Re: [Freesurfer] Fwd: Eccentric lesions

[Bruce Fischl]

Hi Octavian

I wouldn't use control points since it really isn't healthy wm. The only 
thing you can do is edit the wm.mgz and possibly also the brainmask, but 
it's so abnormal looking you may not be able to get accurate surfaces. 
How does the aseg look? If it is ok there may be one other option.

cheers
Bruce


On Tue, 25 Nov 2014, Octavian Lie wrote:

> Dear All,
> any suggestion about this type of problem? I tried control points through
> the middle/axis of the atrophic gyri (intensity 30-90 in T1 or brainmask),
> wm.mgz edits through the same (adding from brainmask by cloning those
> voxels; painting 110; or 255 brush), and modifying brainmask directly by
> painting 110 internsity voxels through the same (gyri interiors, where wm is
> supposed to be). Did not work, the atrophic gyri continue to remain outside
> the pia. Again, this is an example of an eccentric lesion with gyral
> atrophy, without interruption in the gray matter ribbon but very faint wm
> signal through the base of the affected gyri.
> Thanks,
> Octavian
> 
> 
> 
> -- Forwarded message --
> From: Octavian Lie 
> Date: Tue, Nov 18, 2014 at 10:50 AM
> Subject: Eccentric lesions
> To: "freesurfer@nmr.mgh.harvard.edu" 
> 
> 
> Dear All,
> 
> I am interested at getting as good pial/cortical reconstructions as possible
> on a series of epilepsy pt scans, some showing eccentric (cortical) lesions
> (focal encephalomalacias, infarcts, or after focal resections). One
> particularly difficult lesion type to get an accurate cortical surface is
> where there are prongs of grey matter bulging out (like a bag of worms),
> (mostly) without visible wm, see attached picture. These prongs are
> maintained in the brainmask.mgz and brain.finalsurfs.mgz, but not included
> in the pia with the default recon. Lesion voxel intensities vary from 30-90.
> I tried cp, wm edits (using brainmask or T1 as referece), both, did not
> matter, it did not work.
> 
> Since I am not intested in wm/subcortical segmentation but just in a good
> pia, I was wondering if I 'create' thin wm tracts through the center of
> these gm prongs to help pial segmentation. If this is a valid option, should
> I create those in brainmask, brain.finalsurfs or wm.mgz, and should I use
> 110 or 255 for the brush?
> Any other suggestions are appreciated. Nevertheless, I know there is a lot
> of tweaking of each lesion, and I try for more of a global approach to these
> kinds of lesions.
> 
> Thank you,
> 
> Octavian.
> 
> 
>
___
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: Eccentric lesions

[Bruce Fischl]

so the GM is properly labeled by the aseg there? What about the faint wm?
On 
Tue, 25 Nov 2014, Octavian Lie wrote:

