Re: [Freesurfer] aparc & wm underestimation

[Douglas N. Greve]

Can you send pictures of the slices showing the problem?

On 3/3/2024 3:18 PM, Stanica, Maria wrote:


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Hello FS developers,

I ran my subjects through skullstripping and recon-all. Everything 
processed correctly (and exited without errors), except 4 images which 
have an underestimation in coronal subcortical region. The 
underestimation is significant and goes on for about 10-12 slices (for 
one image it was 153-162, for another it was 150-164).


After searching the list, we attempted control points, which ended up 
not working (I don’t believe this was the right method to correct the 
error). Then we tried white matter edits, and one of the images was 
resolved, but the other 3 did not get better. Is there anything else 
we could do to try to resolve the issue? I can provide any other 
information needed. Any help would be appreciated!


 1. Freesurfer version: FreeSurfer/7.1.1-centos7_x86_64
 2. Operating System: Red Hat Enterprise Linux 7
 3. OS Version: 7.9 (Maipo)

Best,

Maria

*Maria St**ǎ**nic**ǎ**, B.A.| **Graduate Student*

Medical/Clinical Psychology Doctoral Program

UAB |/The University of Alabama at Birmingham/

mstan...@uab.edu 

Pronouns: she/her/hers

Image


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Re: [Freesurfer] Freesurfer white matter overestimated

[Douglas N. Greve]

Can you include an image with and without the surfaces? Make sure to 
include slices where you think the white surface extends too far.


On 2/28/2024 9:13 AM, Luisa Klahn wrote:


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Dear Douglas,
Please find the nu.mgz screenshot attached.
Best,
Luisa



*Von:* Luisa Klahn 
*Gesendet:* Montag, 26. Februar 2024 08:53
*An:* dgr...@mgh.harvard.edu 
*Betreff:* Re: [Freesurfer] Freesurfer white matter overestimated
Dear Douglas,
Please find attached the pictures for the following issue:
I am processing structural data from a 3T scanner using Freesurfer
version 7.3.2. For some subjects, the grey matter looks very thin, and
the white matter looks overestimated. I'll attach screenshots of the
brainmask, wm mask, and T1 including wm and pial surface lines.
I have tried to set control points into the wm but this did not change
the results.
Does anyone have an idea? Would it be possible to change the intensity
settings in the recon-all command?

Thanks for helping!
Best,
Luisa
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Re: [Freesurfer] Is the slice delay of each slice needed for slice time correction with preprocess-sess?

[Douglas N. Greve]

Yes, you can use the siemens STC option (ie, -stc siemens)

On 2/26/2024 9:02 PM, Maria Hakonen wrote:


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Dear all,

Have I understood correctly that the slice delay of each slice is not 
needed when performing slice time correction with preprocess-sess?


I am processing an open OASIS fMRI dataset. The dataset has fMRI data 
in nifti format and JSON files that contain information about the data.
In the instructions they say: "Slice timing is included in the JSON 
when available. Some original DICOM files did not have slice timing 
info. When slice timing information is unavailable use the ratio 
TR/#slices."


The data is collected with a Siemens scanner.
If the slice timing is available it seems to be interleaved:

"SliceTiming": [
    1.1025,
    0,
    1.165,
    0.059998,
    1.2251,
    0.1225,
    1.28750001,
    0.1825,
    1.3474,
    0.245,
    1.4099,
    0.30499,
    1.47,
    0.36749,
    1.5325,
    0.42749,
    1.595,
    0.48999,
    1.655,
    0.55004,
    1.7175,

Could I just run slice time correction with the siemens option?

Best regards,
Maria



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[Freesurfer] aparc & wm underestimation

[Stanica, Maria]

External Email - Use Caution

Hello FS developers,

I ran my subjects through skullstripping and recon-all. Everything processed 
correctly (and exited without errors), except 4 images which have an 
underestimation in coronal subcortical region. The underestimation is 
significant and goes on for about 10-12 slices (for one image it was 153-162, 
for another it was 150-164).

After searching the list, we attempted control points, which ended up not 
working (I don’t believe this was the right method to correct the error). Then 
we tried white matter edits, and one of the images was resolved, but the other 
3 did not get better. Is there anything else we could do to try to resolve the 
issue? I can provide any other information needed. Any help would be 
appreciated!


  1.  Freesurfer version: FreeSurfer/7.1.1-centos7_x86_64
  2.  Operating System: Red Hat Enterprise Linux 7
  3.  OS Version: 7.9 (Maipo)

Best,
Maria

Maria Stǎnicǎ, B.A. | Graduate Student
Medical/Clinical Psychology Doctoral Program
UAB |The University of Alabama at Birmingham
mstan...@uab.edu
Pronouns: she/her/hers
[Image]


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Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
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continue to communicate over unencrypted e-mail.