[Freesurfer] Can FS use the recon all command to automatically divide it into DKT32 areas?

[1248742467]

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Hello, Fs
I saw an article that gave the Dice coefficient and ACC of Freesurfer's 
automatic segmentation, so I am curious, can Fs automatically divide it into 32 
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Re: [Freesurfer] Talairach Failed: Distorted T1

[Douglas N. Greve]

That is an axial scan that only covers 25mm of the brain 
inferior-superior. This is not whole brain coverage, which is causing 
the problem


On 3/25/2021 9:07 PM, Harkey, Thomas Jarrott wrote:


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Douglas,
Thank you for your help. I have pasted the result below.

Volume information for 2020-24axialScalarvolumeall/mri/orig/001.mgz
          type: MGH
    dimensions: 384 x 384 x 25
   voxel sizes: 0.598958, 0.598958, 1.00
          type: SHORT (4)
           fov: 230.000
           dof: 1
        xstart: -115.0, xend: 115.0
        ystart: -115.0, yend: 115.0
        zstart: -12.5, zend: 12.5
            TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 
0.00 degrees

       nframes: 1
       PhEncDir: UNKNOWN
       FieldStrength: 0.00
ras xform present
    xform info: x_r =  -0.9841, y_r =  -0.0087, z_r =  -0.1777, c_r = 
   15.3722
              : x_a =   0.0272, y_a =  -0.9944, z_a =  -0.1022, c_a = 
   14.0701
              : x_s =  -0.1758, y_s =  -0.1054, z_s = 0.9788, c_s =   
-75.3479


talairach xfm :
Orientation   : LPS
Primary Slice Direction: axial

voxel to ras transform:
               -0.5894  -0.0052  -0.1777   131.7540
                0.0163  -0.5956  -0.1022   126.5760
               -0.1053  -0.0631   0.9788   -55.2497
                0.   0.   0.     1.

voxel-to-ras determinant 0.358751

ras to voxel transform:
               -1.6429   0.0454  -0.2935   194.5030
               -0.0144  -1.6602  -0.1759   202.3262
               -0.1777  -0.1022   0.9788    90.4171
                0.   0.   0.     1.

Kindly,
Thomas Harkey
UAMS College of Medicine class of 2022

*From:* freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Douglas N. Greve 


*Sent:* Thursday, March 25, 2021 9:11 AM
*To:* freesurfer@nmr.mgh.harvard.edu 
*Subject:* Re: [Freesurfer] Talairach Failed: Distorted T1
It looks like something is wrong with your input. For starters, the 
voxel size looks huge. Run

mri_info subject/mri/orig/001.mgz
and send the result

On 3/23/2021 10:54 PM, Harkey, Thomas Jarrott wrote:


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Hello,

My name is Thomas Harkey and I am conducting research using 
FreeSurfer. After running recon-all on this patient, the Talairach 
failed according to the .log file. No stats were calculated but 
loading the orig.mgz file into FreeView looks like this (see image 
attached). This DICOM file was successfully uploaded into other 
programs.


How can I fix this error?

Kind regards,

--

*Thomas Harkey **
University of Arkansas for Medical Sciences***

*College of Medicine, Class of 2022
501-553-6318*

*tjhar...@uams.edu *


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Re: [Freesurfer] Talairach Failed: Distorted T1

[Harkey, Thomas Jarrott]

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Douglas,
Thank you for your help. I have pasted the result below.

Volume information for 2020-24axialScalarvolumeall/mri/orig/001.mgz
  type: MGH
dimensions: 384 x 384 x 25
   voxel sizes: 0.598958, 0.598958, 1.00
  type: SHORT (4)
   fov: 230.000
   dof: 1
xstart: -115.0, xend: 115.0
ystart: -115.0, yend: 115.0
zstart: -12.5, zend: 12.5
TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 
degrees
   nframes: 1
   PhEncDir: UNKNOWN
   FieldStrength: 0.00
ras xform present
xform info: x_r =  -0.9841, y_r =  -0.0087, z_r =  -0.1777, c_r =15.3722
  : x_a =   0.0272, y_a =  -0.9944, z_a =  -0.1022, c_a =14.0701
  : x_s =  -0.1758, y_s =  -0.1054, z_s =   0.9788, c_s =   -75.3479

talairach xfm :
Orientation   : LPS
Primary Slice Direction: axial

voxel to ras transform:
   -0.5894  -0.0052  -0.1777   131.7540
0.0163  -0.5956  -0.1022   126.5760
   -0.1053  -0.0631   0.9788   -55.2497
0.   0.   0. 1.

voxel-to-ras determinant 0.358751

ras to voxel transform:
   -1.6429   0.0454  -0.2935   194.5030
   -0.0144  -1.6602  -0.1759   202.3262
   -0.1777  -0.1022   0.978890.4171
0.   0.   0. 1.

