Re: [Freesurfer] MRI image quality metrics

[Douglas N. Greve]

You probably don't have write permission to that folder.
Also, you can try
mri_segstats --qa-stats subject subject.qa.dat
Run mri_segstats with --help to understand what is in the qa.dat file

On 2/17/2023 7:43 PM, MANSON ERIC NAAB wrote:


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Thank you once again for your reply.
After running the command wm-anat-snr --s  to determine 
the white matter signal-to-noise ratio, I receive an error about the 
output. It fails to write the output. Please, how do I solve this?


MACs-MacBook-Pro:~ mac$  export 
FREESURFER_HOME=/Applications/freesurfer/7.1.1


MACs-MacBook-Pro:~ mac$ export SUBJECTS_DIR=$FREESURFER_HOME/subjects

MACs-MacBook-Pro:~ mac$ source $FREESURFER_HOME/SetUpFreeSurfer.sh

 freesurfer-darwin-macOS-7.1.1-20200811-8b40551 

Setting up environment for FreeSurfer/FS-FAST (and FSL)

FREESURFER_HOME   /Applications/freesurfer/7.1.1

FSFAST_HOME       /Applications/freesurfer/7.1.1/fsfast

FSF_OUTPUT_FORMAT nii.gz

SUBJECTS_DIR     /Applications/freesurfer/7.1.1/subjects

MNI_DIR           /Applications/freesurfer/7.1.1/mni

FSL_DIR           /Users/mac/fsl

MACs-MacBook-Pro:~ mac$ cd $SUBJECTS_DIR

MACs-MacBook-Pro:subjects mac$ wm-anat-snr --s bert

ERROR: cannot write to /Applications/freesurfer/7.1.1/subjects/bert/stats


On Sat, Feb 11, 2023 at 2:11 PM John Anderson  
wrote:


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export SUBJECTS_DIR=

mri_cnr $SUBJECTS_DIR//surf/ $SUBJECTS_DIR/ /mri/norm.mgz > output_CNR.txt
wm-anat-snr --s  check stats/wmsnr.e3.dat  the
output is snr for the whole white matter.

if you need snr for every roi in aseg.stats or wmparc.stats, then
you can add the flag --snr to the command mri_segstats as follows:

mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv
mri/norm.mgz --empty --brainmask mri/brainmask.mgz
--brain-vol-from-seg --excludeid 0 --excl-ctxgmwm --supratent
--subcortgray --in mri/norm.mgz --in-intensity-name norm
--in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol
--totalgray --euler --ctab
/usr/local/freesurfer/6.0/ASegStatsLUT.txt --subject 
--snr

do the same for wmparc.stats:
mri_segstats --seg mri/wmparc.mgz --sum stats/wmparc.stats --pv
mri/norm.mgz --excludeid 0 --brainmask mri/brainmask.mgz --in
mri/norm.mgz --in-intensity-name norm --in-intensity-units MR
--subject  --surf-wm-vol --ctab
/usr/local/freesurfer/6.0/WMParcStatsLUT.txt --etiv --snr

make sure to change /usr/local/freesurfer/6.0/ASegStatsLUT.txt  in
the previous command to the FS folder on your system
The last two commands update aseg.stats and wmparc.stats. They
both will get a new column for SNR values for every roi.


On Fri, Feb 10, 2023 at 10:25 PM MANSON ERIC NAAB
 wrote:

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Thank you very much for your quick response. I still have a
challenge locating the output file after running the suggested
 command
( mri_cnr $SUBJECTS_DIR/bert/surf/
$SUBJECTS_DIR/bert/mri/norm.mgz) with my subject.
Can you please provide me with the full command for
calculating contrast-to-noise ratio and signal-to-noise ratio
of white matter, gray matter and CSF since am a beginner Or a
video link to calculate them.

This is what i see after running the command

mri_cnr
/Applications/freesurfer/7.1.1/SUBNEW/PA1//label/lh.cortex.label

mri_cnr -- compute the gray/white/csf contrast-to-noise ratio
for volumes.

usage: mri_cnr [options]...

usage example (assumes fs pipeline has finished for subject
subj1): mri_cnr subj1/surf subj1/mri/orig.mgz

Available options:

-s :
compute slope based on given values, write it to slope and
offset files labeled  (e.g.,
`lh..slope.mgz')

-t : print only the total CNR to stdout (stderr still contains
more information)

-l : log cnr to file . Will contain 8 values
in the following order: gray_white_cnr, gray_csf_cnr,
white_mean, gray_mean, csf_mean, sqrt(white_var),
sqrt(gray_var), sqrt(csf_var)

label  : read hemisphere labels from  and 

-u, -?, -help : print usage information and quit

-version : print software version information and quit.


On Thu, Feb 9, 2023 at 3:46 PM John Anderson
 wrote:

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You might consider the command wm-anat-snr to compute SNR

On Thu, Feb 9, 2023 at 10:38 AM Kumar, Avnish
 wrote:

You could also use these:

 1. For CNR you can use the mri_cnr tool:

mri_cnr [options]  

 For example:

mri_cnr $SUBJECTS_DIR/bert/surf/
$SUBJECTS_DIR/bert/mri/norm.mgz


 2. 

