Re: [Freesurfer] Hippocampal segmentation - data processed in different fs version

[Iglesias Gonzalez, Juan E.]

Yes! As long as you explain it clearly in whatever paper you may write with the 
results ;-)

Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jeiglesias.com

On Jan 10, 2022, at 23:28, Katarina Vulić 
mailto:vulic.katari...@gmail.com>> wrote:


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Hello Freesurfer Developers,

We have data that has been initially processed by Freesurfer v6.0.1.
Is it ok if we run hippocampal subfield segmentation (MailScanner has detected 
a possible fraud attempt from "secure-web.cisco.com" claiming to be 
https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldsAndNucleiOfAmygdala)
 with v7.1.1 that we currently have on our machine?

Thanks in advance,
Katarina
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[Freesurfer] Hippocampal segmentation - data processed in different fs version

[Katarina Vulić]

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Hello Freesurfer Developers,

We have data that has been initially processed by Freesurfer v6.0.1.
Is it ok if we run hippocampal subfield segmentation (
https://secure-web.cisco.com/1jE-n3Hq6P8vcsBZUmGPkR42g9WznVSWKUxrDeSXYoSnRiQ7w9sPdFxkojCvOKSo7MwK2yxjWiL_dOWKwm3TSkiyIW2o5SZP_vM93pe9jws3DKRsSEz1mSMqpCIceNcJIyPe2LlgE56f8lZYOHJkVluik1MP-Zz5RXAckFBYX2RtE-sd7PD-5hk2yGonbMxiwF5289LFQleIvmATT5uDH_sZj5ndSZ1f1XNTSZ0L5OXFfoAlxRxVf2EN3i2Rsq9Q91RICL1dwFy9vGTl9jqmIRwZWgsdD5vQLXQpnGBASku7ncsLZ0Fx-9eaWd4NJWLuBWIZXYJSA25g5JAMV-70_8A/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FHippocampalSubfieldsAndNucleiOfAmygdala)
with v7.1.1 that we currently have on our machine?

Thanks in advance,
Katarina
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Re: [Freesurfer] Trac-all -prep -c error

[Salar Dini, Elaheh]

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Thank you for constantly improving TRACULA. I believe we don't have reverse 
polarity scan or a field-map. We might be able to acquire the field-map though 
since the MRI has been acquired locally.


Having that in mind, and just for clarification and making sure I have 
understood you correctly, do you still propose to choose bbregister for 
intera-subject, nonlinear FA-to-FA with SyN for inter-subject and intradof=12?


Or do you propose to try both bbregister and Flirt for intra-subject 
registration in addition to trying different intradof ?


I would love to run both bbregister and Flirt and compare the results between 
the two methods, but I believe we can't run Flirt because the 
trctrain/hcp/mgh_10xx/mni folder, doesn't contain acomm.flt.prep.trk file; This 
folder, however, has the acomm.bbr.prep.trk in it. I believe that is why we can 
run trac-all -prep without an error setting the registration method as 
bbregister but we get error when we change it to Flirt. This is at least true 
for the freesurfer 7.2.0 that we installed on our server using 
freesurfer-linux-centos7_x86_64-7.2.0.tar.gz package.


My best wishesm

Ela


From: Yendiki, 
Anastasia

Sent: Sun, 09 Jan 2022 19:06:53 
-0800
To: elaheh.salard...@yale.edu
Subject: Re: Trac-all -prep -c error


Interesting! I had not observed that, but I was not specifically looking for
it. I imagine that this may vary depending on how much EPI distortion there is
in the diffusion data to being with, if a field map or reverse polarity scan is
used to correct this distortion, etc.

In the new version, there is an option to set the degrees of freedom for the
affine inter-subject registration, in your config file. (This should work
either with bbregister or with flirt.)

For example, this gives you rigid registration (rotation + translation only):
set intradof = 6

This gives you rigid + scaling:
set intradof = 9

This gives you full affine:
set intradof = 12

Depending on how much distortion there is in your diffusion data, increasing
the DoF in the registration to the T1 may give you better results. I'd actually
be very interested in hearing what worked best for you.

Thanks to you and your instructor for bringing this to our attention!

Anastasia.



From: Salar Dini, Elaheh 
Sent: Sunday, January 9, 2022 8:26 PM
To: Freesurfer support list 
Subject: Re: Trac-all -prep -c error

Dear Anastasia,

I just wanted to share with you that after following up with our instructor, 
asking him why he recommended FLIRT rather than bbregister, he clarified that 
4-5 years ago when he was using TRACULA for his project,
registration using bbregister either worked well for the hemispheres or for the 
brainstem, but not both. He provided the slides that can be found at 
https://secure-web.cisco.com/1uCi2IyvVBHy3tX6oJBB9QNrkGz4S4DgkdtGlSxcNZe-0xF5zGiBkx0cNxUT6AkRgXWY1k8ZPeTsa54H_4GgkkMyhq8jHZAqOEQGQ_A0KHzqyK0RKHa_D16ybsNfPcamBZxAQGykqpzeOObVaUmSzkekbuRPcyD3n1gGz51MZFKTgdb1YSBmC4RKtSr6YKrxIewlX1p8H_ow_AWTj9cKOOIaWKCLyvc8daBWQ3xSHNChBtOVA7RtiHMJSu3kKJvPwmRiTkQ-WNRStTc0nizdwBwWJYkNt4x10wZeFzJiAQ33-FF-6bCBY6x16bB2nQ6_a8VM8XkEwW6gaiWmnbuItkw/https%3A%2F%2Fwww.dropbox.com%2Fs%2Fffkz8kqqdyxojno%2Fdiff_to_anat_reg.pdf%3Fdl%3D0
to share with you. He also mentioned that there is a possibility that you have 
fixed this issue in the newer version of FreeSurfer. Is that true? Has this 
problem been fixed in the most recent version?

