Re: [Freesurfer] hippocampal subfield segmentation question

[Iglesias Gonzalez, Juan E.]

Dear Gabor,
It’s all about the physical coordinates, so (b) is the right answer!
/Eugenio

Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jeiglesias.com


From:  on behalf of Gabor Perlaki 

Reply-To: Freesurfer support list 
Date: Saturday, 11 January 2020 at 20:43
To: freesurfer 
Subject: [Freesurfer] hippocampal subfield segmentation question


External Email - Use Caution
We have a sagittal 1 mm isotropic whole-brain 3D T1 mprage (morphometry 
protocol suggested on Freesurfer's page) and a coronal anisotropic (0.4mm 
inplane, 2mm thickness, similar to ADNI protocol) T2 measurement acquired 
perpendicular to the hippocampus. We'd like to use both measurements 
simultaneously in the segmentation. However, on the fswiki it is suggested that 
T2 should be coarsely aligned to the main T1 scan, but I'm not sure about how 
to understand it, especially since our 3D T1 is acquired in sagittal plane, 
while T2 is in coronal.
(a) Should T1 and T2 acquired in the same (e.g. coronal plane) with the same or 
little angulation?
or
(b) Is it enough if they are just aligned based on the physical/anatomical 
coordinate system (which is automatically ensured if both images were  acquired 
in the same session with no repositioning and little or no head movement of the 
subject between the two measurements)?

Best,
Gabor
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Re: [Freesurfer] (no subject)

[Boris Rauchmann]

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Thanks, that solution seems to work finally. I just ignored the remaining 
voxels labeled according to the standard aseg scheme and proceeded with the the 
PET analysis and the combined LUT.
I will ignore the remaining fragment labels from the original aseg and only use 
the output from the BN labels (starting with 211), these are the only results 
im really interested in. Is that ok?

Here an example stats file I got:

  12 Left-Cerebral-White-Matter  wm 41550 13909.534
0.989   0.0935
  27 Left-Cerebellum-White-Matterwm  2276 1037.525
0.854   0.0811
  38 Left-Cerebellum-Cortex  cortex 10936 6010.637
1.015   0.1339
  4   10 Left-Thalamus-Propersubcort_gm 30.024   
-0.815   0.2251
  5   11 Left-Caudatesubcort_gm 30.035   
21.480   0.1746
  6   12 Left-Putamensubcort_gm250.459
3.161   0.0615
  7   13 Left-Pallidum   subcort_gm491.497
1.474   0.0667
  8   16 Brain-Stem  subcort_gm  4599 2714.856
0.929   0.1000
  9   17 Left-Hippocampussubcort_gm 20.023   
-3.152   0.1702
 10   18 Left-Amygdala   subcort_gm 10.005   
-7.082   0.1060
 11   24 CSF csf 7468 2623.527
0.251   0.2568
 12   26 Left-Accumbens-area subcort_gm 00.004
0.879  nan
 13   28 Left-VentralDC  subcort_gm   714  205.288
1.358   0.1427
 14   31 Left-choroid-plexus csf  220   18.333
5.945   0.6080
 15   41 Right-Cerebral-White-Matter wm 40645 13911.597
0.987   0.0841
 16   46 Right-Cerebellum-White-Matter   wm  2146  990.941
0.862   0.0826
 17   47 Right-Cerebellum-Cortex cortex 11029 6187.241
0.985   0.1317
 18   49 Right-Thalamus-Proper   subcort_gm110.140
0.032   0.2024
 19   50 Right-Caudate   subcort_gm 10.009   
-2.162   0.0258
 20   51 Right-Putamen   subcort_gm442.020
3.727   0.1893
 21   52 Right-Pallidum  subcort_gm240.316
5.739   0.1814
 22   53 Right-Hippocampus   subcort_gm 30.026   
16.575   0.2951
 23   54 Right-Amygdala  subcort_gm 70.081
4.637   0.0897
 24   58 Right-Accumbens-areasubcort_gm 00.000   
-4.474  nan
 25   60 Right-VentralDC subcort_gm   728  198.051
1.430   0.2142
 26   63 Right-choroid-plexuscsf  136   10.088
6.633   0.5924
 27  211 mAmyg_L subcort_gm   264   48.960
1.126   0.1262
 28  212 mAmyg_R subcort_gm   268   46.429
1.292   0.1920
 29  213 lAmyg_L subcort_gm   1316.503
1.889   0.1003
 30  214 lAmyg_R subcort_gm   181   13.490
1.382   0.1237
 31  215 rHipp_L subcort_gm  1020  260.090
1.166   0.1828
 32  216 rHipp_R subcort_gm   833  241.777
1.149   0.2291
 33  217 cHipp_L subcort_gm   911  288.346
1.578   0.3201
 34  218 cHipp_R subcort_gm  1050  330.445
1.273   0.2312
 35  219 vCa_L   subcort_gm   626  170.254
1.205   0.0829
 36  220 vCa_R   subcort_gm   477   84.269
1.491   0.0933
 37  221 GP_Lsubcort_gm   597  133.161
1.369   0.0977
 38  222 GP_Rsubcort_gm   514   93.978
1.491   0.0811
 39  223 NAC_L   subcort_gm   412   67.647
1.348   0.1591
 40  224 NAC_R   subcort_gm   503   87.917
1.240   0.1258
 41  225 vmPu_L  subcort_gm   465  128.509
1.740   0.0783
 42  226 vmPu_R  subcort_gm   367   83.411
1.588   0.0699
 43  227 dCa_L   subcort_gm   997  255.259
0.821   0.1448
 44  228 dCa_R   subcort_gm  1271  405.156
1.017   0.1380
 45  229 dlPu_L  subcort_gm   678  122.256
1.356   0.0960
 46  230 dlPu_R  subcort_gm   585  150.878
1.319   0.0942
 47  231 mPFtha_L  