Kindly,
Thomas Harkey
UAMS College of Medicine class of 2022

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Douglas N. Greve 

Sent: Thursday, March 25, 2021 9:11 AM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] Talairach Failed: Distorted T1

It looks like something is wrong with your input. For starters, the voxel size 
looks huge. Run
mri_info subject/mri/orig/001.mgz
and send the result

On 3/23/2021 10:54 PM, Harkey, Thomas Jarrott wrote:

External Email - Use Caution

Hello,

My name is Thomas Harkey and I am conducting research using FreeSurfer. After 
running recon-all on this patient, the Talairach failed according to the .log 
file. No stats were calculated but loading the orig.mgz file into FreeView 
looks like this (see image attached). This DICOM file was successfully uploaded 
into other programs.

How can I fix this error?

Kind regards,

--

Thomas Harkey
University of Arkansas for Medical Sciences

College of Medicine, Class of 2022
501-553-6318

tjhar...@uams.edu




Confidentiality Notice: This e-mail message, including any attachments, is for 
the sole use of the intended recipient(s) and may contain confidential and 
privileged information. Any unauthorized review, use, disclosure or 
distribution is prohibited. If you are not the intended recipient, please 
contact the sender by reply e-mail and destroy all copies of the original 
message.



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Re: [Freesurfer] cross sectional vs longitudinal TRACULA reliability

[Yendiki, Anastasia]

Hi Carissa - Any QA issues aside, the first reason for a difference that I can 
think of is that the same % threshold for the tract probability distribution 
(e.g., 20% of the max) would not be equivalent between cross and long streams. 
In the long stream I'd expect the distributions to be tighter because they're 
derived from twice as much data, so there is reduced uncertainty.

In the 2016 longitudinal TRACULA paper we looked at test-retest reliability, 
but that was reliability between two scans of the same subject when analyzed 
with the same stream. That was higher when the two scans were analyzed jointly 
with the long stream than when they were analyzed as independent data points 
with the cross stream. But, there is no expectation of reliability between the 
cross and the long stream on the same data set. They are two different analysis 
methods and there is no reason to expect that they will give the same result or 
that the result will scale linearly. If they did, both streams would give the 
same answer when comparing two populations, so there would be no reason to have 
a long stream.

Hope this helps,
Anastasia.



From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Carissa Nicole Weis 

Sent: Thursday, March 25, 2021 6:06 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: [Freesurfer] cross sectional vs longitudinal TRACULA reliability


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Hello,



I’ve run both longitudinal and cross-sectional TRACULA pipelines on the same 
dataset, and I’ve found surprisingly low correlations of FA measurements for 
several tracts (as low as r= .1 in some cases). Which measurement should be 
considered more reliable? I’m having a hard time deciding which set of results 
to carry forward to group analysis.



Thanks,



Carissa




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[Freesurfer] cross sectional vs longitudinal TRACULA reliability

[Carissa Nicole Weis]

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Hello,

I’ve run both longitudinal and cross-sectional TRACULA pipelines on the same 
dataset, and I’ve found surprisingly low correlations of FA measurements for 
several tracts (as low as r= .1 in some cases). Which measurement should be 
considered more reliable? I’m having a hard time deciding which set of results 
to carry forward to group analysis.