Re: [Freesurfer] mri_robust_register --minsize

[Douglas N. Greve]

Yes, but you have to get it started in about the right place.

On 2/23/2023 9:47 AM, Fischl, Bruce R.,PHD wrote:


Hi Sebastien

I believe that Doug has had success using bbregister for this. You 
might give it a try


Cheers

Bruce

*From:* freesurfer-boun...@nmr.mgh.harvard.edu 
 *On Behalf Of *Reuter, 
Martin,Ph.D.

*Sent:* Thursday, February 23, 2023 4:19 AM
*To:* Freesurfer support list 
*Subject:* Re: [Freesurfer] mri_robust_register --minsize

Hi Sebastien,

Robust register cannot register a slice into a 3D volume. It can only 
register 3d to 3d (or 2d to 2d, although that has not been tested much).


Sorry,

Martin



On 30. Jan 2023, at 21:09, Proulx, Jean Sebastien
 wrote:

Hello,

I am trying to register a full volume to a single slice, and I
follow example 3 of mri_robust_register's help. I get the
following error:

 Input image is smaller than min dimension: 1 < 16

 Input dimensions (after conformalizing) MOV: 64 64 64

 Input dimensions (after conformalizing) DST: 64 64 1

 Specify larger minimum ...

This error stays after adding --minsize 1 or --minsize, despite
mri_robust_register recognizing the flag, as suggested by this
terminal output:

--minsize: Smallest dimension > 0 .

Registration ran ok when replacing the single-slice with a
40-slice volume.

Any idea on what is going on here?

Thanks a lot for the good work and

Have a good day!

Sebastien

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Re: [Freesurfer] Visualizing transparent surface with non transparent annotations

[Douglas N. Greve]

Under "Render" select "Mesh"
Under "Annotation" hit the View/Edit button. From there you can turn any 
annotation on or off.


On 2/22/2023 2:34 PM, Leonardo Tozzi wrote:


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Dear Experts,

I would like to use Freeview to achieve the following.

I would like to visualize a transparent brain surface, with only some 
annotations visible. In other words, I would like the surface to be 
transparent, but the annotations I choose to visualize to not be 
transparent.


Is there a way to achieve this?

Thank you,

Leonardo Tozzi, MD, PhD

Director of Computational Neuroscience & Neuroimaging Program

Stanford Center for Precision Mental Health and Wellness

Stanford University

lto...@stanford.edu  | (650) 5615738

*/Connect with us!/*

signature_1075933358 
signature_1282923475 
signature_911042299 




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Re: [Freesurfer] How to find topological defects

[Douglas N. Greve]

If you are using 7.X, you can run
tkmeditfv subject norm.mgz -defects
This will load a "segmentation" with the defects in the volume, an 
annotation (surface segmentation) showing them on the surface, and a 
point set that you can go to any of the points.


On 2/21/2023 7:21 PM, KennethSPrice wrote:


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Hello Freesurfers,

I've found the tutorial for editing wm.mgz (*MailScanner has detected 
a possible fraud attempt from "secure-web.cisco.com" claiming to be* 
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TopologicalDefect_freeview 
).


I'm curious if there is a way to find the topological defects easily? 
Is there a text file in the stats folder, for example, which locates 
the coordinates of topological defects?


Thanks, Ken


Sent with Proton Mail 
 
secure email.


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[Freesurfer] Substantia nigra segmentation status

[Christian Owen]

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 Hi,

The latest post I could find about substantia nigra segmentation in
FreeSurfer is from May 2020
.
As of that post, it was not possible. Is it still not possible? If that's
the case:

- is substantia nigra segmentation on the roadmap?
- is there anything a software engineer could do to help make it happen? I
cannot promise any resources atm, but there's a chance we could help out
(if it turns out to be enough of a priority).

Best,
Christian
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Re: [Freesurfer] Mac OS 13 Ventura

[fsbuild]

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Hello Elmira,

  

You can try downloading an installing the 7.3.2 package file, 
freesurfer-darwin-macOS-7.3.2.pkg, from 
https://secure-web.cisco.com/19NKhoH2W5uSEES-6x2_z8s-Qx5RJB0qwAFyHKCorvYwKi4BblORpORzTbDKNkRqhhdQnW5ym2WsYK_PgrOrKX2IfdxlxfegISVI2161dJMAwmxKaRzQvb8YDvnHIdxB-6ysq7tMKsidZ84QPazeBaTIZ8oQNGeK7gt1X48PhQupIjC5kgjtgnXLQXIzhOVSE6rxxBS1mbOY4pFPNHkjvPN06y91Gv10qyMWnUbyb-Ti4Rhe3OXEGDTzKSowxqFifdzkr8_O_tc_JMYgo3iEy29Ccfudsjub2RbVMJI5b-fZ93N1hJvI7NQfpTpRkvJbWM3BMhv6d2IX-vEQ5BvybHw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2Frel7downloads

  

Once downloaded, right-clicking on the package file and then selecting open 
should work. There should also be a link to setup instructions on that 
page.

  

- R.