Re: [Freesurfer] Edit surface in Freeview

[Davide Momi]

External Email - Use Caution

Thanks Doug,

I followed your tips and try to run mris_remove_intersection. However  the
result looks like the same than before. Maybe I am doing something wrong.
Could you please provide me more details?

Do you have any other suggestions?

Thanks again for your help

Dave

Il giorno sab 11 gen 2020 alle ore 15:56 Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> ha scritto:

> YOu can try running mris_remove_intersection (or something like that)
>
> On 1/11/2020 12:48 PM, Davide Momi wrote:
>
> External Email - Use Caution
> Dear Freesurfer expert,
>
> I am working with bem model and I have created the outer and the inner
> skull. Unfortunately, for few subjects the two surfaces intersect each
> other (see attached). I've tried to edit it manually but I had hard time in
> figuring it out. Could you please help me with this?
>
> thanks
>
> Dave
>
> ___
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>
>
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Re: [Freesurfer] Noise reduction + Eddy current reduction

[Glasser, Matthew]

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In general these days the more recent “eddy” tool is preferred for eddy current 
correction of diffusion data.

Matt.

From:  on behalf of "Greve, Douglas 
N.,Ph.D." 
Reply-To: Freesurfer support list 
Date: Saturday, January 11, 2020 at 2:54 PM
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: Re: [Freesurfer] Noise reduction + Eddy current reduction

No, I've always used FSL's eddy_correct
On 1/11/2020 2:17 AM, Adam Rytina wrote:

External Email - Use Caution
Hi Greve,

thanks for your answer. I will try ANTS DenoiseImage.

Regarding Eddy Current - moreover, i have to reduce the eddy current on DWI 
images. Does Freesurfer enable to perform the eddy current reduction?

Thanks a lot
Regards
Adam


Od: 
freesurfer-boun...@nmr.mgh.harvard.edu
 

 za uživatele Greve, Douglas N.,Ph.D. 

