External Email - Use Caution        

Hi Bruce,

Thank you very much for your response. I would like to calculate this distance error for specific regions on the flatmap after the transformation, so I can formulate cuts to minimize it for the region I am interested in. Do you have any suggestions on how I can do it?

From reading your paper : Fischl B, Sereno MI, Dale AM. Cortical surface-based analysis. II: Inflation, flattening, and a surface-based coordinate system. Neuroimage. 1999 Feb;9(2):195-207. doi: 10.1006/nimg.1998.0396. PMID: 9931269, I understand that distances are calculated using the corrected Dijkstra algorithm as an estimator of geodesic distances. 

In your response, you said that the distance error is calculated with:

100 * (mean(abs(distance error)) /  mean(original_distances))

Are the original_distances = the geodesic distances (gd) calculated (using the Dijkstra algorithm) for each vertex  on the inflated surface? 

Is the distance error = (gd on the flatmap) - (gd on the inflated surface)?

Do you know how I can do this in matlab for just one region using the DKTaltas? for example, the superior frontal?

Any help would be greatly appreciated!

Kind regards,
Sarah

On Wed, 9 Nov 2022 at 17:02, <freesurfer-request@nmr.mgh.harvard.edu> wrote:
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Today's Topics:

   1. Calculating Distortion in mris_flatten() (Sarah Lavelle)
   2. Fwd: average lobar cortical thickness (James Brown)
   3. Re: Calculating Distortion in mris_flatten()
      (Fischl, Bruce R.,PHD)
   4. Re: volumes/surfaces FS6.0 vs FS7.2/3.2 (Nolan, Jackson)
   5. Re: [External] Re: Mapping the labels onto the aparc atlas
      (Zeng, Victor (BIDMC - Keshavan - Psychiatry))
   6. Question about a skullstripping error (dimitra kokkinou)
   7. Re: Fwd: Longitudinal FS pipeline consistently interrupts at
      -Sphere for all participants (Huang, Yujing)
   8. cortical thickness in frontal lobe (James Brown)
   9. Re: [External] Re: Mapping the labels onto the aparc atlas
      (Huang, Yujing)
  10. Re: Option -contrasurfreg in FreeSurfer 7.X (Douglas N. Greve)
  11. Re: FreeSurfer Hippocampus Segmentation Question
      (Douglas N. Greve)
  12. Re: Question about freesurfer default settings. (Douglas N. Greve)
  13. Re: Help: Vertex Properties (Douglas N. Greve)
  14. Re: acompcor in fsfast (Douglas N. Greve)
  15. Re: Fwd: average lobar cortical thickness (Douglas N. Greve)
  16. Re: Question about a skullstripping error (Douglas N. Greve)
  17. Re: cortical thickness in frontal lobe (Douglas N. Greve)
  18. Re: Fwd: average lobar cortical thickness
      (Fernanda Hansen P. de Moraes)
  19. Cerebellum segmentation pipeline (AJ)


----------------------------------------------------------------------

Message: 1
Date: Tue, 8 Nov 2022 17:20:22 +0000
From: Sarah Lavelle <lavells1@tcd.ie>
Subject: [Freesurfer] Calculating Distortion in mris_flatten()
To: freesurfer@nmr.mgh.harvard.edu
Message-ID:
        <CABRNrkfJFpcKP0jhBX4Fmv6OKr1KamrNr5Tap_5bM3H5v--eyQ@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"

        External Email - Use Caution       

Hi freesurfers,

Does anyone know how to measure the distortion of your inflated surface ->
flatmap transformation (using mris_flatten)?

When being run, the function outputs "final distance error ...%" in the
terminal. What exactly does this mean? and how is this calculated?

I would like to research optimal cuts for flatmaps, depending on the region
of interest (ROI), so we can minimize the distortion of the ROI itself
on the 2D map. If anyone has any ideas on how this can be done or is
interested in working with me on this, please contact me via <
lavells1@tcd.ie>

Kind regards,
Sarah
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Message: 2
Date: Tue, 8 Nov 2022 12:20:34 -0500
From: James Brown <jb1979000@gmail.com>
Subject: [Freesurfer] Fwd: average lobar cortical thickness
To: freesurfer@nmr.mgh.harvard.edu
Message-ID:
        <CACJ7YcdZ_vfUxUkR8dcN8kp+KYAMwZ-H5EsHkSWC3UtzW5xOWg@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"