> Dear Bruce,
> 
> I am not sure how an ok aseg.mgz would look like for a lesion like that, but
> it looks like it includes one larger gyrus excluded by the pia, see
> attached, I would be happy to retrieve that one as it is the bulkiest of all
> the ones left out.
> Thank you,
> 
> Octavian
> 
> On Tue, Nov 25, 2014 at 7:38 AM, Bruce Fischl 
> wrote:
>   Hi Octavian
>
>   I wouldn't use control points since it really isn't healthy wm.
>   The only
>   thing you can do is edit the wm.mgz and possibly also the
>   brainmask, but
>   it's so abnormal looking you may not be able to get accurate
>   surfaces.
>   How does the aseg look? If it is ok there may be one other
>   option.
>
>   cheers
>   Bruce
> 
>
>   On Tue, 25 Nov 2014, Octavian Lie wrote:
>
>   > Dear All,
>   > any suggestion about this type of problem? I tried control
>   points through
>   > the middle/axis of the atrophic gyri (intensity 30-90 in T1 or
>   brainmask),
>   > wm.mgz edits through the same (adding from brainmask by
>   cloning those
>   > voxels; painting 110; or 255 brush), and modifying brainmask
>   directly by
>   > painting 110 internsity voxels through the same (gyri
>   interiors, where wm is
>   > supposed to be). Did not work, the atrophic gyri continue to
>   remain outside
>   > the pia. Again, this is an example of an eccentric lesion with
>   gyral
>   > atrophy, without interruption in the gray matter ribbon but
>   very faint wm
>   > signal through the base of the affected gyri.
>   > Thanks,
>   > Octavian
>   >
>   >
>   >
>   > -- Forwarded message --
>   > From: Octavian Lie 
>   > Date: Tue, Nov 18, 2014 at 10:50 AM
>   > Subject: Eccentric lesions
>   > To: "freesurfer@nmr.mgh.harvard.edu"
>   
>   >
>   >
>   > Dear All,
>   >
>   > I am interested at getting as good pial/cortical
>   reconstructions as possible
>   > on a series of epilepsy pt scans, some showing eccentric
>   (cortical) lesions
>   > (focal encephalomalacias, infarcts, or after focal
>   resections). One
>   > particularly difficult lesion type to get an accurate cortical
>   surface is
>   > where there are prongs of grey matter bulging out (like a bag
>   of worms),
>   > (mostly) without visible wm, see attached picture. These
>   prongs are
>   > maintained in the brainmask.mgz and brain.finalsurfs.mgz, but
>   not included
>   > in the pia with the default recon. Lesion voxel intensities
>   vary from 30-90.
>   > I tried cp, wm edits (using brainmask or T1 as referece),
>   both, did not
>   > matter, it did not work.
>   >
>   > Since I am not intested in wm/subcortical segmentation but
>   just in a good
>   > pia, I was wondering if I 'create' thin wm tracts through the
>   center of
>   > these gm prongs to help pial segmentation. If this is a valid
>   option, should
>   > I create those in brainmask, brain.finalsurfs or wm.mgz, and
>   should I use
>   > 110 or 255 for the brush?
>   > Any other suggestions are appreciated. Nevertheless, I know
>   there is a lot
>   > of tweaking of each lesion, and I try for more of a global
>   approach to these
>   > kinds of lesions.
>   >
>   > Thank you,
>   >
>   > Octavian.
>   >
>   >
>   >
> ___
> 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] Fwd: Eccentric lesions

[Octavian Lie]

It looks like there is only gray matter (int 42), similar to cortical
ribbon gray, no white matter in that gyrus in aseg, both in the original
recon, and after painting gyral centers in brainmask.
Octavian

On Tue, Nov 25, 2014 at 7:51 AM, Octavian Lie 
wrote:

> Dear Bruce,
>
> I am not sure how an ok aseg.mgz would look like for a lesion like that,
> but it looks like it includes one larger gyrus excluded by the pia, see
> attached, I would be happy to retrieve that one as it is the bulkiest of
> all the ones left out.
> Thank you,
>
> Octavian
>
> On Tue, Nov 25, 2014 at 7:38 AM, Bruce Fischl 
> wrote:
>
>> Hi Octavian
>>
>> I wouldn't use control points since it really isn't healthy wm. The only
>> thing you can do is edit the wm.mgz and possibly also the brainmask, but
>> it's so abnormal looking you may not be able to get accurate surfaces.
>> How does the aseg look? If it is ok there may be one other option.
>>
>> cheers
>> Bruce
>>
>>
>> On Tue, 25 Nov 2014, Octavian Lie wrote:
>>
>> > Dear All,
>> > any suggestion about this type of problem? I tried control points
>> through
>> > the middle/axis of the atrophic gyri (intensity 30-90 in T1 or
>> brainmask),
>> > wm.mgz edits through the same (adding from brainmask by cloning those
>> > voxels; painting 110; or 255 brush), and modifying brainmask directly by
>> > painting 110 internsity voxels through the same (gyri interiors, where
>> wm is
>> > supposed to be). Did not work, the atrophic gyri continue to remain
>> outside
>> > the pia. Again, this is an example of an eccentric lesion with gyral
>> > atrophy, without interruption in the gray matter ribbon but very faint
>> wm
>> > signal through the base of the affected gyri.
>> > Thanks,
>> > Octavian
>> >
>> >
>> >
>> > -- Forwarded message --
>> > From: Octavian Lie 
>> > Date: Tue, Nov 18, 2014 at 10:50 AM
>> > Subject: Eccentric lesions
>> > To: "freesurfer@nmr.mgh.harvard.edu" 
>> >
>> >
>> > Dear All,
>> >
>> > I am interested at getting as good pial/cortical reconstructions as
>> possible
>> > on a series of epilepsy pt scans, some showing eccentric (cortical)
>> lesions
>> > (focal encephalomalacias, infarcts, or after focal resections). One
>> > particularly difficult lesion type to get an accurate cortical surface
>> is
>> > where there are prongs of grey matter bulging out (like a bag of worms),
>> > (mostly) without visible wm, see attached picture. These prongs are
>> > maintained in the brainmask.mgz and brain.finalsurfs.mgz, but not
>> included
>> > in the pia with the default recon. Lesion voxel intensities vary from
>> 30-90.
>> > I tried cp, wm edits (using brainmask or T1 as referece), both, did not
>> > matter, it did not work.
>> >
>> > Since I am not intested in wm/subcortical segmentation but just in a
>> good
>> > pia, I was wondering if I 'create' thin wm tracts through the center of
>> > these gm prongs to help pial segmentation. If this is a valid option,
>> should
>> > I create those in brainmask, brain.finalsurfs or wm.mgz, and should I
>> use
>> > 110 or 255 for the brush?
>> > Any other suggestions are appreciated. Nevertheless, I know there is a
>> lot
>> > of tweaking of each lesion, and I try for more of a global approach to
>> these
>> > kinds of lesions.
>> >
>> > Thank you,
>> >
>> > Octavian.
>> >
>> >
>> >
>> ___
>> 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] Poor subcortical segmentation