Odesláno: sobota 11. ledna 2020 0:03
Komu: freesurfer@nmr.mgh.harvard.edu 

Předmět: Re: [Freesurfer] Noise reduction + Eddy current reduction

We don't have anything to denoise. You can try using ANTS DenoiseImage, but 
using on the input might change where the surface is placed. We are 
experimenting with using it inside the stream in a place where it is less 
likely to bias the surface placement.

I don't understand the eddy current question as there should not be eddy 
currents in a typical T1 or FLAIR
On 1/10/2020 2:53 PM, Adam Rytina wrote:

External Email - Use Caution
Hello all,

I want to apply the denoising and eddy current reduction on input images 3DT1 
and 3D Flair. Are there any algorithms in Freesurfer to perform the noise and 
eddy current reduction? Does recon-all involve denoising and eddy current 
reduction? If so, in which processing stage?

Thanks a lot
Regards
Adam



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Re: [Freesurfer] Noise reduction + Eddy current reduction

[Greve, Douglas N.,Ph.D.]

No, I've always used FSL's eddy_correct

On 1/11/2020 2:17 AM, Adam Rytina wrote:

External Email - Use Caution

Hi Greve,

thanks for your answer. I will try ANTS DenoiseImage.

Regarding Eddy Current - moreover, i have to reduce the eddy current on DWI 
images. Does Freesurfer enable to perform the eddy current reduction?

Thanks a lot
Regards
Adam


Od: 
freesurfer-boun...@nmr.mgh.harvard.edu
 

 za uživatele Greve, Douglas N.,Ph.D. 

Odesláno: sobota 11. ledna 2020 0:03
Komu: freesurfer@nmr.mgh.harvard.edu 

Předmět: Re: [Freesurfer] Noise reduction + Eddy current reduction

We don't have anything to denoise. You can try using ANTS DenoiseImage, but 
using on the input might change where the surface is placed. We are 
experimenting with using it inside the stream in a place where it is less 
likely to bias the surface placement.

I don't understand the eddy current question as there should not be eddy 
currents in a typical T1 or FLAIR

On 1/10/2020 2:53 PM, Adam Rytina wrote:

External Email - Use Caution

Hello all,

I want to apply the denoising and eddy current reduction on input images 3DT1 
and 3D Flair. Are there any algorithms in Freesurfer to perform the noise and 
eddy current reduction? Does recon-all involve denoising and eddy current 
reduction? If so, in which processing stage?

Thanks a lot
Regards
Adam



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Re: [Freesurfer] Edit surface in Freeview

[Greve, Douglas N.,Ph.D.]

YOu can try running mris_remove_intersection (or something like that)

On 1/11/2020 12:48 PM, Davide Momi wrote:

External Email - Use Caution

Dear Freesurfer expert,

I am working with bem model and I have created the outer and the inner skull. 
Unfortunately, for few subjects the two surfaces intersect each other (see 
attached). I've tried to edit it manually but I had hard time in figuring it 
out. Could you please help me with this?

thanks

Dave



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[Freesurfer] hippocampal subfield segmentation question

[Gabor Perlaki]

External Email - Use Caution

 We have a sagittal 1 mm isotropic whole-brain 3D T1 mprage (morphometry
protocol suggested on Freesurfer's page) and a coronal anisotropic (0.4mm
inplane, 2mm thickness, similar to ADNI protocol) T2 measurement acquired
perpendicular to the hippocampus. We'd like to use both measurements
simultaneously in the segmentation. However, on the fswiki it is suggested
that T2 should be coarsely aligned to the main T1 scan, but I'm not sure
about how to understand it, especially since our 3D T1 is acquired in
sagittal plane, while T2 is in coronal.
(a) Should T1 and T2 acquired in the same (e.g. coronal plane) with the
same or little angulation?
or
(b) Is it enough if they are just aligned based on the physical/anatomical
coordinate system (which is automatically ensured if both images were
acquired in the same session with no repositioning and little or no head
movement of the subject between the two measurements)?