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Dear Freesurfer experts,
I would like to know if this procedure is correct.
I have cortical thickness data from aparc+aseg for every ROI in DTK atlas
(i.e. output of recon-all). I need average cortical thickness in frontal,
parietal, temporal, cingulate and occipital lobes. Is it correct to average
thickness measurement of every sub lobe roi (e.g. average thickness in
frontal lobe = average of:

   - Superior Frontal
   - Rostral and Caudal Middle Frontal
   - Pars Opercularis, Pars Triangularis, and Pars Orbitalis
   - Lateral and Medial Orbitofrontal
   - Precentral
   - Paracentral
   - Frontal Pole

and so on for other lobes...

Do we need to correct for the number of vertices in every region when we
measure the lobar average thickness?

Alternatively, do I need to run these commands to generate lobes then
measure thickness in every lobe?

# mri_annotation2label --subject subject --hemi lh --lobesStrict lobes
# mri_annotation2label --subject subject --hemi rh --lobesStrict lobes
# mri_aparc2aseg --s subject --labelwm --hypo-as-wm --rip-unknown \
#   --volmask --o wmparc.lobes.mgz --ctxseg aparc+aseg.mgz \
#   --annot lobes --base-offset 200 [--base-offset must be last arg]


Thank you
James
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Message: 3
Date: Tue, 8 Nov 2022 17:55:30 +0000
From: "Fischl, Bruce R.,PHD" <BFISCHL@mgh.harvard.edu>
Subject: Re: [Freesurfer] Calculating Distortion in mris_flatten()
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
        <DM8PR04MB79769F168821AACCB16C076FEF3F9@DM8PR04MB7976.namprd04.prod.outlook.com>

Content-Type: text/plain; charset="utf-8"

Hi Sarah

It is something like:

100 * (mean(abs(distance error)) /  mean(original_distances))

Cheers
Bruce

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Sarah Lavelle
Sent: Tuesday, November 8, 2022 12:20 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Calculating Distortion in mris_flatten()


        External Email - Use Caution
Hi freesurfers,

Does anyone know how to measure the distortion of your inflated surface -> flatmap transformation (using mris_flatten)?

When being run, the function outputs "final distance error ...%" in the terminal. What exactly does this mean? and how is this calculated?

I would like to research optimal cuts for flatmaps, depending on the region of interest (ROI), so we can minimize the distortion of the ROI itself on the 2D map. If anyone has any ideas on how this can be done or is interested in working with me on this, please contact me via <lavells1@tcd.ie<mailto:lavells1@tcd.ie>>

Kind regards,
Sarah


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Message: 4
Date: Tue, 8 Nov 2022 19:33:59 +0000
From: "Nolan, Jackson" <JNOLAN5@mgh.harvard.edu>
Subject: Re: [Freesurfer] volumes/surfaces FS6.0 vs FS7.2/3.2
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
        <DM8PR04MB8149D7082BE8DF97ACF9898AAB3F9@DM8PR04MB8149.namprd04.prod.outlook.com>

Content-Type: text/plain; charset="utf-8"

Hello Jim,

All subjects should be processed with the same version of freesurfer, especially for longitudinal studies.
Either v6.x or 7.x should work for your purposes.

If you decide to go with v7.x, you can make a copy of the subjects run in v6.0, then run v7.x using the outputs of v6.0, and the new outputs should respect the edits made using v6.0.
??????- Note: Running recon-all on processed subjects will overwrite the outputs, so make a copy of your older data so it is not destroyed.

Best,
Jackson


________________________________
From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Alexopoulos, Dimitrios <dimitriosalexopoulos@wustl.edu>
Sent: Friday, November 4, 2022 5:20 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] volumes/surfaces FS6.0 vs FS7.2/3.2


        External Email - Use Caution

We have processed a large pediatric cohort (9-10 y.o. subjects) acquired with 1 mm isotopic voxels using FS 6.0.



We are now beginning to rescan the same cohort at 15-16 y.o. using the exact same imaging protocol and scanner (3T, Prizma).

If we process with FS 7.2/7.3.2, can we analyze the surface/volume measures/outputs with the earlier FS.6.0. structural outputs?

We?d like to look at volume changes and cortical expansion analysis between the 2 timepoints.



Is this reasonable or should we run the new cohort using 6.0 as well? Or rerun the earlier cohort at 7.2/MailScanner warning: numerical links are often malicious: 7.3.2.

