[Freesurfer] delete skull part in GM by tkmedit

[Rujing Zha]

Dear all,
I have read the troubleshooting in the website 
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/ControlPoints_tktools. I 
want to know if thereis a similar method to remove skull part in GM? I donot 
want to use -gcut and watershed option. I think control point method is better 
than -gcut option in my case.
Thanks,
All the best. 

2013-12-03



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


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

Re: [Freesurfer] DTI - tracula - satisfactory cntrl pnts

[Anastasia Yendiki]

Hi Skyler - I would *highly* recommend using the version of tracula in 
5.3, as there have been improvements in both performance and speed.


You can check the DWI to anatomical registration by overlaying the 
aparc+aseg from the dlabel/diff directory (which is in diffusion space) on 
the FA map. Does that look ok?


a.y

On Mon, 2 Dec 2013, Skyler Gabriel Shollenbarger wrote:


Hi Anastasia,

We're using 5.1. It's likely poor registration. The aparc+aseg. looked fine. Is 
there anything to do about poor registration?

Thank you for the fast reply. Truly appreciated.
Skyler

- Original Message -
From: "Anastasia Yendiki" 
To: "Skyler Gabriel Shollenbarger" 
Cc: Freesurfer@nmr.mgh.harvard.edu
Sent: Monday, December 2, 2013 4:27:37 PM
Subject: Re: [Freesurfer] DTI - tracula - satisfactory cntrl pnts


Hi Skyler - Are you using freesurfer 5.1 or 5.3?

Most likely this issue is due to poor registration, either from the
individual DWI to the individual T1, or from the individual T1 to the
template space. Or it could be that there is a problem with the
aparc+aseg.

a.y

On Mon, 2 Dec 2013, Skyler Gabriel Shollenbarger wrote:


Hi all,

I've been running DTI using tracula (fs version 5) for over 1 week on 2 
subjects. It appears that it is having difficulty finding satisfactory control 
point fit and has attempted over 1600 tries. Any help is greatly appreciated.
See error below:

INFO: Distances between consecutive points are 25 24 25 26
WARN: Could not find satisfactory control point fit - try 1665
Finding center streamline
INFO: Step is 4 voxels
WARN: Turning off FA check for center streamline
INFO: Step is 4 voxels
WARN: Turning off deviation check for center streamline
INFO: Step is 4 voxels
INFO: Length of center streamline is 96 voxels
Selecting 5 points on center streamline
INFO: Step is 4 voxels
WARN: Defaulting to equidistant control points
INFO: Selected control points are
 108 193 84
 112 173 72
 98 153 75
 74 157 75
 74 184 86
INFO: Distances between consecutive points are 24 25 24 29
WARN: Could not find satisfactory control point fit - try 1666
Finding center streamline
INFO: Step is 4 voxels
WARN: Turning off FA check for center streamline
INFO: Step is 4 voxels
WARN: Turning off deviation check for center streamline
INFO: Step is 4 voxels


Best,
Skyler





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


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


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

Re: [Freesurfer] mri_vol2surf

[Arash Nazeri]

Thank you very much for all the help.

> On Dec 2, 2013, at 11:27 AM, Douglas N Greve  
> wrote:
> 
> 
>> On 12/01/2013 11:40 PM, Arash Nazeri wrote:
>> Hi all,
>> 
>> I wanted to make sure how one could assign intensities from the 
>> subjacent white matter voxels to the cortical surfaces using mri_vol2surf.
>> 
>> Based on the documentation page --projfrac, if used with negative 
>> values, would assign white matter values to the surface. I was 
>> wondering if this holds true for other options such as projfrac-avg, 
>> projfrac-max, projdist-max ... . Further, I wanted to make sure if the 
>> third value, designated as del, means the minimum value that could be 
>> projected to the surface.
>> For instance: --projdist-max 0 -4 0.1 means to assign the maximum 
>> value in the distance 0-4 mm of the gray/white matter boundary to the 
>> white matter, that is larger than 0.1 .
> You basically have the right idea (ie, negative values go into the white 
> matter). I'm not sure exactly what you are asking in your example. If 
> you want to go from the gray/white surface into the WM by 4 mm, I would 
> use --projdist-max -4 0 0.1 or --projdist-max 0 4 -0.1
> This will sample along the normal in 40 places spaced 0.1mm apart and 
> return the maximum. Note that this does not assure that all points will 
> be in WM because 4mm may put you into the GM on an adjacent bank (but 
> for a T1 this will be dark so probably does not affect the max).
>> 
>> In case of the local/global outliers, is there any good way of 
>> finding, discarding, and replacement of these values, through 
>> thresholding+resampling for instance?
> We don't have anything.
>> 
>> Finally, I was wondering how it is possible to use these resulting mgh 
>> files for group comparison in an uncached dataset, presumably using 
>> mris_preproc.
> You can save them in the surf folder and then use "--meas yourfile.mgh" 
> with mris_preproc.
> 
> I'm not sure what you are aiming for, but David Salat did a similar 
> analysis http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2750073
> This was done using the pctsurfcon program, so you might want to take a 
> look at that
> doug
> 
> 
>> 
>> Bests,
>> Arash
>> 
>> 
>> ___
>> 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

Re: [Freesurfer] recon-all strip skull and neck by brain volume mask

[Bruce Fischl]

when you say there is some skull considered to be gray matter, do you 
mean in the aseg or does the pial surface contain it? If it's the aseg 
then it probably doesn't matter as we don't use the asegs for cortical 
stuff in any case


cheers
Bruce
On Tue, 3 Dec 2013, Rujing Zha wrote:


Dear Louis,
Thanks for your helpful prompt in advance.
I see. In my case, there is a not properly stripping, there is a not
properly gray matter(there are a some skull considered as gray matter). Did
you mean I can draw the segmentation without considering the skull
stripping? And a bad brainmask.mgz will not influence the GM thickness
analysis?
Thanks in advance.
All the best.
 
2013-12-03


Rujing Zha


发件人：Louis Nicholas Vinke 
发送时间：2013-12-03 03:58
主题：Re: [Freesurfer] recon-all strip skull and neck by brain volume mask
收件人："Rujing Zha"
抄送："freesurfer"
 
Hi Rujing, 
Even if there is some skull/dura left after the skullstrip step in  
recon-all, it still may not negatively impact the surfaces.  It might be  
worth running the remaining recon-all steps to see how the surfaces turn  
out. 
 
If you want to swap-in a better skullstripped volume into the recon-all  
stream then you just need to replace the brainmask.mgz and continue with  
autorecon2 and autorecon3. 
 
Keep in mind that the new brainmask.mgz volume still needs to be in the  
conformed anatomical space, so use the T1.mgz or brainmask.mgz to create  
the improved skullstrip volume which will replace the existing  
brainmask.mgz. 
 
-Louis 
 
On Mon, 2 Dec 2013, Rujing Zha wrote: 
 
> Dear all, 
> Part of subjects 3d images cannot be stripped skull and neck properly in

?? ?> recon-all default. I have got the brain volume mask, how I can using the
?? ?> existing proper mask to help strip skull in recon-all and next workflow?
?? ?> Thanks.Any reply will be appreciated. 

> All the best. 
>   
> 2013-12-02 
>  
> _
___ 
> Rujing Zha 
>  
> 
___ 
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 i
s 
addressed. If you believe this e-mail was sent to you in error and the e-ma
il 
contains patient information, please contact the Partners Compliance HelpLi
ne at 
http://www.partners.org/complianceline . If the e-mail was sent to you in e
rror 
but does not contain patient information, please contact the sender and pro
perly 
dispose of the e-mail. 
 

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


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

Re: [Freesurfer] recon-all strip skull and neck by brain volume mask

[Rujing Zha]

Dear Louis,
Thanks for your helpful prompt in advance.
I see. In my case, there is a not properly stripping, there is a not properly 
gray matter(there are a some skull considered as gray matter). Did you mean I 
can draw the segmentation without considering the skull stripping? And a bad 
brainmask.mgz will not influence the GM thickness analysis?
Thanks in advance.
All the best.

2013-12-03



Rujing Zha



发件人：Louis Nicholas Vinke 
发送时间：2013-12-03 03:58
主题：Re: [Freesurfer] recon-all strip skull and neck by brain volume mask
收件人："Rujing Zha"
抄送："freesurfer"

Hi Rujing, 
Even if there is some skull/dura left after the skullstrip step in  
recon-all, it still may not negatively impact the surfaces.  It might be  
worth running the remaining recon-all steps to see how the surfaces turn  
out. 

If you want to swap-in a better skullstripped volume into the recon-all  
stream then you just need to replace the brainmask.mgz and continue with  
autorecon2 and autorecon3. 

Keep in mind that the new brainmask.mgz volume still needs to be in the  
conformed anatomical space, so use the T1.mgz or brainmask.mgz to create  
the improved skullstrip volume which will replace the existing  
brainmask.mgz. 

-Louis 

On Mon, 2 Dec 2013, Rujing Zha wrote: 

> Dear all, 
> Part of subjects 3d images cannot be stripped skull and neck properly in 
> recon-all default. I have got the brain volume mask, how I can using the 
> existing proper mask to help strip skull in recon-all and next workflow? 
> Thanks.Any reply will be appreciated. 
> All the best. 
>   
> 2013-12-02 
>  
>  
> Rujing Zha 
>  
> 
___ 
Freesurfer mailing list 
Freesurfer@nmr.mgh.harvard.edu 
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 


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


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

Re: [Freesurfer] viewing slices dynamically by tkmedit

[Rujing Zha]

Hi Louis,
Thanks for your helpful suggestion. 
Maybe I just click the "slice -/+" module if I want to view all the slices of 
one subject's volume in tkmedit. But I do not want to click the button 
continuously to view all the slices. I want to press a button/key once, then I 
can see all the slices one by one in a volume automatically; the automatically 
view will halt if I press a button/key again or other button/key.
Thanks in advance.
All the best.
2013-12-03



Rujing Zha



发件人：Louis Nicholas Vinke 
发送时间：2013-12-03 03:50
主题：Re: [Freesurfer] viewing slices dynamically by tkmedit
收件人："Rujing Zha"
抄送："freesurfer"

Hi Rujing, 
You can use a tcl script to take several snapshots in tkmedit, then you  
could use the convert command (part of ImageMagick distro) or  
something similar to create an animated gif.  With the convert command you  
would use the -adjoin and -delay flags.  You could use one of the tcl  
scripts from the QA tools scripts as a good start (e.g. snap_tkmedit.tcl). 

You could also get multiple snapshots with freeview using command line  
flags and a shell script. 
-Louis 

On Sat, 30 Nov 2013, Rujing Zha wrote: 

> Dear all, 
> I want to see the slices as a shape of movie in tkmedit. Do anyone can tell 
> me how to do it? 
> Thanks. 
> All the best. 
>   
> 2013-11-30 
>  
>  
> Rujing Zha 
>  
> 


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


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

Re: [Freesurfer] Which boost version is used in CVS, mris_resample

[André Ribeiro]

Hi Martin,

In November 27 I posted a similar question, which later I found a solution.
See if it works for you.

Hi Lilla,
> Thank you for your reply. I have boost installed, yet it is not the
> version required (v. 1.49). Although, even after installing an older
> version such as the 1.41 it is not straightforward to use this libboost
> with freesurfer. The doc from libboost is not easy to understand and even
> if done correctly you will not be able to use this installation as there is
> no libboost_program_options.so.5. Nevertheless, I got it to work so here
> goes the solution that worked for me.
> >Download libboost v. 1.41 and untar
> >cd libboost_folder
> >mkdir libraries
> >./bootstrap.sh --prefix=./libraries
> >./bjam install
> >cd libraries/lib
> > ln -s libboost_program_options.so.1.41.0 libboost_program_options.so.5
> >export LD_LIBRARY_PATH=.../boost_1_41_0/libraries/lib:$LD_LIBRARY_PATH
> Cheers,
> Andre Santos Ribeiro


regards,
Andre Santos Ribeiro


On Mon, Dec 2, 2013 at 9:57 PM, Martin Kavec  wrote:

> Hi Zeke,
>
> Thanks a lot for explanation. I think I will install centOS into a virtual
> machine for quick solution. I only need it to run CVS.
>
> Thanks and best regards,
>
> Martin
>
> Sent from my iPad
>
> > On 2.12.2013, at 22:50, Z K  wrote:
> >
> > Martin,
> >
> > Upx (http://upx.sourceforge.net) is an executable packaging utility we
> run on all our binaries before shipping to reduce their overall size. One
> consequence of upx is that it changes the way the "file" and "ld" commands
> process the binaries. In this case it makes the "file" command say they are
> statically linked when infact it is dynamically linked. You can view this
> for yourself by running upx in reverse (upx -d mris_resample) and indeed
> you will see that it says dynamically linked.
> >
> > libboost1.41 is what comes by default on our centOS6_x86_64 platforms
> and it is what freesurfer builds against. All I can suggest is that you
> install the same version, or one very close to it.
> >
> > -Zeke
> >
> >
> >
> >> On 12/02/2013 02:50 PM, Martin Kavec wrote:
> >> Hi Zeke,
> >>
> >> Thanks for response. Well it was the first thing for me to try to
> compile boost on gentoo, which went fine. However the libraries were not
> compatible. Gentoo has 1.52 version, while the one needed is about 4 years
> old.
> >>
> >> When I do "ldd mris_resample" I get "not a dynamic executable" and when
> I do "file mris_resample" I get that it is a statically linked executable,
> stripped. I think something could have happened with when stripping the
> executable. I get the same output from file mris_rescale, but mris_rescale
> runs fine.
> >>
> >> I am using Freesurfer-5.3.0 for Centos6 x86_64.
> >>
> >> Thanks,
> >>
> >> Martin
> >>
> >> Sent from my iPad
> >>
> >>> On 2.12.2013, at 17:33, Z K  wrote:
> >>>
> >>> Martin,
> >>>
> >>> libboost is not a static library, it is a shared library. It comes by
> >>> default on centOS platforms and freesurfer compiles against it during
> >>> the the build process. Typing 'ldd mris_resample' and examining the
> >>> output confirms this:
> >>>
> >>> $>ldd mris_resample
> >>> linux-vdso.so.1 =>  (0x7fffd2773000)
> >>> libboost_program_options.so.5 =>
> >>> /usr/lib64/libboost_program_options.so.5 (0x7fe2e588d000)
> >>> etc...
> >>>
> >>> Also, many of the freesurfer binaries do require the libboost library.
> >>>
> >>> Freesurfer works on most linux distribution, but we specifically build
> >>> on and support centOS platforms. We do not have Gentoo linux machines
> to
> >>> try and replicate your error but I am confident that if you get the
> >>> libboost libraries on your machine, the program will work properly.
> >>>
> >>> -Zeke
> >>>
> >>>
> >>>
> >>>
>  On 11/28/2013 05:09 PM, Martin Kavec wrote:
>  Hi Lilla,
> 
>  thanks for coming back. Unfortunately I was not able to compile
>  appropriate boost for my operating system Gentoo linux. Nevertheless I
>  do not understand why mris_resample misses the library if it should be
>  statically linked. Other binaries do not need it. Could you please
> check
>  if mris_resample in 64-bit linux version of CentOS is correct?
> 
>  Otherwise I cannot run cvs.
> 
>  Thanks a lot,
> 
>  Martin
> 
> 
>  On Mon, Nov 25, 2013 at 5:32 PM, Lilla Zollei
>  mailto:lzol...@nmr.mgh.harvard.edu>>
> wrote:
> 
> 
> This is a bit delayed response (my apologies) to an earlier
> question to
> the list:
> 
> The boost library is installed by default on CentOS platforms. If
> a user
> gets the libboost error then they are using a different platform
> which
> doesn't have boost installed by default. On RedHat systems libboost
> can be
> installed by typing the follwing command:
> $>yum install boost-devel"
> 
> The version of libboost that we use for our latest release is 1.41.
> 
> Lilla
> 

Re: [Freesurfer] DTI - tracula - satisfactory cntrl pnts

[Anastasia Yendiki]

Hi Skyler - Are you using freesurfer 5.1 or 5.3?

Most likely this issue is due to poor registration, either from the 
individual DWI to the individual T1, or from the individual T1 to the 
template space. Or it could be that there is a problem with the 
aparc+aseg.


a.y

On Mon, 2 Dec 2013, Skyler Gabriel Shollenbarger wrote:


Hi all,

I've been running DTI using tracula (fs version 5) for over 1 week on 2 
subjects. It appears that it is having difficulty finding satisfactory control 
point fit and has attempted over 1600 tries. Any help is greatly appreciated.
See error below:

INFO: Distances between consecutive points are 25 24 25 26
WARN: Could not find satisfactory control point fit - try 1665
Finding center streamline
INFO: Step is 4 voxels
WARN: Turning off FA check for center streamline
INFO: Step is 4 voxels
WARN: Turning off deviation check for center streamline
INFO: Step is 4 voxels
INFO: Length of center streamline is 96 voxels
Selecting 5 points on center streamline
INFO: Step is 4 voxels
WARN: Defaulting to equidistant control points
INFO: Selected control points are
 108 193 84
 112 173 72
 98 153 75
 74 157 75
 74 184 86
INFO: Distances between consecutive points are 24 25 24 29
WARN: Could not find satisfactory control point fit - try 1666
Finding center streamline
INFO: Step is 4 voxels
WARN: Turning off FA check for center streamline
INFO: Step is 4 voxels
WARN: Turning off deviation check for center streamline
INFO: Step is 4 voxels


Best,
Skyler

___
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] DTI - tracula - satisfactory cntrl pnts

[Skyler Gabriel Shollenbarger]

Hi all,

I've been running DTI using tracula (fs version 5) for over 1 week on 2 
subjects. It appears that it is having difficulty finding satisfactory control 
point fit and has attempted over 1600 tries. Any help is greatly appreciated. 
See error below:

INFO: Distances between consecutive points are 25 24 25 26
WARN: Could not find satisfactory control point fit - try 1665
Finding center streamline
INFO: Step is 4 voxels
WARN: Turning off FA check for center streamline
INFO: Step is 4 voxels
WARN: Turning off deviation check for center streamline
INFO: Step is 4 voxels
INFO: Length of center streamline is 96 voxels
Selecting 5 points on center streamline
INFO: Step is 4 voxels
WARN: Defaulting to equidistant control points
INFO: Selected control points are
 108 193 84
 112 173 72
 98 153 75
 74 157 75
 74 184 86
INFO: Distances between consecutive points are 24 25 24 29
WARN: Could not find satisfactory control point fit - try 1666
Finding center streamline
INFO: Step is 4 voxels
WARN: Turning off FA check for center streamline
INFO: Step is 4 voxels
WARN: Turning off deviation check for center streamline
INFO: Step is 4 voxels


Best,
Skyler

-- 

Skyler G. Shollenbarger 
Graduate Student - UWM Brain Lab 
Clinical Psychology & Neurospychology 
University of Wisconsin-Milwaukee 


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


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

Re: [Freesurfer] Which boost version is used in CVS, mris_resample

[Martin Kavec]

Hi Zeke,

Thanks a lot for explanation. I think I will install centOS into a virtual 
machine for quick solution. I only need it to run CVS.

Thanks and best regards,

Martin

Sent from my iPad

> On 2.12.2013, at 22:50, Z K  wrote:
> 
> Martin,
> 
> Upx (http://upx.sourceforge.net) is an executable packaging utility we run on 
> all our binaries before shipping to reduce their overall size. One 
> consequence of upx is that it changes the way the "file" and "ld" commands 
> process the binaries. In this case it makes the "file" command say they are 
> statically linked when infact it is dynamically linked. You can view this for 
> yourself by running upx in reverse (upx -d mris_resample) and indeed you will 
> see that it says dynamically linked.
> 
> libboost1.41 is what comes by default on our centOS6_x86_64 platforms and it 
> is what freesurfer builds against. All I can suggest is that you install the 
> same version, or one very close to it.
> 
> -Zeke
> 
> 
> 
>> On 12/02/2013 02:50 PM, Martin Kavec wrote:
>> Hi Zeke,
>> 
>> Thanks for response. Well it was the first thing for me to try to compile 
>> boost on gentoo, which went fine. However the libraries were not compatible. 
>> Gentoo has 1.52 version, while the one needed is about 4 years old.
>> 
>> When I do "ldd mris_resample" I get "not a dynamic executable" and when I do 
>> "file mris_resample" I get that it is a statically linked executable, 
>> stripped. I think something could have happened with when stripping the 
>> executable. I get the same output from file mris_rescale, but mris_rescale 
>> runs fine.
>> 
>> I am using Freesurfer-5.3.0 for Centos6 x86_64.
>> 
>> Thanks,
>> 
>> Martin
>> 
>> Sent from my iPad
>> 
>>> On 2.12.2013, at 17:33, Z K  wrote:
>>> 
>>> Martin,
>>> 
>>> libboost is not a static library, it is a shared library. It comes by
>>> default on centOS platforms and freesurfer compiles against it during
>>> the the build process. Typing 'ldd mris_resample' and examining the
>>> output confirms this:
>>> 
>>> $>ldd mris_resample
>>> linux-vdso.so.1 =>  (0x7fffd2773000)
>>> libboost_program_options.so.5 =>
>>> /usr/lib64/libboost_program_options.so.5 (0x7fe2e588d000)
>>> etc...
>>> 
>>> Also, many of the freesurfer binaries do require the libboost library.
>>> 
>>> Freesurfer works on most linux distribution, but we specifically build
>>> on and support centOS platforms. We do not have Gentoo linux machines to
>>> try and replicate your error but I am confident that if you get the
>>> libboost libraries on your machine, the program will work properly.
>>> 
>>> -Zeke
>>> 
>>> 
>>> 
>>> 
 On 11/28/2013 05:09 PM, Martin Kavec wrote:
 Hi Lilla,
 
 thanks for coming back. Unfortunately I was not able to compile
 appropriate boost for my operating system Gentoo linux. Nevertheless I
 do not understand why mris_resample misses the library if it should be
 statically linked. Other binaries do not need it. Could you please check
 if mris_resample in 64-bit linux version of CentOS is correct?
 
 Otherwise I cannot run cvs.
 
 Thanks a lot,
 
 Martin
 
 
 On Mon, Nov 25, 2013 at 5:32 PM, Lilla Zollei
 mailto:lzol...@nmr.mgh.harvard.edu>> wrote:
 
 
This is a bit delayed response (my apologies) to an earlier question to
the list:
 
The boost library is installed by default on CentOS platforms. If a user
gets the libboost error then they are using a different platform which
doesn't have boost installed by default. On RedHat systems libboost
can be
installed by typing the follwing command:
$>yum install boost-devel"
 
The version of libboost that we use for our latest release is 1.41.
 
Lilla
 
-
Martin Kavec Mon, 04 Nov 2013 14:10:53 -0800
 
Hi guys,
 
When running mri_cvs_register on linux (5.3.0), I get into problem with
mris_resample, which cannot find libboost_programs_options.so.5. I
installed
the latest version of boost-1.52.0 for my system, but there are
unresolved
symbols.
 
Which version is suitable for mris_resample?
 
Thanks,
 
Martin
 
Sent from my iPad
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu 
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu 
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
 
 
The information in this e-mail is intended only for the person to
whom it is
addressed. If you believe this e-mail was se

Re: [Freesurfer] Which boost version is used in CVS, mris_resample

[Z K]

Martin,

Upx (http://upx.sourceforge.net) is an executable packaging utility we 
run on all our binaries before shipping to reduce their overall size. 
One consequence of upx is that it changes the way the "file" and "ld" 
commands process the binaries. In this case it makes the "file" command 
say they are statically linked when infact it is dynamically linked. You 
can view this for yourself by running upx in reverse (upx -d 
mris_resample) and indeed you will see that it says dynamically linked.

libboost1.41 is what comes by default on our centOS6_x86_64 platforms 
and it is what freesurfer builds against. All I can suggest is that you 
install the same version, or one very close to it.

-Zeke



On 12/02/2013 02:50 PM, Martin Kavec wrote:
> Hi Zeke,
>
> Thanks for response. Well it was the first thing for me to try to compile 
> boost on gentoo, which went fine. However the libraries were not compatible. 
> Gentoo has 1.52 version, while the one needed is about 4 years old.
>
> When I do "ldd mris_resample" I get "not a dynamic executable" and when I do 
> "file mris_resample" I get that it is a statically linked executable, 
> stripped. I think something could have happened with when stripping the 
> executable. I get the same output from file mris_rescale, but mris_rescale 
> runs fine.
>
> I am using Freesurfer-5.3.0 for Centos6 x86_64.
>
> Thanks,
>
> Martin
>
> Sent from my iPad
>
>> On 2.12.2013, at 17:33, Z K  wrote:
>>
>> Martin,
>>
>> libboost is not a static library, it is a shared library. It comes by
>> default on centOS platforms and freesurfer compiles against it during
>> the the build process. Typing 'ldd mris_resample' and examining the
>> output confirms this:
>>
>> $>ldd mris_resample
>> linux-vdso.so.1 =>  (0x7fffd2773000)
>> libboost_program_options.so.5 =>
>> /usr/lib64/libboost_program_options.so.5 (0x7fe2e588d000)
>> etc...
>>
>> Also, many of the freesurfer binaries do require the libboost library.
>>
>> Freesurfer works on most linux distribution, but we specifically build
>> on and support centOS platforms. We do not have Gentoo linux machines to
>> try and replicate your error but I am confident that if you get the
>> libboost libraries on your machine, the program will work properly.
>>
>> -Zeke
>>
>>
>>
>>
>>> On 11/28/2013 05:09 PM, Martin Kavec wrote:
>>> Hi Lilla,
>>>
>>> thanks for coming back. Unfortunately I was not able to compile
>>> appropriate boost for my operating system Gentoo linux. Nevertheless I
>>> do not understand why mris_resample misses the library if it should be
>>> statically linked. Other binaries do not need it. Could you please check
>>> if mris_resample in 64-bit linux version of CentOS is correct?
>>>
>>> Otherwise I cannot run cvs.
>>>
>>> Thanks a lot,
>>>
>>> Martin
>>>
>>>
>>> On Mon, Nov 25, 2013 at 5:32 PM, Lilla Zollei
>>> mailto:lzol...@nmr.mgh.harvard.edu>> wrote:
>>>
>>>
>>> This is a bit delayed response (my apologies) to an earlier question to
>>> the list:
>>>
>>> The boost library is installed by default on CentOS platforms. If a user
>>> gets the libboost error then they are using a different platform which
>>> doesn't have boost installed by default. On RedHat systems libboost
>>> can be
>>> installed by typing the follwing command:
>>> $>yum install boost-devel"
>>>
>>> The version of libboost that we use for our latest release is 1.41.
>>>
>>> Lilla
>>>
>>> -
>>> Martin Kavec Mon, 04 Nov 2013 14:10:53 -0800
>>>
>>> Hi guys,
>>>
>>> When running mri_cvs_register on linux (5.3.0), I get into problem with
>>> mris_resample, which cannot find libboost_programs_options.so.5. I
>>> installed
>>> the latest version of boost-1.52.0 for my system, but there are
>>> unresolved
>>> symbols.
>>>
>>> Which version is suitable for mris_resample?
>>>
>>> Thanks,
>>>
>>> Martin
>>>
>>> Sent from my iPad
>>> ___
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu 
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>> ___
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu 
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>
>>>
>>> The information in this e-mail is intended only for the person to
>>> whom it is
>>> addressed. If you believe this e-mail was sent to you in error and
>>> the e-mail
>>> contains patient information, please contact the Partners Compliance
>>> HelpLine at
>>> http://www.partners.org/complianceline . If the e-mail was sent to
>>> you in error
>>> but does not contain patient information, please contact the sender
>>> and properly
>>> dispose of the e-mail.
>>>
>>>
>>>
>>>
>>> 

Re: [Freesurfer] LONG stream questions

[Martin Reuter]

Hi,

so far that wiki page only had the commands for cross sectional runs. I 
added the commands for the longitudinal runs (see my mail and also the 
one for the surface mapping) to that page for future reference.

