External Email - Use Caution        

Many thanks for this quick response!
From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of freesurfer-request@nmr.mgh.harvard.edu <freesurfer-request@nmr.mgh.harvard.edu>
Sent: Thursday, July 22, 2021 1:22 AM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: [EXT] Freesurfer Digest, Vol 209, Issue 33
 
External email: Please exercise caution

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Today's Topics:

   1. Re: Developer password (Eli Bulger)
   2. Re: dwi_orig_las issue trac-all -prep (AmirHussein Abdolalizadeh)
   3. DOSS Question (WON JONG CHWA)
   4. Re: dwi_orig_las issue trac-all -prep (Yendiki, Anastasia)
   5. sbTIV versus eTIV (AJ)
   6. Re: sbTIV versus eTIV (Douglas N. Greve)
   7. Re: sbTIV versus eTIV (AJ)
   8. Total WM surface area (Alexopoulos, Dimitrios)
   9. Intensity equalization (AJ)
  10. delineating gyral boundaries in native space (Robin Cash)
  11. Re: dwi_orig_las issue trac-all -prep (AmirHussein Abdolalizadeh)
  12. Control points and white matter segmentation
      (Rosalia Dacosta Aguayo)
  13. Re: dwi_orig_las issue trac-all -prep (Yendiki, Anastasia)
  14. Re: Intensity equalization (Fischl, Bruce)
  15. Re: delineating gyral boundaries in native space (Fischl, Bruce)
  16. Re: Control points and white matter segmentation (Fischl, Bruce)
  17. Re: Control points and white matter segmentation
      (Rosalia Dacosta Aguayo)
  18. shortest distance between two points along the    gray/white
      boundary (Krieger, Donald N.)
  19. Re: Control points and white matter segmentation (Fischl, Bruce)
  20. Re: shortest distance between two points along    the     gray/white
      boundary (Fischl, Bruce)
  21. Re: (no subject) (Stephanie K)
  22. Re: shortest distance between two points  along   the     gray/white
      boundary (Krieger, Donald N.)


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

Message: 1
Date: Tue, 20 Jul 2021 18:06:31 +0000
From: Eli Bulger <esbulger@cmu.edu>
Subject: Re: [Freesurfer] Developer password
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <6451b1940990455c966dacc981f091a9@cmu.edu>
Content-Type: text/plain; charset="windows-1252"

        External Email - Use Caution       

Hello,

I am also in need of the developer password for running freesurfer through VirtualBox. Is it possible to get the info sent to my email?

Thank you,
Eli
________________________________
From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of fsbuild <fsbuild@contbay.com>
Sent: Monday, July 19, 2021 1:26:29 PM
To: freesurfer@nmr.mgh.harvard.edu
Cc: cmielach@mailbox.org
Subject: Re: [Freesurfer] Developer password


        External Email - Use Caution

I?ll send the info to your private email shortly.

- R.

On Jul 19, 2021, at 07:07, Clemens M <cmielach@mailbox.org> wrote:


        External Email - Use Caution

Dear Freesurfer Team,

I am currently setting up freesurfer using the Ubuntu VM but I can't log in because I don't have the developer password. Would it be possible to provide me with the password? Thank you!

Best,
Clemens
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------------------------------

Message: 2
Date: Tue, 20 Jul 2021 22:47:17 +0430
From: AmirHussein Abdolalizadeh <amirhussein.a@gmail.com>
Subject: Re: [Freesurfer] dwi_orig_las issue trac-all -prep
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
        <CAJmCTXN3=8xBQWd+WTo-okG0mNY_5WrAMPVPaGQqzB9RjaBhAg@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"

        External Email - Use Caution       

Hi Anastasia,

I installed the beta version and tried TRACULA on one of my subjects. The
results were satisfying but there were a few issues that I had to address
manually:

   - I did thalamic segmentation using the T2 beside the T1 sequence, thus
   the thalamic segmentation had "*.T2.*" instead of T1 and I had to manually
   rename them.
   - During trac-all -prep there were errors of pathlist and trclist; it
   was looking for them in $FREESURFER_HOME/trclist instead of trclist/hcp. So
   I copied them a directory above (into trclist).
   - trac-all -bedp had an ubuntu-related issue: bedpostx_mgh errored with
   a syntax error, and I had to change the first line of bedpostx_mgh into
   /bin/bash.