Best,
Gabor
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[Freesurfer] Edit surface in Freeview

[Davide Momi]

External Email - Use Caution

Dear Freesurfer expert,

I am working with bem model and I have created the outer and the inner
skull. Unfortunately, for few subjects the two surfaces intersect each
other (see attached). I've tried to edit it manually but I had hard time in
figuring it out. Could you please help me with this?

thanks

Dave
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[Freesurfer] Extract specific LGI values

[Tien Pham]

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Dear FreeSurfer Experts,

I am Tien Pham, I am stucked at this situation. I calculated longitudinal
LGI changes in my data set with two time points using longitudinal
pipeline. Now I would like to extract the regional LGI and gray matter
volume in my longitudinal results using QDEC to draw the ROIs which is
showed significant differences, label it and map to all subjects. Then I
get the LGI value of the ROI I saved before using the command below:

cd $SUBJECTS_DIR
mris_anatomical_stats -l lh.untitled.label \
 -t lh.pial_lgi \
 -b \
 -f subject_id/stats/lh.untitled.stats subject_id lh

And this is the result:

[toyama-no-iMac:/applications/freesurfer/subjects] toyama%
mris_anatomical_stats -l lh.frontoinsula.label \

? -t lh.pial_lgi \

? -b \

? -f VC019_1/stats/lh.frontoinsula.stats VC019_1 lh

limiting computations to label lh.frontoinsula.label.

using thickness file lh.pial_lgi.

reading volume /applications/freesurfer/subjects/VC019_1/mri/wm.mgz...

reading input surface
/applications/freesurfer/subjects/VC019_1/surf/lh.white...

reading input pial surface
/applications/freesurfer/subjects/VC019_1/surf/lh.pial...

reading input white surface
/applications/freesurfer/subjects/VC019_1/surf/lh.white...



table columns are:

number of vertices

total surface area (mm^2)

total gray matter volume (mm^3)

average cortical thickness +- standard deviation (mm)

integrated rectified mean curvature

integrated rectified Gaussian curvature

folding index

intrinsic curvature index

structure name



 6595   4368  15935  3.311 0.895 0.158 0.077  13519.7
lh.frontoinsula.label


As I saw there was no columns showing the LGI value, I did similar with
gray matter volume, the result displayed the different in some values of
the columns.
Could you please help me to explain about this?

Thank you very much.


Best regards,

Tien Pham
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Re: [Freesurfer] Noise reduction + Eddy current reduction

[Adam Rytina]

External Email - Use Caution

Hi Greve,

thanks for your answer. I will try ANTS DenoiseImage.

Regarding Eddy Current - moreover, i have to reduce the eddy current on DWI 
images. Does Freesurfer enable to perform the eddy current reduction?

Thanks a lot
Regards
Adam


Od: freesurfer-boun...@nmr.mgh.harvard.edu 
 za uživatele Greve, Douglas N.,Ph.D. 

Odesláno: sobota 11. ledna 2020 0:03
Komu: freesurfer@nmr.mgh.harvard.edu 
Předmět: Re: [Freesurfer] Noise reduction + Eddy current reduction

We don't have anything to denoise. You can try using ANTS DenoiseImage, but 
using on the input might change where the surface is placed. We are 
experimenting with using it inside the stream in a place where it is less 
likely to bias the surface placement.

I don't understand the eddy current question as there should not be eddy 
currents in a typical T1 or FLAIR

On 1/10/2020 2:53 PM, Adam Rytina wrote:

External Email - Use Caution

Hello all,

I want to apply the denoising and eddy current reduction on input images 3DT1 
and 3D Flair. Are there any algorithms in Freesurfer to perform the noise and 
eddy current reduction? Does recon-all involve denoising and eddy current 
reduction? If so, in which processing stage?

Thanks a lot
Regards
Adam



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