[Freesurfer] SAMSEG - modification of the template files

[Mikolaj Pawlak]

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Dear Freesurfers,
I have been using samseg for a while and like it a lot. Thank you for this
tool. How do you modify the template for this tool? Is there a guideline
for this?
I would like to divide Fluid_Inside_Eyes label to left and right and
improve the bone information in the template. What is the procedure?
thanks,
Mikolaj Pawlak
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Re: [Freesurfer] Longitudinal PET analysis

[Douglas N. Greve]

You may be able to use one of the paired diff options in mris_preproc. 
Run it with --help. I also put some info on it below. QDEC has been 
deprecated




--paired-diff

After concatenating all the inputs together, create a new output file by
computing paired differences, ie, Input1-Input2, Input3-Input4, etc.
There must be an even number of inputs. The inputs are "pruned" before
taking the difference, meaning that values for all inputs are set to 0
if any individual is 0.

--paired-diff-norm

Same as --paired-diff, but normalizes by average of time points, ie,
(Input1-Input2)/((Input1+Input2)/2).

--paired-diff-norm1

Same as --paired-diff, but normalizes by time point 1, ie,
(Input1-Input2)/Input1.

--paired-diff-norm2

Same as --paired-diff, but normalizes by time point 2, ie,
(Input1-Input2)/Input2.



On 9/20/2022 3:31 PM, Gomar, Jesus wrote:


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Hello Freesurfer developers,

I am interested in analyzing PET data following a longitudinal design.

I have co-registered each PET image to the closest MRI in time 
processed through the longitudinal stream.


I have sampled each co-registered PET image time-point onto fsaverage 
surface via the individual's subject surface (mri_vol2surf).


From this point:

1.Is it possible to obtain spc (symmetrized percent change) using 
long_mris_slopes for each subject?


2.Is there a way to input the sampled surfaces into a qdec file for 
long_mris_slopes command?


1) FreeSurfer version: freesurfer-linux-centos6_x86_64-7.2.0.

2) Platform: Ubuntu 18,04.6 LTS

3) uname -a: Linux ubuntu 5.4.0-122-generic-Ubuntu UTC 2022 x86_64 
x86_64 x86_64 GNU/Linux


Thank you!

Jesus

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Re: [Freesurfer] SAMSEG - modification of the template files

[Douglas N. Greve]

by template I'm assuming you mean the atlas. There is not an easy way to 
create a new atlas or modify the existing one (though we are developing 
methods to do both). For the eyes, you could probably just write 
something to look at the column index in the eyes. If it is less than 
128, then set it to left otherwise right.


On 9/21/2022 6:01 AM, Mikolaj Pawlak wrote:


External Email - Use Caution

Dear Freesurfers,
I have been using samseg for a while and like it a lot. Thank you for 
this tool. How do you modify the template for this tool? Is there a 
guideline for this?
I would like to divide Fluid_Inside_Eyes label to left and right and 
improve the bone information in the template. What is the procedure?

thanks,
Mikolaj Pawlak

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[Freesurfer] White matter normalization of FLAIR images

[James Brown]

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Dear Freesurfer experts,
In order to normalize white matter intensity of T1 images and correct for
bias field. We do the following steps:
mri_convert T1.nii.gz T1.mgz
mri_nu_correct.mni --i T1.mgz --o T1_N3.mgz --n 2
mri_normalize -g 1 T1_N3.mgzT1_norm.mgz
mri_convert T1_norm.mgz T1_norm.nii.gz

We would like to apply bias field correction on FLAIR images then
normalize white matter intensity.
We tried N4biasfieldcorrection from ANTS but it didn't work as expected.
Reviewing documents about N4biasfieldcorrection we realize that the
algorithm has been developed to correct bias field correction in T1 not
clear if it works on FLAIR images.

Are the steps above valid for normalizing FLAIR images or can it only be
applied on T1 images? I would like to send a "recon-all.log" file that
includes the processing steps of FLAIR. Is there any link I can use to
upload the file. It gets rejected every time I send it due to size
limitations.

We appreciate any feedback about the proper way to correct FLAIR images for
bias fields and normalize white matter intensity in FLAIR images.

Thank you
JamesB
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[Freesurfer] unziping problems

[TAIB Simon]

External Email - Use Caution

Good afternoon,

I am having trouble unzipping the freesurfer folder downloaded from your 
website as a password is required and I could not find it. I have done my 
registration and got the licence.txt file, but I don't know if the password is 
in it. Is there something I am missing ? If so, please enlight me.

Have a good day

Dr Simon TAIB
Centre Régional Psychotraumatisme Occitanie - CHU de Purpan
INSERM U1214 ToNIC - Université Toulouse 3




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Re: [Freesurfer] [EXTERNAL] Re: Longitudinal PET analysis

[Gomar, Jesus]

External Email - Use Caution

Thank you Doug, I will follow your suggestion.