Best, Martin

On 12/02/2013 03:21 PM, Douglas N Greve wrote:
> For #2 you can use the method described here
> http://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat
>
>
> On 12/02/2013 03:01 PM, Martin Reuter wrote:
>> Hi Ivan,
>>
>> 1) it means that the voxel sizes across your images are different. Do
>> mri_info on the images to see what's going on. Usually this is no
>> problem if the differences are tiny. Just a warning.
>>
>> 2) yes, the longs are all in the same space as the base, you can map
>> images to the rawavg from the cross runs with a single command:
>>
>> cd $SUBJECTS_DIR/.long./mri
>>
>> mri_convert -ait transforms/_to_.long..lta \
>>  -rl $SUBJCECTS_DIR//mri/rawavg.mgz \
>>  -rt nearest aseg.mgz aseg-in-rawavg.mgz
>>
>> for other images (not segmentations, e.g. brainmask, use '-rt cubic'
>> instead of nearest neighbor).
>>
>> Best, Martin
>>
>>
>> On 11/22/2013 09:22 PM, Kirov, Ivan wrote:
>>> Dear FreeSurfer group/Dr. Reuter,
>>>
>>> My questions are in regards to the LONG stream.
>>>
>>> My version is: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
>>>
>>> 1) Error message
>>> During the creation of the BASE, I get the following error in the
>>> beginning of the recon:
>> WARNING: Image geometries differ across time, maybe due to
>>> aquisition changes?
>>>   This can potentially bias a longitudinal study! Will
>>> continue in 10s.
>>> What should I be aware of in regards to this error?
>>>
>>> The images were all acquired using the same MPRAGE protocol.
>>> All timepoints were fed MPRAGEs reconstructed in the axial
>>> orientation, but some may have been reconstructed at an angle. I was
>>> assured that this is not an issue for FreeSurfer, but could this be
>>> the reason for the error?
>>>
>>>
>>> 2) Conversion of LONG run aseg.mgz segmentations to native anatomical
>>> space
>>>
>>> Executing the commands for converting aseg.mgz to native space (as
>>> noted in the FsAnat-to-NativeAnat wiki entry) in the folder of a long
>>> run (me1.long.me_base) does not convert.
>>>
>>> It seems to me that (unlike the cross runs) the long runs are all in
>>> the same space (in the template/ base space?) and their rawavg.mgz
>>> does not match that of the corresponding cross run. Some insight on
>>> this would be appreciated.
>>>
>>> The question is how to convert an individual long run's aseg.mgz into
>>> native anatomical space. Perhaps using the rawavg.mgz from the
>>> corresponding cross run?
>>>
>>> Thank you very much!
>>> Ivan
>>>
>>> --
>>> Ivan Kirov, PhD
>>> Postdoctoral fellow
>>> New York University School of Medicine
>>> Center for Biomedical Imaging
>>> 660 1st Ave, 4th floor, New York, NY 10016
>>> Tel: 212-263-3337
>>> Fax: 212-263-7541
>>> 
>>> This email message, including any attachments, is for the sole use of
>>> the intended recipient(s) and may contain information that is
>>> proprietary, confidential, and exempt from disclosure under
>>> applicable law. Any unauthorized review, use, disclosure, or
>>> distribution is prohibited. If you have received this email in error
>>> please notify the sender by return email and delete the original
>>> message. Please note, the recipient should check this email and any
>>> attachments for the presence of viruses. The organization accepts no
>>> liability for any damage caused by any virus transmitted by this email.
>>> =
>>>
>>>
>>> ___
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> -- 
>> Martin Reuter, Ph.D.
>> Assistant in Neuroscience - Massachusetts General Hospital
>> Instructor in Neurology   - Harvard Medical School
>> MGH / HMS / MIT
>>
>> A.A.Martinos Center for Biomedical Imaging
>> 149 Thirteenth Street, Suite 2301
>> Charlestown, MA 02129
>>
>> Phone: +1-617-724-5652
>> Email:
>>  mreu...@nmr.mgh.harvard.edu
>>  reu...@mit.edu
>> Web  :http://reuter.mit.edu
>>
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- 
Martin Reuter, Ph.D.
Assistant in Neuroscience - Massachusetts General Hospital
Instructor in Neurology   - Harvard Medical School
MGH / HMS / MIT

A.A.Martinos Center for Biomedical Imaging
149 Thirteenth Street, Suite 2301
Charlestown, MA 02129

Phone: +1-617-724-5652
Email:
mreu...@nmr.mgh.harvard.edu
reu...@mit.edu
Web  : http://reuter.mit.edu

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

Re: [Freesurfer] Fwd: converting to fsaverage space

[Paul Beach]

Doug,

Thank you for your very helpful suggestion. Indeed, doing so made it so I
could quickly take any parts (or all) of each Greicius network and put them
in individual subject space.

In case this may help anyone else, the final series of commands were (in
this case, for the whole anterior salience network):

*mni152reg --s [subj]*

mri_label2vol
*--seg anterior_Salience.nii.gz \*
--reg $SUBJECTS_DIR/[subj]/mri/transforms/reg.mni152.2mm.dat \
--invertmtx --o anterior_Salience_[subj].nii.gz \
--temp $SUBJECTS_DIR/[subj]/mri/orig.mgz


Cheers,
Paul


On Sun, Dec 1, 2013 at 7:28 PM, Douglas Greve wrote:

>
> Don't go through fsaverage. Instead use mni152reg to create a registration
> matrix from an individual to the 152 (stored in
> $SUBJECTS_DIR/$subject/mri/transforms). Then use the command below with
> this registration matrix instead of mni152.register.dat
>
> doug
>
>
>
> On 11/27/13 2:57 PM, Paul Beach wrote:
>
>  Freesurfer experts,
>
>  I am interested in converting functional ROIs defined by the Greicius
> lab (http://findlab.stanford.edu/functional_ROIs.html) into individual
> subject space. Originally I had converted the fROIs from an FSL-based
> MNI152 to Freesurfer-based MNI305 space. To do this I used this command (in
> this case for the precuneus network fROI):
>
>  *mri_label2vol \*
> *--seg Precuneus.nii.gz \*
> *--reg $FREESURFER_HOME/average/mni152.register.dat \*
> *--invertmtx --o Precuneus_FS.nii.gz \*
>  *--temp $FREESURFER_HOME/subjects/fsaverage/mri/mni305.cor.mgz*
>
>  *The output file's information, provided by 3dinfo, is as follows:*
>  Template Space:  ORIG
>  Dataset Type:Anat Bucket (-abuc)
> Byte Order:  LSB_FIRST {assumed} [this CPU native = LSB_FIRST]
> Storage Mode:NIFTI
> Storage Space:   67,108,864 (67 million [mega]) bytes
> Geometry String: "MATRIX(1,0,0,-128,0,0,-1,128,0,-1,0,128):256,256,256"
> Data Axes Tilt:  Plumb
> Data Axes Orientation:
>   first  (x) = Right-to-Left
>   second (y) = Superior-to-Inferior
>   third  (z) = Posterior-to-Anterior   [-orient RSP]
> R-to-L extent:  -128.000 [R] -to-   127.000 [L] -step- 1.000 mm [256
> voxels]
> A-to-P extent:  -127.000 [A] -to-   128.000 [P] -step- 1.000 mm [256
> voxels]
> I-to-S extent:  -127.000 [I] -to-   128.000 [S] -step- 1.000 mm [256
> voxels]
> Number of values stored at each pixel = 1
>   -- At sub-brick #0 '?' datum type is float
>
>
>  I would like to take the output of this command and convert it to an
> individual subject's space. However, I'm not really sure how to proceed.
>
>  Originally I thought the above command, in using the mni305.cor.mgz file
> in fsaverage's mri folder, would put the output file into fsaverage's
> space. I could then, I figured, use some other commands I have for moving
> things in fsaverage space to individual subject space. Unfortunately, when
> I try to load the above output file into tkmedit for fsaverage as an aux
> volume it's essentially off screen (i.e. not in the brain). Obviously the
> output file is not in fsaverage space, per se.
>
>  Any thoughts on how to proceed?
>
>  Thanks,
> Paul
> --
> Paul Beach
> DO/PhD candidate - Year VI
> Michigan State University
> - College of Osteopathic Medicine
> - Neuroscience Program
>- Bozoki Lab: Neurology/Radiology
>
>
> ___
> Freesurfer mailing 
> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> The information in this e-mail is intended only for the person to whom it
> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
>


-- 
Paul Beach
DO/PhD candidate - Year VI
Michigan State University
- College of Osteopathic Medicine
- Neuroscience Program
   - Bozoki Lab: Neurology/Radiology
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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

Re: [Freesurfer] LONG stream questions

[Douglas N Greve]

For #2 you can use the method described here
http://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat


On 12/02/2013 03:01 PM, Martin Reuter wrote:
> Hi Ivan,
>
> 1) it means that the voxel sizes across your images are different. Do 
> mri_info on the images to see what's going on. Usually this is no 
> problem if the differences are tiny. Just a warning.
>
> 2) yes, the longs are all in the same space as the base, you can map 
> images to the rawavg from the cross runs with a single command:
>
> cd $SUBJECTS_DIR/.long./mri
>
> mri_convert -ait transforms/_to_.long..lta \
> -rl $SUBJCECTS_DIR//mri/rawavg.mgz \
> -rt nearest aseg.mgz aseg-in-rawavg.mgz
>
> for other images (not segmentations, e.g. brainmask, use '-rt cubic' 
> instead of nearest neighbor).
>
> Best, Martin
>
>
> On 11/22/2013 09:22 PM, Kirov, Ivan wrote:
>> Dear FreeSurfer group/Dr. Reuter,
>>
>> My questions are in regards to the LONG stream.
>>
>> My version is: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
>>
>> 1) Error message
>> During the creation of the BASE, I get the following error in the 
>> beginning of the recon:
>> >>>WARNING: Image geometries differ across time, maybe due to 
>> aquisition changes?
>>  This can potentially bias a longitudinal study! Will 
>> continue in 10s.
>> What should I be aware of in regards to this error?
>>
>> The images were all acquired using the same MPRAGE protocol.
>> All timepoints were fed MPRAGEs reconstructed in the axial 
>> orientation, but some may have been reconstructed at an angle. I was 
>> assured that this is not an issue for FreeSurfer, but could this be 
>> the reason for the error?
>>
>>
>> 2) Conversion of LONG run aseg.mgz segmentations to native anatomical 
>> space
>>
>> Executing the commands for converting aseg.mgz to native space (as 
>> noted in the FsAnat-to-NativeAnat wiki entry) in the folder of a long 
>> run (me1.long.me_base) does not convert.
>>
>> It seems to me that (unlike the cross runs) the long runs are all in 
>> the same space (in the template/ base space?) and their rawavg.mgz 
>> does not match that of the corresponding cross run. Some insight on 
>> this would be appreciated.
>>
>> The question is how to convert an individual long run's aseg.mgz into 
>> native anatomical space. Perhaps using the rawavg.mgz from the 
>> corresponding cross run?
>>
>> Thank you very much!
>> Ivan
>>
>> --
>> Ivan Kirov, PhD
>> Postdoctoral fellow
>> New York University School of Medicine
>> Center for Biomedical Imaging
>> 660 1st Ave, 4th floor, New York, NY 10016
>> Tel: 212-263-3337
>> Fax: 212-263-7541
>> 
>> This email message, including any attachments, is for the sole use of 
>> the intended recipient(s) and may contain information that is 
>> proprietary, confidential, and exempt from disclosure under 
>> applicable law. Any unauthorized review, use, disclosure, or 
>> distribution is prohibited. If you have received this email in error 
>> please notify the sender by return email and delete the original 
>> message. Please note, the recipient should check this email and any 
>> attachments for the presence of viruses. The organization accepts no 
>> liability for any damage caused by any virus transmitted by this email.
>> =
>>
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> -- 
> Martin Reuter, Ph.D.
> Assistant in Neuroscience - Massachusetts General Hospital
> Instructor in Neurology   - Harvard Medical School
> MGH / HMS / MIT
>
> A.A.Martinos Center for Biomedical Imaging
> 149 Thirteenth Street, Suite 2301
> Charlestown, MA 02129
>
> Phone: +1-617-724-5652
> Email:
> mreu...@nmr.mgh.harvard.edu
> reu...@mit.edu
> Web  :http://reuter.mit.edu  
>
>
> ___
> 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 co

Re: [Freesurfer] trac-all inquiry

[Anastasia Yendiki]

Hi David - I am not convinced that all the regisrtrations have worked well 
for this subject. The fact that some of the coordinates of the control 
points, which are mapped from template to individual space, are negative 
in individual space (see INFO messages in log file), means that some part 
of the brain in templated space is mapped outside the field of view in 
individual DWI space. Can you send any screenshots that show the quality 
of the DWI to anatomical and DWI to MNI registrations?


