freesurfer/subjects/TGT_N61AvgSubject/mri_annotation2label/rh.S_temporal_inf.label
> This is the terminal output:
> >> Reading ctab
> >>
> /Data/freesurfer/subjects/TGT_N61AvgSubject/label/aparc.annot.a2009s_comp2RH.ctab
> Number of ctab entries 76
> >> $Id: mris_label2annot.c,v 1.17 2011/03/02 00:04:32 nicks Exp $
> >> cwd /home/woodward
> >> cmdline mris_label2annot --s TGT_N61AvgSubject --h rh --ctab
> >>
> /Data/freesurfer/subjects/TGT_N61AvgSubject/label/aparc.annot.a2009s_comp2RH.ctab
> --a Comp2RH_TGTN61_properGreyRH --l
> >>
> /Data/freesurfer/subjects/TGT_N61AvgSubject/mri_annotation2label/rh.S_collat_transv_ant.label
> --l
> >>
> /Data/freesurfer/subjects/TGT_N61AvgSubject/mri_annotation2label/rh.S_oc-temp_med_and_Lingual.label
> --l
> >>
> /Data/freesurfer/subjects/TGT_N61AvgSubject/mri_annotation2label/rh.G_oc-temp_med-Lingual.label
> --l
> >>
> /Data/freesurfer/subjects/TGT_N61AvgSubject/mri_annotation2label/rh.G_oc-temp_lat-fusifor.label
> --l
> >>
> /Data/freesurfer/subjects//TGT_N61AvgSubject/mri_annotation2label/rh.S_occipital_ant.label
> --l
> >>
> /Data/freesurfer/subjects/TGT_N61AvgSubject/mri_annotation2label/rh.S_temporal_inf.label
> sysname  Linux
> >> hostname Bambi
> >> machine  x86_64
> >> user woodward
> >> subject TGT_N61AvgSubject
> >> hemirh
> >> SUBJECTS_DIR /Data/freesurfer/subjects
> >> ColorTable
> >>
> /Data/freesurfer/subjects/TGT_N61AvgSubject/label/aparc.annot.a2009s_comp2RH.ctab
> AnnotName  Comp2RH_TGTN61_properGreyRH
> >> nlables 6
> >> LabelThresh 0 0.00
> >> Loading /Data/freesurfer/subjects/TGT_N61AvgSubject/surf/rh.orig
> >>  1 8355711 G_and_S_frontomargin
> >>  2 8355711 G_and_S_occipital_inf
> >>  3 8355711 G_and_S_paracentral
> >>  4 8355711 G_and_S_subcentral
> >>  5 8355711 G_and_S_transv_frontopol
> >>  6 8355711 G_and_S_cingul-Ant
> >> Mapping unhit to unknown
> >> Found 154540 unhit vertices
> >> Writing annot to
> >>
> /Data/freesurfer/subjects/TGT_N61AvgSubject/label/rh.Comp2RH_TGTN61_properGreyRH.annot
> colortab file:
> >>
> /Data/freesurfer/subjects/TGT_N61AvgSubject/label/aparc.annot.a2009s_comp2RH.ctab
> >>  0  Unknown   0   0   00
> >>   1  G_and_S_frontomargin 127 127 127   0
> >>   2  G_and_S_occipital_inf127 127 127   0
> >>   3

Re: [Freesurfer] Mac OSX installations incomplete? What to do?

[Z K]

There are 3 missing fsl files from the OSX snow leopard installation. 
They can be downloaded from here:

ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/fsdev/zkaufman/fsl

Copy them into your "$FREESURFER_HOME/bin" directory.

-Zeke



On 04/04/2014 12:32 PM, Markus Gschwind wrote:
> Dear Freesurfers,
>
> As discovered here,
>
> http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg35160.html
>
> it seams that some Mac OSX installations suffered from incomplete files.
>
> I just veryfied that I had downloaded the complete image and wget says yes:
>
> Logging in as anonymous ... Logged in!
> ==> SYST ... done.==> PWD ... done.
> ==> TYPE I ... done.  ==> CWD (1) /pub/dist/freesurfer/5.3.0 ... done.
> ==> SIZE freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0.dmg
> ... 3394499614
> File has already been retrieved.
> 2014-04-04 18:24:26 (0.00 B/s) -
> ‘freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0.dmg’ saved
> [3394499614]
>
>
> So this is what I installed recently and it seems that there are some
> files missing (at least some of the fsl-functions in bin).
>
> Doug, you said that you suspected that it could be a problem of the
> installer script?
>
> What should we do (also Eiran) in order to complete the installation?
>
> Thanks for you work!
> Markus
>
>
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[Freesurfer] Mac OSX installations incomplete? What to do?