[Bruce Fischl]

Hi Mihaela

if you want to upload a representative subject we will take a look
cheers
Bruce
On Tue, 
25 Nov 2014, Mihaela Stefan wrote:

> Hello Freesurfers,
> We noticed that our subcortical segmentations have a poor quality (see
> attachment). Is there a way to improve the segmentation in an automated
> fashion (avoiding long hours of manual editing)?
> 
> We use FS 5.3 on Ubuntu 12.04.
> 
> Thanks!
> Mihaela
> 
>
___
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] Poor subcortical segmentation

[Mihaela Stefan]

Hi Bruce,
I uploaded a subject.

Thanks!
Mihaela

On Tue, Nov 25, 2014 at 10:13 AM, Bruce Fischl 
wrote:

> Hi Mihaela
>
> if you want to upload a representative subject we will take a look
> cheers
> Bruce
> On Tue,
> 25 Nov 2014, Mihaela Stefan wrote:
>
> > Hello Freesurfers,
> > We noticed that our subcortical segmentations have a poor quality (see
> > attachment). Is there a way to improve the segmentation in an automated
> > fashion (avoiding long hours of manual editing)?
> >
> > We use FS 5.3 on Ubuntu 12.04.
> >
> > Thanks!
> > Mihaela
> >
> >
> ___
> 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] Tracula mri_convert error

[Douglas Greve]

Can you send the full terminal output?
doug

On 11/24/14 10:18 PM, Janosch Linkersdörfer wrote:
> Hi experts,
>
> I wanted to play with Tracula. Strangely, already the first preprocessing 
> step, i.e., conversion to .nii.gz, fails.
>
> Apparently, mri_convert (falsely) recognizes my dicom files as MGH dicoms 
> ("This looks like an MGH DTI volume"). Could this be the reason why it fails?
>
> Thanks,
>
> Janosch
>
>
>
>
>
>
>
> ___
> 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] TRACULA- DKI?

[Cat Chong]

Dear Tracula Team,
Quick question: Is Tracula able to to process diffusion kurtosis data, and 
yield, let's say, 'mean kurtosis' parameters for specific fiber 
tracts?cheers,Cat___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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

Re: [Freesurfer] Freesurfer Version

[zkaufman]

The 64bit Lion version. It should probably be made a little more clear
that that version is for 10.7 and higher. Ill fix that.

https://surfer.nmr.mgh.harvard.edu/fswiki/Download

-Zeke


> Gentleman
> Which Version of Freesurfer should I download for use with the OS X
> Yosemite 10.10.1?
> Thanks
> Cristian
> ___
> 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] Freesurfer Version

[Cristian Zeni]

Thanks, Zeke!!!