I hope they've been addressed in the released 7.2 version.

Bests,
Amir

On Mon, Jul 19, 2021 at 6:06 AM Yendiki, Anastasia <AYENDIKI@mgh.harvard.edu>
wrote:

> Hi Amir - You can check the build stamp in your log file:
>
> build-stamp.txt: freesurfer-linux-ubuntu18_x86_64-*dev-20210207*-440e8c2
>
> You're using a development version of freesurfer that was built on Feb
> 7th, 2021 ("dev-20210207") . This is neither 7.1.1 (which was released on
> July 27th, 2020: MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://protect-au.mimecast.com/s/YTq7CVAGLrsxYgxkpSQhC37?domain=secure-web.cisco.com),
> nor 7.2 (which is about to be released). It's an unstable version somewhere
> in between.
>
> I checked your trac-all output against the trac-all in 7.2, and I don't
> expect that you'll get this error in 7.2. You can try out the 7.2 beta
> here: MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://protect-au.mimecast.com/s/aXFhCWLJMvF5VD5XnSpreEt?domain=secure-web.cisco.com
>
> Let us know how it goes! ?
>
> Anastasia.
>
>
>
> ------------------------------
> *From:* freesurfer-bounces@nmr.mgh.harvard.edu <
> freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of AmirHussein
> Abdolalizadeh <amirhussein.a@gmail.com>
> *Sent:* Sunday, July 18, 2021 2:18 AM
> *To:* freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
> *Subject:* Re: [Freesurfer] dwi_orig_las issue trac-all -prep
>
>
>         External Email - Use Caution
>
> Hi Anastasia and thanks for your reply. Here I have attached trac-all.log.
> I think I installed the official FS 7.1.1 version and not the beta (not
> sure btw). Is there a way to get which one that I am using?
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://protect-au.mimecast.com/s/FQEWCXLKNwFXWOXDLs7EK2r?domain=secure-web.cisco.com
> The information in this e-mail is intended only for the person to whom it
> is addressed. If you believe this e-mail was sent to you in error and the
> e-mail contains patient information, please contact the Mass General
> Brigham Compliance HelpLine at
> MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://protect-au.mimecast.com/s/mayvCYWLOxhLwALpyIjy69G?domain=secure-web.cisco.com . If the e-mail was sent
> to you in error but does not contain patient information, please contact
> the sender and properly dispose of the e-mail.
> 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 this message immediately.  Continuing to send or respond to
> e-mail after receiving this message means you understand and accept this
> risk and wish to continue to communicate over unencrypted e-mail.
>
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------------------------------

Message: 3
Date: Tue, 20 Jul 2021 13:49:27 -0500
From: WON JONG CHWA <williamchwa@ucla.edu>
Subject: [Freesurfer] DOSS Question
To: freesurfer@nmr.mgh.harvard.edu
Message-ID:
        <CACj1kb=+=fxnDDfT6qVrWbHrAPjvudKYdznVkMVLsTpdrd=SoA@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"

        External Email - Use Caution       

Dear FreeSurfer Experts,

I have been having trouble with performing DOSS analyses with mri_glmfit.
One of the groups in my sample is too small to be performed with DODS, but
when I try to call the DOSS option in mri_glmfit, it returns the same
error, saying that DODS is not possible with this sample. I even tried
defining the design matrix manually using --X, but it returns the same
error.

mri_glmfit --glmdir lh.rate.CI.paired-diff.thickness.DOSS --y
mgh/rates/lh.thickness-rate.stack.fwhm10.mgh --fsgd
FSGD/CI_baselines/paired-diff-demean-CI.fsgd doss --surf fsaverage lh --C
Contrasts/BMICorrelationCI_DOSS.mtx
gdfRead(): reading FSGD/CI_baselines/paired-diff-demean-CI.fsgd
INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done.
Continuous Variable Means (all subjects)
0 BMIatBaseline -1.49788e-08 3.57667
1 AgeAtFirstTP -5.62933e-08 3.40434
Class Size and Means of each Continuous Variable
1 MaleNormal 26  -0.5852   0.2393
2 MaleCI  2   0.8115   2.2778
3 FemaleNormal 38   0.2564  -0.2749
4 FemaleCI  6   0.6414  -0.0556
ERROR: Class MaleCI has 2 members. With 2 variables and using DODS, you
need at least 3 members

If anyone has any ideas on how to go about this, that would be greatly
appreciated.