On 3/6/23 10:41, Elmira Hassanzadeh (elm...@gmail.com) wrote:



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Caution
  Hi everyone,
Could someone please direct me to the workaround instructions on installing 
Freesurfer on Mac M1 ultra on OS 13.0 Ventura?
Thank you,Elmira



  

  
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Re: [Freesurfer] Segment the centrum semiovale

[Douglas N. Greve]

These are segments in the wmparc.mgz file. Originally, I called these 
centrum semiovale, but I realized that, while they might overlap heavily 
with CS, it they were really just voxels left unsegmented by the main 
process and I did not really know that they were a good segmentation of CS.


On 3/6/2023 11:43 AM, Julie Ottoy wrote:


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Dear Freesurfer team,

I was wondering if FS has a way to segment the centrum semiovale?
The freesurfer colorLUT table mentions "Centrum semiovale is also 
labled with 5001 (left) and 5002 (right)." (see *MailScanner has 
detected a possible fraud attempt from "secure-web.cisco.com" claiming 
to be* 
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/AnatomicalROI/FreeSurferColorLUT 
) 



What does the "also" refer to in this description?

Do the following rois represent the centrum semiovale ? :
5001Left-UnsegmentedWhiteMatter 20  30  40  0
5002Right-UnsegmentedWhiteMatter20  30  40  0
Thank you for your help!

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[Freesurfer] Fwd: Pass code to open FS_7_2_0_Ubuntu_18_04_06.ova.7z

[Idaiane Batista de Assunção Leme]

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Dear,

Please, request to pass code to open the file
FS_7_2_0_Ubuntu_18_04_06.ova.7z


Kind regards,


-- 
Idaiane Batista de Assunção Leme
Biomédica, PhD
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[Freesurfer] Password request for FS_7_2_0_ubuntu_18_04_06.ova.7z

[Michael Wagner]

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Dear Team,

I'm about to install Freesurfer in a VirtualBox VM under Windows., 
following the instructions in
https://secure-web.cisco.com/1Vo2zDB0YAGmcpr2LU_XN4jEZ1O0S0gevSS9oIAxajv6IyTSDJ8zmsWSBEOO5zsAXSeHDvh4omN9EFw_WjOLzRH8pDeEHrwUC2eVMMmLUFG06cCRvTHJihivwSDoXA5zKY1L5vJ25tN516uTZNX6HL4E-OtYbue4aaVHAc1EP_hqnLb4ChRYBtPE6FxNdrk7ntFspjx2qc3lJmbgpFrQ2NW5fmas9jF0vx24J1Fy9__hxH9TtziSRI0GmYTYliP4zRHEn9KUJvFshH-afufpWvBJqZJrpFgtX0Pgbet3spjHk4OX4etzxmQWeS0xGpcF3KB0UBrsS3b-_zTCVum0ZhA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FVM_67

I believe I will need a password to unpack
FS_7_2_0_ubuntu_18_04_06.ova.7z
(currently downloading).

Later on, I might also need a license file:
"Once the VM starts and you have added your FreeSurfer license file, you 
can start a terminal"

Can you please help me with either of these?

Thanks,

Michael

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[Freesurfer] Segment the centrum semiovale

[Julie Ottoy]

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Dear Freesurfer team,

I was wondering if FS has a way to segment the centrum semiovale?
The freesurfer colorLUT table mentions "Centrum semiovale is also labled
with 5001 (left) and 5002 (right)." (see
https://secure-web.cisco.com/16ntnqYurxLXfYvZCsM5evs9fxRFquoTnxIkD0H4vCmJ3wyz1ILXajrnEbC8QyD23IXTjhznWNEd6JY41T_1i4pFiAhYAmIiof9tTBS1o1Uv6Xe0jQ8zZK9BhCaaj7eG9eskRi7K2wraMBF5F1EQuFvn37XsurmsDLZ0IDBk02St-7AjIKjoN_btWKXbQQ_GjGriTaQKWn4oNTTT1J4WJiO73HLMdnC4N3JLqbQ0M7Rv8LV2WSnPMBUXHQA8R1nK869ZmYnfSz43n0gGUGW4dwGx6BqLbae0K35hubuWgxRFxCSpAMGc4xDZWv753Hyn8XTc1jpc5Dq57MVQ-eWsDRQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FAnatomicalROI%2FFreeSurferColorLUT
)

What does the "also" refer to in this description?

Do the following rois represent the centrum semiovale ? :

5001Left-UnsegmentedWhiteMatter 20  30  40  0
5002Right-UnsegmentedWhiteMatter20  30  40  0

Thank you for your help!
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[Freesurfer] Omar: VirtualBox image password request

[Omar Salah Mohammed Mostafa Ahmed]

External Email - Use Caution

Hello, I'd like to request the password for FS_7_2_0_ubuntu_18_04_06.ova.7z 
in
order to install the virtual image and run Freesurfer in a Virtualbox VM.

Thank you!

Omar Ahmed


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Re: [Freesurfer] infant freesurfer - input and output questions

[Zollei, Lilla,Ph.D.]

Hi Inga,

Did you infant_recon_all run through without any errors? If you see the regular 
FS directory structure in your subejct directory that woudl mean the 
infant_recon_all successfull completed. If there is only a "work" directory 
there, that means the process quit in the middle of the processing.