On Tue, Nov 25, 2014 at 10:59 AM,  wrote:

>
> The 64bit Lion version. It should probably be made a little more clear
> that that version is for 10.7 and higher. Ill fix that.
>
> https://surfer.nmr.mgh.harvard.edu/fswiki/Download
>
> -Zeke
>
>
> > Gentleman
> > Which Version of Freesurfer should I download for use with the OS X
> > Yosemite 10.10.1?
> > Thanks
> > Cristian
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> >
> >
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> The information in this e-mail is intended only for the person to whom it
> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
>
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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

[Freesurfer] Freeview in a VM (Debian)

[Elena Molina]

Hi all,

I am running FS in a VM (Debian, wheezy) and I would like to create a 3D
reconstruction of the hippocampus in .png. For that, I executed the
following code lines:

>> mri_extract_label aseg.mgz 17 lh.nii
>> mri_extract_label aseg.mgz 53 rh.nii
>> freeview -slice 500 500 500 -v lh.nii:isosurface=on rh.nii:isosurface=on
-viewport 3d -cam azimuth -90 elevation 25 dolly 5 -ras 0 0 10 -ss
3dhipo.png

But I have an error with the freeview command: freeview.bin: cannot connect
to X server

How can I solve it? Is there another way to generate the .png?

Best Regards,

Elena
___
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] Digest mode for mailing list and responding to mails

[Janosch Linkersdörfer]

Hi list,

I recently switched to the digest mode for the mailing list. Since then, I 
don't receive answers to my mails as mails anymore, making it harder to respond 
to them (or any other mail on the list). 

Does anybody experience the same issues? How did you solve them?

Thanks,

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


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

Re: [Freesurfer] tksurfer curvature and overlay displays

[Graham Wideman]

At 11/24/2014 08:23 AM, Bruce Fischl wrote:
>Hi Graham
>
>have you tried freeview? We stopped development on the tktools some time 
>ago.
>
>cheers
>Bruce

Hi Bruce, thanks for replying.

Yes, I did proceed to try the same task in Freeview (which in general has a 
nicer UI, to be sure). Some notes:

Test case: For subject bert, display principal curvature k1 (of smoothwm) on 
smoothwm and on inflated. Using Freeview latest version, in Linux Mint 15.

Freeview Problems/Bugs
---
1. The Threshold frequency histogram widget with color adjustment handles is a 
great idea, but has several problems.

a. Horizontal range of the freq hist defaults to entire range of the variable, 
which, for k1, is one to two orders of magnitude larger than the range of the 
bulk of the data. Consequence: the bulk of the data appears compressed to a 
tiny range near zero, in a tiny number of bins, and it's impossible to set the 
adjustment handles. 

This mechanism needs to accept manual upper and lower limits (and options to 
clip outliers to that value, or exclude them).

b. The "Use percentile" checkbox doesn't seem to do anything that I could 
discover.

c. The mouse hit detection for selecting and dragging the color adjustment 
handles often doesn't work. This is some combination of:

-- The target area of the handles is too small.

-- Clicking the handle but missing instead moves some other handle to the 
clicked location

-- Sometimes the hit detection seems to think you're pressing/clicking on the 
mirror-image side of the graph. Press at +10, and it's like you pressed at -10.

2. It would be great to be able to clone (or save/load) display settings 
associated with one surface onto another. This way, time spent configuring the 
display of a particular variable on, say, smoothwm, would not have to be redone 
(inevitably imperfectly) to display the same variable on another surface like 
inflated, which is a frequent need.

mris_convert
-
3. crv->text, text->crv.  I didn't find a tool that would convert between crv 
and text format and back, to make it easy to use some other tool to clip k1 to 
tractable limits. 

Maybe mris_convert does this, but if so, the help for that program could use 
some revision:
---
Usage: mris_convert [options]  
...
-c   input is scalar curv overlay file (must still specify surface)
---

a. 'curv' perhaps also includes 'crv'?

b. Why is 'surface' needed? The curv/crv files contain everything they need for 
conversion. Requiring surface makes it seem like the conversion is going to do 
something more elaborate than just convert binary <--> text.

c. And does 'surface' mean just an argument like 'orig' or 'pial', or the name 
of a surface file? Perhaps it just means that mris_convert still looks for an 
 argument, but doesn't use it?

Anyhow, I didn't trust that this was going to do what I intended.
 
---
I DID end up getting the display I wanted: I inspected a k1.crv file in a hex 
editor, discovered it was the same as old "new" .curv format, and wrote some 
python code to read/write/filter such a file. With this I could produce a 
clipped version of k1, which did work tractably in Freeview and produced a nice 
display.