Thank you.
William
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------------------------------

Message: 4
Date: Tue, 20 Jul 2021 19:07:06 +0000
From: "Yendiki, Anastasia" <AYENDIKI@mgh.harvard.edu>
Subject: Re: [Freesurfer] dwi_orig_las issue trac-all -prep
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
        <MN2PR04MB6816DDDEBF097919A60134338AE29@MN2PR04MB6816.namprd04.prod.outlook.com>
       
Content-Type: text/plain; charset="utf-8"

Hi Amir - Glad the results were satisfying! I'm afraid that it's a bit hard to address issues before they are reported ?

About the second issue, was there something in your config file about where to find the training data, or did you just use the default?

Thanks,
Anastasia.

________________________________
From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of AmirHussein Abdolalizadeh <amirhussein.a@gmail.com>
Sent: Tuesday, July 20, 2021 2:17 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] dwi_orig_las issue trac-all -prep


        External Email - Use Caution

Hi Anastasia,

I installed the beta version and tried TRACULA on one of my subjects. The results were satisfying but there were a few issues that I had to address manually:

  *   I did thalamic segmentation using the T2 beside the T1 sequence, thus the thalamic segmentation had "*.T2.*" instead of T1 and I had to manually rename them.
  *   During trac-all -prep there were errors of pathlist and trclist; it was looking for them in $FREESURFER_HOME/trclist instead of trclist/hcp. So I copied them a directory above (into trclist).
  *   trac-all -bedp had an ubuntu-related issue: bedpostx_mgh errored with a syntax error, and I had to change the first line of bedpostx_mgh into /bin/bash.

I hope they've been addressed in the released 7.2 version.

Bests,
Amir

On Mon, Jul 19, 2021 at 6:06 AM Yendiki, Anastasia <AYENDIKI@mgh.harvard.edu<mailto:AYENDIKI@mgh.harvard.edu>> wrote:
Hi Amir - You can check the build stamp in your log file:

build-stamp.txt: freesurfer-linux-ubuntu18_x86_64-dev-20210207-440e8c2

You're using a development version of freesurfer that was built on Feb 7th, 2021 ("dev-20210207") . This is neither 7.1.1 (which was released on July 27th, 2020: MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://protect-au.mimecast.com/s/7NKRC2xZLrcpg8pZDHpZCCS?domain=surfer.nmr.mgh.harvard.edu<https://protect-au.mimecast.com/s/KnFyC3Q8MvCpO2p9rH99SLY?domain=secure-web.cisco.com>), nor 7.2 (which is about to be released). It's an unstable version somewhere in between.

I checked your trac-all output against the trac-all in 7.2, and I don't expect that you'll get this error in 7.2. You can try out the 7.2 beta here: MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://protect-au.mimecast.com/s/w10cC4QZNwCBqlB9wUo_aJe?domain=surfer.nmr.mgh.harvard.edu<https://protect-au.mimecast.com/s/aXFhCWLJMvF5VD5XnSpreEt?domain=secure-web.cisco.com>

Let us know how it goes! ?

Anastasia.



________________________________
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 AmirHussein Abdolalizadeh <amirhussein.a@gmail.com<mailto:amirhussein.a@gmail.com>>
Sent: Sunday, July 18, 2021 2:18 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: Re: [Freesurfer] dwi_orig_las issue trac-all -prep


        External Email - Use Caution

Hi Anastasia and thanks for your reply. Here I have attached trac-all.log. I think I installed the official FS 7.1.1 version and not the beta (not sure btw). Is there a way to get which one that I am using?
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
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The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://protect-au.mimecast.com/s/s1ioC5QZOxCZ26ZpriwibXr?domain=massgeneralbrigham.org<https://protect-au.mimecast.com/s/mayvCYWLOxhLwALpyIjy69G?domain=secure-web.cisco.com> . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
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 this message immediately.  Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
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------------------------------

Message: 5
Date: Tue, 20 Jul 2021 14:24:57 -0500
From: AJ <ajcns1969@gmail.com>
Subject: [Freesurfer] sbTIV versus eTIV
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
        <CAMF0Jn=rqPLELuhW0mx+WrucAAOt7g-2sHRZQGfEiUh1bp0Kug@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"

        External Email - Use Caution       

Hi,
I am looking at interscanner differences between Philip and GE.  I get
significantly less variation between the scanners when looking at sbTIV
(coefficient of variation < 1.5 %)  than  eTIV (12%) within subjects.   Any
thought as to why?  Normalizing ROIs with sbTIV improves these differences
even more.