Thanks,

Carissa


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Re: [Freesurfer] make_average_subject without Talairach transform

[Trisanna Sprung-Much]

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Ah, neat! Ok, will give this a go!
Thanks a bunch

Trisanna Sprung-Much
Research Associate
McGill University
MD Anderson Cancer Centre
--


From:  on behalf of "Douglas N. Greve" 

Reply-To: Freesurfer support list 
Date: Thursday, March 25, 2021 at 11:36 AM
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: Re: [Freesurfer] make_average_subject without Talairach transform

If you have the transform in the form of an LTA file, I think all you need to 
do is put it in the subject/mri/transforms folder, then spec --xfrom your.lta 
when running make_average_subject
On 3/25/2021 11:33 AM, Trisanna Sprung-Much wrote:

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Hi Doug

The scans were registered (6 parameter) to a common chimp template prior to 
input to recon-all. The surfaces have reconstructed nicely and match the input 
volumes.
I would now like to create an average surface from these surfaces that are “in 
the space of the average chimp volume”.

Trisanna
--


From: 

 on behalf of "Douglas N. Greve" 

Reply-To: Freesurfer support list 

Date: Thursday, March 25, 2021 at 11:24 AM
To: "freesurfer@nmr.mgh.harvard.edu" 

Subject: Re: [Freesurfer] make_average_subject without Talairach transform

If you don't have a transform, how will you align the subjects into a common 
space?
On 3/25/2021 10:19 AM, Trisanna Sprung-Much wrote:

External Email - Use Caution

External Email - Use Caution
Hi there

I’d like to know if it is possible to create an average volume and average 
surface of several subjects without having to incorporate the Talairach 
transform and no transform at all.

Thank you,

Trisanna Sprung-Much
Research Associate
McGill University
MD Anderson Cancer Centre
--





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Re: [Freesurfer] make_average_subject without Talairach transform

[Douglas N. Greve]

If you have the transform in the form of an LTA file, I think all you 
need to do is put it in the subject/mri/transforms folder, then spec 
--xfrom your.lta when running make_average_subject


On 3/25/2021 11:33 AM, Trisanna Sprung-Much wrote:


External Email - Use Caution

External Email - Use Caution

Hi Doug

The scans were registered (6 parameter) to a common chimp template 
prior to input to recon-all. The surfaces have reconstructed nicely 
and match the input volumes.


I would now like to create an average surface from these surfaces that 
are “in the space of the average chimp volume”.


Trisanna

--

*From: * on behalf of "Douglas 
N. Greve" 

*Reply-To: *Freesurfer support list 
*Date: *Thursday, March 25, 2021 at 11:24 AM
*To: *"freesurfer@nmr.mgh.harvard.edu" 
*Subject: *Re: [Freesurfer] make_average_subject without Talairach 
transform


If you don't have a transform, how will you align the subjects into a 
common space?


On 3/25/2021 10:19 AM, Trisanna Sprung-Much wrote:

*External Email - Use Caution *

*External Email - Use Caution *

Hi there

I’d like to know if it is possible to create an average volume and
average surface of several subjects without having to incorporate
the Talairach transform and no transform at all.

Thank you,

Trisanna Sprung-Much

Research Associate

McGill University

MD Anderson Cancer Centre

-- 




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Re: [Freesurfer] make_average_subject without Talairach transform

[Trisanna Sprung-Much]

External Email - Use Caution

Hi Doug

The scans were registered (6 parameter) to a common chimp template prior to 
input to recon-all. The surfaces have reconstructed nicely and match the input 
volumes.
I would now like to create an average surface from these surfaces that are “in 
the space of the average chimp volume”.

Trisanna
--


From:  on behalf of "Douglas N. Greve" 

Reply-To: Freesurfer support list 
Date: Thursday, March 25, 2021 at 11:24 AM
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: Re: [Freesurfer] make_average_subject without Talairach transform

If you don't have a transform, how will you align the subjects into a common 
space?
On 3/25/2021 10:19 AM, Trisanna Sprung-Much wrote:

External Email - Use Caution

External Email - Use Caution
Hi there

I’d like to know if it is possible to create an average volume and average 
surface of several subjects without having to incorporate the Talairach 
transform and no transform at all.

Thank you,

Trisanna Sprung-Much
Research Associate
McGill University
MD Anderson Cancer Centre
--




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Re: [Freesurfer] make_average_subject without Talairach transform

[Douglas N. Greve]

You can just use the identity matrix. The white and pial surfaces will 
be bogus (probably the inflated too), but the atlas created from it will 
be valid


On 3/25/2021 11:17 AM, Trisanna Sprung-Much wrote:


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External Email - Use Caution

Thanks Bruce for your speedy response.