Thanks,
a.y

On Mon, 2 Dec 2013, David Soto wrote:


hi - thanks , not sure though...the no_dif brain maskseems ok, if that is
what you meant...

I did re-run the processing and
in the last run I can not see the WARN you mentioned
the latest preprocessing output from the preprocessing can be
found  here:  https://dl.dropboxusercontent.com/u/8209026/prepro.txt

the dlabel/diff output got stuck with the
rh.ilf_AS_avg33 which only contains thee  _mni_bbr_cpts_5.txt but nothing
else

thanks so much

ds



On Mon, Dec 2, 2013 at 10:59 AM, Anastasia Yendiki
 wrote:

  Hi David - Sorry for the delayed response due to traveling.

  There's a warning about the right ILF in the log file that may
  offer a
  clue:

  WARN: Initial control point 37 56 -6 is not in DWI volume - is
  DWI cropped?
  WARN: Replacing with closest point in volume (37 56 0)
  WARN: Initial control point 38 45 -1 is not in DWI volume - is
  DWI cropped?
  WARN: Replacing with closest point in volume (38 45 0)
  WARN: Initial start point 37 56 0 is not in start ROI
  WARN: Replacing with closest point in start ROI (31 56 0)

  Is the brain mask cropped on either end of the right ILF? You
  mentioned
  that you already checked the registration of the FA map to the
  template
  space (dmri/mni/dtifit_FA.bbr.nii.gz), so I'm assuming there's
  nothing
  wrong there.

  a.y

  On Sat, 16 Nov 2013, David Soto wrote:

  > Thanks!
  > for some weird unknown reason
  > the log for the preprocessing file of this
  > subject is unusually big (2.8 megabytes)
  >  please get it from this link
  > https://dl.dropboxusercontent.com/u/8209026/Archive.zip
  > cheers
  > ds
  >
  >
  > On Sat, Nov 16, 2013 at 3:13 PM, Anastasia Yendiki
  >  wrote:
  >
  >       Hi David - This log only shows output from the -path
  step and
  >       not from the -prep step. The file that's missing should
  be
  >       created during the -prep step, so there's no way to
  figure out
  >       what went wrong without seeing the output from the
  >       pre-processing.
  >
  >       Please cc the freesurfer list on your reply.
  >
  >       Thank you,
  >       a.y
  >
  >
  >       On Sat, 16 Nov 2013, David Soto wrote:
  >
  >             Thanks, please see attachedI only noticed this 
  >             ERROR: 
Couldnotopen/home/dsoto/Documents/fmri/rsdtianawmgui/14AB/dlabel/diff/rh.ilf_AS_
  avg
  >             33_m
  >             ni_bbr_cpts_5_std.txt
  >             cheers
  >             DS
  >
  >
  >             On Fri, Nov 15, 2013 at 8:55 PM, Anastasia Yendiki
  >              wrote:
  >
  >                   Hi David - Can you please send us the
  >             trac-all.log file for this
  >                   subject?
  >                   Without seeing where it stopped and what
  error
  >             messages there
  >                   are it's
  >                   hard to guess what's going on.
  >
  >                   Thanks,
  >                   a.y
  >
  >                   On Fri, 15 Nov 2013, David Soto wrote:
  >
  >                   >  Hi -  
  >                   > trac-all completed in all my Ps except one
  >                   > and I noticed that the  dlabel/diff output
  >             does not contain
  >                   all the files
  >                   >
  >                   > I assessed whether it could be do to poor
  >             registration, by
  >                   checking
  >                   > the  aparc+aseg
  >                   > file and looks allright
  >                   >
  >                   > I also checked the registration of FA maps
  >             to standard space
  >                   by 
  >                   > freeview -v
  >             $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz
  >                   > dtifit_FA.bbr.nii.gz 
  >                   > and seems fine
  >                   >
  >                   > also
  >                   >
  >                   > freeview -v brain_anat_orig.nii.gz
  >             lowb_brain.nii.gz 
  >                   >
  >                   > which also seems fine
  >   

[Freesurfer] R: Re: Linear regression

[stdp82]

Tank you very much.
A-Do you mean the partial correlation coeff (PCC) at each voxel averaged over 
region? Finally a linear regression is done between cortical thickness of a 
composite region and NPS. However the authors discuss every individual region 
as related to disease. So a table with partials correlations of individuals 
ROIs with NPS seems useful to support the discussion. B- I'd like to obtain the 
covariance matrix of the regression made between cortical thickness, group and 
covariates. How can I do it?I'm not sure what you mean. Would this be a 
different matrix for each  vertex?I cite the referee: "The authors must provide 
the covariance matrix of the regression made between cortical thickness, group 
and covariates as supplementary information in order to increase the value of 
the results."
I don't have Matlab for mri_glmfit_pcc matlab.
Stefano





Messaggio originale
Da: gr...@nmr.mgh.harvard.edu
Data: 2-dic-2013 20.47
A: 
Ogg: Re: [Freesurfer] Linear regression


On 12/02/2013 02:22 PM, std...@virgilio.it wrote:
> Hi list,
>
> I have some questions, please.
>
> I performed linear regression by qdec to find the regions where the 
> cortical thinning correlates with neuropsychological test (NPS), 
> taking in account 3 nuisance factors.
>
> A- I individuated some posterior regions and now I'd like to build a 
> table with partials correlations of individuals ROIs with NPS. How can 
> I obtain the values for each region?
Do you mean the partial correlation coeff (PCC) at each voxel averaged 
over region? You can get PCC maps using the mri_glmfit_pcc matlab 
command. You can then do the averaging over region using mri_segstats.
>
> B- I'd like to obtain the covariance matrix of the regression made 
> between cortical thickness,  group and covariates. How can I do it?
I'm not sure what you mean. Would this be a different matrix for each 
vertex?
>
> C- Is there a specific reference for qdec?
No, it is just a GLM so any GLM reference will do.
>
> Thank you very much,
>
>
> Stefano
>
>
>
>
>
> ___
> 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


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] LONG stream questions

[Martin Reuter]

Hi Ivan,

1) it means that the voxel sizes across your images are different. Do 
mri_info on the images to see what's going on. Usually this is no 
problem if the differences are tiny. Just a warning.


2) yes, the longs are all in the same space as the base, you can map 
images to the rawavg from the cross runs with a single command:


cd $SUBJECTS_DIR/.long./mri

mri_convert -ait transforms/_to_.long..lta \
-rl $SUBJCECTS_DIR//mri/rawavg.mgz \
-rt nearest aseg.mgz aseg-in-rawavg.mgz

for other images (not segmentations, e.g. brainmask, use '-rt cubic' 
instead of nearest neighbor).


Best, Martin


On 11/22/2013 09:22 PM, Kirov, Ivan wrote:

Dear FreeSurfer group/Dr. Reuter,

My questions are in regards to the LONG stream.

My version is: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0

1) Error message
During the creation of the BASE, I get the following error in the 
beginning of the recon:
>>>WARNING: Image geometries differ across time, maybe due to 
aquisition changes?
 This can potentially bias a longitudinal study! Will continue 
in 10s.

What should I be aware of in regards to this error?

The images were all acquired using the same MPRAGE protocol.
All timepoints were fed MPRAGEs reconstructed in the axial 
orientation, but some may have been reconstructed at an angle. I was 
assured that this is not an issue for FreeSurfer, but could this be 
the reason for the error?



2) Conversion of LONG run aseg.mgz segmentations to native anatomical 
space


Executing the commands for converting aseg.mgz to native space (as 
noted in the FsAnat-to-NativeAnat wiki entry) in the folder of a long 
run (me1.long.me_base) does not convert.


It seems to me that (unlike the cross runs) the long runs are all in 
the same space (in the template/ base space?) and their rawavg.mgz 
does not match that of the corresponding cross run. Some insight on 
this would be appreciated.


The question is how to convert an individual long run's aseg.mgz into 
native anatomical space. Perhaps using the rawavg.mgz from the 
corresponding cross run?


Thank you very much!
Ivan

--
Ivan Kirov, PhD
Postdoctoral fellow
New York University School of Medicine
Center for Biomedical Imaging
660 1st Ave, 4th floor, New York, NY 10016
Tel: 212-263-3337
Fax: 212-263-7541

This email message, including any attachments, is for the sole use of 
the intended recipient(s) and may contain information that is 
proprietary, confidential, and exempt from disclosure under applicable 
law. Any unauthorized review, use, disclosure, or distribution is 
prohibited. If you have received this email in error please notify the 
sender by return email and delete the original message. Please note, 
the recipient should check this email and any attachments for the 
presence of viruses. The organization accepts no liability for any 
damage caused by any virus transmitted by this email.

=


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


--
Martin Reuter, Ph.D.
Assistant in Neuroscience - Massachusetts General Hospital
Instructor in Neurology   - Harvard Medical School
MGH / HMS / MIT

A.A.Martinos Center for Biomedical Imaging
149 Thirteenth Street, Suite 2301
Charlestown, MA 02129

Phone: +1-617-724-5652
Email:
   mreu...@nmr.mgh.harvard.edu
   reu...@mit.edu
Web  : http://reuter.mit.edu

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


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

Re: [Freesurfer] recon-all strip skull and neck by brain volume mask

[Louis Nicholas Vinke]

Hi Rujing,
Even if there is some skull/dura left after the skullstrip step in 
recon-all, it still may not negatively impact the surfaces.  It might be 
worth running the remaining recon-all steps to see how the surfaces turn 
out.


If you want to swap-in a better skullstripped volume into the recon-all 
stream then you just need to replace the brainmask.mgz and continue with 
autorecon2 and autorecon3.


Keep in mind that the new brainmask.mgz volume still needs to be in the 
conformed anatomical space, so use the T1.mgz or brainmask.mgz to create 
the improved skullstrip volume which will replace the existing 
brainmask.mgz.


-Louis

On Mon, 2 Dec 2013, Rujing Zha wrote:


Dear all,
Part of subjects 3d images cannot be stripped skull and neck properly in
recon-all default. I have got the brain volume mask, how I can using the
existing proper mask to help strip skull in recon-all and next workflow?
Thanks.Any reply will be appreciated.
All the best.
 
2013-12-02


Rujing Zha

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


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

Re: [Freesurfer] Which boost version is used in CVS, mris_resample

[Martin Kavec]

Hi Zeke,

Thanks for response. Well it was the first thing for me to try to compile boost 
on gentoo, which went fine. However the libraries were not compatible. Gentoo 
has 1.52 version, while the one needed is about 4 years old.

When I do "ldd mris_resample" I get "not a dynamic executable" and when I do 
"file mris_resample" I get that it is a statically linked executable, stripped. 
I think something could have happened with when stripping the executable. I get 
the same output from file mris_rescale, but mris_rescale runs fine.

I am using Freesurfer-5.3.0 for Centos6 x86_64.

Thanks,

Martin

Sent from my iPad

> On 2.12.2013, at 17:33, Z K  wrote:
> 
> Martin,
> 
> libboost is not a static library, it is a shared library. It comes by 
> default on centOS platforms and freesurfer compiles against it during 
> the the build process. Typing 'ldd mris_resample' and examining the 
> output confirms this:
> 
> $>ldd mris_resample
> linux-vdso.so.1 =>  (0x7fffd2773000)
> libboost_program_options.so.5 => 
> /usr/lib64/libboost_program_options.so.5 (0x7fe2e588d000)
> etc...
> 
> Also, many of the freesurfer binaries do require the libboost library.
> 
> Freesurfer works on most linux distribution, but we specifically build 
> on and support centOS platforms. We do not have Gentoo linux machines to 
> try and replicate your error but I am confident that if you get the 
> libboost libraries on your machine, the program will work properly.
> 
> -Zeke
> 
> 
> 
> 
>> On 11/28/2013 05:09 PM, Martin Kavec wrote:
>> Hi Lilla,
>> 
>> thanks for coming back. Unfortunately I was not able to compile
>> appropriate boost for my operating system Gentoo linux. Nevertheless I
>> do not understand why mris_resample misses the library if it should be
>> statically linked. Other binaries do not need it. Could you please check
>> if mris_resample in 64-bit linux version of CentOS is correct?
>> 
>> Otherwise I cannot run cvs.
>> 
>> Thanks a lot,
>> 
>> Martin
>> 
>> 
>> On Mon, Nov 25, 2013 at 5:32 PM, Lilla Zollei
>> mailto:lzol...@nmr.mgh.harvard.edu>> wrote:
>> 
>> 
>>This is a bit delayed response (my apologies) to an earlier question to
>>the list:
>> 
>>The boost library is installed by default on CentOS platforms. If a user
>>gets the libboost error then they are using a different platform which
>>doesn't have boost installed by default. On RedHat systems libboost
>>can be
>>installed by typing the follwing command:
>>$>yum install boost-devel"
>> 
>>The version of libboost that we use for our latest release is 1.41.
>> 
>>Lilla
>> 
>>-
>>Martin Kavec Mon, 04 Nov 2013 14:10:53 -0800
>> 
>>Hi guys,
>> 
>>When running mri_cvs_register on linux (5.3.0), I get into problem with
>>mris_resample, which cannot find libboost_programs_options.so.5. I
>>installed
>>the latest version of boost-1.52.0 for my system, but there are
>>unresolved
>>symbols.
>> 
>>Which version is suitable for mris_resample?
>> 
>>Thanks,
>> 
>>Martin
>> 
>>Sent from my iPad
>>___
>>Freesurfer mailing list
>>Freesurfer@nmr.mgh.harvard.edu 
>>https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>___
>>Freesurfer mailing list
>>Freesurfer@nmr.mgh.harvard.edu 
>>https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> 
>> 
>>The information in this e-mail is intended only for the person to
>>whom it is
>>addressed. If you believe this e-mail was sent to you in error and
>>the e-mail
>>contains patient information, please contact the Partners Compliance
>>HelpLine at
>>http://www.partners.org/complianceline . If the e-mail was sent to
>>you in error
>>but does not contain patient information, please contact the sender
>>and properly
>>dispose of the e-mail.
>> 
>> 
>> 
>> 
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> 
> ___
> Freesurfer 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

Re: [Freesurfer] viewing slices dynamically by tkmedit

[Louis Nicholas Vinke]

Hi Rujing,
You can use a tcl script to take several snapshots in tkmedit, then you 
could use the convert command (part of ImageMagick distro) or 
something similar to create an animated gif.  With the convert command you 
would use the -adjoin and -delay flags.  You could use one of the tcl 
scripts from the QA tools scripts as a good start (e.g. snap_tkmedit.tcl).


