subject:"\[Freesurfer\] thickness"

Re: [Freesurfer] Thickness vs surface area

2021-01-25 Thread Fischl, Bruce

Hi Stephanie

I’m not sure you can really compare their accuracy. Thickness is easier to 
interpret though and is also a point measure and relatively insensitive to head 
size, so is frequently an easier surrogate biomarker than surface area. That 
said, we have done studies of surface area change

Cheers
Bruce

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Stephanie K
Sent: Monday, January 25, 2021 1:09 PM
To: Freesurfer support list 
Subject: [Freesurfer] Thickness vs surface area


External Email - Use Caution
Hello,

I am performing analyses looking at brain measures for a neurodegenerative 
disorder. I wanted to ask whether the accuracy for surface area is as high as 
is for thickness? I would appreciate your advice or any references.

Thanks

[https://secure-web.cisco.com/1VSxjZQrTWn2bAajNapNegjX50Tu8iavxXhlBJ8rSANZo-XwbJkojP4r84JrgaYuBAGmonml7yvKeWgjJMVxgsOF-hBq4a7Xj51OmHQD9xch7yeAWzqYonUoLwA9BQyAOFMMvfB6-FNuA9WpQJhdkzB-u3py99MhKoNR74vWCQYEQUqpb8Dh-huAF-CaPSMlYw69_lj2MsxdZjptvxg1nUpAm7TFvcpLno]<http://secure-web.cisco.com/1s2WxUEm6XSL6Os4QbhWGVNh9SslHbUxbpObZbT9zlKw4O9NZtyLSPrt6V5BF6PZWJc9kgG5yVViHluW0cVeWbR7mtYObJcSo42KId00-1ep8cUpZMcP30KF_CvYBf_hplvOCq5Ap3tyq8T_-p3AlKhpTT7Jdh3WaU5iirNzquiNu6ASgl0wsqhAgMS9nvmlq7U_uzf8w-3s-VwgTslO8uW2mmTb2PWKuNWvjAWogUfulpz637pW83aeW5FCSEaXJeIVA8DVwbqfSCMOWPKCRAw/http%3A%2F%2Fwww.avg.com%2Femail-signature%3Futm_medium%3Demail%26utm_source%3Dlink%26utm_campaign%3Dsig-email%26utm_content%3Dwebmail>
Virus-free. MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to be 
www.avg.com<http://secure-web.cisco.com/1s2WxUEm6XSL6Os4QbhWGVNh9SslHbUxbpObZbT9zlKw4O9NZtyLSPrt6V5BF6PZWJc9kgG5yVViHluW0cVeWbR7mtYObJcSo42KId00-1ep8cUpZMcP30KF_CvYBf_hplvOCq5Ap3tyq8T_-p3AlKhpTT7Jdh3WaU5iirNzquiNu6ASgl0wsqhAgMS9nvmlq7U_uzf8w-3s-VwgTslO8uW2mmTb2PWKuNWvjAWogUfulpz637pW83aeW5FCSEaXJeIVA8DVwbqfSCMOWPKCRAw/http%3A%2F%2Fwww.avg.com%2Femail-signature%3Futm_medium%3Demail%26utm_source%3Dlink%26utm_campaign%3Dsig-email%26utm_content%3Dwebmail>

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

[Freesurfer] Thickness vs surface area

2021-01-25 Thread Stephanie K

External Email - Use Caution

Hello,

I am performing analyses looking at brain measures for a neurodegenerative
disorder. I wanted to ask whether the accuracy for surface area is as high
as is for thickness? I would appreciate your advice or any references.

Thanks


Virus-free.
http://secure-web.cisco.com/1bMTKfkeHqBmt5B7Whj8ClEmtAkQLnLLsXYt4JTx1GtIZMKZ38qYhne45E3Kt9boCNv6e6bO9AJR8demZjnAKApMFwLti-xffu3xdXttDhWa1JLW1AbqkO5LasUtAEwyMnDg23iV4EN28BAecSwd8R-UDEE4xz6JkYItEGFsw9O5A0VSQi2qhrKXDbO_eq63iwCw0KEo_PgaepuMYs8CZSLLWtvlycADZmk2lSaKhnPS6SStlQwAjBWC7vix2m3Yf07gPQPIpqrN0OMI-xwL4AA/http%3A%2F%2Fwww.avg.com