I am dealing with chimp scans and therefore am trying to avoid 
anything to do with Talairach. The surfaces have reconstructed pretty 
nicely using recon-all, but I’d like to create an average surface now.


I will try as you suggest

Trisanna Sprung-Much

Research Associate

McGill University

MD Anderson Cancer Centre

--

*From: * on behalf of "Fischl, 
Bruce" 

*Reply-To: *Freesurfer support list 
*Date: *Thursday, March 25, 2021 at 10:59 AM
*To: *Freesurfer support list 
*Subject: *Re: [Freesurfer] make_average_subject without Talairach 
transform


Sure, I guess you can just run mri_average. I think also if you 
specify the file name for the transform as identity.nofile to any 
binary that takes an lta file, the code will internally create an 
identity transform.


I won’t look pretty though….

Cheers

Bruce

*From:*freesurfer-boun...@nmr.mgh.harvard.edu 
 *On Behalf Of *Trisanna 
Sprung-Much

*Sent:* Thursday, March 25, 2021 10:19 AM
*To:* Freesurfer support list 
*Subject:* [Freesurfer] make_average_subject without Talairach transform

*External Email - Use Caution *

*External Email - Use Caution *

Hi there

I’d like to know if it is possible to create an average volume and 
average surface of several subjects without having to incorporate the 
Talairach transform and no transform at all.


Thank you,

Trisanna Sprung-Much

Research Associate

McGill University

MD Anderson Cancer Centre

--


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Re: [Freesurfer] make_average_subject without Talairach transform

[Douglas N. Greve]

If you don't have a transform, how will you align the subjects into a 
common space?


On 3/25/2021 10:19 AM, Trisanna Sprung-Much wrote:


External Email - Use Caution

External Email - Use Caution

Hi there

I’d like to know if it is possible to create an average volume and 
average surface of several subjects without having to incorporate the 
Talairach transform and no transform at all.


Thank you,

Trisanna Sprung-Much

Research Associate

McGill University

MD Anderson Cancer Centre

--


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Re: [Freesurfer] make_average_subject without Talairach transform

[Trisanna Sprung-Much]

External Email - Use Caution

Thanks Bruce for your speedy response.

I am dealing with chimp scans and therefore am trying to avoid anything to do 
with Talairach. The surfaces have reconstructed pretty nicely using recon-all, 
but I’d like to create an average surface now.

I will try as you suggest

Trisanna Sprung-Much
Research Associate
McGill University
MD Anderson Cancer Centre
--


From:  on behalf of "Fischl, Bruce" 

Reply-To: Freesurfer support list 
Date: Thursday, March 25, 2021 at 10:59 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] make_average_subject without Talairach transform

Sure, I guess you can just run mri_average. I think also if you specify the 
file name for the transform as identity.nofile to any binary that takes an lta 
file, the code will internally create an identity transform.

I won’t look pretty though….
Cheers
Bruce

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Trisanna Sprung-Much
Sent: Thursday, March 25, 2021 10:19 AM
To: Freesurfer support list 
Subject: [Freesurfer] make_average_subject without Talairach transform


External Email - Use Caution

External Email - Use Caution
Hi there

I’d like to know if it is possible to create an average volume and average 
surface of several subjects without having to incorporate the Talairach 
transform and no transform at all.

Thank you,

Trisanna Sprung-Much
Research Associate
McGill University
MD Anderson Cancer Centre
--

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Re: [Freesurfer] make_average_subject without Talairach transform

[Fischl, Bruce]

Sure, I guess you can just run mri_average. I think also if you specify the 
file name for the transform as identity.nofile to any binary that takes an lta 
file, the code will internally create an identity transform.

I won’t look pretty though….
Cheers
Bruce

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Trisanna Sprung-Much
Sent: Thursday, March 25, 2021 10:19 AM
To: Freesurfer support list 
Subject: [Freesurfer] make_average_subject without Talairach transform


External Email - Use Caution

External Email - Use Caution
Hi there

I’d like to know if it is possible to create an average volume and average 
surface of several subjects without having to incorporate the Talairach 
transform and no transform at all.