Lilla

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Inga Harting 

Sent: Wednesday, October 19, 2022 8:03 AM
To: freesurfer@nmr.mgh.harvard.edu 
Cc: Inga_klinik 
Subject: Re: [Freesurfer] infant freesurfer - input and output questions

External Email - Use Caution

Hello again.

Please forget about my first question. I just realised I had moved my
Inga/local directory (new after installing freesurfer) before data
backup. Just moved it back and now iFS is running again.

But, I'm still new to infant freesufer, trying to find my way, am
stumbling and glad for some help:

Looking at the results using freeview and following along the lines of
FS tutorial on FS output, there is no T1.mgz in /mri and brainmask.mgz
is referred to norm.mgz which is empty. Does this indicate the analysis
went through but didn't work?

Is there a tutorial for infant freesurfer which I've missed and which
might answer (some of) my (current and future) questions?

Best, Inga

--output copy from my screen for the directory /mri

inga@XPS-15-9510:~/Inga/Daten/test/pmd2-0/iFS_output_2022-10-05/mri$ ls -la
insgesamt 4824
drwxrwxr-x 3 inga inga4096 Oct  5 15:44 .
drwxrwxr-x 7 inga inga4096 Oct 19 11:44 ..
-rw-rw-r-- 1 inga inga  232837 Oct  5 15:44 aparc+aseg.mgz
-rw-rw-r-- 1 inga inga  39 Oct  5 15:44 aseg.count.txt
-rw-rw-r-- 1 inga inga  186355 Oct  5 15:44 aseg.mgz
-rw-rw-r-- 1 inga inga  186080 Oct  5 15:44 aseg.nii.gz
-rw-rw-r-- 1 inga inga  186355 Oct  5 15:44 aseg.presurf.mgz
-rw-rw-r-- 1 inga inga  606165 Oct  5 15:44 brain.finalsurfs.mgz
lrwxrwxrwx 1 inga inga   8 Oct  5 15:44 brainmask.mgz -> norm.mgz
lrwxrwxrwx 1 inga inga  11 Oct  5 15:44 brainmask.nii.gz -> norm.nii.gz
lrwxrwxrwx 1 inga inga   8 Oct  5 15:44 brain.mgz -> norm.mgz
lrwxrwxrwx 1 inga inga  11 Oct  5 15:44 brain.nii.gz -> norm.nii.gz
-rw-rw-r-- 1 inga inga  102107 Oct  5 15:44 filled.mgz
-rw-rw-r-- 1 inga inga 169 Oct  5 15:44 lh.dpial.ribbon.mgz
-rw-rw-r-- 1 inga inga  598075 Oct  5 15:44 lh.dwhite.ribbon.mgz
-rw-rw-r-- 1 inga inga   53037 Oct  5 15:44 lh.ribbon.mgz
-rw-rw-r-- 1 inga inga   0 Oct 18 19:08 norm.mgz
-rw-rw-r-- 1 inga inga   0 Oct 18 19:08 norm.nii.gz
-rw-rw-r-- 1 inga inga 1011650 Oct  5 15:44 rh.dpial.ribbon.mgz
-rw-rw-r-- 1 inga inga  372114 Oct  5 15:44 rh.dwhite.ribbon.mgz
-rw-rw-r-- 1 inga inga   54091 Oct  5 15:44 rh.ribbon.mgz
-rw-rw-r-- 1 inga inga   93026 Oct  5 15:44 ribbon.mgz
drwxrwxr-x 2 inga inga4096 Oct  5 15:44 transforms
-rw-rw-r-- 1 inga inga   62243 Oct  5 15:44 wm.mgz
--


--
Inga Harting
private email: inga.hart...@gmx.de

Dpt. Neuroradiology
Heidelberg University Medical Center
INF400, 69120 Heidelberg
inga.hart...@med.uni-heidelberg.de


Am 19/10/2022 um 12:53 schrieb Inga Harting:
> Hello,
>
> I'm new to infant freesurfer. I was initially relieved when a first run
> of a test patient went through after I created mprage.nii.gz using
> mri_convert.
>
> 1. Today I wanted to rerun it, but it gives me an error message although
> the "original" file mprage.nii.gz is sitting unchanged right there in
> the directory (ERROR: must have the input file in
> home/inga/Inga/Daten/test/pmd2-0/mprage.nii.gz!). Could you help me find
> my error? I've copied the output on my screen below.
>
> 2. I wanted to look at the results using freeview and following along
> the lines of FS tutorial on FS output. However there is no T1.mgz in
> /mri and brainmask.mgz is referred to norm.mgz which is empty. Does this
> indicate the analysis went through but didn't work?
>
> 3. Is there a tutorial for infant freesurfer which I've missed and which
> might answer (some of) my questions?
>
> Best, Inga.
>
> --
> Inga Harting
> private email: inga.hart...@gmx.de
>
> Dpt. Neuroradiology
> Heidelberg University Medical Center
> INF400, 69120 Heidelberg
> inga.hart...@med.uni-heidelberg.de
>
> --
>
> error for infant_revon_all--
>
> inga@XPS-15-9510:~/Inga/Daten/test/pmd2-0$ pwd
> /home/inga/Inga/Daten/test/pmd2-0
> inga@XPS-15-9510:~/Inga/Daten/test/pmd2-0$ ls -la
> insgesamt 33808
> drwxrwxrwx 11 inga inga 4096 Oct 19 12:10 .
> drwxrwxr-x 10 inga inga 4096 Oct 19 12:10 ..
> drwxrwxrwx  2 inga inga 4096 Apr  6  2019
> 1.2.840.113619.2.322.2807.4236267.23758.1434086473.218
> drwxrwxrwx  2 inga inga36864 Apr  6  2019
> 1.2.840.113619.2.322.2807.4236267.23758.1434086473.219
> drwxrwxrwx  2 inga inga12288 Apr  6  2019
> 1.2.840.113619.2.322.2807.4236267.23758.1434086473.223
> drwxrwxrwx  2 inga inga16384 Apr  6  2019
> 1.2.840.113619.2.322.2807.4236267.23758.1434086473.224
> drwxrwxrwx  2 inga inga12288 Apr  6  2019
> 