Any suggestions as to the best approach.



Jim





________________________________

The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.
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Message: 5
Date: Tue, 8 Nov 2022 21:04:57 +0000
From: "Zeng, Victor (BIDMC - Keshavan - Psychiatry)"
        <vzeng@bidmc.harvard.edu>
Subject: Re: [Freesurfer] [External] Re: Mapping the labels onto the
        aparc atlas
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Cc: "jsritharan@student.ethz.ch" <jsritharan@student.ethz.ch>
Message-ID:
        <CO6PR06MB720460A06BE7EC68443ED9E8F53F9@CO6PR06MB7204.namprd06.prod.outlook.com>

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

        External Email - Use Caution       

Hi,

I'm assuming the .annot is wrong because it doesn't map the entire gray matter ribbon, whereas when the .annot is mapped unto the gray matter ribbon using mri_aparc2aseg, its grabbing the surround gray matter. I am attaching a picture as illustration. This is the rh FG4 (from the Stanford atlas), in the sagittal view. The yellow is the .label file for the FG4, and when its mapped unto the gray matter, the brown region is mapped as the FG4. Is this the procedure that's suppose to happen?

Victor Zeng
Beth Israel Deaconess Medical Center
Keshavan Lab
--
________________________________
From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Douglas N. Greve <dgreve@mgh.harvard.edu>
Sent: Tuesday, November 8, 2022 9:14 AM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: [External] Re: [Freesurfer] Mapping the labels onto the aparc atlas

I'm not sure what you are saying. Are you saying that the annot/surf looks right but the seg in the volume looks wrong or that they both look wrong?

On 10/31/2022 2:58 PM, Zeng, Victor (BIDMC - Keshavan - Psychiatry) wrote:

        External Email - Use Caution

Hi Freesurfer devs,

We have used mri_aparc2aseg to map the Stanford mpm/vpnl labels unto the gray matter ribbon. We notice that when analyzing the resulting mpm.vpnl+aseg.mgz that the regions/voxels of the mpm.vpnl+aseg.mgz stretch out the corresponding voxels that the labels identify as the mpm/vpnl. Can we reliably use the mpm.vpnl+aseg.mgz, and are the stats created from that file, or from the annot file? We are asking because we are using the mpm.vpnl+aseg.mgz as a mask for blood perfusion measurements.

Thanks,

Victor Zeng
Beth Israel Deaconess Medical Center
Keshavan Lab
--



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Message: 6
Date: Wed, 9 Nov 2022 11:47:14 +0000
From: dimitra kokkinou <dimkokkinou1@hotmail.com>
Subject: [Freesurfer] Question about a skullstripping error
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
        <PAXP193MB1166AFD9E9080C3A9FACA786873E9@PAXP193MB1166.EURP193.PROD.OUTLOOK.COM>

Content-Type: text/plain; charset="iso-8859-1"

        External Email - Use Caution       

Dear freesurfer experts,

I am analysing some MP2RAGE images on freesurfer and found an error I am unable to correct.

After the recon-all finished successfully, I looked at the T1 and brainmask images on freeview and I noticed a skullstripping error on the brainmask volume. On one side of the brain there was also skull (and other non brain parts), and on the other half there was a lot of missing cortex.

I tried to change the watershed threshold but this didn't work, I also tried to put control points but most of them were ignored since they were outside of the estimated pial surface.

What would be the best way to correct this problem?

Regards,

DK

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Message: 7
Date: Wed, 9 Nov 2022 12:42:01 +0000
From: "Huang, Yujing" <YHUANG43@mgh.harvard.edu>
Subject: Re: [Freesurfer] Fwd: Longitudinal FS pipeline consistently
        interrupts at -Sphere for all participants
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>, fsbuild
        <fsbuild@contbay.com>
Message-ID:
        <MN2PR04MB59822D423AE99BD99B5B5F809D3E9@MN2PR04MB5982.namprd04.prod.outlook.com>

Content-Type: text/plain; charset="utf-8"

Hi Julie,

Thank you for using Freesurfer and bought the problem to our attention.

We are looking into the issue.