Thank you,

Trisanna Sprung-Much
Research Associate
McGill University
MD Anderson Cancer Centre
--

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[Freesurfer] make_average_subject without Talairach transform

[Trisanna Sprung-Much]

External Email - Use Caution

Hi there

I’d like to know if it is possible to create an average volume and average 
surface of several subjects without having to incorporate the Talairach 
transform and no transform at all.

Thank you,

Trisanna Sprung-Much
Research Associate
McGill University
MD Anderson Cancer Centre
--

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Re: [Freesurfer] read_surf surface

[Douglas N. Greve]

The surface coordinates are in "tkregister" coordinates whereas freeview 
is giving you scanner coordinates.
See https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems for how 
to convert between them


On 3/25/2021 7:14 AM, Shizuka Hayashi wrote:


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Dear Freesurfer team,

I have a question about the inconsistency between the vertex read from 
read_surf and vertex shown in Freeview.
I have a volume from the hippocampal subfield pipeline and I converted 
it to surface mesh using
mri_tessellate mri/lh.hippoAmygLabels-T1.long.v21.mgz -an 
surf/lh.hippoAmygLabels-T1.long.v21.surf.


Then I smoothed the surface using mris_smooth 
surf/lh.hippoAmygLabels-T1.long.v21.surf 
surf/lh.hippoAmygLabels-T1.long.v21.surf


Now I want to get the corresponding voxel of 
lh.hippoAmygLabels-T1.long.v21.mgz with the vertex. In Freeview, for 
example, the vertex 0 is [5.17, -19.5, 4.83]. I know how to convert 
this vertex to the corresponding voxel.
However, when I read the surf/lh.hippoAmygLabels-T1.long.v21.surf from 
Matlab using read_surf, the first vertex ( vertex(1,:,:)) is equal to 
[165.4900,217.3600,-159.7300].


Are there any ways to solve the issue?


Thank you.


Regards,

Shizuka


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Re: [Freesurfer] Questions regarding atlas labels

[Douglas N. Greve]

On 3/24/2021 5:11 PM, Blanpain, Lou wrote:


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Hello,

I had the following 2 general questions regarding Freesurfer:

 1. Is there an extensive list of anatomical labels for each atlas
used? For instance, what are all the potential labels used in
wmparc.mgz? I am aware of the extensive list of labels in
‘FreeSurferColorLUT.txt’, but this list does not seem to indicate
which labels are included in which atlas.

The easiest thing to do is to look in the corresponding .stats file (eg, 
subject/stats/wmparc.stats)


1.


 2. Do we know of Freesurfer users who have already worked on
categorizing labels from such atlases? For instance, I would be
interested in categorizing labels belonging to the visual system
network vs the auditory system network.


Not that I know of.


1.

Thank you so much for your assistance.

Warm regards,

Lou Blanpain




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Re: [Freesurfer] Talairach Failed: Distorted T1

[Douglas N. Greve]

It looks like something is wrong with your input. For starters, the 
voxel size looks huge. Run

mri_info subject/mri/orig/001.mgz
and send the result

On 3/23/2021 10:54 PM, Harkey, Thomas Jarrott wrote:


External Email - Use Caution

Hello,

My name is Thomas Harkey and I am conducting research using 
FreeSurfer. After running recon-all on this patient, the Talairach 
failed according to the .log file. No stats were calculated but 
loading the orig.mgz file into FreeView looks like this (see image 
attached). This DICOM file was successfully uploaded into other programs.


How can I fix this error?

Kind regards,

--

*Thomas Harkey **
University of Arkansas for Medical Sciences***

*College of Medicine, Class of 2022
501-553-6318*

*tjhar...@uams.edu *


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Re: [Freesurfer] mri_label2vol - Questions about label file and missing voxels?

[Douglas N. Greve]

On 3/23/2021 4:54 PM, Devavrat Vartak wrote:


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Hello freesurfer experts,

I am using mri_label2vol to convert my surface drawn label (of 
functional activity) to functional space (nifti) for more analysis (prf).


When I open the label file in text editor - it shows two lines at the top
#!ascii label  , from subject  vox2ras=TkReg
1287

1) Does the number 1287 represent selected voxels or does it represent 
something else?