You could also get multiple snapshots with freeview using command line 
flags and a shell script.

-Louis

On Sat, 30 Nov 2013, Rujing Zha wrote:


Dear all,
I want to see the slices as a shape of movie in tkmedit. Do anyone can tell
me how to do it?
Thanks.
All the best.
 
2013-11-30


Rujing Zha

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


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

Re: [Freesurfer] Linear regression

[Douglas N Greve]

On 12/02/2013 02:22 PM, std...@virgilio.it wrote:
> Hi list,
>
> I have some questions, please.
>
> I performed linear regression by qdec to find the regions where the 
> cortical thinning correlates with neuropsychological test (NPS), 
> taking in account 3 nuisance factors.
>
> A- I individuated some posterior regions and now I'd like to build a 
> table with partials correlations of individuals ROIs with NPS. How can 
> I obtain the values for each region?
Do you mean the partial correlation coeff (PCC) at each voxel averaged 
over region? You can get PCC maps using the mri_glmfit_pcc matlab 
command. You can then do the averaging over region using mri_segstats.
>
> B- I'd like to obtain the covariance matrix of the regression made 
> between cortical thickness,  group and covariates. How can I do it?
I'm not sure what you mean. Would this be a different matrix for each 
vertex?
>
> C- Is there a specific reference for qdec?
No, it is just a GLM so any GLM reference will do.
>
> Thank you very much,
>
>
> Stefano
>
>
>
>
>
> ___
> 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.

Re: [Freesurfer] talairach_mixed_with_skull.gca file missing in average directory of local version stable5_3_0

[Koene Van Dijk]

Yes, that's correct! Thanks for the follow up
~koene


On 12/2/13 2:27 PM, Louis Nicholas Vinke wrote:
> Hi Koene,
> It looks like Nick copied that volume over on 11/27.  Thanks for 
> pointing that out.
> -Louis
>
> On Tue, 26 Nov 2013, Koene Van Dijk wrote:
>
>> Hi there,
>>
>> We've been using this local version of Freesurfer:
>> /cluster/freesurfer/centos6_x86_64/stable5
>>
>> And this file was relevant:
>> /cluster/freesurfer/centos6_x86_64/stable5/average/talairach_mixed_with_skull.gca
>>  
>>
>>
>> We want to switch to the newest version of Freesurfer at the beginning
>> of a new study but we can't find that "talairach_mixed_with_skull.gca"
>> file in the /cluster/freesurfer/centos6_x86_64/stable5_3_0 directory.
>>
>> Is it possible to also include the "talairach_mixed_with_skull.gca" 
>> file in:
>> /cluster/freesurfer/centos6_x86_64/stable5_3_0/average/?
>>
>> Thanks,
>>
>> Koene
>>
>>
>
>

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


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

Re: [Freesurfer] talairach_mixed_with_skull.gca file missing in average directory of local version stable5_3_0

[Louis Nicholas Vinke]

Hi Koene,
It looks like Nick copied that volume over on 11/27.  Thanks for pointing 
that out.
-Louis

On Tue, 26 Nov 2013, Koene Van Dijk wrote:

> Hi there,
>
> We've been using this local version of Freesurfer:
> /cluster/freesurfer/centos6_x86_64/stable5
>
> And this file was relevant:
> /cluster/freesurfer/centos6_x86_64/stable5/average/talairach_mixed_with_skull.gca
>
> We want to switch to the newest version of Freesurfer at the beginning
> of a new study but we can't find that "talairach_mixed_with_skull.gca"
> file in the /cluster/freesurfer/centos6_x86_64/stable5_3_0 directory.
>
> Is it possible to also include the "talairach_mixed_with_skull.gca" file in:
> /cluster/freesurfer/centos6_x86_64/stable5_3_0/average/?
>
> Thanks,
>
> Koene
>
>
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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

Re: [Freesurfer] Fixed-Effects Analysis carried out by mri_glmfit

[Douglas N Greve]

yep, you should be able to do that

On 12/02/2013 02:08 PM, Clark Fisher wrote:
> Thanks for the reply.  That makes sense.  With your modified approach, maybe 
> I could even work the scalings into the contrast weights?  Thanks for the 
> feedback.
>
> -Clark
>
>
> On Dec 2, 2013, at 12:50 PM, Douglas N Greve  
> wrote:
>
>> Hi Clark, I think Approach A should work ok. As you imply, there could be 
>> different scalings, so take that into account somehow. A slightly modified 
>> approach would be do define a different set of conditions for each subject 
>> in the paradigm file. They create a contrast with mkcontrast-sess that 
>> averages over subjects while testing the contrast you are interested in. 
>> Does that make sense?
>> doug
>>
>>
>> On 12/02/2013 12:27 PM, Clark Fisher wrote:
>>> Hi Doug (and other Freesurfers),
>>>
>>> Hope you had a pleasant Thanksgiving.  My thread last left off before 
>>> everyone left for the holidays.  I just wanted to re-raise this question, 
>>> as it's still a pressing one for me.
>>>
>>> Thanks,
>>> Clark
>>>
>>>
>>> On Nov 27, 2013, at 11:06 AM, Clark Fisher >> > wrote:
>>>
 Hmm, it looks like my formatting didn't survive the internet (at least in 
 my e-mail program). . I'm going to try it one more time (I'm going to 
 include the complete original message).

 Hi Doug,

 I sidestepped the registration issue because I am performing the analysis 
 on 5 ROIs per subject (5x1x1 volumes), which are aligned by design.  I'm 
 doing this using the lab's semi-manual NHP processing stream, so usual 
 assumptions you have about which FS-fast steps have been performed may not 
 hold.

 Just to clarify things, I'll try to outline where I stand more completely.

 I have a block design study with 3 subjects, and ~30 runs per subject. 
 Each run contains every condition occurs twice in each run. These runs 
 have been collected over 2-3 days for each subject. Within each subject, I 
 aligned all of the different sessions and combined them into a single 
 metasession.  Within these 3 metasessions, I defined ROIs, and created new 
 ROI volumes by averaging the time courses within each ROI.  From here I 
 have taken 2 approaches.

 Approach A: Combine all of the ROI volumes (~30 runs X 3 subjects), which 
 are pre-aligned with each other, into a single bold folder.  Run 
 selxavg3-sess on this data using my contrasts of interest.

 Approach B: Keep the ROI volumes from each subject in their own bold 
 folder, and run selxavg3-sess 3 times (once for each subject). Then I used 
 mri_glmfit to attempt fixed effects meta-analysis. Here there's another 
 split.
 Approach B.1:  I ran the contrasts for each individual subject, then used 
 mri_glmfit --osgm on the ces and cesvar volumes of each contrast to test 
 for significance of the contrast over the group. This does not work for 
 F-tests.
 Approach B.2:  I ran an omnibus contrast on each subject separately, and 
 use the ces and cesvar for each condition in each subject.  I assembled 
 this for input to mri_glmfit.  The fsgd file looks roughly like:

 GroupDescriptorFile 1
 Class Subj1
 Class Subj2
 Class Subj3
 Variables  Condition1 Condition2 Condition3Condition4
 Input Subj1-Cond1  Subj1 10  0  0
 Input Subj1-Cond2  Subj1 0  1  0  0
 Input Subj1-Cond3  Subj1 0  0  1  0
 Input Subj1-Cond4  Subj1 0  0  0  1
 Input Subj1-Cond00 Subj1 00  0  0
 Input Subj2-Cond1  Subj2 1  0  0  0
 Input Subj2-Cond2  Subj2 0  1  0  0
 Input Subj2-Cond3  Subj2 0  0  1  0
 Input Subj2-Cond4  Subj2 0  0  0  1
 Input Subj2-Cond00 Subj2 0  0  0  0
 Input Subj3-Cond1  Subj3 10  0  0
 Input Subj3-Cond2  Subj3 01  0  0
 Input Subj3-Cond3  Subj3 00  1  0
 Input Subj3-Cond4  Subj3 00  0  1
 Input Subj3-Cond00 Subj3 00  0  0

 Approach B.2 (continued): I then define contrasts comparing conditions 
 (Condition1 vs Condition2, etc.) and run these contrasts using mri_glmfit 
 --C. With this method, I have no problem defining F contrasts (what they 
 are actually testing is another question).

 My actual experiment is a 6 condition, 2x3 factorial design. The 2 
 contrasts of interest that I need an F test for are one of the main 
 effects (these contrasts are shown without the 3 leading columns of zeros 
 for the different subjects):
 1   1   -1  -1  0   0
 1   1   0   0   -1  -1

 and the interaction effect:
 

[Freesurfer] Linear regression

[stdp82]

Hi list, 
I have some questions, please.
I performed linear regression by qdec to find the regions where the cortical 
thinning correlates with neuropsychological test (NPS), taking in account 3 
nuisance factors.
A- I individuated some posterior regions and now I'd like to build a table with 
partials correlations of individuals ROIs with NPS. How can I obtain the values 
for each region?
B- I'd like to obtain the covariance matrix of the regression made between 
cortical thickness,  group and covariates. How can I do it?
C- Is there a specific reference for qdec?
Thank you very much,

Stefano


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


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

Re: [Freesurfer] Fixed-Effects Analysis carried out by mri_glmfit

[Clark Fisher]

Thanks for the reply.  That makes sense.  With your modified approach, maybe I 
could even work the scalings into the contrast weights?  Thanks for the 
feedback.

-Clark


On Dec 2, 2013, at 12:50 PM, Douglas N Greve  wrote:

> 
> Hi Clark, I think Approach A should work ok. As you imply, there could be 
> different scalings, so take that into account somehow. A slightly modified 
> approach would be do define a different set of conditions for each subject in 
> the paradigm file. They create a contrast with mkcontrast-sess that averages 
> over subjects while testing the contrast you are interested in. Does that 
> make sense?
> doug
> 
> 
> On 12/02/2013 12:27 PM, Clark Fisher wrote:
>> Hi Doug (and other Freesurfers),
>> 
>> Hope you had a pleasant Thanksgiving.  My thread last left off before 
>> everyone left for the holidays.  I just wanted to re-raise this question, as 
>> it's still a pressing one for me.
>> 
>> Thanks,
>> Clark
>> 
>> 
>> On Nov 27, 2013, at 11:06 AM, Clark Fisher > > wrote:
>> 
>>> Hmm, it looks like my formatting didn't survive the internet (at least in 
>>> my e-mail program). . I'm going to try it one more time (I'm going to 
>>> include the complete original message).
>>> 
>>> Hi Doug,
>>> 
>>> I sidestepped the registration issue because I am performing the analysis 
>>> on 5 ROIs per subject (5x1x1 volumes), which are aligned by design.  I'm 
>>> doing this using the lab's semi-manual NHP processing stream, so usual 
>>> assumptions you have about which FS-fast steps have been performed may not 
>>> hold.
>>> 
>>> Just to clarify things, I'll try to outline where I stand more completely.
>>> 
>>> I have a block design study with 3 subjects, and ~30 runs per subject. Each 
>>> run contains every condition occurs twice in each run. These runs have been 
>>> collected over 2-3 days for each subject. Within each subject, I aligned 
>>> all of the different sessions and combined them into a single metasession.  
>>> Within these 3 metasessions, I defined ROIs, and created new ROI volumes by 
>>> averaging the time courses within each ROI.  From here I have taken 2 
>>> approaches.
>>> 
>>> Approach A: Combine all of the ROI volumes (~30 runs X 3 subjects), which 
>>> are pre-aligned with each other, into a single bold folder.  Run 
>>> selxavg3-sess on this data using my contrasts of interest.
>>> 
>>> Approach B: Keep the ROI volumes from each subject in their own bold 
>>> folder, and run selxavg3-sess 3 times (once for each subject). Then I used 
>>> mri_glmfit to attempt fixed effects meta-analysis. Here there's another 
>>> split.
>>> Approach B.1:  I ran the contrasts for each individual subject, then used 
>>> mri_glmfit --osgm on the ces and cesvar volumes of each contrast to test 
>>> for significance of the contrast over the group. This does not work for 
>>> F-tests.
>>> Approach B.2:  I ran an omnibus contrast on each subject separately, and 
>>> use the ces and cesvar for each condition in each subject.  I assembled 
>>> this for input to mri_glmfit.  The fsgd file looks roughly like:
>>> 
>>> GroupDescriptorFile 1
>>> Class Subj1
>>> Class Subj2
>>> Class Subj3
>>> Variables  Condition1 Condition2 Condition3Condition4
>>> Input Subj1-Cond1  Subj1 10  0  0
>>> Input Subj1-Cond2  Subj1 0  1  0  0
>>> Input Subj1-Cond3  Subj1 0  0  1  0
>>> Input Subj1-Cond4  Subj1 0  0  0  1
>>> Input Subj1-Cond00 Subj1 00  0  0
>>> Input Subj2-Cond1  Subj2 1  0  0  0
>>> Input Subj2-Cond2  Subj2 0  1  0  0
>>> Input Subj2-Cond3  Subj2 0  0  1  0
>>> Input Subj2-Cond4  Subj2 0  0  0  1
>>> Input Subj2-Cond00 Subj2 0  0  0  0
>>> Input Subj3-Cond1  Subj3 10  0  0
>>> Input Subj3-Cond2  Subj3 01  0  0
>>> Input Subj3-Cond3  Subj3 00  1  0
>>> Input Subj3-Cond4  Subj3 00  0  1
>>> Input Subj3-Cond00 Subj3 00  0  0
>>> 
>>> Approach B.2 (continued): I then define contrasts comparing conditions 
>>> (Condition1 vs Condition2, etc.) and run these contrasts using mri_glmfit 
>>> --C. With this method, I have no problem defining F contrasts (what they 
>>> are actually testing is another question).
>>> 
>>> My actual experiment is a 6 condition, 2x3 factorial design. The 2 
>>> contrasts of interest that I need an F test for are one of the main effects 
>>> (these contrasts are shown without the 3 leading columns of zeros for the 
>>> different subjects):
>>> 1   1   -1  -1  0   0
>>> 1   1   0   0   -1  -1
>>> 
>>> and the interaction effect:
>>> 1   -1  -1  1   0   0
>>> 1   -1  0   0   -1  1
>>> 
>>> I switched to Approach B because I want to scale the condition betas 
>>> per-subject before running the analysis ac