[Markus Gschwind]

Dear Freesurfers,

As discovered here,

http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg35160.html

it seams that some Mac OSX installations suffered from incomplete files.

I just veryfied that I had downloaded the complete image and wget says yes:

Logging in as anonymous ... Logged in!
> ==> SYST ... done.==> PWD ... done.
> ==> TYPE I ... done.  ==> CWD (1) /pub/dist/freesurfer/5.3.0 ... done.
> ==> SIZE freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0.dmg ...
> 3394499614
> File has already been retrieved.
> 2014-04-04 18:24:26 (0.00 B/s) -
> 'freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0.dmg' saved
> [3394499614]


So this is what I installed recently and it seems that there are some files
missing (at least some of the fsl-functions in bin).

Doug, you said that you suspected that it could be a problem of the
installer script?

What should we do (also Eiran) in order to complete the installation?

Thanks for you work!
Markus
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Re: [Freesurfer] tracula and libnetcdf

[Anastasia Yendiki]

Hi Satra - We've been talking about a 5.3.1, yes. On my end, it would 
include the tracula updates that are currently available and possibly some 
more (I've been working on some improvements to longitudinal tracula).


Not sure about libnetcdf but this is a good time to add things to the wish 
list :)


a.y

On Fri, 4 Apr 2014, Satrajit Ghosh wrote:


hi folks,
we are setting up freesurfer on a new cluster and trying to be as modular as
possible in terms of dependencies. at present we are only installing 5.3.0 +
tracula updates.

will libnetcdf (required by tracula) be included in freesurfer? or is it
considered a dependency?

and talking of which, is there a patch (a 5.3.1) in the horizon which will
include the tracula updates and perhaps netcdf in the freesurfer download.

cheers,

satra

On Wed, Feb 5, 2014 at 11:07 PM, Satrajit Ghosh  wrote:
  update: the lack of libnetcdf eventually makes it fail.
i found a libnetcdf.so.7 on the cluster and soft linked it to
libnetcdf.so.6 and added the path to LD_LIBRARY_PATH. 

that let trac-all -prep run to completion.

cheers,

satra


On Wed, Feb 5, 2014 at 9:02 PM, Satrajit Ghosh  wrote:
  hi a.y.,
when running trac-preproc i'm getting this error (for
dmri_motion and dmri_group), but it continues running:

/software/freesurfer/bin/dmri_motion: error while loading shared
libraries: libnetcdf.so.6: cannot open shared object file: No
such file or directory

what will this fail to do?

also is libnetcdf now a dependency for freesurfer? the reason i
ask is that i'm running this on a remote cluster for which i
don't have admin privileges.

cheers,

satra




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Re: [Freesurfer] TRACULA longitudinal stream - length of Center variable

[Anastasia Yendiki]

Hi Vincent - I suspect that this problem would be fixed by some recent 
changes that I've implemented for the longitudinal stream of tracula, and 
that I'm in the process of testing. As soon as we can get a new dev 
version built, I'll let you know so you can test it.

Thank you for your patience!

a.y

On Fri, 4 Apr 2014, Vincent Brunsch wrote:

> Dear TRACULA experts,
>
> I have used the longitudinal version and find that for some subjects'
> tracts Len_Min is larger than Len_Center. How is this possible? (An
> extreme example is Len_Min: 36, Len_Max: 75, Len_Center: 4.)
>
> Best, Vincent
>
> ---
> This email is free from viruses and malware because avast! Antivirus 
> protection is active.
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>
>
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[Freesurfer] Postdoctoral Fellowship in Aging Research

[Anqi Qiu]

Job description:
National University of Singapore (NUS) is a leading global university
centre in Asia. It offers a global approach to education and research,
with a focus on Asian perspectives and expertise. Computation functional
anatomy laboratory at NUS (http://www.bioeng.nus.edu.sg/cfa) focuses on
brain and cognition studies using neuroimaging techniques. Our group is
leading a large-scale aging neuroimaging project from birth in Singapore.
The project examines neurocognition, high angular resolution diffusion
imaging (HARDI), resting-state fMRI, and structural MRI. We are looking
for a research fellow who is interested in multi-modal MRI studies in
aging, especially, who is interested in understanding aging processes of
anatomical and functional connectivity and their relations with cognition
as well as genetic regulation on aging brain processes. We offer high
salary with medical and other benefits.