Best,

Yujing

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Julie Ottoy
Sent: Tuesday, November 8, 2022 9:27 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>; fsbuild <fsbuild@contbay.com>
Subject: [Freesurfer] Fwd: Longitudinal FS pipeline consistently interrupts at -Sphere for all participants


        External Email - Use Caution
Hi FS team,

Just wanted to follow up with my question below. Thanks!
Julie
---------- Forwarded message ---------
From: Julie Ottoy <julie.jj.ottoy@gmail.com<mailto:julie.jj.ottoy@gmail.com>>
Date: Fri, 4 Nov 2022 at 00:11
Subject: Re: [Freesurfer] Longitudinal FS pipeline consistently interrupts at -Sphere for all participants
To: fsbuild <fsbuild@contbay.com<mailto:fsbuild@contbay.com>>

Hi Fsbuild team,

Thank you for your reply. Sorry for the confusion, my system was actually Linux, not Windows. It did not run on top of Windows (sorry again for the confusion).
In any case, I tried both the longitudinal pipeline FS v7.1.1 and v7.2 consistently on Linux. I also used two different machines (our institute server as well as ComputeCanada, hence I do not believe it's a memory issue). Each run got stuck at the -Sphere x.long.x step as indicated in my previous email. Interestingly, I tried today with the longitudinal FS v6.0.0 (kept all the rest the same) and it ran fine! Could there be any bug in the v7 series for longitudinal processing that was not present in the v6 series? I tried on two different types of input T1w data acquired from different centers and they point to the same issue => -Sphere error in x.long.x for v7 , while it runs fine for v6. Please see attached log files and screenshots for both.

I am also thinking if it would be ok to run the longitudinal with v6 since we ran the baseline data with v7.2. Could you please advise on this?

Last, I was wondering if there is a way to receive more detailed log/error files? As indicated from my previous email and screenshots, the code just exited at Sphere but did not indicate why it went wrong there.

Thank you for your help!
Best regards
Julie

On Wed, 2 Nov 2022 at 17:02, fsbuild <fsbuild@contbay.com<mailto:fsbuild@contbay.com>> wrote:
One way we?ve seen recon-all eventually fail running on Linux hosted on Windows is whatever is virtualizing Linux to run on top of the Windows OS - simply runs out of memory at some point in the processing pipeline.  That can result in a message in the recon-all.log like a file was not found, i.e., a computation fails and the results are not saved in a file that later on is expected to be found, opened and read.  I don?t see messages like that in your log.

It might be helpful to know more about how you are running Linux on windows, e.g., if you are using the built-in Windows Subsystem for Linux (WSL) or using a VM running on something like VirtualBox.

You could also send along the output in the linux terminal from:
$ cat /etc/os-release
$ cat $FREESURFER_HOME/build-stamp.txt

- R.


On Nov 2, 2022, at 15:03, Julie Ottoy <julie.jj.ottoy@gmail.com<mailto:julie.jj.ottoy@gmail.com>> wrote:

<recon-all.log>

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Message: 8
Date: Wed, 9 Nov 2022 08:01:13 -0500
From: James Brown <jb1979000@gmail.com>
Subject: [Freesurfer] cortical thickness in frontal lobe
To: freesurfer@nmr.mgh.harvard.edu
Message-ID:
        <CACJ7YccMh8D2AOzZkW2EgZ8aoTD0VuYj0mAuw6hNaBFJsZS2UA@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"

        External Email - Use Caution       

Dear Freesurfer experts,
We are new to Freesurfer. We appreciate your help & apologize if the
question is simple.
We need cortical thickness in lobes instead of parcellates. Is it correct
to take the average of the parcelates from the aparc+aseg.stats file under
subjid/stats folder. For example,
cortical thickness of frontal lobe = sum of frontal parcellates  divided by
number of parcallates .
Do we need to do any correction such as weighing the surface area
measurements ?

Thank you
James
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Message: 9
Date: Wed, 9 Nov 2022 13:18:15 +0000
From: "Huang, Yujing" <YHUANG43@mgh.harvard.edu>
Subject: Re: [Freesurfer] [External] Re: Mapping the labels onto the
        aparc atlas
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Cc: "jsritharan@student.ethz.ch" <jsritharan@student.ethz.ch>
Message-ID:
        <MN2PR04MB598245AB87EA6E1CDAA703C79D3E9@MN2PR04MB5982.namprd04.prod.outlook.com>

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

Hi Victor,

I'm trying to understand what you described,  and re-produce it here. Which .annot are you referring to? Also, can you provide the command sequences that you used to generate mpm.vpnl+aseg.mgz?

Thanks.