Re: [Freesurfer] infant Freesurfer - subcortical/white matter segmentation

[Zollei, Lilla,Ph.D.]

Hi Inga,

Sorry, I missed this message on the mailing list.

This is a new issue to me, so I will take a look at the label fusion step.

And yes, we are working on including T2w images in the pipeline as at the 
newborn stage it would help with the GM/WM segmentation accuracy.

Best, Lilla



From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Inga Harting 

Sent: Monday, October 31, 2022 3:11 PM
To: freesurfer@nmr.mgh.harvard.edu 
Cc: Inga_klinik 
Subject: [Freesurfer] infant Freesurfer - subcortical/white matter segmentation

External Email - Use Caution

Hello experts,

I've begun using infantFS for neonates and I'am interested in the
subcortical segmentation.

I noticed that the internal capsule is delineated in the
manseg-tsubj2subj.NIFTYREG volumes (irrespective of the template's
having gmwm or not), but that ist lost after mri_label_fusion when the
thalamus has suddenly increased, swallowing PLIC and corona radiata, the
basal ganglia have also expanded and the corpus of the caudate nucleus
is large and pushed upwards.

Is there a way to preserve the subcortical anatomy?

Would labelling e.g. capsula interna help? Is there a way to include 2D
T2axial to help with gmwm contrast?

Best regards, Inga.


--
Dr.med. Inga Harting

Dpt. Neuroradiology
Heidelberg University Medical Center
INF 400
69120 Heidelberg
inga.hart...@med.uni-heidelberg.de

Mühltalstr. 124b
69121 Heidelberg
inga.hart...@gmx.de


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Re: [Freesurfer] Infant freesurfer issue

[Zollei, Lilla,Ph.D.]

Hi Chris,

Are you setting the environment path correctly? It seems that infant_recon_all 
cannot find the relevant folder.

Best, Lilla

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Sayre, Christopher 

Sent: Wednesday, January 25, 2023 9:13 AM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: [Freesurfer] Infant freesurfer issue


External Email - Use Caution

Hello all,



I am having an issue when trying to run infant_recon_all. The error that I am 
getting is  
/opt/apps/software/FreeSurfer.7.2.0-centos7_x86_64/bin/atlassubjects.csh No 
such file or directory.



I have searched through the bin folder  xç  xfor the atlassubjects.csh 
and indeed it does not exist. I have looked at the github for FreeSurfer and I 
was able to find the file under the infant folder. Am I missing something here 
or can anyone offer anything that would assist me in resolving this error?



Thanks,



Chris Sayre
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Re: [Freesurfer] Infant Freesurfer - manual edits

[Zollei, Lilla,Ph.D.]

Hi Jee Won,

Currently the infant stream does not allow for a rerun after manual edits. 
Editing the thalamus though would not impact the surface computations though.

Best, Lilla

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Kang, Jee Won 

Sent: Thursday, February 16, 2023 8:38 AM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] Infant Freesurfer - manual edits


External Email - Use Caution

Dear Freesurfer experts,


Hello, I have started experimenting with Infant Freesurfer (version 4a14499), 
and we have run into a problem with very poor segmentation of the thalamus in 
one of our subjects.


Is there a way to incorporate manual edits, as in adult Freesurfer, to improve 
the segmentation? From this post: MailScanner has detected a possible fraud 
attempt from "secure-web.cisco.com" claiming to be 
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg65925.html,
 it looks like the option to make manual edits was a feature in the works, but 
I am not sure if that is still the case.


I am guessing it would be inadvisable to re-run the infant data after making 
edits (to wm or aseg.presurf) in adult Freesurfer?


Thank you for your advice on this!


Sincerely,

Jee Won
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Re: [Freesurfer] How to get individual betas (parameter estimates) in certain ROI?

[Douglas N. Greve]

You'll probably have to use matlab, eg,
 [vertices, label, colortable] = read_annotation(filename)
ind = find(label==yourlabel);
beta = fast_vol2mat(MRIread('beta.nii.gz'));
yourlabelbeta = beta(:,ind);


On 3/6/2023 10:08 AM, Huang, Yujing wrote:


Hi Andy,

Can you try the mask option?

https://surfer.nmr.mgh.harvard.edu/fswiki/mri_glmfit

Best,

Yujing

*From:* freesurfer-boun...@nmr.mgh.harvard.edu 
 *On Behalf Of *Andy Kim

*Sent:* Tuesday, February 28, 2023 10:47 PM
*To:* freesurfer 
*Subject:* [Freesurfer] How to get individual betas (parameter 
estimates) in certain ROI?