Thanks again for the help.
Kindly,
Ela




From: Yendiki, 
Anastasia

Re: [Freesurfer] Spatial distance between regions

[Julie Ottoy]

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Hi Doug

Thank you, worked as a charm!

I was wondering if I can apply this code on other atlases, for example I
have the schaefer atlas (in MNI152) space. Can I just run the
mri_segcentroids on the schaefer as input to extract the centroid
coordinates of the schaefer parcels? (My final goal is to calculate the
distances between each of the centroids)

Thank you! Best wishes for the new year.
Julie

On Sun, 2 Jan 2022 at 16:11, Douglas N. Greve 
wrote:

> Try mri_segcentroids. Run it with --help to get docs
>
> On 12/20/2021 3:34 AM, Julie Ottoy wrote:
>
> External Email - Use Caution
> Hi Doug,
>
> Just checking in with the question below. Does Freesurfer have such an
> option?
>
> Thanks,
> Julie
>
> On Tue, 14 Dec 2021 at 18:38, Julie Ottoy 
> wrote:
>
>> Hello FreeSurfer team,
>>
>> I was wondering if there is a way to calculate a distance matrix between
>> atlas-based regions (e.g. between their centers of mass) in volumetric
>> space (MNI152) space?
>>
>> Thank you for the information!
>> Best regards
>> Julie
>>
>
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[Freesurfer] mri_info orientation string ???

[Xiaojiang Yang]

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Dear Freesurfer Experts,

I have a question regarding the orientation string gotten from mri_info.
When I apply mri_info command to a DIOM series I generated
programmatically, I get the "???" result, and hence primary slice direction
is also unknown:

..
Orientation   : ???
Primary Slice Direction: unknown
..

I already had the " Image Position Patient" and "Image Orientation
Patient" written in the DICOM header. Don't know what other important info
is missing.

Could you tell me what key information is used in DICOM header to
determine this orientation when using mri_info?

Thanks!
John
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Re: [Freesurfer] Ventricle segmentation issue - ventricle mislabeled as white matter

[Kang, Jee Won]

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Hello all,

Apologies for the delay in response! 

For the applications in my group's work, we are looking at ventricular volume, 
as well as white matter volume. To that degree, we are interested in whether 
there are any processing steps earlier in the pipeline that we can implement 
just to minimize the manual editing required - just anecdotally, there have 
been cases where lateral ventricle volume increases over 5% after making manual 
edits, and I was unable to identify if there was a common element to the 
subjects with ventricle problems.

Thank you for your work on this! We really appreciate it.

Thank you,
Jee Won



Message: 2
Date: Tue, 4 Jan 2022 22:11:53 +
From: "Nadar, Priyanka (NIH/CC/OCRTME) [F]" 
Subject: Re: [Freesurfer] [EXTERNAL] Re: Ventricle segmentation issue
- ventricle mislabeled as white matter
To: Freesurfer support list 
Message-ID:



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

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I am not part of Jee Won's team: just generally interested. For my work, I am 
looking at ventricular volume and so it would be good to not have to manually 
correct a large number of my scans.

From: Douglas N. Greve 
Sent: Tuesday, January 4, 2022 1:19 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: [EXTERNAL] Re: [Freesurfer] Ventricle segmentation issue - ventricle 
mislabeled as white matter


CAUTION: This email originated from outside of the organization. Do not click 
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Hi Jee Won and Priyanka, there are several things going on here. First, the 
original aseg (aseg.presurf.mgz) has these areas labeled as nothing (0); they 
show up as WM in aseg.mgz and aparc+aseg.mgz. Obviously, it would be good to 
have them properly labeled, but is this critical to your applications? Eg, are 
you looking at ventricular volume?

On 12/21/2021 9:19 AM, Kang, Jee Won wrote:

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Hello all,


I found a very common error in our data while I was correcting recons. The 
lateral ventricles (usually the horns) are being misclassified as white matter 
in aseg.mgz. This happened in around 1/3 of our 108 subjects.


We were able to fix this issue by manually filling in the ventricles in 
aseg.presurf.mgz and re-running Freesurfer with the command autorecon2-noaseg 
-autorecon3, but this is obviously quite a labor-intensive fix for a 
substantial portion of our data. This was also the only way to fix the 
segmentation - filling in the mislabeled areas as 255 in the wm.mgz did not fix 
the problem. I'm not sure why Freesurfer is having issues here, as the areas it 
is mislabeling have very distinct intensity boundaries - the T1 intensity is 
usually between 20 and 45 in the areas that are being mislabeled. I've attached 
a screenshot of a subject's aseg.presurf.mgz who had this ventricle 
segmentation issue, and you can see that a large portion of the right ventricle 
has just not been segmented properly; the intensity of the area in the 
aseg.presurf.mgz and wm.mgz volumes is just 0, and it was 41 (R cerebral white 
matter) in aseg.mgz.


Would you be able to provide some insight into why this might have been 
happening, and what we could do in the future to prevent such extensive manual 
editing in the future? I can also say that this data was processed with a T2 
image as well, and supplying that flag didn't help with the segmentation issue.


Thank you,

Jee Won



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