Thanks for your help.

AJ
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------------------------------

Message: 6
Date: Tue, 20 Jul 2021 15:35:46 -0400
From: "Douglas N. Greve" <dgreve@mgh.harvard.edu>
Subject: Re: [Freesurfer] sbTIV versus eTIV
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <b3eaa953-c32f-69b1-e904-fd3da865c6b2@mgh.harvard.edu>
Content-Type: text/plain; charset="utf-8"

The two methods are totally different. See
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://surfer.nmr.mgh.harvard.edu/fswiki/sbTIV
the sb version actually performs a skull segmentation? and counts voxels
within skull. The eTIV is computed from the talairach registration,
which is going to be inherently more variable (eg, more or less neck
will affect it).

On 7/20/2021 3:24 PM, AJ wrote:
>
> ????????External Email - Use Caution
>
> Hi,
> I am looking at interscanner differences between Philip and GE.? I get
> significantly less variation between the scanners when looking at
> sbTIV (coefficient of variation < 1.5 %)? than? eTIV (12%) within
> subjects.? ?Any thought as to why?? Normalizing ROIs with sbTIV
> improves these differences even more.
>
> Thanks for your?help.
>
> AJ
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://protect-au.mimecast.com/s/7aoiCOMxAkspMvpZBHEAOAK?domain=mail.nmr.mgh.harvard.edu

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

Message: 7
Date: Tue, 20 Jul 2021 14:46:59 -0500
From: AJ <ajcns1969@gmail.com>
Subject: Re: [Freesurfer] sbTIV versus eTIV
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
        <CAMF0JnnXJnK1Up9h2ojRNAjDabTYoJmS21KCY9jweYH7YiMcRQ@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"

        External Email - Use Caution       

Many thanks.
Best


On Tue, Jul 20, 2021, 14:36 Douglas N. Greve <dgreve@mgh.harvard.edu> wrote:

> The two methods are totally different. See
> MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://protect-au.mimecast.com/s/qW8dC0YZJpCGpmGgACVq7Je?domain=secure-web.cisco.com
> the sb version actually performs a skull segmentation  and counts voxels
> within skull. The eTIV is computed from the talairach registration, which
> is going to be inherently more variable (eg, more or less neck will affect
> it).
>
> On 7/20/2021 3:24 PM, AJ wrote:
>
>         External Email - Use Caution
> Hi,
> I am looking at interscanner differences between Philip and GE.  I get
> significantly less variation between the scanners when looking at sbTIV
> (coefficient of variation < 1.5 %)  than  eTIV (12%) within subjects.   Any
> thought as to why?  Normalizing ROIs with sbTIV improves these differences
> even more.
>
> Thanks for your help.
>
> AJ
>
> _______________________________________________
> Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://protect-au.mimecast.com/s/XEpzCgZolKFADGAwzfBwfsy?domain=secure-web.cisco.com
> The information in this e-mail is intended only for the person to whom it
> is addressed. If you believe this e-mail was sent to you in error and the
> e-mail contains patient information, please contact the Mass General
> Brigham Compliance HelpLine at
> MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://protect-au.mimecast.com/s/5ej1CjZroMFnVRnGxfBbQfc?domain=secure-web.cisco.com . If the e-mail was sent
> to you in error but does not contain patient information, please contact
> the sender and properly dispose of the e-mail.
> 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 this message immediately.  Continuing to send or respond to
> e-mail after receiving this message means you understand and accept this
> risk and wish to continue to communicate over unencrypted e-mail.
>
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------------------------------

Message: 8
Date: Tue, 20 Jul 2021 20:16:05 +0000
From: "Alexopoulos, Dimitrios" <dimitriosalexopoulos@wustl.edu>
Subject: [Freesurfer] Total WM surface area
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
        <CH2PR02MB6215EBA8F4CE38D70F87BEFCD6E29@CH2PR02MB6215.namprd02.prod.outlook.com>
       
Content-Type: text/plain; charset="windows-1252"

        External Email - Use Caution       

Hi,

Are the total lh/rh cortical surface areas in stats/aparc.stats = parcel1 surface area + parcel2 surface area??