<#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] Thickness group normalization

2020-02-14 Thread Douglas N. Greve


You need to register your subjects to the new average subject with
surfreg --s subject --t 0_1


On 2/11/2020 12:36 PM, Vyacheslav Yarkin wrote:


External Email - Use Caution

I got the idea but faced an issue with mris_preproc, the command is:


mris_preproc --target 0_1 --s avg_subject_91_noexpopts --hemi lh 
--meas thickness --out avg_91_to_lh.mgh



where 0_1 is target patient to map thickness, from 
avg_subject_91_noexpopts, optained from make_average_subject.



i get the error running mris_preproc:

Reading source surface reg

  /input/HCP_T1_fs6/avg_subject_91_noexpopts/surf/lh.0_1.sphere.reg

  No such file or directory

  mri_surf2surf: could not read surface

  /input/HCP_T1_fs6/avg_subject_91_noexpopts/surf/lh.0_1.sphere.reg

  No such file or directory


Why there should be lh.0_1.sphere.reg? Have i missed some intermediate 
steps?







*От:* freesurfer-boun...@nmr.mgh.harvard.edu 
 от имени Vyacheslav Yarkin 


*Отправлено:* 5 февраля 2020 г. 11:47
*Кому:* Freesurfer support list
*Тема:* Re: [Freesurfer] Thickness group normalization

External Email - Use Caution

I got the idea but faced an issue with mris_preproc, the command is:


mris_preproc --target 0_1 --s avg_subject_91_noexpopts --hemi lh 
--meas thickness --out avg_91_to_lh.mgh



where 0_1 is target patient to map thickness, from 
avg_subject_91_noexpopts, optained from make_average_subject.



i get the error running mris_preproc:

Reading source surface reg

  /input/HCP_T1_fs6/avg_subject_91_noexpopts/surf/lh.0_1.sphere.reg

  No such file or directory

  mri_surf2surf: could not read surface

  /input/HCP_T1_fs6/avg_subject_91_noexpopts/surf/lh.0_1.sphere.reg

  No such file or directory


Why there should be lh.0_1.sphere.reg? Have i missed some intermediate 
steps?







*От:* freesurfer-boun...@nmr.mgh.harvard.edu 
 от имени Douglas N. Greve 


*Отправлено:* 3 февраля 2020 г. 20:51
*Кому:* freesurfer@nmr.mgh.harvard.edu
*Тема:* Re: [Freesurfer] Thickness group normalization

Do you have a group of subjects that you want to use as an average? If 
so, you can just map all their thickness maps to your patient subject 
with

mris_preproc --target patientsubjectname [then usual arguments]
Compute the mean with
mri_concat outputofmris_preproc.mgz --mean --o groupmean.mgz
You can then compare groupmean.mgz to your patient on a 
vertex-by-vertex baiss



On 2/3/2020 12:16 PM, Vyacheslav Yarkin wrote:


External Email - Use Caution

Hello Freesurfer Team,


Would you be so kind to provide freesurfer steps to implement warping 
fsaverage mean thickness data on individual subject inflated brains ?




I am using expert opts to disable cortical thickness restriction, and 
set mris_thickness -max 20 as I want to find fcd to cortical 
surfaces. The reason i need normalization is that there is zones like 
sulci orbitales have bigger thickness accross subjects group ( 
control ) and have red LUTs on inflated thickness map. So i would 
like to normalize thickness over control group, to use it on patients 
to exclude "normal" thickness excedings to include only increased FCD 
zones. The main issue I faced is how to warp fsaverage mean thickness 
data on individual subject's inflated brain as they have vertices 
number missmatch.


Steps I tried:

1) make_average_subject

2) mri_concat --mean to create mean thicknesses over group


Thank you


___
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] Thickness group normalization

2020-02-11 Thread Vyacheslav Yarkin

External Email - Use Caution

I got the idea but faced an issue with mris_preproc, the command is:


mris_preproc --target 0_1 --s avg_subject_91_noexpopts --hemi lh --meas 
thickness --out avg_91_to_lh.mgh


where 0_1 is target patient to map thickness, from avg_subject_91_noexpopts,  
optained from make_average_subject.


i get the error running mris_preproc:

   Reading source surface reg

/input/HCP_T1_fs6/avg_subject_91_noexpopts/surf/lh.0_1.sphere.reg

No such file or directory

mri_surf2surf: could not read surface

/input/HCP_T1_fs6/avg_subject_91_noexpopts/surf/lh.0_1.sphere.reg

No such file or directory


Why there should be lh.0_1.sphere.reg? Have i missed some intermediate steps??