Requirements:
•   Ph. D or MD
•   Research background on infant brain is preferable but necessary
•   Knowledge in statistical analysis is necessary
•   Good communication and writing skills in English language

If you are interested in the jobs listed above, please send your CV to
Associate Prof. Anqi QIU
Department of Biomedical Engineering
National University of Singapore
Email: bi...@nus.edu.sg
Phone: +(65) 6516 7002


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[Freesurfer] question about how to calculate COV for MNE

[Joseph Dien]

Hi,
   I have a question about how to calculate the COV for the MNE software.  As I 
understand it from Section 4.17 of the 2.7.3 MNE manual, if one is averaging 
together COV matrices, one weights them by the number of observations going 
into each one.  I also see from Section 4.17.2 that these are technically not 
covariance matrices so much as sum-of-squares matrices where the epochs going 
into each variable has been baseline corrected.

   Assuming my understanding so far is correct, my question is about how to 
proceed when making linear combinations of COV matrices, as in a difference 
wave, as discussed in Section 6.3.  Would the following be the correct 
procedure?

   Compute the COV separately for the two conditions (say standard and rare 
oddballs).  Subtract the two COV matrices to obtain C0. Then calculate C by 
dividing by Leff, which in turn is calculated as Leff= (L1*L2)/(L1+L2) where L1 
is the number of observations in the first COV matrix and L2 is for the second.

   But if done in this way, the two COV matrices would not be weighted by their 
relative sample sizes.  So would I also weight them by L1 and L2 during the 
subtraction, as done for averaging per 4.17?  But then what is the purpose of 
the Leff calculation? Or is the idea that one would calculate a single COV 
based on both conditions and then one would modify COV by Leff to reflect that 
the signal-to-noise ratio has been reduced by combining two averages with 
differing sample sizes?  But in the case where both samples equal, say, 10, 
Leff would end up equalling 100/20=5.  Dividing C by 5 seems like too much.  
Anyway, very confused.  Any guidance would be appreciated.

Respectfully,

Joe






Joseph Dien,
Senior Research Scientist
Maryland Neuroimaging Center
University of Maryland 

E-mail: jdie...@mac.com
Phone: 202-297-8117
http://joedien.com














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Re: [Freesurfer] tracula and libnetcdf

[Satrajit Ghosh]

hi folks,

we are setting up freesurfer on a new cluster and trying to be as modular
as possible in terms of dependencies. at present we are only installing
5.3.0 + tracula updates.

will libnetcdf (required by tracula) be included in freesurfer? or is it
considered a dependency?

and talking of which, is there a patch (a 5.3.1) in the horizon which will
include the tracula updates and perhaps netcdf in the freesurfer download.

cheers,

satra

On Wed, Feb 5, 2014 at 11:07 PM, Satrajit Ghosh  wrote:

> update: the lack of libnetcdf eventually makes it fail.
>
> i found a libnetcdf.so.7 on the cluster and soft linked it to
> libnetcdf.so.6 and added the path to LD_LIBRARY_PATH.
>
> that let trac-all -prep run to completion.
>
> cheers,
>
> satra
>
>
> On Wed, Feb 5, 2014 at 9:02 PM, Satrajit Ghosh  wrote:
>
>> hi a.y.,
>>
>> when running trac-preproc i'm getting this error (for dmri_motion and
>> dmri_group), but it continues running:
>>
>> /software/freesurfer/bin/dmri_motion: error while loading shared
>> libraries: libnetcdf.so.6: cannot open shared object file: No such file or
>> directory
>>
>> what will this fail to do?
>>
>> also is libnetcdf now a dependency for freesurfer? the reason i ask is
>> that i'm running this on a remote cluster for which i don't have admin
>> privileges.
>>
>> cheers,
>>
>> satra
>>
>>
>
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Re: [Freesurfer] Standard surface tessellation

[Chris McNorgan]

Hi Justin,
This is quite similar to a question I had asked previously:
https://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg33421.html
I believe the solution is to generate a 14000 vertex template, and then 
appy mri_surf2surf to all 10 subjects, which will map the vertices of 
all 10 subjects to your template. The 10 transformed surfaces should 
then correspond with one another.


Chris


   Subject:
   [Freesurfer] Standard surface tessellation
   From:
   jeong...@pet.wayne.edu
   Date:
   14-04-03 03:47 PM
   To:
   freesurfer@nmr.mgh.harvard.edu

   Dear FreeSurfer,

   I am a beginner in FreeSurfer and wonder if it is possible in FreeSurfer
   to apply the same triangulation across multiple subjects, i.e. the same
   number of vertices and triangles at the anatomically identical
   locations.
   For instance, I have 10 subjects and want to have pial (or white matter)
   surfaces of individual subjects consisting of 14000 vertices which are
   anatomically matched. Any suggestion will be greatly appreciated.