*External Email - Use Caution *

Dear FreeSurfer Developers,

Hi. Thanks to FreeSurfer, I finished a group activation analysis with 
FS-FAST.


Now I want to draw a ROC curve to check how well my task conditions 
can distinguish M1 and S1. (M1 is more activated under certain 
condition of my task and S1 is more activated under another condition.)


To do so, I need to get every betas of individual nodes in certain 
ROIs (which I created my own, but let's just say M1 and S1).


Betas are in beta.mgh file which is a product of mri_glmfit. Then how 
do I get betas of only M1 nodes or only S1 nodes?


Kind Regards,

Andy (Junghyun) Kim


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[Freesurfer] Mac OS 13 Ventura

[Elmira Hassanzadeh]

External Email - Use Caution

Hi everyone,

Could someone please direct me to the workaround instructions on installing
Freesurfer on Mac M1 ultra on OS 13.0 Ventura?

Thank you,
Elmira
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Re: [Freesurfer] different results for gtmpvc with different tracers

[Douglas N. Greve]

can you send an example?

On 2/17/2023 9:38 AM, Federica Di Antonio wrote:


External Email - Use Caution

Dear experts,

I hope this email finds you well.
I run the pvc correction with mri_gtmpvc for subjects data obtained 
with two different PET tracers.
In gtm.stats.dat, for every subject and every region, the number of 
voxels evaluated for amyloid tracer is approximately twice the volume 
evaluated for the second tracer.
I'd expect that the volume of a region for the same subject doesn't 
change with the tracer.


Do you think this error can result from previous errors in the 
analysis? Or is it in some way plausible?


Thank you for your patience,
Federica


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Re: [Freesurfer] cvs clarifications with petsurfer

[Douglas N. Greve]

On 2/17/2023 9:21 AM, Federica Di Antonio wrote:


External Email - Use Caution

Dear Freesurfer experts,

I'm using PETsurfer. I've done the standard pipeline for all my 
subjects, using the cvs registration.
I was wondering (maybe it's very stupid) when the standard pipeline 
"uses" the cvs resulting files (except for subcortical volume-based 
analysis and final resampling).

This is the only time it uses it.


Moreover, when I obtain a resampled file (like 
subctxgm.cvs.2mm.sm00.nii.gz ) should I process it with freesurfer?
I'm not sure what you mean to process it in freesurfer? Do you mean 
recon-all anatomical anlaysis? That is only for T1weighted MRI images.


Sorry for my english, maybe what I ask is not very clear, but I hope 
you can help me.

Thank you so much for your time and kindness!

Sincerely,
Federica

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Re: [Freesurfer] Samseg cortex parcellation

[Douglas N. Greve]

when you say that it is better cortex segmentation, do you mean better 
than the aseg.mgz=aparc+aseg.mgz or better than the aseg.presurf.mgz? Do 
you mean in general or just near the WMH? The aseg/aparc+aseg use the 
surfaces to refine the gray/white boundary, and usually the surfaces do 
a much better job there.


On 2/16/2023 6:32 PM, Stepanov, Valentin wrote:


External Email - Use Caution

Hello, I hope this email finds you well.

I am using Samseg for the MS patients' data and am very impressed with 
its performance in terms of lesions segmentation along with posteriors 
and probability maps saving. Also, compared to freesurfer, it has a 
remarkably better quality of cortical gray matter segmentation, 
particularly in subjects with juxta/intracortical lesions. However, to 
my knowledge, it does not allow doing a cortex parcellation. I used it 
with the —recon option, but in that case, the output (aparc+aseg.mgz) 
is identical or very close to those freesurfer provides and commonly 
has some segmentation errors, whereas seg.mgz saved in samseg 
directory demonstrates significantly better segmentation.


I wonder if there is any way to run cortex parcellation using exact 
samseg seg.mgz output?


I have attached a couple of images demonstrating the difference of 
segmentation output for freesurfer and samseg.


Thank you,

Best regards

Valentin

*Valentin Stepanov*

Postdoctoral Fellow

Center for Biomedical imaging

Department of Radiology

NYU Grossman School of Medicine

660 1^st Avenue, office 212

New York, NY 10016


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Re: [Freesurfer] -pctsurfcon --fsvol default

[Douglas N. Greve]

On 2/15/2023 5:35 PM, Antonio #30 wrote:


External Email - Use Caution

Hello again,

I would like to ask one last thing.
How can the class averages computed from csdbase.y.ocn.dat not match 
the gamma.mgh values in the cluster?


e.g. How can gamma show +29 in a vertex that is part of the 
significantly positive cluster in an A-B contrast, while the average 
of all values taken from csdbase.y.ocn.dat referring to class A in 
that same cluster is lower than that of class B (average of values of 
input y for class A = 20.367; average for class B = 20.401)?
The cluster is defined after thresholding. So there might be some 
vertices that have a huge effect in one direction, but from the cluster 
perspective, they don't count anymore than a vertex that has a small but 
suprathreshold effect. The computed average will be affected though.