Re: [Freesurfer] Fixed-Effects Analysis carried out by mri_glmfit

[Douglas N Greve]

Hi Clark, I think Approach A should work ok. As you imply, there could 
be different scalings, so take that into account somehow. A slightly 
modified approach would be do define a different set of conditions for 
each subject in the paradigm file. They create a contrast with 
mkcontrast-sess that averages over subjects while testing the contrast 
you are interested in. Does that make sense?
doug


On 12/02/2013 12:27 PM, Clark Fisher wrote:
> Hi Doug (and other Freesurfers),
>
> Hope you had a pleasant Thanksgiving.  My thread last left off before 
> everyone left for the holidays.  I just wanted to re-raise this 
> question, as it's still a pressing one for me.
>
> Thanks,
> Clark
>
>
> On Nov 27, 2013, at 11:06 AM, Clark Fisher  > wrote:
>
>> Hmm, it looks like my formatting didn't survive the internet (at 
>> least in my e-mail program). . I'm going to try it one more time (I'm 
>> going to include the complete original message).
>>
>> Hi Doug,
>>
>> I sidestepped the registration issue because I am performing the 
>> analysis on 5 ROIs per subject (5x1x1 volumes), which are aligned by 
>> design.  I'm doing this using the lab's semi-manual NHP processing 
>> stream, so usual assumptions you have about which FS-fast steps have 
>> been performed may not hold.
>>
>> Just to clarify things, I'll try to outline where I stand more 
>> completely.
>>
>> I have a block design study with 3 subjects, and ~30 runs per 
>> subject. Each run contains every condition occurs twice in each run. 
>> These runs have been collected over 2-3 days for each subject. Within 
>> each subject, I aligned all of the different sessions and combined 
>> them into a single metasession.  Within these 3 metasessions, I 
>> defined ROIs, and created new ROI volumes by averaging the time 
>> courses within each ROI.  From here I have taken 2 approaches.
>>
>> Approach A: Combine all of the ROI volumes (~30 runs X 3 subjects), 
>> which are pre-aligned with each other, into a single bold folder. 
>>  Run selxavg3-sess on this data using my contrasts of interest.
>>
>> Approach B: Keep the ROI volumes from each subject in their own bold 
>> folder, and run selxavg3-sess 3 times (once for each subject). Then I 
>> used mri_glmfit to attempt fixed effects meta-analysis. Here there's 
>> another split.
>> Approach B.1:  I ran the contrasts for each individual subject, then 
>> used mri_glmfit --osgm on the ces and cesvar volumes of each contrast 
>> to test for significance of the contrast over the group. This does 
>> not work for F-tests.
>> Approach B.2:  I ran an omnibus contrast on each subject separately, 
>> and use the ces and cesvar for each condition in each subject.  I 
>> assembled this for input to mri_glmfit.  The fsgd file looks roughly 
>> like:
>>
>> GroupDescriptorFile 1
>> Class Subj1
>> Class Subj2
>> Class Subj3
>> Variables  Condition1 Condition2 Condition3Condition4
>> Input Subj1-Cond1  Subj1 10  0  0
>> Input Subj1-Cond2  Subj1 0  1  0  0
>> Input Subj1-Cond3  Subj1 0  0  1  0
>> Input Subj1-Cond4  Subj1 0  0  0  1
>> Input Subj1-Cond00 Subj1 00  0  0
>> Input Subj2-Cond1  Subj2 1  0  0  0
>> Input Subj2-Cond2  Subj2 0  1  0  0
>> Input Subj2-Cond3  Subj2 0  0  1  0
>> Input Subj2-Cond4  Subj2 0  0  0  1
>> Input Subj2-Cond00 Subj2 0  0  0  0
>> Input Subj3-Cond1  Subj3 10  0  0
>> Input Subj3-Cond2  Subj3 01  0  0
>> Input Subj3-Cond3  Subj3 00  1  0
>> Input Subj3-Cond4  Subj3 00  0  1
>> Input Subj3-Cond00 Subj3 00  0  0
>>
>> Approach B.2 (continued): I then define contrasts comparing 
>> conditions (Condition1 vs Condition2, etc.) and run these contrasts 
>> using mri_glmfit --C. With this method, I have no problem defining F 
>> contrasts (what they are actually testing is another question).
>>
>> My actual experiment is a 6 condition, 2x3 factorial design. The 2 
>> contrasts of interest that I need an F test for are one of the main 
>> effects (these contrasts are shown without the 3 leading columns of 
>> zeros for the different subjects):
>> 1   1   -1  -1  0   0
>> 1   1   0   0   -1  -1
>>
>> and the interaction effect:
>> 1   -1  -1  1   0   0
>> 1   -1  0   0   -1  1
>>
>> I switched to Approach B because I want to scale the condition betas 
>> per-subject before running the analysis across all subjects (this is 
>> to correct for potentially different levels of a contrast agent). I 
>> was worried that if I scaled the raw time courses that are the input 
>> to Approach A, that the normalization step built into selxavg3-sess 
>> would interact with my manual normalization in ways that would be 
>> difficult to figure out.  Wit

Re: [Freesurfer] Fixed-Effects Analysis carried out by mri_glmfit

[Clark Fisher]

Hi Doug (and other Freesurfers),

Hope you had a pleasant Thanksgiving.  My thread last left off before everyone 
left for the holidays.  I just wanted to re-raise this question, as it's still 
a pressing one for me.

Thanks,
Clark


On Nov 27, 2013, at 11:06 AM, Clark Fisher 
mailto:cfis...@rockefeller.edu>> wrote:

Hmm, it looks like my formatting didn't survive the internet (at least in my 
e-mail program). . I'm going to try it one more time (I'm going to include the 
complete original message).

Hi Doug,

I sidestepped the registration issue because I am performing the analysis on 5 
ROIs per subject (5x1x1 volumes), which are aligned by design.  I'm doing this 
using the lab's semi-manual NHP processing stream, so usual assumptions you 
have about which FS-fast steps have been performed may not hold.

Just to clarify things, I'll try to outline where I stand more completely.

I have a block design study with 3 subjects, and ~30 runs per subject. Each run 
contains every condition occurs twice in each run. These runs have been 
collected over 2-3 days for each subject. Within each subject, I aligned all of 
the different sessions and combined them into a single metasession.  Within 
these 3 metasessions, I defined ROIs, and created new ROI volumes by averaging 
the time courses within each ROI.  From here I have taken 2 approaches.

Approach A: Combine all of the ROI volumes (~30 runs X 3 subjects), which are 
pre-aligned with each other, into a single bold folder.  Run selxavg3-sess on 
this data using my contrasts of interest.

Approach B: Keep the ROI volumes from each subject in their own bold folder, 
and run selxavg3-sess 3 times (once for each subject). Then I used mri_glmfit 
to attempt fixed effects meta-analysis. Here there's another split.
Approach B.1:  I ran the contrasts for each individual subject, then used 
mri_glmfit --osgm on the ces and cesvar volumes of each contrast to test for 
significance of the contrast over the group. This does not work for F-tests.
Approach B.2:  I ran an omnibus contrast on each subject separately, and use 
the ces and cesvar for each condition in each subject.  I assembled this for 
input to mri_glmfit.  The fsgd file looks roughly like:

GroupDescriptorFile 1
Class Subj1
Class Subj2
Class Subj3
VariablesCondition1 Condition2 Condition3 Condition4
Input Subj1-Cond1  Subj1 1  0  0  0
Input Subj1-Cond2  Subj1 0  1  0  0
Input Subj1-Cond3  Subj1 0  0  1  0
Input Subj1-Cond4  Subj1 0  0  0  1
Input Subj1-Cond00 Subj1 0  0  0  0
Input Subj2-Cond1  Subj2 1  0  0  0
Input Subj2-Cond2  Subj2 0  1  0  0
Input Subj2-Cond3  Subj2 0  0  1  0
Input Subj2-Cond4  Subj2 0  0  0  1
Input Subj2-Cond00 Subj2 0  0  0  0
Input Subj3-Cond1  Subj3 1  0  0  0
Input Subj3-Cond2  Subj3 0  1  0  0
Input Subj3-Cond3  Subj3 0  0  1  0
Input Subj3-Cond4  Subj3 0  0  0  1
Input Subj3-Cond00 Subj3 0  0  0  0

Approach B.2 (continued): I then define contrasts comparing conditions 
(Condition1 vs Condition2, etc.) and run these contrasts using mri_glmfit --C. 
With this method, I have no problem defining F contrasts (what they are 
actually testing is another question).

My actual experiment is a 6 condition, 2x3 factorial design. The 2 contrasts of 
interest that I need an F test for are one of the main effects (these contrasts 
are shown without the 3 leading columns of zeros for the different subjects):
1   1   -1  -1  0   0
1   1   0   0   -1  -1

and the interaction effect:
1   -1  -1  1   0   0
1   -1  0   0   -1  1

I switched to Approach B because I want to scale the condition betas 
per-subject before running the analysis across all subjects (this is to correct 
for potentially different levels of a contrast agent). I was worried that if I 
scaled the raw time courses that are the input to Approach A, that the 
normalization step built into selxavg3-sess would interact with my manual 
normalization in ways that would be difficult to figure out.  With approach B, 
I can directly scale the contrast ces and cesvars (B.1) or betas (B.2) for each 
subject.


OK, given all of that background information, what is the best way to approach 
this? Should I:
a) Try to scale the time courses that go into Approach A
b) Work with Approach B.1, and live without knowing the significance of my 
main/interaction effects (not a nice thought)
c) Work with Approach B.2
d) Take some other tack

If I take Approach B.2, would any violation within-subject independence 
decrease my power, or artificially inflate my significance?  Some loss of power 
could be acceptable.