?



От: freesurfer-boun...@nmr.mgh.harvard.edu 
 от имени Vyacheslav Yarkin 

Отправлено: 5 февраля 2020 г. 11:47
Кому: Freesurfer support list
Тема: Re: [Freesurfer] Thickness group normalization


External Email - Use Caution

I got the idea but faced an issue with mris_preproc, the command is:


mris_preproc --target 0_1 --s avg_subject_91_noexpopts --hemi lh --meas 
thickness --out avg_91_to_lh.mgh


where 0_1 is target patient to map thickness, from avg_subject_91_noexpopts,  
optained from make_average_subject.


i get the error running mris_preproc:

   Reading source surface reg

/input/HCP_T1_fs6/avg_subject_91_noexpopts/surf/lh.0_1.sphere.reg

No such file or directory

mri_surf2surf: could not read surface

/input/HCP_T1_fs6/avg_subject_91_noexpopts/surf/lh.0_1.sphere.reg

No such file or directory


Why there should be lh.0_1.sphere.reg? Have i missed some intermediate steps??






От: freesurfer-boun...@nmr.mgh.harvard.edu 
 от имени Douglas N. Greve 

Отправлено: 3 февраля 2020 г. 20:51
Кому: freesurfer@nmr.mgh.harvard.edu
Тема: Re: [Freesurfer] Thickness group normalization


Do you have a group of subjects that you want to use as an average? If so, you 
can just map all their thickness maps to your patient subject with
mris_preproc --target patientsubjectname [then usual arguments]
Compute the mean with
mri_concat outputofmris_preproc.mgz --mean --o groupmean.mgz
You can then compare groupmean.mgz to your patient on a vertex-by-vertex baiss


On 2/3/2020 12:16 PM, Vyacheslav Yarkin wrote:

External Email - Use Caution

Hello Freesurfer Team,


Would you be so kind to provide freesurfer steps to implement warping fsaverage 
mean thickness data on individual subject inflated brains ?


I am using expert opts to disable cortical thickness restriction, and set 
mris_thickness -max 20 as I want to find fcd to cortical surfaces. The reason i 
need normalization is that there is zones like sulci orbitales have bigger 
thickness accross subjects group ( control ) and have red LUTs on inflated 
thickness map. So i would like to normalize thickness over control group, to 
use it on patients to exclude "normal" thickness excedings to include only 
increased FCD zones. The main issue I faced is how to warp fsaverage mean 
thickness data on individual subject's inflated brain as they have vertices 
number missmatch.

Steps I tried:

1) make_average_subject

2) mri_concat --mean to create mean thicknesses over group?


Thank you



___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu<mailto: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] Thickness group normalization

2020-02-05 Thread Vyacheslav Yarkin

External Email - Use Caution

I got the idea but faced an issue with mris_preproc, the command is:


mris_preproc --target 0_1 --s avg_subject_91_noexpopts --hemi lh --meas 
thickness --out avg_91_to_lh.mgh


where 0_1 is target patient to map thickness, from avg_subject_91_noexpopts,  
optained from make_average_subject.


i get the error running mris_preproc:

   Reading source surface reg

/input/HCP_T1_fs6/avg_subject_91_noexpopts/surf/lh.0_1.sphere.reg

No such file or directory

mri_surf2surf: could not read surface

/input/HCP_T1_fs6/avg_subject_91_noexpopts/surf/lh.0_1.sphere.reg

No such file or directory


Why there should be lh.0_1.sphere.reg? Have i missed some intermediate steps??






От: freesurfer-boun...@nmr.mgh.harvard.edu 
 от имени Douglas N. Greve 

Отправлено: 3 февраля 2020 г. 20:51
Кому: freesurfer@nmr.mgh.harvard.edu
Тема: Re: [Freesurfer] Thickness group normalization


Do you have a group of subjects that you want to use as an average? If so, you 
can just map all their thickness maps to your patient subject with
mris_preproc --target patientsubjectname [then usual arguments]
Compute the mean with
mri_concat outputofmris_preproc.mgz --mean --o groupmean.mgz
You can then compare groupmean.mgz to your patient on a vertex-by-vertex baiss


On 2/3/2020 12:16 PM, Vyacheslav Yarkin wrote:

External Email - Use Caution

Hello Freesurfer Team,


Would you be so kind to provide freesurfer steps to implement warping fsaverage 
mean thickness data on individual subject inflated brains ?