Get Outlook for Android<https://secure-web.cisco.com/1r8EgoSfTlXwlAPQCeMBRYJ0_aOaAble6354Xo7obkuwMZIUCW7FD9nDWvuGW0goRdLbGEvsn1w_Mv9raIy9xrKEdAYiu53vMsBXBT9szBBOP31IJvV-tfg6usq4SHkx4xO--kn7xjYiZgMlz1zfDHjXbf1eex8W3G5XJN4wJFSzEqhIZRVgw1hPhaB5ZiZU5iKZQavqo9YDzWfjrEPrmaBUKPmwF8X7wbcS6nTx2N4SuYAAKZI0kjoLdP4rj6s8kqShdI3tmUrYjirb-FnNo3Q/https%3A%2F%2Faka.ms%2FAAb9ysg>

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Message: 9
Date: Wed, 21 Jul 2021 00:27:23 -0500
From: AJ <ajcns1969@gmail.com>
Subject: [Freesurfer] Intensity equalization
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
        <CAMF0JnmmDqB=UGtFuTji4s5vO3nOZKBAWrfNf+o=2FUV_+BGWQ@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"

        External Email - Use Caution       

Hi,
I have 2 MRIs on different scanners. The tissue contrasts are slightly off
and there is slight differences in the volumes of ROIs. Is there a way to
make both MRIs have the same intensity? I.e., Im2's intensity follows Im1's
intensity?
Many thanks
AJ
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------------------------------

Message: 10
Date: Wed, 21 Jul 2021 05:34:41 +0000
From: Robin Cash <robin.cash@unimelb.edu.au>
Subject: [Freesurfer] delineating gyral boundaries in native space
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Cc: Andrew Zalesky <andrewzalesky@gmail.com>
Message-ID:
        <ME2PR01MB3841F2D61A56BD79C6278AA4A1E39@ME2PR01MB3841.ausprd01.prod.outlook.com>
       
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Hi,
Is there a tool within freesurfer that can be used to delineate gyral boundaries (delineate sulci) from an individual's T1 scan in native space?
To be clear, the purpose wouldn't be to broadly identify or parcellate different gyri, but to delineate the boundary between gyri and sulci.
Many thanks,
Robin




Dr. Robin Cash (PhD) | ARC Senior Research Fellow

Department of Biomedical Engineering,

UNIVERSITY OF MELBOURNE

Melbourne Neuropsychiatry Centre,
Level 3,

Alan Gilbert Building,

161 Barry St,

Carlton VIC 3053 Australia


Twitter<https://secure-web.cisco.com/1acjuoQqXB1dkDPlCJpMqGSMi53R45KVmVJko7Ik-Kfmqdei2_TeX-UQX0bSJPNnsZU1t8imxMKzRQzG-j14T-ZQAwFQyD9rQ76B6maeiNcTvKj24mm6yjPklLfoTUpQR8422RC0pC3U-fBgCx6RAFLoGjJRbKKfTQzqWqGfo35yVGvIk6R7pSZyhNRDVKBnXd-OrgZFwgKZK4oGw9760p1sZonwomML2TswzWN36Nkdn8YbnLubqJxDXpwKEADp6vLq5uz2mpkGmPvuessRwsQ/https%3A%2F%2Ftwitter.com%2Fcashmachine15>  |  Google Scholar<https://secure-web.cisco.com/1Z4EkX_ch_GUS5nKc90QaGpU6mdLSm8Xs315eYJQOYKtpdpHaAoUsvaPR5I__5SvRzlHsLAOWKFZBGHM_FVKbkF5c3wgLpiEbNgz3BXElGmaf0op_-WMjomz6oQjXa_geERMj01Xv3wayLEbcU5bS7_mf6wXRt5wLvTGeqDMN4Kto_PkpNt-iUeCO0Z3fWFEQ1Z8Zyc69YpspLU5F9qc4bVjN77izyIUT_ogR3PW4ihg70J3n4MtzvcPzB1rYESRQmxHHj27yDXEuou6TiV54Xg/https%3A%2F%2Fscholar.google.com.au%2Fcitations%3Fuser%3DfykZRhYAAAAJ%26hl%3Den%26oi%3Dao>
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Message: 11
Date: Wed, 21 Jul 2021 11:24:15 +0430
From: AmirHussein Abdolalizadeh <amirhussein.a@gmail.com>
Subject: Re: [Freesurfer] dwi_orig_las issue trac-all -prep
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
        <CAJmCTXMFwDasYe9PAxMDiaZv9Y=jms4i7Ap75UnMYVdFerBO8Q@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"