   Justin.





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Re: [Freesurfer] Display tkmedit image of surface after mri_vol2surf with projfrac or projdist

[Bruce Fischl]

Hi Ruthger

no, they are not the same. mris_expand generates a smooth 
non-self-intersecting surface, which is definitely not guaranteed by 
simple projection.


cheers
Bruce
On Fri, 4 Apr 2014, Righart, Ruthger wrote:


Hi Markus,
Thank you, excellent tool and gives exactly what I was searching for!
Is the resulting surface the same for mris_expand taken at 50% as the
one that is used in mri_vol2surf with flag projfrac 0.5? I wondered if
something is done differently as processing time for mris_expand is much
longer (at about 14 min.) as compared with mri_vol2surf (couple of
minutes). Any ideas on this would be welcome!
Ruthger

Le 2014-04-03 16:39, Markus Gschwind a écrit :

Hi Ruthger!

Use mris_expand to create a surf inside or outside of white

e.g. 

mris_expand surf/lh.white -1 surf/lh.white_1mm_inside
# use positive values for outside ?h.white border

mris_expand -thickness surf/lh.white -1
surf/lh.white_in100%_thickness 
# this samples in % of GM thickness, use positive values for outside
white 

Cheers!
Markus

2014-04-03 16:24 GMT+02:00 Righart, Ruthger
:


Hi All,

mri_vol2surf has the flags --projfrac and --projdist. If I
understand
these flags correctly, the volume is sampled inbetween the
white-matter
surface and the pial surface (for ex. --projfrac 0.5 is midway). Is
there a possibility in tkmedit/Freeview to display with a colored
line
for ex. --projfrac 0.5 for a given subject? (actually similar to
what
was done by Salat et al., NeuroImage 2009, 48, p23, fig 1A,
http://surfer.nmr.mgh.harvard.edu/pub/articles/salat_2009.pdf [1]).

Thank you very much in advance for your help!

All the best,

Ruthger
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Links:
--
[1] http://surfer.nmr.mgh.harvard.edu/pub/articles/salat_2009.pdf
[2] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[3] http://www.partners.org/complianceline

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Re: [Freesurfer] Display tkmedit image of surface after mri_vol2surf with projfrac or projdist

[Righart, Ruthger]

Hi Markus,
Thank you, excellent tool and gives exactly what I was searching for! 
Is the resulting surface the same for mris_expand taken at 50% as the 
one that is used in mri_vol2surf with flag projfrac 0.5? I wondered if 
something is done differently as processing time for mris_expand is much 
longer (at about 14 min.) as compared with mri_vol2surf (couple of 
minutes). Any ideas on this would be welcome!
Ruthger

Le 2014-04-03 16:39, Markus Gschwind a écrit :
> Hi Ruthger!
>
> Use mris_expand to create a surf inside or outside of white
>
> e.g. 
>
> mris_expand surf/lh.white -1 surf/lh.white_1mm_inside
> # use positive values for outside ?h.white border
>
> mris_expand -thickness surf/lh.white -1 
> surf/lh.white_in100%_thickness 
> # this samples in % of GM thickness, use positive values for outside 
> white 
>
> Cheers!
> Markus
>
> 2014-04-03 16:24 GMT+02:00 Righart, Ruthger 
> :
>
>> Hi All,
>>
>> mri_vol2surf has the flags --projfrac and --projdist. If I 
>> understand
>> these flags correctly, the volume is sampled inbetween the 
>> white-matter
>> surface and the pial surface (for ex. --projfrac 0.5 is midway). Is
>> there a possibility in tkmedit/Freeview to display with a colored 
>> line
>> for ex. --projfrac 0.5 for a given subject? (actually similar to 
>> what
>> was done by Salat et al., NeuroImage 2009, 48, p23, fig 1A,
>> http://surfer.nmr.mgh.harvard.edu/pub/articles/salat_2009.pdf [1]).
>>
>> Thank you very much in advance for your help!
>>
>> All the best,
>>
>> Ruthger
>> ___
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>>
>> The information in this e-mail is intended only for the person to 
>> whom it is
>> addressed. If you believe this e-mail was sent to you in error and 
>> the e-mail
>> contains patient information, please contact the Partners Compliance 
>> HelpLine at
>> http://www.partners.org/complianceline [3] . 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.
>
>
>
> Links:
> --
> [1] http://surfer.nmr.mgh.harvard.edu/pub/articles/salat_2009.pdf
> [2] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> [3] http://www.partners.org/complianceline
>
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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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