Yujing

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Zeng, Victor (BIDMC - Keshavan - Psychiatry)
Sent: Tuesday, November 8, 2022 4:05 PM
To: freesurfer@nmr.mgh.harvard.edu
Cc: jsritharan@student.ethz.ch
Subject: Re: [Freesurfer] [External] Re: Mapping the labels onto the aparc atlas


        External Email - Use Caution

Hi,

I'm assuming the .annot is wrong because it doesn't map the entire gray matter ribbon, whereas when the .annot is mapped unto the gray matter ribbon using mri_aparc2aseg, its grabbing the surround gray matter. I am attaching a picture as illustration. This is the rh FG4 (from the Stanford atlas), in the sagittal view. The yellow is the .label file for the FG4, and when its mapped unto the gray matter, the brown region is mapped as the FG4. Is this the procedure that's suppose to happen?

Victor Zeng
Beth Israel Deaconess Medical Center
Keshavan Lab
--
________________________________
From: freesurfer-bounces@nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu> <freesurfer-bounces@nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu>> on behalf of Douglas N. Greve <dgreve@mgh.harvard.edu<mailto:dgreve@mgh.harvard.edu>>
Sent: Tuesday, November 8, 2022 9:14 AM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> <freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [External] Re: [Freesurfer] Mapping the labels onto the aparc atlas

I'm not sure what you are saying. Are you saying that the annot/surf looks right but the seg in the volume looks wrong or that they both look wrong?
On 10/31/2022 2:58 PM, Zeng, Victor (BIDMC - Keshavan - Psychiatry) wrote:

        External Email - Use Caution
Hi Freesurfer devs,

We have used mri_aparc2aseg to map the Stanford mpm/vpnl labels unto the gray matter ribbon. We notice that when analyzing the resulting mpm.vpnl+aseg.mgz that the regions/voxels of the mpm.vpnl+aseg.mgz stretch out the corresponding voxels that the labels identify as the mpm/vpnl. Can we reliably use the mpm.vpnl+aseg.mgz, and are the stats created from that file, or from the annot file? We are asking because we are using the mpm.vpnl+aseg.mgz as a mask for blood perfusion measurements.

Thanks,

Victor Zeng
Beth Israel Deaconess Medical Center
Keshavan Lab
--



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Message: 10
Date: Wed, 9 Nov 2022 09:11:28 -0500
From: "Douglas N. Greve" <dgreve@mgh.harvard.edu>
Subject: Re: [Freesurfer] Option -contrasurfreg in FreeSurfer 7.X
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <431edf2f-eeed-e815-1a91-f6cce40a113d@mgh.harvard.edu>
Content-Type: text/plain; charset=UTF-8; format=flowed

I think I took it out because it was a bad idea (can't really remember).
If you want to do cross-hemi analysis, better to use the xhemi tool
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On 11/7/2022 8:46 AM, Francois Tadel, Mr [Affiliate] wrote:
>          External Email - Use Caution
>
> Hello,
>
> Does anybody know what happened to the recon-all option -contrasurfreg.
> It is still documented, but recon-all crashes when trying to use it
> ("ERROR: Flag -contrasurfreg unrecognized.")
>
> How can we obtain the files lh.rh.sphere.reg and rh.lh.sphere.reg with
> FreeSurfer 7.X?
>
> Thanks,
> Francois
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
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------------------------------

Message: 11
Date: Wed, 9 Nov 2022 09:12:42 -0500
From: "Douglas N. Greve" <dgreve@mgh.harvard.edu>
Subject: Re: [Freesurfer] FreeSurfer Hippocampus Segmentation Question
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <f39d725e-3133-0ecb-8940-c9595ed06d52@mgh.harvard.edu>
Content-Type: text/plain; charset="utf-8"

are you talking about the whole hippo seg? That will have some WM in it.
You can also try the hippo subfield segmentation which will give you a
more refined segmentation separating GM and WM.

On 11/7/2022 11:16 AM, Jun Yeon Won wrote:
>
> ????????External Email - Use Caution
>
> Dear Freesurfer experts,
>
> I have a question about hippocampal segmentation. For the hippocampal
> mask after completing recon-all, is it purely gray matter or does it
> also include some aspects of white matter and others? Please advise.
>
> Best,
> JW
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
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Message: 12
Date: Wed, 9 Nov 2022 09:13:21 -0500
From: "Douglas N. Greve" <dgreve@mgh.harvard.edu>
Subject: Re: [Freesurfer] Question about freesurfer default settings.
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <97dbcd3a-0144-a57d-1ca5-19c27f710d25@mgh.harvard.edu>
Content-Type: text/plain; charset="utf-8"

FS does not warp any images. No smoothing is ever applied.