From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N. Greve
Sent: Wednesday, September 21, 2022 9:58 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [EXTERNAL] Re: [Freesurfer] Longitudinal PET analysis


External Email. Do not click links or open attachments unless you trust the 
sender and content. Report suspicious emails using Report Phishing button or 
forward email to ph...@northwell.edu
You may be able to use one of the paired diff options in mris_preproc. Run it 
with --help. I also put some info on it below. QDEC has been deprecated



--paired-diff

After concatenating all the inputs together, create a new output file by
computing paired differences, ie, Input1-Input2, Input3-Input4, etc.
There must be an even number of inputs. The inputs are "pruned" before
taking the difference, meaning that values for all inputs are set to 0
if any individual is 0.

--paired-diff-norm

Same as --paired-diff, but normalizes by average of time points, ie,
(Input1-Input2)/((Input1+Input2)/2).

--paired-diff-norm1

Same as --paired-diff, but normalizes by time point 1, ie,
(Input1-Input2)/Input1.

--paired-diff-norm2

Same as --paired-diff, but normalizes by time point 2, ie,
(Input1-Input2)/Input2.


On 9/20/2022 3:31 PM, Gomar, Jesus wrote:

External Email - Use Caution
Hello Freesurfer developers,

I am interested in analyzing PET data following a longitudinal design.
I have co-registered each PET image to the closest MRI in time processed 
through the longitudinal stream.
I have sampled each co-registered PET image time-point onto fsaverage surface 
via the individual's subject surface (mri_vol2surf).
From this point:

1.   Is it possible to obtain spc (symmetrized percent change) using 
long_mris_slopes for each subject?

2.   Is there a way to input the sampled surfaces into a qdec file for 
long_mris_slopes command?

1) FreeSurfer version: freesurfer-linux-centos6_x86_64-7.2.0.
2) Platform: Ubuntu 18,04.6 LTS
3) uname -a: Linux ubuntu 5.4.0-122-generic-Ubuntu UTC 2022 x86_64 x86_64 
x86_64 GNU/Linux


Thank you!

Jesus
The information contained in this electronic e-mail transmission and any 
attachments are intended only for the use of the individual or entity to whom 
or to which it is addressed, and may contain information that is privileged, 
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responsible for delivering this communication to the intended recipient, you 
are hereby notified that any dissemination, distribution, copying or disclosure 
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telephone and electronic mail, and delete the original communication and any 
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Re: [Freesurfer] [EXTERNAL] Re: Longitudinal PET analysis

[Adam Martersteck]

External Email - Use Caution

On other thought: You may want to do Doug's suggestion of calculating the
paired-diff in the longitudinal stream's subject-specific unbiased template
space of each participant instead of doing it all in fsaverage. Then take
the resultant file, the symmetrized percent change, or pc1, etc. from the
subject-specific template space to fsaverage for your group statistics.

On Wed, Sep 21, 2022 at 12:39 PM Gomar, Jesus  wrote:

> External Email - Use Caution
>
> Thank you Doug, I will follow your suggestion.
>
>
>
>
>
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu [mailto:
> freesurfer-boun...@nmr.mgh.harvard.edu] *On Behalf Of *Douglas N. Greve
> *Sent:* Wednesday, September 21, 2022 9:58 AM
> *To:* freesurfer@nmr.mgh.harvard.edu
> *Subject:* [EXTERNAL] Re: [Freesurfer] Longitudinal PET analysis
>
>
>
> *External Email. Do not click links or open attachments unless you trust
> the sender and content. Report suspicious emails using Report Phishing
> button or forward email to ph...@northwell.edu *
>
> You may be able to use one of the paired diff options in mris_preproc. Run
> it with --help. I also put some info on it below. QDEC has been deprecated
>
>
>
> --paired-diff
>
> After concatenating all the inputs together, create a new output file by
> computing paired differences, ie, Input1-Input2, Input3-Input4, etc.
> There must be an even number of inputs. The inputs are "pruned" before
> taking the difference, meaning that values for all inputs are set to 0
> if any individual is 0.
>
> --paired-diff-norm
>
> Same as --paired-diff, but normalizes by average of time points, ie,
> (Input1-Input2)/((Input1+Input2)/2).
>
> --paired-diff-norm1
>
> Same as --paired-diff, but normalizes by time point 1, ie,
> (Input1-Input2)/Input1.
>
> --paired-diff-norm2
>
> Same as --paired-diff, but normalizes by time point 2, ie,
> (Input1-Input2)/Input2.
>
>
> On 9/20/2022 3:31 PM, Gomar, Jesus wrote:
>
> *External Email - Use Caution*
>
> Hello Freesurfer developers,
>
>
>
> I am interested in analyzing PET data following a longitudinal design.
>
> I have co-registered each PET image to the closest MRI in time processed
> through the longitudinal stream.
>
> I have sampled each co-registered PET image time-point onto fsaverage
> surface via the individual's subject surface (mri_vol2surf).
>
> From this point:
>
> 1.   Is it possible to obtain spc (symmetrized percent change) using
> long_mris_slopes for each subject?
>
> 2.   Is there a way to input the sampled surfaces into a qdec file
> for long_mris_slopes command?
>
>
>
> 1) FreeSurfer version: freesurfer-linux-centos6_x86_64-7.2.0.
>
> 2) Platform: Ubuntu 18,04.6 LTS
>
> 3) uname -a: Linux ubuntu 5.4.0-122-generic-Ubuntu UTC 2022 x86_64 x86_64
> x86_64 GNU/Linux
>
>
>
>
>
> Thank you!
>
>
>
> Jesus
>
> The information contained in this electronic e-mail transmission and any
> attachments are intended only for the use of the individual or entity to
> whom or to which it is addressed, and may contain information that is
> privileged, confidential and exempt from disclosure under applicable law.
> If the reader of this communication is not the intended recipient, or the
> employee or agent responsible for delivering this communication to the
> intended recipient, you are hereby notified that any dissemination,
> distribution, copying or disclosure of this communication and any
> attachment is strictly prohibited. If you have received this transmission
> in error, please notify the sender immediately by telephone and electronic
> mail, and delete the original communication and any attachment from any
> computer, server or other electronic recording or storage device or medium.
> Receipt by anyone other than the intended recipient is not a waiver of any
> attorney-client, physician-patient or other privilege.
>
>
>
> ___
>
> Freesurfer mailing list
>
> Freesurfer@nmr.mgh.harvard.edu
>
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>  
> 