It is the number of points in the label


I use the following command to convert:

mri_label2vol --subject sub-01 --hemi lh --label 
CustomLabel/lh.V1.label --regheader /sub-01/mri/orig.mgz --temp 
/sub-01/ses-1/mri_files/func_ref_file.nii.gz --o 
/prfdata/prfroi_mask/lh.V1.nii --fillthresh .3 --proj frac 0 1 .1


2) When I load the nifti file in python, I do not get 1287 voxels, I 
get only ~300 voxels. Why do I get so few voxels ?


You mean 300 active voxels, right? There should be as many voxels as in 
func_ref. Probably func_ref has a much larger voxels size, so there are 
fewer voxels.


Any help is appreciated.

Cheers,

Dev






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Re: [Freesurfer] Missing 'brainstemSsLabels.v10.mgz' file

[Douglas N. Greve]

Can you send the recon-all.log file?

On 3/23/2021 3:31 PM, Taylor, Lisa Marie wrote:


External Email - Use Caution

Hi,

This is the first time I have encountered this problem.  I have a 
participant that has been through recon all, but when trying to create 
PET masks, the error that comes up is that the 
'brainstemSsLabels.v10.mgz' file is missing in the MRI directory. I am 
unsure of how to have this label created when it has been created in 
other participants from freesurfer.


Here is the command and the arguments used when running this 
participant (every one of our participants has had the same command):


${FREESURFER_HOME}/bin/recon-all -s /pub/ltaylor2/*PARTICIPANT* 
-no-isrunning -all -hippocampal-subfields-T1 -brainstem-structures -qcache




Any understanding as to why this particular participant is not having 
this file created?


Any leads would be greatly appreciated!

Lisa




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Re: [Freesurfer] Lesion Heatmap question - follow up

[Douglas N. Greve]

Do you want to do it on a voxel-wise (map) basis? I guess you could just run
mri_concat subj1/lesionmap.mni152.mgz subj2/lesionmap.mni152.mgz ... 
subjN/lesionmap.mni152.mgz --o stack.lesionmaps.mgz
Then run a voxel-wise GLM on the stack. This tricky. You'll probably 
want to smooth it some (mri_fwhm). When you run mri_glmfit make sure to 
add --no-prune. You should also use permutation when you do correction 
for multiple comparisons (mri_glmfit-sim)



On 3/23/2021 10:07 AM, XY XY wrote:


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Thanks Douglas, "mri_convert lesionmap.mgz -at samseg.m3z 
lesionmap.mni152.mgz" worked fabulously after some tweaks in the 
command line!


What would be the best approach to compare population-wise lesion heat 
maps between groups of subjects using the output from SAMSEG? (the 
full FS pipeline cannot process my data due to brain defects and time 
restrictions).


Thanks for all the support for these fantastic tools!



Stay safe!

*-*
*David Olayinka Kamson, MD PhD*
Clinical and Research Fellow
/Joint Neuro-Oncology Program of/
/Johns Hopkins Medicine &/
/National Institutes of Health /
dkams...@jhmi.edu 

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Re: [Freesurfer] Which pial surface to trust

[Douglas N. Greve]