Are the values in csdbase.y.ocn.dat not corrected by the variables 
chosen as covariates?

The gamma values are corrected.


Thanks again!

Antonio Bonifanti

Il giorno mer 15 feb 2023 alle ore 18:36 Antonio #30 
 ha scritto:


Hi,

1. I was wondering why the --fsvol argument in -pctsurfcon takes
rawavg.mgz by default, when most literature on grey/white contrast
tends to compute it from nu.mgz.
Is the intensity-corrected volume to be preferred in all cases or
was there a reason for choosing rawavg as a default while writing
the script?

I don't think it matters as the computation is very local (ie, wm a few 
mm from gm) so the bias field will be minimal.



2. I would also like to ask whether or not you believe the values
of smoothing kernels seen in literature for grey-white contrast
(which often are over 20mm) to be adequate for such a measure.


I don't know, I've never looked into it. 20mm seems like a lot.



3. As a final note, would you say it is appropriate, from a
statistical standpoint, to compare the results of group analyses
conducted on the two hemispheres with different covariates? (e.g.
with mean left cortical thickness and mean right cortical
thickness rather than mean whole cortical thickness)

It just leads to a different interpretation. If the interpretation is 
reasonable and you can explain it, then it is ok.



Thank you for your time!

Antonio Bonifanti


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Re: [Freesurfer] WMH in aparc+aseg

[Douglas N. Greve]

I think it is  basically the same procedure as the other segmentations, 
ie, a set of 40 subjects' whole brains were manually labeled, many of 
them had WMH, then it is just the normal Bayesian labeling as in Bruce 
Fischl's 2002 Neuron paper.


On 2/13/2023 12:37 PM, Alberto Del Cerro Leon wrote:


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Hello FS team! I am using the volumetric data of WMH obtained during 
the recon-all in the apar+aseg.mgz file. Where I could find the 
description of the method throught it is segmented? I find the 
Automated Labeling of Neuroanatomical Structures in the Human Brain 
but the label WMH doesn't figure on that.


Thanks in advance


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Re: [Freesurfer] Recon-all exited without errors

[Douglas N. Greve]

That one looks like there was a massive failure of the registration. One 
thing you can try is to add -samseg-reg to the command line. This will 
use samseg to do this registration, which may be more robust. Is there 
anything amiss with your image?


On 2/13/2023 10:25 AM, Goeckner, Bryna wrote:


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Thanks for the response.  I should have been more clear in my first 
email.  I have used tkregister2 in the past to fix talairachs, but 
this one does not appear to be fixable with the in-plane shifting, 
scaling, and rotating that is available within the tkregister2 GUI.  
The moveable appears to be in a different plane than the target. I’m 
attaching a screenshot from tkregister2.


Is there a different way to fix the talairach or another recon fix 
(especially considering the apparent brainmask issue) that should be 
pursued?


Thanks again for your help!

*Bryna Goeckner* (she/her)

Graduate Student

Meier Lab

Medical College of Wisconsin

Neuroscience Doctoral Program

Date: Fri, 10 Feb 2023 20:48:26 +
From: "Huang, Yujing" 
Subject: Re: [Freesurfer] Recon-all exited with errors
To: Freesurfer support list 
Message-ID:


Content-Type: text/plain; charset="us-ascii"

Hi Bryna,

In this tutorial, it talks about how to fix bad output from the 
talairach registration:


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https://urldefense.com/v3/__https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach__;!!H8mHWRdzp34!_l_gOh7Vnn8ovwqfR_EqP1dOfB-MrgDNoaNiCUIahwFJ_aGAOSKGKIk18p6fQDf2snUDr8V7UbYuZ_sgpEWHNY9oikTLS12PI--QGIY$ 



Best,

Yujing



From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Goeckner, Bryna

Sent: Friday, February 10, 2023 3:35 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Recon-all exited with errors


    External Email - Use Caution
Hi All,

I am using FS 7.2.0 and have one subject that exited recon-all with 
errors (looks like for talairach issues) but I am not able to use 
tkregister2 to view and make manual adjustments to the talairach since 
surf/lh.orig was not generated.


I then tried recon-all with the -notal-check flag, which exited 
"without errors" although the talairach is nowhere near correctly 
aligned and while aparc & aseg in freeview appear ok, the brainmask 
appears to have issues (when I turn it off, the entire background 
displays as white).


I'm including the recon-all logs (original & notal-check flag) and 
have listed the actual commands used below as well.  Any help you can 
provide in figuring out how to run this subject is greatly 
appreciated.  Thanks!


The original code was:
recon-all -subject subj# \
    -i rawT1.nii.gz \
    -T2 rawT2.nii.gz \
    -T2pial \
    -parallel -openmp 12 \
    -3T \
    -all

And for the second run, -notal-check was added after -all

For tkregister2:
tkregister2 --s subj# --fstal --surf orig

Bryna Goeckner (she/her)
Graduate Student
Meier Lab
Medical College of Wisconsin
Neuroscience Doctoral Program


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Re: [Freesurfer] How to get individual betas (parameter estimates) in certain ROI?

