[Freesurfer] amount of manual corrections in 5.1 related to aparc+aseg?

[Dorit Kliemann]

Dear FreeSurfers,

I'm working on a structural dataset and after running recon-all -all,  
I had to correct all cases (32 so far) from minimum pial/wm  
corrections to massive pial corrections (only three cases needed  
control points). Mostly, the corrections were needed due to remaining  
dura/skull. Initially, I tried to adjust the skull-stripping (either  
with changing the wsthresh or gcut for individual cases), however,  
those corrections were not always too successful (i.e. still remaining  
dura/skull), so I continued correcting manually.


Are there any known/expected problems that could still arise with the  
aparc+aseg segmentations after (massive) corrections (i.e. all cases),  
even after redoing respective recon-steps with version 5.1?  In the  
release notes, I only found that control points may adversely affect  
aseg...
I checked the segmentations and so far I couldn't recognize any  
obvious/consistent flaws.
I remember from working with version 4.1. that most cases need at  
least some corrections, but I don't have any experience with 5.1, yet.


I'm specifically interested in the amygdala, but of course amygdala  
segmentations will be corrected manually.



Thanks,
Dorit


Data were acquired on a 3T Tim Trio dataset (32 channel-coil, TR  
1900ms, TE 2.52 ms, 1x1x1 voxel-size, TI 900ms, flip angle 9, ipad  
grappa2, bandwidth 170Hz/pixel, prescan-normalize).
Data were initially processed with recon-all -all with version 5.1 on  
a linux cluster (scientific linux 6.1). Data were corrected and then  
re-run with respective recon-steps on a local Mac (OS 10.5.8) with  
freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0.


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[Freesurfer] Lateral ventricles not filled entirely

[Dorit Kliemann]

Hi,

I recently started using freesurfer and finally processed my first subjects
with all three recon steps (using the latest version).

Checking the white matter volume I recognized that all my scans have the
same issue:
The lateral ventricles aren't filled entirely but there are some black spots
within the ventricles..in the tutorial is written that one should handle
this in a described way but I was wondering if this is necessary when recon3
was sucessful without any errors.

Does anyone have experience with that? (see attached picture)


Thanks a lot,
Dorit Kliemann





Bild 6.png
Description: Binary data
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[Freesurfer] again: qdec error

[Dorit Kliemann]

Dear all,

I wanted to open qdec for the first time and experienced an error that was
posted some days ago...
( RE: [Freesurfer] qdec ERROR: Rendering vtkXOpenGLRenderWindow ; Juranek,
Jenifer )


 ERROR: In 
/usr/pubsw/packages/vtk/5.0.4/src/VTK/Rendering/vtkXOpenGLRenderWindow.cxx,
line 219 vtkXOpenGLRenderWindow (0x49220f0): Could not find a decent visual

In contrast to the previously reported incident, I was finally able to open
qdec by just clicking 'ok' on 3 of those exact same error messages. Still -
I could not read in any .dat files.

 I tried to follow the advice given in the previous threat

 In the file /etc/X11/xorg.conf, within the section titled Section
Module, make sure this line exists:

  Load glx

You might need to have your administrator perform this change, as it
requires root access.  You will have to restart your X server after
making this change (Ctrl-Bksp).

..but I don¹t have the referred file in the X11 folder (xorg.conf).

FYI, I¹m using the latest Freesurfer version and for a colleague of mine
qdec works without having that xorg.conf file. It is possible that there
is any other reason for the qdec error?

Thanks,
Dorit
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[Freesurfer] amygdala nuclear subregions

[Dorit Kliemann]

Hi Heidi,
segmentation of amygdalar subregions is currently not yet implemented in 
FreeSurfer, but we are working on including this feature soon.

Best,
Dorit


-

Message: 9
Date: Fri, 8 Jan 2016 13:21:48 +
From: "Jacobs H (NP)" 
Subject: [Freesurfer] amygdala nuclear subregions
To: Freesurfer support list 
Message-ID: 
Content-Type: text/plain; charset="iso-8859-1"

Dear FreeSurfer developers,

In the FreeSurferColorLut file I see labels for the subregions of the amygdala.
Is it possible to extract the volumes for these regions? And how can I do this? 
I don't see them in the aseg or aparc stat files.

Many thanks!
Heidi
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Re: [Freesurfer] Amygdala subfields

[Dorit Kliemann]

Hi Sascha,
yes, we have developed an amygdala nuclei atlas similar to the hippocampal 
subfields . Its currently being tested and to be implemented (hopefully) soon. 
Stay tuned. 

Dorit


> From: "sf" 
> Subject: [Freesurfer] Amygdala subfields
> Date: 31 October 2016 at 15:13:21 GMT
> To: "'Freesurfer support list'" 
> Reply-To: Freesurfer support list 
> 
> Hi all, is there any possibility to segment amygdala subfields with 
> freesurfer? Similar to the hippocampal subfields segmentation?
> Cheers - Sascha
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> 


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Re: [Freesurfer] Amygdala subfields

[Dorit Kliemann]

to clarify: the amygdala subregion atlas is built and will be released early 
2017.

Dorit

On Oct 31, 2016, at 11:46 AM, Dorit Kliemann <do...@mit.edu> wrote:

> Hi Sascha,
> yes, we have developed an amygdala nuclei atlas similar to the hippocampal 
> subfields . Its currently being tested and to be implemented (hopefully) 
> soon. Stay tuned. 
> 
> Dorit
> 
> 
>> From: "sf" <fruehh...@gmail.com>
>> Subject: [Freesurfer] Amygdala subfields
>> Date: 31 October 2016 at 15:13:21 GMT
>> To: "'Freesurfer support list'" <freesurfer@nmr.mgh.harvard.edu>
>> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
>> 
>> Hi all, is there any possibility to segment amygdala subfields with 
>> freesurfer? Similar to the hippocampal subfields segmentation?
>> Cheers - Sascha
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> 



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[Freesurfer] bbregister issues with ?h.only

[Dorit Kliemann]

Hi,

I’m having some troubles with using bbregister on hemispherectomy brains (i.e 
only one hemisphere; data is successfully processed with recon-all dev version 
- thanks to Bruce). 