On 11/7/2022 3:30 PM, Katrina Simon wrote:
>
> ????????External Email - Use Caution
>
> Hi, I have a dataset i have run with the default settings of
> Freesurfer 6.0. A reviewer for a paper recently raised the question
> "Were T1 images warped with the grey matter preserved? Were volumetric
> images for the amygdala and hippocampus smoothed?"
>
> I have tried to look through the archives and freesurfer papers but
> dont see anything that directly addresses these aspects, and some help
> would?be appreciated.
>
> Thank you!
> Katrina
>
> --
> Katrina Simon
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
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Message: 13
Date: Wed, 9 Nov 2022 09:19:31 -0500
From: "Douglas N. Greve" <dgreve@mgh.harvard.edu>
Subject: Re: [Freesurfer] Help: Vertex Properties
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <7d838d49-f1ef-d3b5-bcd8-15785114f9a9@mgh.harvard.edu>
Content-Type: text/plain; charset="utf-8"

The coords are in the surface structure, which you can get by running
mris_convert lh.white lh.white.asc (asc will be an ascii file)? or by
loading into matlab with read_surf.m
The surface area is computed for white (?h.area) and pial
(?h.pial.area). These can be converted to mgz or nifti (mri_convert
lh.area lh.area.{mgz,nii.gz }) or read into matlab with read_curv.m
The other stuff (angles, edge lengths, dist matrix), you will have to do
yourself but you can get it on a vertex-wise basis with something like
 ?mris_info --vx 1000 $SUBJECTS_DIR/fsm011/surf/lh.white
vertexno 1000
xyz? -12.5783 -89.7512 33.0777? # the coords
nxyz -0.9930? 0.0542? 0.1049????? # the normal at this vertex
vertex_area 0.668113?????????????????? # area
neighbors 6
nbr 0??? 994 0.6636 0.3354? 1524 0.2240
nbr 1??? 669 0.8749 0.9553? 1525 0.3357
nbr 2??? 677 0.8132 0.6240? 1538 0.3472
nbr 3?? 1006 1.0009 1.0769? 2226 0.2301
nbr 4?? 1408 0.9042 0.8405? 2227 0.4085
nbr 5?? 1419 0.9977 1.0954? 2238 0.4587

NbrInfo: nbrno, nbrvno, nbrdist, nbrarea, faceno, facearea

On 11/8/2022 3:43 AM, Sarah Lavelle wrote:
>
> ????????External Email - Use Caution
>
> Hi,
>
> I?m wondering if there?s a way to get the properties of individual
> vertices such as:
>
> 1)Coordinates
> 2)Surface area
> 3)angles
> 4) Side lengths
> 5) distance matrix from other vertices
>
> And can you get these properties for individual surfaces/
> transformations (eg. On the spherical map or flatmap) ?
>
> On the FreeSurfer application or else through matlab?
>
> Any help would be greatly appreciated,
> Thanks,
>
> Sarah
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
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Message: 14
Date: Wed, 9 Nov 2022 09:20:41 -0500
From: "Douglas N. Greve" <dgreve@mgh.harvard.edu>
Subject: Re: [Freesurfer] acompcor in fsfast
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <7ed5966d-6944-4624-2476-2622d8027202@mgh.harvard.edu>
Content-Type: text/plain; charset="utf-8"