-- Graham

___
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] kvlQuantifyHippocampalSubfieldSegmentations.sh resultsDirectory 1, 10 gives error line 22: cd: left: No such file or directory

[Knut J Bjuland]

 Dear Freesurfer experts,


I have processed my subject with recon-all and subfields hippocampal
segmentation. . I have tried to use
kvlQuantifyHippocampalSubfieldSegmentations.sh on a subset of my
subjects. I have these subjects A  B  C  D  E  fsaverage in a folder.
When I try to exclude fsaverage by using this command
kvlQuantifyHippocampalSubfieldSegmentations.sh  ~/subjects/hippo 1 5.  I
get this error message.

cd A/
Quantifying subject A/ left
Doing left side
cd left
/usr/local/freesurfer/bin/kvlQuantifyHippocampalSubfieldSegmentations.sh: line
22: cd: left: No such file or directory
failed to do cd left
I have issued this command both in tsch and in bash.
However, when I run the command without any options in the same folder,
it works but bails out as expected when it reaches fsaverage-

Best regards,

Knut J. Bjuland
PhD candidate
NTNU
___
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] Poor subcortical segmentation

[Mihaela Stefan]

Hi Bruce,

I've heard people saying that FS 5.3 is focusing on better output for
cortical thickness and that I should use 5.0 for subcortical segmentation
because it's better. Does that make sense?

Thanks!
Mihaela

On Tue, Nov 25, 2014 at 10:43 AM, Mihaela Stefan 
wrote:

> Hi Bruce,
> I uploaded a subject.
>
> Thanks!
> Mihaela
>
> On Tue, Nov 25, 2014 at 10:13 AM, Bruce Fischl  > wrote:
>
>> Hi Mihaela
>>
>> if you want to upload a representative subject we will take a look
>> cheers
>> Bruce
>> On Tue,
>> 25 Nov 2014, Mihaela Stefan wrote:
>>
>> > Hello Freesurfers,
>> > We noticed that our subcortical segmentations have a poor quality (see
>> > attachment). Is there a way to improve the segmentation in an automated
>> > fashion (avoiding long hours of manual editing)?
>> >
>> > We use FS 5.3 on Ubuntu 12.04.
>> >
>> > Thanks!
>> > Mihaela
>> >
>> >
>> ___
>> 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] Poor subcortical segmentation

[Bruce Fischl]

No, I don't think so
Bruce



> On Nov 25, 2014, at 11:05 PM, Mihaela Stefan  wrote:
> 
> Hi Bruce,
> 
> I've heard people saying that FS 5.3 is focusing on better output for 
> cortical thickness and that I should use 5.0 for subcortical segmentation 
> because it's better. Does that make sense?
> 
> Thanks!
> Mihaela
> 
>> On Tue, Nov 25, 2014 at 10:43 AM, Mihaela Stefan  
>> wrote:
>> Hi Bruce,
>> I uploaded a subject.
>> 
>> Thanks!
>> Mihaela
>> 
>>> On Tue, Nov 25, 2014 at 10:13 AM, Bruce Fischl  
>>> wrote:
>>> Hi Mihaela
>>> 
>>> if you want to upload a representative subject we will take a look
>>> cheers
>>> Bruce
>>> On Tue,
>>> 25 Nov 2014, Mihaela Stefan wrote:
>>> 
>>> > Hello Freesurfers,
>>> > We noticed that our subcortical segmentations have a poor quality (see
>>> > attachment). Is there a way to improve the segmentation in an automated
>>> > fashion (avoiding long hours of manual editing)?
>>> >
>>> > We use FS 5.3 on Ubuntu 12.04.
>>> >
>>> > Thanks!
>>> > Mihaela
>>> >
>>> >
>>> ___
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>> 
>>> 
>>> The information in this e-mail is intended only for the person to whom it is
>>> addressed. If you believe this e-mail was sent to you in error and the 
>>> e-mail
>>> contains patient information, please contact the Partners Compliance 
>>> HelpLine at
>>> http://www.partners.org/complianceline . If the e-mail was sent to you in 
>>> error
>>> but does not contain patient information, please contact the sender and 
>>> properly
>>> dispose of the e-mail.
> 
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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

[Freesurfer] parcellation of group stats maps?