I use bbregister to create a register.dat for the functional (preprocessed with 
fmriprep and registered -but not resampled- to standard space with fmriprep) to 
structural. Goal is to use the aparc+aseg
with mri_label2vol to transform to functional volume space. Ultimate goal is 
then to extract time series with mrisegstats. And this seems to work fine for 3 
out of 5 subjects with hemispherectomy.

However for two subjects the bbregister steps produced a bad output (as in the 
input tilts vertically, see screenshot overlaid on T1). One reason might be 
that for those subjects two heads are in a bid of a ‘funky tilted’ position, 
which maybe causes the automatic registration in bbregister to fail? 
Regardless of the reason, I was just wondering if any of you (Doug?) have 
further suggestions? 

One issue I noticed in the log is its suggested to use the T1 flag (not the 
bold) but its a bold input, just weird intensities probably bc of the ‘empty’ 
hemisphere. I also tried to run it with the T1 flag..same issue

Thank you,
Dorit


Here is the command I use for bbregister
bbregister --s subjx --mov func.nii.gz --init-fsl --reg subjx_register.dat 
--bold --lh-only 

Also happy to upload the relevant data or paste the whole log.
I use Fs 6.0 to run bbregister,mri_label2vol and mri_segstats.



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[Freesurfer] annotation to volume with custom color scheme (Yeo parcellations)

[Dorit Kliemann]

Hi,
I’m trying to use the Yeo2011 annotations to create individual volume masks in 
subject space.

I first use mri_surf2surf to map the annotations from fsaverage to individual 
subjects:

mri_surf2surf --srcsubject fsaverage --trgsubject subject --hemi rh 
--sval-annot fsaverage/label/rh.Yeo2011_7Networks_N1000.annot --tval 
$SUBJECTS_DIR/subject/label/rh.Yeo2011_7Networks_N1000

Then I use mri_apar2aseg to map the annotation from the surface to the volume 
and thought he annot-table flag would use the labels provided in the custom 
color lut file.

mri_aparc2aseg --s subject --o test.mgz --annot Yeo2011_7Networks_N1000 
--annot-table path_to/Yeo2011_7Networks_ColorLUT.txt


However the output is using different segmentation/color assignments. I can 
certainly find out which segmentation corresponds to which color and extract 
them separately (i.e. with fslmath or mri_binarize)..just wandering if I missed 
something or something changed since these posts?


https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg35247.html


Thanks
Dorit






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Re: [Freesurfer] annotation to volume with custom color scheme (Yeo parcellations)

[Dorit Kliemann]

ops. I guess that should have been obvious to me!

Thanks!
Dorit



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[Freesurfer] getting h/o atlas into individual surface (and then volume) space

[Dorit Kliemann]

Hi,
I’m trying to get an atlas (Harvard/Oxford sub) into individual space 
via surface registration. 
Motivation is to replicate a finding in volume space (functional data) in a 
normal population with that atlas in a lesion data set where transformation to 
template volume space is not feasible.

I think I found a way described in principle for one region below but it seems 
clumsy with a lot of steps , so I’d like to check if there is a better/more 
accurate ways with less transforms?

Any feedback appreciated!

Thanks,
Dorit


 1) create a registration file from FSL-MNItemplate to Freesurfer space and 
fsaverage
bbregister --s fsaverage --mov MNI152_T1_1mm_brain.nii.gz --init-fsl 
--init-header --reg mni2fsaverage.dat --T1 --o mni2fsaverage.nii

 2) warp atlas from FSL-MNI space onto surface of fsaverage
mri_vol2surf --mov HarvardOxford-cort-maxprob-thr25-1mm.nii.gz --reg 
mni2fsaverage.dat --projdist-max 0 1 .01 --interp nearest --hemi lh --out 
lh.atlas.mgh

 3) writing label for id = 1
mri_cor2label --i lh.atlas.mgh --surf fsaverage lh --id 1 --l 
./lh.1.atlas

 4) move label from fsaverage onto individual subject space
mri_label2label --srclabel lh.1.atlas --srcsubject fsaverage --trglabel 
lh.1.atlas --trgsubject subject --regmethod surface --hemi lh

 5) create voluem form label
mri_label2vol --label subject/label/lh.1.atlas --subject subject --hemi 
lh --identity --temp subject/mri/brain.mgz --o lh.1.atlas.volume.nii --proj 
frac 0 1 .01

 6) fix wholes/border ribbon
mri_binarize --dilate 1 --erode 1 --i lh.1.atlas.volume.nii --o 
lh.1.atlas.volumebin.nii --min 1
mris_calc -o lh.1.atlas.volumebinfixed.nii lh.1.atlas.volumebin.nii  
mul subject/mri/lh.ribbon.mgz

 7) bring from subject T1-FS space (1mm) into subject's functional space
bbregister --s subject --mov func.nii  --init-fsl --init-header --reg 
anat2func_register.dat --bold 

 8) warp atlas image from individual subject anat space to subject bold space
mri_label2vol --seg lh.1.atlas.volumebinfixed.nii --temp func.nii --reg 
anat2func_register.dat --fillthresh .5 --o lh.atlas.func.nii

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