I am using expert opts to disable cortical thickness restriction, and set 
mris_thickness -max 20 as I want to find fcd to cortical surfaces. The reason i 
need normalization is that there is zones like sulci orbitales have bigger 
thickness accross subjects group ( control ) and have red LUTs on inflated 
thickness map. So i would like to normalize thickness over control group, to 
use it on patients to exclude "normal" thickness excedings to include only 
increased FCD zones. The main issue I faced is how to warp fsaverage mean 
thickness data on individual subject's inflated brain as they have vertices 
number missmatch.

Steps I tried:

1) make_average_subject

2) mri_concat --mean to create mean thicknesses over group?


Thank you



___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu<mailto: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] Thickness group normalization

2020-02-03 Thread Douglas N. Greve



Do you have a group of subjects that you want to use as an average? If 
so, you can just map all their thickness maps to your patient subject with

mris_preproc --target patientsubjectname [then usual arguments]
Compute the mean with
mri_concat outputofmris_preproc.mgz --mean --o groupmean.mgz
You can then compare groupmean.mgz to your patient on a vertex-by-vertex 
baiss



On 2/3/2020 12:16 PM, Vyacheslav Yarkin wrote:


External Email - Use Caution

Hello Freesurfer Team,


Would you be so kind to provide freesurfer steps to implement warping 
fsaverage mean thickness data on individual subject inflated brains ?




I am using expert opts to disable cortical thickness restriction, and 
set mris_thickness -max 20 as I want to find fcd to cortical surfaces. 
The reason i need normalization is that there is zones like sulci 
orbitales have bigger thickness accross subjects group ( control ) and 
have red LUTs on inflated thickness map. So i would like to normalize 
thickness over control group, to use it on patients to exclude 
"normal" thickness excedings to include only increased FCD zones. The 
main issue I faced is how to warp fsaverage mean thickness data on 
individual subject's inflated brain as they have vertices number 
missmatch.


Steps I tried:

1) make_average_subject

2) mri_concat --mean to create mean thicknesses over group


Thank you


___
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] Thickness group normalization

2020-02-03 Thread Vyacheslav Yarkin

External Email - Use Caution

Hello Freesurfer Team,


Would you be so kind to provide freesurfer steps to implement warping fsaverage 
mean thickness data on individual subject inflated brains ?
I am using expert opts to disable cortical thickness restriction, and set 
mris_thickness -max 20 as I want to find fcd to cortical surfaces. The reason i 
need normalization is that there is zones like sulci orbitales have bigger 
thickness accross subjects group ( control ) and have red LUTs on inflated 
thickness map. So i would like to normalize thickness over control group, to 
use it on patients to exclude "normal" thickness excedings to include only 
increased FCD zones. The main issue I faced is how to warp fsaverage mean 
thickness data on individual subject's inflated brain as they have vertices 
number missmatch.

Steps I tried:

1) make_average_subject

2) mri_concat --mean to create mean thicknesses over group?


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

Re: [Freesurfer] Thickness problem

2019-12-20 Thread Greve, Douglas N.,Ph.D.

sig = -log10(p)*sign(contrast), so if p=.01, then sig=2. The sign(contrast) is 
the direction of the contrast

On 12/19/2019 4:14 PM, Gwang-Won Kim wrote:

External Email - Use Caution

Hi Dr. Greve,

Thank you for your comment.
I compared cortical thickness bewteen two groups. I have a question. What does 
the values mean in the "sig.table.dat" file (ex. 0.571)?

Good luck,


 
--

Can you try running the ROI results with mri_glmfit? ie, if you ran 
aparcstats2table to get the ROI results you input to SPSS, then run

mri_glmfit --table table.dat --fsgd g1v4.fsgd --C group.diff.mtx --glmdir 
table.g1v4.glmdir

where table.dat is the result of aparcstats2table

Then look at the sig.table.dat

Oftentimes, the SPSS analysis is not doing exactly the same thing as the 
mri_glmfit analysis.