[Huang, Yujing]

Hi Andy,

Can you try the mask option?

https://surfer.nmr.mgh.harvard.edu/fswiki/mri_glmfit


Best,

Yujing

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Andy Kim
Sent: Tuesday, February 28, 2023 10:47 PM
To: freesurfer 
Subject: [Freesurfer] How to get individual betas (parameter estimates) in 
certain ROI?


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Dear FreeSurfer Developers,

Hi. Thanks to FreeSurfer, I finished a group activation analysis with FS-FAST.
Now I want to draw a ROC curve to check how well my task conditions can 
distinguish M1 and S1. (M1 is more activated under certain condition of my task 
and S1 is more activated under another condition.)
To do so, I need to get every betas of individual nodes in certain ROIs (which 
I created my own, but let's just say M1 and S1).
Betas are in beta.mgh file which is a product of mri_glmfit. Then how do I get 
betas of only M1 nodes or only S1 nodes?

Kind Regards,
Andy (Junghyun) Kim
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Re: [Freesurfer] Question on mri_nu_correct for 3 Tesla data

[Douglas N. Greve]

Hi Philipp, by default, those parameters are not used anymore as we are 
using ANTS N4 (though this is not obvious). There is no separate 
parameter set for for 3T for N4. It is still  possible to use the old 
MNI N3 code, so we have kept it in there.



On 2/25/2023 2:58 PM, Saemann, Philipp wrote:


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Hi FreeSurfer specialists,


we have problems with a strong non-intensity in 3 Tesla data of GE 
(mainly temporal poles and occipital area).


We managed to rescue the occipital errors by a pre-Bias-field 
correction using SPM, but would of course try


to optimize this in recon-all itself.


When I open the recon-all scrip tin FS v7.1.1 I can find no difference 
in the parameters depending on if the


the flag "-3T" is set or not.


In both cases the parameters forwarded are:


--n 1 --proto-iters 1000 --distance 50


(in line 1536 and line 1540 of /bin/recon-all.)


 Could someone explain this?


What could be done (manual corrections etc. are obsolete due to the 
large sample size...) to improve the WM detection


in the temporolateral/polar area (subsequently cortex detection)? The 
brainmask looks okay; the ribbon.mgz shows the


cut off lateral parts of the cortex.


Thanks in advance for any hints,

Philipp



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[Freesurfer] pass code to open the Ubuntu compressed image with Freesurfer

[Chloe Lin]

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Hi,

I do not have the pass code to open the Ubuntu compressed image with
Freesurfer, can you provide me with that?

Thank you very much.

Best regards,

Chloe
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Re: [Freesurfer] To freesurfer

[Huang, Yujing]

Hi,

You can find sources on Freesurfer Wiki - 
https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferWiki

Here the page about conducting an at-home FreeSurfer Course - 
https://surfer.nmr.mgh.harvard.edu/fswiki/TeachYourselfFreeSurfer

Best,

Yujing


-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Kanokwanwijit Wongsook
Sent: Friday, March 3, 2023 10:07 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] To freesurfer

External Email - Use Caution

Dear Freesurfer

My name is nan from Thailand and I’m interest in Freesurfer software but I 
can’t learn from the begin by myself. I’m confused. so please, can you ad rise 
me in the begin point of this Freesurfer or some course to learn.Thankyou


Sincerely yours,
 

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Re: [Freesurfer] Segmentation fault (core dumped)

[Huang, Yujing]

Hi Tracy,

I’m wondering if you have any success with other subjects. Can you attach the 
failed recon-all.log?

Best,

Yujing

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Tracy Riggins
Sent: Sunday, March 5, 2023 1:22 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Segmentation fault (core dumped)


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Greetings FS experts:

We are trying to run recon-all -s -qcache on a handful of brains processed in 
freesurfer v5.1.0.   (it's an old dataset...5.1 makes the most sense for our 
purpose.)

The error is below:

[cid:image001.png@01D95008.DF0111D0]

--
#@# 1/1 HMN080 Fri Mar  3 12:14:44 EST 2023 --
---
mri_surf2surf --srcsubject HMN080 --srchemi lh --srcsurfreg sphere.reg 
--trgsubject fsaverage --trghemi lh --trgsurfreg sphere.reg --tval 
./tmp.mris_preproc.51930/HMN080.1.mgh --sval 
/export/data/seahorse_ncdl/HMN/data/HMN080/surf/lh.thickness --sfmt curv 
--noreshape --no-cortex
Segmentation fault (core dumped)
Linux 
seahorse.umd.edu
 3.10.0-1160.80.1.el7.x86_64 #1 SMP Sat Oct 8 18:13:21 UTC 2022 x86_64 x86_64 
x86_64 GNU/Linux

recon-all -s HMN080 exited with ERRORS at Fri Mar  3 12:14:48 EST 2023

Can you assist?  OR perhaps tell us where to find the core dump file, which may 
have more information?

--
Tracy Riggins, Ph.D.
Pronouns:
 she/her/hers
Associate Professor of Psychology
4094 Campus Drive, Biology/Psychology Building 2147J
University of Maryland, College Park, MD 20742
Zoom Meeting ID: 
6751666548
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