Thanks for reading all of the way through this (twice now),
Clark

Re: [Freesurfer] glmfit error on v5.1

[Douglas N Greve]

The problem is in the noE4female group. You only have 3 subjects and the 
zAPOB and thickness are nearly equal and opposite in sign. The 
correlation between these two regressors exceeds .96. This is probably 
spurious, but it is killing the design matrix.
doug


On 12/02/2013 11:44 AM, Gabriel Gonzalez Escamilla wrote:
> There you are!
>
> Hope it helps
>
> - Mensaje original -
> De: Douglas N Greve 
> Fecha: Lunes, 2 de Diciembre de 2013, 5:09 pm
> Asunto: Re: [Freesurfer] glmfit error on v5.1
> A: freesurfer@nmr.mgh.harvard.edu
>
> > Can you send the matrix that it creates?
> >
> > On 12/02/2013 06:09 AM, Gabriel Gonzalez Escamilla wrote:
> > > Dear Freesurfer experts,
> > >
> > > Sorry for the inconvenience but I posted this message last
> > week, but I
> > > did not receive any answer. I really need to keep going on
> > with my
> > > analyses.
> > >
> > >
> > > I have runned the following command line:
> > > mri_glmfit --surf PLI_MCI_sample7_avg lh --C
> > >
> > 
> /root/trabajo/freesurfer/subjects/PLI_MCI_sample7_avg/stats_MRI_PET_Biomarkers/glm_files/contrast_withinE4_neg.mat
>  
>
> > > --fsgd
> > >
> > 
> /root/trabajo/freesurfer/subjects/PLI_MCI_sample7_avg/stats_MRI_PET_Biomarkers/glm_files/lh.cortex_AVGthickness_APOB_fsgd.txt
>  
>
> > > dods --label
> > >
> > 
> /root/trabajo/freesurfer/subjects/PLI_MCI_sample7_avg/label/lh.cortex.label 
>
> > > --y
> > >
> > 
> /root/trabajo/freesurfer/subjects/PLI_MCI_sample7_avg/stats_MRI_PET_Biomarkers/lh.thickness_s12mm.mgh
>  
>
> > > --no-prune --glmdir
> > >
> > 
> /root/trabajo/freesurfer/subjects/PLI_MCI_sample7_avg/stats_MRI_PET_Biomarkers/resultsthickness_cortex_s12mm_BiomrkrsWithin/lh.cortex_AVGthickness_APOB_contrast_withinE4_neg/
>  
>
> > >
> > >
> > > which is always prompts the following error:
> > >
> > > 
> > > ERROR: matrix is ill-conditioned or badly scaled, condno =
> > 1.75146e+07> 
> > > Possible problem with experimental design
> > >
> > >
> > > I'm sending attached the fsgd.txt and contras.mat files used
> > in case
> > > you need them
> > >
> > >
> > > Does anyone knows what's wrong with my design?
> > >
> > >
> > > Many thanks in advanced,
> > > Gabriel.
> > >
> > >
> > > ___
> > > 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.
> >
>
> --PhD. student Gabriel 
> González-EscamillaLaboratory of Functional Neuroscience />Department of Physiology, Anatomy, and Cell BiologyUniversity 
> Pablo de OlavideCtra. de Utrera, Km.141013 - Seville />- Spain -Email: ggon...@upo.es />http://www.upo.es/neuroaging/es/

-- 
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

Re: [Freesurfer] glmfit error on v5.1

[Gabriel Gonzalez Escamilla]

There you are!Hope it helps- Mensaje original -De: Douglas N Greve Fecha: Lunes, 2 de Diciembre de 2013, 5:09 pmAsunto: Re: [Freesurfer] glmfit error on v5.1A: freesurfer@nmr.mgh.harvard.edu> Can you send the matrix that it creates?> > On 12/02/2013 06:09 AM, Gabriel Gonzalez Escamilla wrote:> > Dear Freesurfer experts,> >> > Sorry for the inconvenience but I posted this message last > week, but I > > did not receive any answer. I really need to keep going on > with my > > analyses.> >> >> > I have runned the following command line:> > mri_glmfit --surf PLI_MCI_sample7_avg lh --C > > > /root/trabajo/freesurfer/subjects/PLI_MCI_sample7_avg/stats_MRI_PET_Biomarkers/glm_files/contrast_withinE4_neg.mat > > --fsgd > > > /root/trabajo/freesurfer/subjects/PLI_MCI_sample7_avg/stats_MRI_PET_Biomarkers/glm_files/lh.cortex_AVGthickness_APOB_fsgd.txt > > dods --label > > > /root/trabajo/freesurfer/subjects/PLI_MCI_sample7_avg/label/lh.cortex.label > > --y > > > /root/trabajo/freesurfer/subjects/PLI_MCI_sample7_avg/stats_MRI_PET_Biomarkers/lh.thickness_s12mm.mgh > > --no-prune --glmdir > > > /root/trabajo/freesurfer/subjects/PLI_MCI_sample7_avg/stats_MRI_PET_Biomarkers/resultsthickness_cortex_s12mm_BiomrkrsWithin/lh.cortex_AVGthickness_APOB_contrast_withinE4_neg/ > >> >> > which is always prompts the following error:> >> > > > ERROR: matrix is ill-conditioned or badly scaled, condno = > 1.75146e+07> > > Possible problem with experimental design> >> >> > I'm sending attached the fsgd.txt and contras.mat files used > in case > > you need them> >> >> > Does anyone knows what's wrong with my design?> >> >> > Many thanks in advanced,> > Gabriel.> >> >> > ___> > 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.> --PhD. student Gabriel González-EscamillaLaboratory of Functional NeuroscienceDepartment of Physiology, Anatomy, and Cell BiologyUniversity Pablo de OlavideCtra. de Utrera, Km.141013 - Seville- Spain -Email: ggon...@upo.eshttp://www.upo.es/neuroaging/es/


Xg.dat
Description: Binary data
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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

Re: [Freesurfer] Which boost version is used in CVS, mris_resample

[Z K]

Martin,

libboost is not a static library, it is a shared library. It comes by 
default on centOS platforms and freesurfer compiles against it during 
the the build process. Typing 'ldd mris_resample' and examining the 
output confirms this:

$>ldd mris_resample
linux-vdso.so.1 =>  (0x7fffd2773000)
libboost_program_options.so.5 => 
/usr/lib64/libboost_program_options.so.5 (0x7fe2e588d000)
etc...

Also, many of the freesurfer binaries do require the libboost library.

Freesurfer works on most linux distribution, but we specifically build 
on and support centOS platforms. We do not have Gentoo linux machines to 
try and replicate your error but I am confident that if you get the 
libboost libraries on your machine, the program will work properly.

-Zeke




On 11/28/2013 05:09 PM, Martin Kavec wrote:
> Hi Lilla,
>
> thanks for coming back. Unfortunately I was not able to compile
> appropriate boost for my operating system Gentoo linux. Nevertheless I
> do not understand why mris_resample misses the library if it should be
> statically linked. Other binaries do not need it. Could you please check
> if mris_resample in 64-bit linux version of CentOS is correct?
>
> Otherwise I cannot run cvs.
>
> Thanks a lot,
>
> Martin
>
>
> On Mon, Nov 25, 2013 at 5:32 PM, Lilla Zollei
> mailto:lzol...@nmr.mgh.harvard.edu>> wrote:
>
>
> This is a bit delayed response (my apologies) to an earlier question to
> the list:
>
> The boost library is installed by default on CentOS platforms. If a user
> gets the libboost error then they are using a different platform which
> doesn't have boost installed by default. On RedHat systems libboost
> can be
> installed by typing the follwing command:
> $>yum install boost-devel"
>
> The version of libboost that we use for our latest release is 1.41.
>
> Lilla
>
> -
> Martin Kavec Mon, 04 Nov 2013 14:10:53 -0800
>
> Hi guys,
>
> When running mri_cvs_register on linux (5.3.0), I get into problem with
> mris_resample, which cannot find libboost_programs_options.so.5. I
> installed
> the latest version of boost-1.52.0 for my system, but there are
> unresolved
> symbols.
>
> Which version is suitable for mris_resample?
>
> Thanks,
>
> Martin
>
> Sent from my iPad
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu 
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu 
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> The information in this e-mail is intended only for the person to
> whom it is
> addressed. If you believe this e-mail was sent to you in error and
> the e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to
> you in error
> but does not contain patient information, please contact the sender
> and properly
> dispose of the e-mail.
>
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] mri_vol2surf

[Douglas N Greve]

On 12/01/2013 11:40 PM, Arash Nazeri wrote:
> Hi all,
>
> I wanted to make sure how one could assign intensities from the 
> subjacent white matter voxels to the cortical surfaces using mri_vol2surf.
>
> Based on the documentation page --projfrac, if used with negative 
> values, would assign white matter values to the surface. I was 
> wondering if this holds true for other options such as projfrac-avg, 
> projfrac-max, projdist-max ... . Further, I wanted to make sure if the 
> third value, designated as del, means the minimum value that could be 
> projected to the surface.
> For instance: --projdist-max 0 -4 0.1 means to assign the maximum 
> value in the distance 0-4 mm of the gray/white matter boundary to the 
> white matter, that is larger than 0.1 .
You basically have the right idea (ie, negative values go into the white 
matter). I'm not sure exactly what you are asking in your example. If 
you want to go from the gray/white surface into the WM by 4 mm, I would 
use --projdist-max -4 0 0.1 or --projdist-max 0 4 -0.1
This will sample along the normal in 40 places spaced 0.1mm apart and 
return the maximum. Note that this does not assure that all points will 
be in WM because 4mm may put you into the GM on an adjacent bank (but 
for a T1 this will be dark so probably does not affect the max).
>
> In case of the local/global outliers, is there any good way of 
> finding, discarding, and replacement of these values, through 
> thresholding+resampling for instance?
We don't have anything.
>
> Finally, I was wondering how it is possible to use these resulting mgh 
> files for group comparison in an uncached dataset, presumably using 
> mris_preproc.
You can save them in the surf folder and then use "--meas yourfile.mgh" 
with mris_preproc.

I'm not sure what you are aiming for, but David Salat did a similar 
analysis http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2750073
This was done using the pctsurfcon program, so you might want to take a 
look at that
doug


>
> Bests,
> Arash
>
>
> ___
> 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.

Re: [Freesurfer] nuisance factors in QDEC

[Douglas N Greve]

On 12/02/2013 09:05 AM, Yolanda Vives wrote:
> Dear FreeSurfer experts,
>
> I am performing a DODS analysis with QDEC to compare cortical 
> thickness of patients and controls and I have some questions regarding 
> the nuisance factors age and global cortical thickness.
>
> 1.- Should I demean both variables or only the age?
Both.
>
> 2.- Which of the following options do you think that would be better?
>
>- To include the global mean thickness of the left 
> hemisphere for the QDEC analysis of the left hemisphere and the right 
> global mean thickness for the QDEC analysis of the right hemisphere.
>
>
>- To include mean cortical thickness calculated like that:
> bh.thickness = (lh.thickness*lh.surfarea + rh.thickness*rh.surfarea) / 
> (lh.surfarea + rh.surfarea)
Global is probably better.
>
> If you think that this is the best option, which surfarea should I 
> use? Would it be correct to use the WhiteSurfArea?
The global mean thickness is included in the ?h.aparc.stats file, so use 
that.
doug

>
> Thank you for your help,
> Yolanda
>
>
>
> ___
> 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.

Re: [Freesurfer] glmfit error on v5.1

[Douglas N Greve]

Can you send the matrix that it creates?

On 12/02/2013 06:09 AM, Gabriel Gonzalez Escamilla wrote:
> Dear Freesurfer experts,
>
> Sorry for the inconvenience but I posted this message last week, but I 
> did not receive any answer. I really need to keep going on with my 
> analyses.
>
>
> I have runned the following command line:
> mri_glmfit --surf PLI_MCI_sample7_avg lh --C 
> /root/trabajo/freesurfer/subjects/PLI_MCI_sample7_avg/stats_MRI_PET_Biomarkers/glm_files/contrast_withinE4_neg.mat
>  
> --fsgd 
> /root/trabajo/freesurfer/subjects/PLI_MCI_sample7_avg/stats_MRI_PET_Biomarkers/glm_files/lh.cortex_AVGthickness_APOB_fsgd.txt
>  
> dods --label 
> /root/trabajo/freesurfer/subjects/PLI_MCI_sample7_avg/label/lh.cortex.label 
> --y 
> /root/trabajo/freesurfer/subjects/PLI_MCI_sample7_avg/stats_MRI_PET_Biomarkers/lh.thickness_s12mm.mgh
>  
> --no-prune --glmdir 
> /root/trabajo/freesurfer/subjects/PLI_MCI_sample7_avg/stats_MRI_PET_Biomarkers/resultsthickness_cortex_s12mm_BiomrkrsWithin/lh.cortex_AVGthickness_APOB_contrast_withinE4_neg/
>  
>
>
> which is always prompts the following error:
>
> 
> ERROR: matrix is ill-conditioned or badly scaled, condno = 1.75146e+07
> 
> Possible problem with experimental design
>
>
> I'm sending attached the fsgd.txt and contras.mat files used in case 
> you need them
>
>
> Does anyone knows what's wrong with my design?
>
>
> Many thanks in advanced,
> Gabriel.
>
>
> ___
> 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.

Re: [Freesurfer] trac-all inquiry

[David Soto]

hi - thanks , not sure though...the no_dif brain mask
seems ok, if that is what you meant...