        External Email - Use Caution       

I used the default settings which is
$FREESURFER_HOME/trctrain/trainlist.txt. I couldn't find a place to type in
the pathlist.txt so I manually copied all the 42 paths into the config. I
have also attached the config file.

Bests,
Amir

On Tue, Jul 20, 2021 at 11:37 PM Yendiki, Anastasia <
AYENDIKI@mgh.harvard.edu> wrote:

> Hi Amir - Glad the results were satisfying! I'm afraid that it's a bit
> hard to address issues before they are reported ?
>
> About the second issue, was there something in your config file about
> where to find the training data, or did you just use the default?
>
> Thanks,
> Anastasia.
>
> ------------------------------
> *From:* freesurfer-bounces@nmr.mgh.harvard.edu <
> freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of AmirHussein
> Abdolalizadeh <amirhussein.a@gmail.com>
> *Sent:* Tuesday, July 20, 2021 2:17 PM
> *To:* Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
> *Subject:* Re: [Freesurfer] dwi_orig_las issue trac-all -prep
>
>
>         External Email - Use Caution
>
> Hi Anastasia,
>
> I installed the beta version and tried TRACULA on one of my subjects. The
> results were satisfying but there were a few issues that I had to address
> manually:
>
>    - I did thalamic segmentation using the T2 beside the T1 sequence,
>    thus the thalamic segmentation had "*.T2.*" instead of T1 and I had to
>    manually rename them.
>    - During trac-all -prep there were errors of pathlist and trclist; it
>    was looking for them in $FREESURFER_HOME/trclist instead of trclist/hcp. So
>    I copied them a directory above (into trclist).
>    - trac-all -bedp had an ubuntu-related issue: bedpostx_mgh errored
>    with a syntax error, and I had to change the first line of bedpostx_mgh
>    into /bin/bash.
>
> I hope they've been addressed in the released 7.2 version.
>
> Bests,
> Amir
>
> On Mon, Jul 19, 2021 at 6:06 AM Yendiki, Anastasia <
> AYENDIKI@mgh.harvard.edu> wrote:
>
> Hi Amir - You can check the build stamp in your log file:
>
> build-stamp.txt: freesurfer-linux-ubuntu18_x86_64-*dev-20210207*-440e8c2
>
> You're using a development version of freesurfer that was built on Feb
> 7th, 2021 ("dev-20210207") . This is neither 7.1.1 (which was released on
> July 27th, 2020: *MailScanner has detected a possible fraud attempt from
> "secure-web.cisco.com" claiming to be*
> MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://protect-au.mimecast.com/s/wfiuCr8Dz5s8W28nBcoy7Ui?domain=secure-web.cisco.com
> <https://secure-web.cisco.com/1WvPRjsqUvLcDnvLYoFDVPqDm8_TjDHwRNJm4IIMIdyA6Ty_EUKNSEo66F7YNmVoxfH3sqArHg8B3QopYClSCDPJY_SC3ETIn5vrDXB4g7hKfjMCzhwv4cvm88aLcn-F91rylg6yIYiAawFXpcVkdnepCh7uXkCPA8MaJq6RqxaKteOg4eOUu_v_yqp56LW_O7SSCuTr6z1DFF004lyJUyty_IVdQ4Vf08nwb_dJEQZIdtspfefXe7B2sexiEl5F46G0E217c5in2LAPRoURWIw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FReleaseNotes>),
> nor 7.2 (which is about to be released). It's an unstable version somewhere
> in between.
>
> I checked your trac-all output against the trac-all in 7.2, and I don't
> expect that you'll get this error in 7.2. You can try out the 7.2 beta
> here: *MailScanner has detected a possible fraud attempt from
> "secure-web.cisco.com" claiming to be*
> MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://protect-au.mimecast.com/s/UslnCvl0E5u7RA7LkiOMF_y?domain=secure-web.cisco.com
> <https://secure-web.cisco.com/1cj1SgkkGGbnVwrDeUlw1jR7O0jCdIDXqhTwWUb6tGXTsvGfOA-6Nc5QTGa0iS7G8_W9HhNNlgd0vhd2sQwQDGuH23ThOReTds7XOiYNJTSxHaPow0HJzA2b2cc-I5-F2U2-C24PwPHgPMdpc8TaBEyC9kEwLrSEbg7nW1Xpx3XyqZwB_YJUKtHWPMqdxqYcKUqMpUB60tiEbELoQCU_YqYQ6Kq6m3Flzk-n-UjCwL4IBkk-MyU4HBGDPaqPGlmGehx6OB0z9cdF0vi8JgFuY4w/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2F7.2.0-beta%2F>
>
> Let us know how it goes! ?
>
> Anastasia.
>
>
>
> ------------------------------
> *From:* freesurfer-bounces@nmr.mgh.harvard.edu <
> freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of AmirHussein
> Abdolalizadeh <amirhussein.a@gmail.com>
> *Sent:* Sunday, July 18, 2021 2:18 AM
> *To:* freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
> *Subject:* Re: [Freesurfer] dwi_orig_las issue trac-all -prep
>
>
>         External Email - Use Caution
>
> Hi Anastasia and thanks for your reply. Here I have attached trac-all.log.
> I think I installed the official FS 7.1.1 version and not the beta (not
> sure btw). Is there a way to get which one that I am using?
> _______________________________________________
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> Brigham Compliance HelpLine at *MailScanner has detected a possible fraud
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> . If the e-mail was sent to you in error but does not contain patient
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> 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 this message immediately.  Continuing to send or respond to
> e-mail after receiving this message means you understand and accept this
> risk and wish to continue to communicate over unencrypted e-mail.
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://protect-au.mimecast.com/s/SKdJCwVLG5hG2yGVwCO5V7M?domain=secure-web.cisco.com
> The information in this e-mail is intended only for the person to whom it
> is addressed. If you believe this e-mail was sent to you in error and the
> e-mail contains patient information, please contact the Mass General
> Brigham Compliance HelpLine at
> MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://protect-au.mimecast.com/s/KKuqCxnMJ5s1zx1RWU18Di-?domain=secure-web.cisco.com . If the e-mail was sent
> to you in error but does not contain patient information, please contact
> the sender and properly dispose of the e-mail.
> 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 this message immediately.  Continuing to send or respond to
> e-mail after receiving this message means you understand and accept this
> risk and wish to continue to communicate over unencrypted e-mail.
>
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------------------------------