On 3/22/2021 2:56 PM, Jones, Richard wrote:
>  External Email - Use Caution
>
> A couple of questions:-
> 1) Do you experience similar variability with the T2 and FLAIR options or is 
> FLAIR more variable due to it's generally lower SNR?
I have not run it enough to really say. I would think that both would do 
a pretty good job. FLAIR is a little more predictable because both 
vessels and CSF are dark.
> 2) Should the spatial resolution of the T2/FLAIR scan match that of the T1 
> scan?
Yes. And they should be bandwidth matched if possible so that there is 
not differential distortion between them.
>
> Richard
>
> Message: 8
> Date: Wed, 17 Mar 2021 17:51:51 -0400
> From: "Douglas N. Greve" 
> Subject: Re: [Freesurfer] Which pial surface to trust, with or without
>  -FLAIR option
> To: 
> Message-ID: <3c789103-dad7-974a-0d76-58a02cba2...@mgh.harvard.edu>
> Content-Type: text/plain; charset="utf-8"
>
> We get a lot of variable results with FLAIR. Sometimes it helps,
> sometimes it hurts. FLAIR scans themselves can be very variable across
> sites. If it is looking like it is hurting your results, then just run
> without it.
>
> On 3/12/2021 11:07 AM, Xiaojiang Yang wrote:
>> External Email - Use Caution
>>
>> Dear FS developers,
>>
>> I have run FS?s recon-all on many cases, with and without -FLAIR
>> options. I found the pial? surface results (?h.pial) I obtained
>> without -FLAIR option fit to the original image
>> (subjected/mri/orig.mgz) much better than those with -FLAIR option, at
>> least from my visual judgment. See *MailScanner has detected a
>> possible fraud attempt from "secure-web.cisco.com" claiming to be*
>> https://secure-web.cisco.com/1kdfPWDTAquCY3qAKfDNtc8TRiBI5hNHL96VYA9_mTvUn4qpO75SL3h5c4SdXB7ViTEwQr3qvBdcNSLFjdejtW60w8ivtHhUzNRG8q3lZ1xbTIeqmxzu5UakhOAKktPA6QRnwdwkJndw3FM8BTgEY5zvq8wxfJDDr0yrIvj-8mnF4PHlJi1y3SfCiVWPakRs0mSeQjRO-dRiFpl7IoDxugFH1C4OHRgZGkARvy-KxV4pKw_0ubMRqVmKUV5rqXP3m0SDssF44schYVSa5wqU_Bg/https%3A%2F%2Fimgur.com%2Fa%2FwrY0HTY
>> ?for
>> one example.
>>
>> I know -FLAIR option was introduced to improve the quality of pial
>> surface segmentation. Now for many cases, my intuition is that -FLAIR
>> option decreases the pial quality. My questions are:
>>
>>* Is this intuition correct?
>>* Should I trust the pial surface that?s obtained with or without
>>  -FLAIR option in general?
>>
>> In addition, when I use the -FLAIR option, I sometimes get failed when
>> running recon-all. After I did some manual edits to the brainmask
>> image, and re-run the recon-all:
>>
>> recon-all -autorecon-pial -subjid 
>>
>> I can get recon-all successful. But if I run recon-all without -FLAIR
>> option, I can get successful results without needing to manually edit
>> the brainmask image.
>>
>> So my last question is:
>>
>>* Should I just run recon-all without -FLAIR option, or, with -FLAIR
>>  option + manual edit + re-run with -autorecon-pial? Which is better?
>>
>> Thank you very much!
>>
>> John
>>
>
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Re: [Freesurfer] Problem with freesurfer measures

[Douglas N. Greve]

Look in recon-all.log to find the command that creates the wmparc.mgz. 
Run that command changing the aparc annot to your annot and the output 
to a new file name. Look in wmparc.stats; at the top will be an 
mri_segstats command line. Copy that command line changing the file 
names as needed.


On 3/22/2021 9:06 AM, Alberto Del Cerro Leon wrote:


External Email - Use Caution

Thanks!, how can I obtain the white matter volume stats using my 
annotation file?


El mar, 16 mar 2021 a las 16:59, Douglas N. Greve 
(mailto:dgr...@mgh.harvard.edu>>) escribió:


I think they will give very similar results, but my guess is that
#1 is a little better

On 3/8/2021 11:40 AM, Alberto Del Cerro Leon wrote:


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I want to use the annotation file created by myself in fsaverage
to calculate the anatomical stats, but i dont know what is the
best workflow.

1. Convert the annotation file to each subject space using
mri_sur2surf and using mri_anatomical_stats in each subject
2. Convert the surface of each subject to fsaverage space and use
mri_segstats to obtain the data, in this case i dont know what
surface i have to convert to fsaverage space to do it (i can see
thickness (lh/rh.thickness) and volume (lh/rh.volume) but not
folding index and white matter volume)

Any idea?

El lun, 8 mar 2021 a las 16:04, Fischl, Bruce
(mailto:bfis...@mgh.harvard.edu>>)
escribió:

Hi Alberto

 1. And 4. Are not properties of single surfaces – they are
computed from the white and the pial. For 2 and 3 that is
really up to you

Cheers
Bruce

*From:* freesurfer-boun...@nmr.mgh.harvard.edu

mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> *On Behalf
Of *Alberto Del Cerro Leon
*Sent:* Monday, March 8, 2021 7:02 AM
*To:* Freesurfer support list mailto:freesurfer@nmr.mgh.harvard.edu>>
*Subject:* [Freesurfer] Problem with freesurfer measures

*External Email - Use Caution *

Hello Freesurfer team, I am using an annotation file that
i've created previously to obtain the measures of some ROIs.
To do that i am using de commands mri_surf2surf and
mri_segstats. I want to obtain the following measures:

1. Gray and White Matter Volume

2. Folding Index

3. Curvature measures

4. Thickness

However I don't know what surface in the surf folder of each
subject I have to use. Could u help me?