On 12/6/2019 11:25 AM, Gwang-Won Kim wrote:

External Email - Use Caution

Hi there,

I obtained results for right thickness using aparcstats2table.
Then, ANCOVA was used to compared right thickness between two group (age, sex, 
edu, ICV as covariates)using SPSS.
A group showed higher right thickness in the superior frontal gyrus compared 
with B group (p=0.001).

To see voxel-wise map in same data, I tried to process "mris_preporc", 
"mri_surf2surf", and "mri_glmfit"

But the group showed higher right thickness in the middle frontal gyrus 
compared with B group (p<0.005).

I don't understand why data is different.

In ROI analysis, the group showed higher right thickness in the superior 
frontal gyrus compared with B group, but the group showed higher right 
thickness in the middle frontal gyrus compared with B group in the voxel-wise 
map (p<0.005).

Please recommend me about it.



mris_preproc --fsgd g1v4.fsgd --target fsaverage --hemi rh --meas thickness 
--out rh.g1v4.thickness.00.mgh



mri_surf2surf --hemi rh --s fsaverage --sval rh.g1v4.thickness.00.mgh --fwhm 10 
--cortex --tval rh.g1v4.thickness.10B.mgh



itmri_glmfit --y lh.g1v4.thickness.10B.mgh --fsgd g1v4.fsgd --C group.diff.mtx 
--surf fsaverage rh --cortex --glmdir rh.g1v4.glmdir





g1g4.fsgd (subjects 50)

Class Group1

Class Group2

Variables age sex edu ICV

Input eewe Group1 34 1 13 1753213

Input ffds Group2 32 1 13 1753213

Input erfg Group2 33 1 13 1753213

Input gdds Group1 31 2 12 1753213





group.diff.mtx

1 -1 0 0 0 0 0 0 0 0




___
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] Thickness problem

2019-12-19 Thread Gwang-Won Kim

External Email - Use CautionHi Dr. Greve, Thank you for your comment.I compared cortical thickness bewteen two groups. I have a question. What does the values mean in the "sig.table.dat" file (ex. 0.571)? Good luck, -- Can you try running the ROI results with mri_glmfit? ie, if you ran aparcstats2table to get the ROI results you input to SPSS, then run mri_glmfit --table table.dat --fsgd g1v4.fsgd --C group.diff.mtx --glmdir table.g1v4.glmdir where table.dat is the result of aparcstats2table Then look at the sig.table.dat Oftentimes, the SPSS analysis is not doing exactly the same thing as the mri_glmfit analysis. On 12/6/2019 11:25 AM, Gwang-Won Kim wrote: External Email - Use Caution Hi there, I obtained results for right thickness using aparcstats2table. Then, ANCOVA was used to compared right thickness between two group (age, sex, edu, ICV as covariates)using SPSS. A group showed higher right thickness in the superior frontal gyrus compared with B group (p=0.001). To see voxel-wise map in same data, I tried to process "mris_preporc", "mri_surf2surf", and "mri_glmfit" But the group showed higher right thickness in the middle frontal gyrus compared with B group (p<0.005). I don't understand why data is different. In ROI analysis, the group showed higher right thickness in the superior frontal gyrus compared with B group, but the group showed higher right thickness in the middle frontal gyrus compared with B group in the voxel-wise map (p<0.005). Please recommend me about it. mris_preproc --fsgd g1v4.fsgd --target fsaverage --hemi rh --meas thickness --out rh.g1v4.thickness.00.mgh mri_surf2surf --hemi rh --s fsaverage --sval rh.g1v4.thickness.00.mgh --fwhm 10 --cortex --tval rh.g1v4.thickness.10B.mgh itmri_glmfit --y lh.g1v4.thickness.10B.mgh --fsgd g1v4.fsgd --C group.diff.mtx --surf fsaverage rh --cortex --glmdir rh.g1v4.glmdir g1g4.fsgd (subjects 50) Class Group1 Class Group2 Variables age sex edu ICV Input eewe Group1 34 1 13 1753213 Input ffds Group2 32 1 13 1753213 Input erfg Group2 33 1 13 1753213 Input gdds Group1 31 2 12 1753213 group.diff.mtx 1 -1 0 0 0 0 0 0 0 0

1 2 >

1 - 100 of 143 matches

Mail list logo