On 11/8/2022 11:27 AM, Addison, Reuben wrote:
>
> Just as a quick verification and follow up using
>
>  1. Specifying the number of components eg. if I want 5 -nuisreg the
>     various components I want to regress out ?-comp 6 ? comp 7 comp 8
>     comp 9
>
not sure what you mean here. The format is -nuisreg filename Ncomponents
>
> 1.
>
>
>  2. Also just a follow up, how do I go ahead and run an ICA instead of
>     the regular connectivity analysis
>
I don't have ICA in fsfast
>
> *From: *freesurfer-bounces@nmr.mgh.harvard.edu
> <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Douglas N. Greve
> <dgreve@mgh.harvard.edu>
> *Date: *Tuesday, November 8, 2022 at 9:02 AM
> *To: *freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
> *Subject: *Re: [Freesurfer] acompcor in fsfast
>
> When you run fcseed-sess, specify -pca instead of -mean. When you run
> mkanaysis-sess, specify the number of components you want when specify
> -nuisreg
>
> On 10/26/2022 6:29 PM, Addison, Reuben wrote:
>
>     Hi,
>
>     I am running resting State functional connectivity and I want to
>     run everything in freesurfer and fsfast.
>
>     I wanted to know is it is possible to run
>
>     acompcor in fsfast. If so, how do I go about it.
>
>     Thanks.
>
>     Get Outlook for iOS <MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://aka.ms/o0ukef>
>
>
>
>     _______________________________________________
>
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>
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>
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Message: 15
Date: Wed, 9 Nov 2022 09:34:41 -0500
From: "Douglas N. Greve" <dgreve@mgh.harvard.edu>
Subject: Re: [Freesurfer] Fwd: average lobar cortical thickness
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <38ae763d-c827-1539-a5c8-877463b2ef6c@mgh.harvard.edu>
Content-Type: text/plain; charset="utf-8"

I would weight by the number of vertices in each ROI

On 11/8/2022 12:20 PM, James Brown wrote:
>
> ????????External Email - Use Caution
>
>
> Dear Freesurfer experts,
> I would like to know if this procedure?is correct.
> I have cortical thickness data from aparc+aseg for every ROI in DTK
> atlas (i.e. output of recon-all). I need average cortical thickness in
> frontal, parietal, temporal, cingulate and occipital lobes. Is it
> correct to average thickness measurement?of every sub lobe roi (e.g.
> average thickness in frontal lobe = average of:
>
>   * Superior Frontal
>   * Rostral and Caudal Middle Frontal
>   * Pars Opercularis, Pars Triangularis, and Pars Orbitalis
>   * Lateral and Medial Orbitofrontal
>   * Precentral
>   * Paracentral
>   * Frontal Pole
>
> and so on for other lobes...
>
> Do we need to correct for the number of vertices in every region when
> we measure the lobar average thickness?
>
> Alternatively, do I need to run these commands to generate lobes then
> measure thickness in every lobe?
> # mri_annotation2label --subject subject --hemi lh --lobesStrict lobes
> # mri_annotation2label --subject subject --hemi rh --lobesStrict lobes
> # mri_aparc2aseg --s subject --labelwm --hypo-as-wm --rip-unknown \
> #   --volmask --o wmparc.lobes.mgz --ctxseg aparc+aseg.mgz \
> #   --annot lobes --base-offset 200 [--base-offset must be last arg]
>
> Thank you
> James
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
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Message: 16
Date: Wed, 9 Nov 2022 09:37:46 -0500
From: "Douglas N. Greve" <dgreve@mgh.harvard.edu>
Subject: Re: [Freesurfer] Question about a skullstripping error
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <2e262f3b-cde2-e82c-e202-203b5694c944@mgh.harvard.edu>
Content-Type: text/plain; charset="utf-8"

it would be helpful to see some images. Also send the log file

On 11/9/2022 6:47 AM, dimitra kokkinou wrote:
>
> ????????External Email - Use Caution
>
> Dear freesurfer experts,
>
> I am analysing some MP2RAGE images on freesurfer and found an error I
> am unable to correct.
>
> After the recon-all finished successfully, I looked at the T1 and
> brainmask images on freeview and I noticed a skullstripping error on
> the brainmask volume. On one side of the brain there was also skull
> (and other non brain parts), and on the other half there was a lot of
> missing cortex.
>
> I tried to change the watershed threshold but this didn't work, I also
> tried to put control points but most of them were ignored since they
> were outside of the estimated pial surface.
>
> What would be the best way to correct this problem?
>
> Regards,
>
> DK
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
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Message: 17
Date: Wed, 9 Nov 2022 09:38:39 -0500
From: "Douglas N. Greve" <dgreve@mgh.harvard.edu>
Subject: Re: [Freesurfer] cortical thickness in frontal lobe
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <97bbc89e-8970-a764-75ce-7d1139a49cd3@mgh.harvard.edu>
Content-Type: text/plain; charset="utf-8"