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Re: [Freesurfer] Difference between vox2ras and vox2ras-tkr for subject-specific T1w through FreeSurfer

[Douglas N. Greve]

On 3/21/2021 3:33 PM, Adam Li wrote:


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Hi,

I am a bit noob on FreeSurfer and coordinate systems and I had a few 
questions. I am wondering if I have the |T1.mgz| file of FreeSurfer 
after running recon-all and this is the 256^3 image re-scaled and 
re-oriented from your |orig.mgz| file, then how does one define the 
fsnative (volume RAS) vs surface RAS (tkras in FreeSurfer)? Assuming 
there was no preprocessing done on the original scanner nifti, I run 
the following commands:


(base) workstation$ mri_info 
~/bids/derivatives/freesurfer/la02/mri/T1.mgz --vox2ras

  -1.0    0.0    0.0  126.81799
   0.0   -0.0    1.0 -121.57332
   0.0   -1.0    0.0  159.64563
   0.0    0.0    0.0    1.0

(base) workstation$ mri_info 
~/bids/derivatives/freesurfer/la02/mri/T1.mgz --vox2ras-tkr

  -1.0    0.0    0.0  128.0
   0.0    0.0    1.0 -128.0
   0.0   -1.0    0.0  128.0
   0.0    0.0    0.0    1.0

*Questions:*

1. Applying the `vox2ras` to any voxel, I would get RAS xyz 
coordinates right?



Yes, you get Scanner RAS


2. If I apply `vox2ras-tkr` to any voxel, I would also get RAS xyz 
coordinates?


You would get "TKR" coordinates. TKR stands for tkregister, one of our 
old registration GUIs.


3. So what is the difference exactly between these two transforms? Is 
there anything special / consistent in terms of the definition of the 
origin and orientation? E.g. Orientation is always RAS, and origin is 
always... estimated center of the patient's brain? Or is the origin 
somewhere special like the AC?


The surface is in TKR coords (eg, if you take a surface vertex  XYZ and 
apply the inverse vox2ras-tkr, you will get the voxel col, row, slice 
where the vertex lives). The center is at the center of the volume 
(almost).


3. When would I use one transform over the other?

I've searched online and read through the following, but I feel like 
there is not explicit discussion of the above questions:


- *MailScanner has detected a possible fraud attempt from 
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https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems 



- *MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to be* 
http://www.grahamwideman.com/gw/brain/fs/coords/fscoords.htm 




--
Best Regards,

Adam Li (he/him)
PhD Student in Biomedical Engineering
Johns Hopkins University & School of Medicine

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[Freesurfer] read_surf surface

[Shizuka Hayashi]

External Email - Use Caution

Dear Freesurfer team,

I have a question about the inconsistency between the vertex read from 
read_surf and vertex shown in Freeview.
I have a volume from the hippocampal subfield pipeline and I converted it to 
surface mesh using
mri_tessellate mri/lh.hippoAmygLabels-T1.long.v21.mgz -an 
surf/lh.hippoAmygLabels-T1.long.v21.surf.

Then I smoothed the surface using mris_smooth 
surf/lh.hippoAmygLabels-T1.long.v21.surf 
surf/lh.hippoAmygLabels-T1.long.v21.surf

Now I want to get the corresponding voxel of lh.hippoAmygLabels-T1.long.v21.mgz 
with the vertex. In Freeview, for example, the vertex 0 is [5.17, -19.5, 4.83]. 
I know how to convert this vertex to the corresponding voxel.
However, when I read the surf/lh.hippoAmygLabels-T1.long.v21.surf from Matlab 
using read_surf, the first vertex ( vertex(1,:,:)) is equal to 
[165.4900,217.3600,-159.7300].

Are there any ways to solve the issue?

Thank you.

Regards,
Shizuka
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