I did re-run the processing and
in the last run I can not see the WARN you mentioned
the latest preprocessing output from the preprocessing can be
found  here:  https://dl.dropboxusercontent.com/u/8209026/prepro.txt

the dlabel/diff output got stuck with the
rh.ilf_AS_avg33 which only contains thee  _mni_bbr_cpts_5.txt but nothing
else

thanks so much

ds



On Mon, Dec 2, 2013 at 10:59 AM, Anastasia Yendiki <
ayend...@nmr.mgh.harvard.edu> wrote:

>
> Hi David - Sorry for the delayed response due to traveling.
>
> There's a warning about the right ILF in the log file that may offer a
> clue:
>
> WARN: Initial control point 37 56 -6 is not in DWI volume - is DWI cropped?
> WARN: Replacing with closest point in volume (37 56 0)
> WARN: Initial control point 38 45 -1 is not in DWI volume - is DWI cropped?
> WARN: Replacing with closest point in volume (38 45 0)
> WARN: Initial start point 37 56 0 is not in start ROI
> WARN: Replacing with closest point in start ROI (31 56 0)
>
> Is the brain mask cropped on either end of the right ILF? You mentioned
> that you already checked the registration of the FA map to the template
> space (dmri/mni/dtifit_FA.bbr.nii.gz), so I'm assuming there's nothing
> wrong there.
>
> a.y
>
> On Sat, 16 Nov 2013, David Soto wrote:
>
> > Thanks!
> > for some weird unknown reason
> > the log for the preprocessing file of this
> > subject is unusually big (2.8 megabytes)
> >  please get it from this link
> > https://dl.dropboxusercontent.com/u/8209026/Archive.zip
> > cheers
> > ds
> >
> >
> > On Sat, Nov 16, 2013 at 3:13 PM, Anastasia Yendiki
> >  wrote:
> >
> >   Hi David - This log only shows output from the -path step and
> >   not from the -prep step. The file that's missing should be
> >   created during the -prep step, so there's no way to figure out
> >   what went wrong without seeing the output from the
> >   pre-processing.
> >
> >   Please cc the freesurfer list on your reply.
> >
> >   Thank you,
> >   a.y
> >
> >
> >   On Sat, 16 Nov 2013, David Soto wrote:
> >
> > Thanks, please see attachedI only noticed this
> > ERROR: Could
> notopen/home/dsoto/Documents/fmri/rsdtianawmgui/14AB/dlabel/diff/rh.ilf_AS_avg
> > 33_m
> > ni_bbr_cpts_5_std.txt
> > cheers
> > DS
> >
> >
> > On Fri, Nov 15, 2013 at 8:55 PM, Anastasia Yendiki
> >  wrote:
> >
> >   Hi David - Can you please send us the
> > trac-all.log file for this
> >   subject?
> >   Without seeing where it stopped and what error
> > messages there
> >   are it's
> >   hard to guess what's going on.
> >
> >   Thanks,
> >   a.y
> >
> >   On Fri, 15 Nov 2013, David Soto wrote:
> >
> >   >  Hi -
> >   > trac-all completed in all my Ps except one
> >   > and I noticed that the  dlabel/diff output
> > does not contain
> >   all the files
> >   >
> >   > I assessed whether it could be do to poor
> > registration, by
> >   checking
> >   > the  aparc+aseg
> >   > file and looks allright
> >   >
> >   > I also checked the registration of FA maps
> > to standard space
> >   by
> >   > freeview -v
> > $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz
> >   > dtifit_FA.bbr.nii.gz
> >   > and seems fine
> >   >
> >   > also
> >   >
> >   > freeview -v brain_anat_orig.nii.gz
> > lowb_brain.nii.gz
> >   >
> >   > which also seems fine
> >   >
> >   > any ideas pls?
> >   >
> >   > thanks!
> >   >
> >   > ds
> >   >
> >   >
> >   >
> >   > On Fri, Aug 16, 2013 at 5:14 PM, Anastasia
> > Yendiki
> >   >  wrote:
> >   >
> >   >   I suspect the current problem is
> > caused by poor
> >   registration.
> >   >   Have you checked the aparc+aseg and/or
> > the registration
> >   from
> >   >   diffusion to anatomical and from
> > anatomical to MNI?
> >   >
> >   >   On Fri, 16 Aug 2013, David Soto
> > wrote:
> >   >
> >   >
> >   >
> >   > --
> >   

[Freesurfer] nuisance factors in QDEC

[Yolanda Vives]

Dear FreeSurfer experts,

I am performing a DODS analysis with QDEC to compare cortical thickness of
patients and controls and I have some questions regarding the nuisance
factors age and global cortical thickness.

1.- Should I demean both variables or only the age?

2.- Which of the following options do you think that would be better?

   - To include the global mean thickness of the left hemisphere
for the QDEC analysis of the left hemisphere and the right global mean
thickness for the QDEC analysis of the right hemisphere.


   - To include mean cortical thickness calculated like that:
bh.thickness = (lh.thickness*lh.surfarea + rh.thickness*rh.surfarea) /
(lh.surfarea + rh.surfarea)

If you think that this is the best option, which surfarea should I use?
Would it be correct to use the WhiteSurfArea?

Thank you for your help,
Yolanda
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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

[Freesurfer] recon-all strip skull and neck by brain volume mask

[Rujing Zha]

Dear all,
Part of subjects 3d images cannot be stripped skull and neck properly in 
recon-all default. I have got the brain volume mask, how I can using the 
existing proper mask to help strip skull in recon-all and next workflow?
Thanks.Any reply will be appreciated.
All the best.

2013-12-02



Rujing Zha___
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] glmfit error on v5.1

[Gabriel Gonzalez Escamilla]

Dear Freesurfer experts,Sorry for the inconvenience but I posted  this message last week, but I did not receive any answer. I really need to keep  going on with my analyses.I have runned the following command line:mri_glmfit   --surf PLI_MCI_sample7_avg lh --C  /root/trabajo/freesurfer/subjects/PLI_MCI_sample7_avg/stats_MRI_PET_Biomarkers/glm_files/contrast_withinE4_neg.mat   --fsgd  /root/trabajo/freesurfer/subjects/PLI_MCI_sample7_avg/stats_MRI_PET_Biomarkers/glm_files/lh.cortex_AVGthickness_APOB_fsgd.txt   dods --label  /root/trabajo/freesurfer/subjects/PLI_MCI_sample7_avg/label/lh.cortex.label   --y  /root/trabajo/freesurfer/subjects/PLI_MCI_sample7_avg/stats_MRI_PET_Biomarkers/lh.thickness_s12mm.mgh   --no-prune --glmdir  /root/trabajo/freesurfer/subjects/PLI_MCI_sample7_avg/stats_MRI_PET_Biomarkers/resultsthickness_cortex_s12mm_BiomrkrsWithin/lh.cortex_AVGthickness_APOB_contrast_withinE4_neg/   which is always prompts the following error:ERROR: matrix is ill-conditioned or badly scaled, condno = 1.75146e+07Possible problem with experimental designI'm sending attached the fsgd.txt and contras.mat files used in case you need themDoes anyone knows what's wrong with my design?Many thanks in advanced,Gabriel.


contrast_withinE4_neg.mat
Description: Binary data
GroupDescriptorFile 1
Title PVEc-PET_with_MRI in sig_clusters of MC_3000
Class E4female
Class E4male
Class noE4female
Class noE4male
variables zAge zAPOB zlh.cortex_AVGthickness 
Input mci_01_year1 noE4male -0.025380 -0.495746 -0.569553 
Input mci_02_year1 noE4male 0.416237 -0.163064 -1.388804 
Input mci_04_year1 noE4female -0.466997 -1.018533 1.324541 
Input mci_10_year1 noE4male -0.319792 -1.351215 0.286936 
Input mci_11_year1 noE4female 0.563442 -0.400694 -0.384206 
Input mci_14_year1 noE4male -0.466997 -0.281879 0.611082 
Input mci_15_year1 noE4female 1.152265 -0.567035 0.446893 
Input mci_16_year1 noE4male 0.857854 0.549827 -1.563149 
Input mci_20_year1 noE4male -0.614203 -1.066059 -0.254717 
Input mci_23_year1 noE4male 1.299471 -0.780902 -0.043134 
Input mci_25_year1 noE4male -0.761409 -0.899718 0.469744 
Input mci_33_year1 noE4male -0.908614 0.858747 0.584846 
Input mci_36_year1 noE4male -0.025380 2.260766 -0.997798 
Input mci_38_year1 noE4male -2.822288 2.759790 1.354163 
Input mci_39_year1 noE4male -1.350231 2.569685 0.621238 
Input mci_06_year1 E4female -0.172586 -0.234353 -0.633028 
Input mci_07_year1 E4male -1.350231 -0.139301 -0.126075 
Input mci_08_year1 E4female -0.025380 0.383486 -1.171297 
Input mci_09_year1 E4female 0.857854 -0.234353 -0.370665 
Input mci_13_year1 E4male 0.121825 -0.495746 0.904760 
Input mci_17_year1 E4male -0.466997 -0.044248 -0.776059 
Input mci_18_year1 E4female 1.005059 -0.163064 -0.820915 
Input mci_19_year1 E4male 1.152265 0.074567 -2.081952 
Input mci_21_year1 E4female 0.121825 -0.091774 1.423562 
Input mci_27_year1 E4female -1.350231 -0.543272 2.172568 
Input mci_29_year1 E4male 1.888294 0.240908 0.683020 
Input mci_35_year1 E4male 0.710648 -0.567035 1.014783 
Input mci_41_year1 E4female 0.269031 0.169619 -0.510310 
Input mci_42_year1 E4male 0.710648 -0.329405 -0.206476 
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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

Re: [Freesurfer] Bedpost Not successfully completed

[Anastasia Yendiki]

Hi Emily - Sorry for responding late due to traveling.

Does bedpostx not run at all, or does it stop half-way? What files if any 
have been created in the dmri.bedpostX directory?

a.y

On Wed, 20 Nov 2013, ebell...@uwm.edu wrote:

> Hello,
>
> I am finding that my bedposting is not completing successfully. I was able to 
> get my first two subjects to run successfully, however, for the other two 
> subjects that I have run I have gotten the following message:
>
>
> For some reason the bedpostX process DOES NOT appear
> to have successfully completed. Please examine your
> results carefully.
> /opt/psych_imaging/Freesurfer_5.3//bin/bedpostx_mgh: line 345: kill: (30896) 
> - No such process
>
> Any ideas of what I should be looking for or troubleshooting to get this step 
> to work?
>
> Thanks so much,
>
> Emily
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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

Re: [Freesurfer] Fwd: Minimum Dti directions and odf

[Anastasia Yendiki]

Hi Sal - I apologize for the late response due to traveling.

With tracula we have certainly used 30 direction data. It shouldn't be a 
problem, since tracula fits the ball-and-stick model of diffusion of 
Behrens et al 2007, which has been shown to give reasonable results 
fitting 2 crossing fibers with 30 directions.

Hope this helps,
a.y

On Mon, 18 Nov 2013, Salil Soman wrote:

> 
> Hi,
> 
> I hope all is well.
> 
> Was wondering if any of had heard of an explicit minimum number of DTI
> directions necessary for using odf / hardi modeling ? I have run a couple of
> data sets of 30 directions (+ 5 b0) through TRACULA, and have run this same
> data through diffusion toolkit using the hardi / odf model, with reasonable
> looking results. I was wondering if there was any specific reason why using
> these models with 30 directions would be considered in appropriate?
> 
> Thanks!
> 
> Sal
> 
> 
> 
> 
>
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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

Re: [Freesurfer] trac-all inquiry

[Anastasia Yendiki]

Hi David - Sorry for the delayed response due to traveling.

There's a warning about the right ILF in the log file that may offer a 
clue:


WARN: Initial control point 37 56 -6 is not in DWI volume - is DWI cropped?
WARN: Replacing with closest point in volume (37 56 0)
WARN: Initial control point 38 45 -1 is not in DWI volume - is DWI cropped?
WARN: Replacing with closest point in volume (38 45 0)
WARN: Initial start point 37 56 0 is not in start ROI
WARN: Replacing with closest point in start ROI (31 56 0)

Is the brain mask cropped on either end of the right ILF? You mentioned 
that you already checked the registration of the FA map to the template 
space (dmri/mni/dtifit_FA.bbr.nii.gz), so I'm assuming there's nothing 
wrong there.


a.y

On Sat, 16 Nov 2013, David Soto wrote:


Thanks!
for some weird unknown reason
the log for the preprocessing file of this
subject is unusually big (2.8 megabytes)
 please get it from this link
https://dl.dropboxusercontent.com/u/8209026/Archive.zip
cheers
ds


On Sat, Nov 16, 2013 at 3:13 PM, Anastasia Yendiki
 wrote:

  Hi David - This log only shows output from the -path step and
  not from the -prep step. The file that's missing should be
  created during the -prep step, so there's no way to figure out
  what went wrong without seeing the output from the
  pre-processing.

  Please cc the freesurfer list on your reply.

  Thank you,
  a.y


  On Sat, 16 Nov 2013, David Soto wrote:

Thanks, please see attachedI only noticed this 
ERROR: Could 
notopen/home/dsoto/Documents/fmri/rsdtianawmgui/14AB/dlabel/diff/rh.ilf_AS_avg
33_m
ni_bbr_cpts_5_std.txt
cheers
DS


On Fri, Nov 15, 2013 at 8:55 PM, Anastasia Yendiki
 wrote:

      Hi David - Can you please send us the
trac-all.log file for this
      subject?
      Without seeing where it stopped and what error
messages there
      are it's
      hard to guess what's going on.

      Thanks,
      a.y

      On Fri, 15 Nov 2013, David Soto wrote:

      >  Hi -  
      > trac-all completed in all my Ps except one
      > and I noticed that the  dlabel/diff output
does not contain
      all the files
      >
      > I assessed whether it could be do to poor
registration, by
      checking
      > the  aparc+aseg
      > file and looks allright
      >
      > I also checked the registration of FA maps
to standard space
      by 
      > freeview -v
$FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz
      > dtifit_FA.bbr.nii.gz 
      > and seems fine
      >
      > also
      >
      > freeview -v brain_anat_orig.nii.gz
lowb_brain.nii.gz 
      >
      > which also seems fine
      >
      > any ideas pls?
      >
      > thanks!
      >
      > ds
      >
      >
      >
      > On Fri, Aug 16, 2013 at 5:14 PM, Anastasia
Yendiki
      >  wrote:
      >        
      >       I suspect the current problem is
caused by poor
      registration.
      >       Have you checked the aparc+aseg and/or
the registration
      from
      >       diffusion to anatomical and from
anatomical to MNI?
      >
      >       On Fri, 16 Aug 2013, David Soto
wrote: 
      >
      >
      >
      > --
      >
http://www1.imperial.ac.uk/medicine/people/d.soto/
      >
      >
      >  
      >
      >


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.




--
http://www1.imperial.ac.uk/medicine/people/d.soto/

--
http://www1.imperial.ac.uk/medicine/people/d.soto/


___

Re: [Freesurfer] Cortical thickness/surface area in volume-defined ROIs

[Anita van Loenhoud]

Hi Bruce,

Thank you for your response. Now at least I know what went wrong; I'll
try your solution.

Thanks!

Anita
___
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.