[Freesurfer] Voxel to mm coordinates

[Fotiadis, Panagiotis]

External Email - Use Caution

Hello,

I was wondering what the best way would be to extract the coordinates of each 
voxel in my nifti volume in mm. I have used MRIread to load the nifti volume 
into Matlab (=mri) and wanted to essentially create a new variable that takes 
each (voxel) entry in mri.vol and exports its three coordinates in mm. Would I 
just need to multiply the mri.vox2ras 4x4 matrix to each voxel’s [X Y Z 1]’ 
(where X,Y,Z are the voxel’s coordinates in mri.vol) or are there different 
steps involved?

Thank you in advance for your time and help!

Best,
Panos
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Re: [Freesurfer] Voxel to mm coordinates

[Wighton, Paul]

Hi Panos,

Yes that is correct.  Taking a voxel value and multiplying it by the vox2ras 
matrix will give you a coordinate in the "patient coordinate system" which is 
in mm. RAS denotes that the directions (R)ight, (A)nterior and (S)uperior are 
positive.

-Paul

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Fotiadis, Panagiotis 

Sent: Wednesday, September 21, 2022 5:07 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: [Freesurfer] Voxel to mm coordinates


External Email - Use Caution

Hello,



I was wondering what the best way would be to extract the coordinates of each 
voxel in my nifti volume in mm. I have used MRIread to load the nifti volume 
into Matlab (=mri) and wanted to essentially create a new variable that takes 
each (voxel) entry in mri.vol and exports its three coordinates in mm. Would I 
just need to multiply the mri.vox2ras 4x4 matrix to each voxel’s [X Y Z 1]’ 
(where X,Y,Z are the voxel’s coordinates in mri.vol) or are there different 
steps involved?



Thank you in advance for your time and help!



Best,

Panos
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Re: [Freesurfer] Voxel to mm coordinates

[Fotiadis, Panagiotis]

External Email - Use Caution

Awesome, thank you Paul!

Best,
Panos

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Wighton, Paul 

Date: Wednesday, September 21, 2022 at 5:24 PM
To: Freesurfer support list 
Subject: [External] Re: [Freesurfer] Voxel to mm coordinates
Hi Panos,

Yes that is correct.  Taking a voxel value and multiplying it by the vox2ras 
matrix will give you a coordinate in the "patient coordinate system" which is 
in mm. RAS denotes that the directions (R)ight, (A)nterior and (S)uperior are 
positive.

-Paul

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Fotiadis, Panagiotis 

Sent: Wednesday, September 21, 2022 5:07 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: [Freesurfer] Voxel to mm coordinates


External Email - Use Caution

Hello,



I was wondering what the best way would be to extract the coordinates of each 
voxel in my nifti volume in mm. I have used MRIread to load the nifti volume 
into Matlab (=mri) and wanted to essentially create a new variable that takes 
each (voxel) entry in mri.vol and exports its three coordinates in mm. Would I 
just need to multiply the mri.vox2ras 4x4 matrix to each voxel’s [X Y Z 1]’ 
(where X,Y,Z are the voxel’s coordinates in mri.vol) or are there different 
steps involved?



Thank you in advance for your time and help!



Best,

Panos
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