[Scott Hayes]

Hi,
Is there a way to generate an intersection between a cortical thickness
stats map (e.g., sig.mgh) in fsaverage space and native space neuroanatomy
using FS parcellations (e.g., lh.apac.anot.)?  We would like to plot
cortical thickness of the significant clusters for each subject, but
separate the significant clusters by the parcellations, e.g., if the
significant cluster spans parahippocampal and fusiform cortex, I would like
those plotted separately (preferably w/o drawing ROIs--and again, not using
the entire PHC or fusiform parcellation--only the portion that is
significant in the group analysis).

It seems like this might be possible to accomplish w/ a single command, but
we have not been able to pinpoint the exact command w/ the necessary
flags.  Any guidance would be appreciated.

Thanks,
Scott
___
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] Different significant regions with different cluster wise thresholds

[Bronwyn Overs]

Hi Douglas,

How exactly should I upload the glmdir?

Kind regards,

Bronwyn Overs
Research Assistant

Neuroscience Research Australia

Neuroscience Research Australia
Margarete Ainsworth Building
Barker Street Randwick Sydney NSW 2031 Australia
*M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265

neura.edu.au 

Follow @neuraustralia on twitter 
Follow NeuRA on facebook 
Subscribe to the 
NeuRA Magazine 


On 11/11/2014 4:19 am, Douglas N Greve wrote:

Can you upload the gtlmdir and I'll take a look?

On 11/06/2014 08:19 PM, Bronwyn Overs wrote:

I believe it is the cluster-forming threshold. I was running the
following:
mri_glmfit-sim --glmdir site-gender-group-prothaplotype.glmdir --cache
1.3 abs --cwpvalthresh  0.05 --2spaces
mri_glmfit-sim --glmdir site-gender-group-prothaplotype.glmdir --cache
2 abs --cwpvalthresh  0.05 --2spaces

Kind regards,

Bronwyn Overs
Research Assistant

Neuroscience Research Australia

Neuroscience Research Australia
Margarete Ainsworth Building
Barker Street Randwick Sydney NSW 2031 Australia
*M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265

neura.edu.au 

Follow @neuraustralia on twitter
Follow NeuRA on facebook
Subscribe to
the NeuRA Magazine 

On 7/11/2014 4:03 am, Douglas N Greve wrote:

Do you mean cluster-wise threshold or cluster-forming threshold?

On 11/06/2014 01:12 AM, Bronwyn Overs wrote:

Dear Freesurfer Mailing list,

While running a glm anlaysis with monte carlo correction (using
cluster wise thresholds of .05 & .01), I encountered the following issue:
When examining the clusters formed for each of the different cluster
wise thresholds, the .05 threshold resulted in a superior temporal
cluster, while the .01 threshold resulted in a two lateral occipital
clusters that did not overlap with the cluster from the .05 threshold.

Do you know why there would be no overlap between significant regions
at different cluster wise thresholds? I was aware that a cluster which
is significant at .05 may split or be smaller at .01, but I do not
know why entirely different regions would be significant.
--

Kind regards,

Bronwyn Overs
Research Assistant

Neuroscience Research Australia

Neuroscience Research Australia
Margarete Ainsworth Building
Barker Street Randwick Sydney NSW 2031 Australia
*M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265

neura.edu.au

Follow @neuraustralia on twitter
Follow NeuRA on facebook
Subscribe to
the NeuRA Magazine



___
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


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] mri_glmfit-sim

[Jürgen Hänggi]

Dear FS experts

We would like to force FS's mri_glmfit-sim function of FS 5.3.0 to report
all results and not only the significant results.
This was the behavior of this function until FS version 4.5.0.

Please can you guide as to the relevant lines in the mri_glmfit-sim function
and indicate what have to be changed.

Thanks in advance
Best regards
Jürgen Hänggi


Jürgen Hänggi, Ph.D.
Division Neuropsychology
Institute of Psychology
University of Zurich
Binzmuehlestrasse 14, PO Box 25
8050 Zurich, Switzerland
0041 44 635 73 97 (phone office)
0041 76 445 86 84 (phone mobile)
0041 44 635 74 09 (fax office)
BIN 4.D.04 (office room number)
j.haenggi[at]psychologie.uzh.ch (email)
http://www.psychologie.uzh.ch/neuropsy/ (website)
http://www.juergenhaenggi.ch (private website)

This e-mail (and any attachment/s) contains confidential and/or privileged
information. If you are not the intended recipient (or have received this
e-mail in error) please notify the sender immediately and destroy this
e-mail. Any unauthorised copying, disclosure or distribution of the
material in this e-mail is strictly forbidden.




___
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.