you should weight by the number of vertices in each roi

On 11/9/2022 8:01 AM, James Brown wrote:
>
> ????????External Email - Use Caution
>
> Dear?Freesurfer experts,
> We are new to Freesurfer. We appreciate your help & apologize?if the
> question is simple.
> We need cortical thickness in lobes instead of parcellates. Is it
> correct to take the average of the parcelates from the
> aparc+aseg.stats file under subjid/stats folder.?For example,
> cortical thickness of frontal lobe = sum of frontal parcellates?
> divided?by number of parcallates .
> Do we need to do any correction such as weighing?the surface area
> measurements ?
>
> Thank?you
> James
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
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Message: 18
Date: Wed, 9 Nov 2022 12:12:43 -0300
From: "Fernanda Hansen P. de Moraes" <fernandahmoraes@gmail.com>
Subject: Re: [Freesurfer] Fwd: average lobar cortical thickness
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
        <CAKQPGqEmZH=d=4jBSzq_w02VKZPdgY0rv3qMKca+2K_C585t7g@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"

        External Email - Use Caution       

Dear James and FreeSurfer experts,
for lobes average cortical thickness we use this solution
https://secure-web.cisco.com/12kn5RGwkDP8VJQa9PtCWSWT_3GfJlJYy06k6EpiyBm3DNksk5cBO1m_9Le5zbQFSumsT0NoxwNy2VNIh9LcoRkXkj5UlRW4ZVXK_mdgK-47PUJnpHKrnofShRBd4hn04wUndNIeo9qSFfwRuTCFZskpYzu_dEmSTfNuVH1YD9HszB8ZT58BL0-Oeu3k-_DzqTnsZDIIXHLZvQCrbQ7piw80BQs5FRBpW6WPRUf_ESj7p9BCvwjmzbrdNpfar1S9GUTa01DctAIO9o7810uXB9HXlros3aZXIKNPSevhYnE6HxGRs49xo3zx4Onil9efsTKtHy2JNy2TAmbw8Ze37eg/https%3A%2F%2Fgithub.com%2Fcnnp-lab%2FCorticalFoldingAnalysisTools, hope it helps!

Best,
Fernanda

Fernanda Hansen P. de Moraes
fernandahmoraes@gmail.com
Doutora em Ci?ncias M?dicas |  metaBIO (IF-UFRJ) e Instituto D'Or de
Pesquisa e Ensino

On Wed, Nov 9, 2022 at 11:35 AM Douglas N. Greve <dgreve@mgh.harvard.edu>
wrote:

> I would weight by the number of vertices in each ROI
>
> On 11/8/2022 12:20 PM, James Brown wrote:
>
>         External Email - Use Caution
>
> Dear Freesurfer experts,
> I would like to know if this procedure is correct.
> I have cortical thickness data from aparc+aseg for every ROI in DTK atlas
> (i.e. output of recon-all). I need average cortical thickness in frontal,
> parietal, temporal, cingulate and occipital lobes. Is it correct to average
> thickness measurement of every sub lobe roi (e.g. average thickness in
> frontal lobe = average of:
>
>    - Superior Frontal
>    - Rostral and Caudal Middle Frontal
>    - Pars Opercularis, Pars Triangularis, and Pars Orbitalis
>    - Lateral and Medial Orbitofrontal
>    - Precentral
>    - Paracentral
>    - Frontal Pole
>
> and so on for other lobes...
>
> Do we need to correct for the number of vertices in every region when we
> measure the lobar average thickness?
>
> Alternatively, do I need to run these commands to generate lobes then
> measure thickness in every lobe?
>
> # mri_annotation2label --subject subject --hemi lh --lobesStrict lobes
> # mri_annotation2label --subject subject --hemi rh --lobesStrict lobes
> # mri_aparc2aseg --s subject --labelwm --hypo-as-wm --rip-unknown \
> #   --volmask --o wmparc.lobes.mgz --ctxseg aparc+aseg.mgz \
> #   --annot lobes --base-offset 200 [--base-offset must be last arg]
>
>
> Thank you
> James
>
> _______________________________________________
> Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
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--
Fernanda Hansen P. de Moraes

fernandahmoraes@gmail.com
Doutora em Ci?ncias M?dicas | Instituto D'Or de Pesquisa e Ensino e metaBIO
(IF-UFRJ)
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Message: 19
Date: Wed, 9 Nov 2022 10:39:29 -0600
From: AJ <ajcns1969@gmail.com>
Subject: [Freesurfer] Cerebellum segmentation pipeline
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
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        External Email - Use Caution       

Hi,
Is there a specific pipeline for segmenting the cerebellum, cortical gray
and deep nuclei?  Like the one for hippocampus and thalamus?
Best
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