Message: 12
Date: Wed, 21 Jul 2021 11:09:37 +0200
From: Rosalia Dacosta Aguayo <rdacostaa@gmail.com>
Subject: [Freesurfer] Control points and white matter segmentation
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
        <CAPBdvhh1KdHauUz-jq9EdwvXUDmG7HDpSNE+=-R0wvGDrPRP7Q@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"

        External Email - Use Caution       

Dear Freesurfer team,

Sorry for this basic question.

I wonder if once I have edited the white matter (topological defects), I
can run control points without deleting what I have done to white matter
segmentation.

Kind regards,
Rosie
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------------------------------

Message: 13
Date: Wed, 21 Jul 2021 13:17:08 +0000
From: "Yendiki, Anastasia" <AYENDIKI@mgh.harvard.edu>
Subject: Re: [Freesurfer] dwi_orig_las issue trac-all -prep
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
        <MN2PR04MB6816EA54E11021CC6187A6098AE39@MN2PR04MB6816.namprd04.prod.outlook.com>
       
Content-Type: text/plain; charset="utf-8"

Hi Amir - I should make it clearer in the documentation that, unless you have a specific need to change one of the configuration variables, you should just leave it out of your configuration file entirely. This is the best way to make sure that the defaults are being used. Only have in your config file the variables that you specifically need to change for your study.

The error is actually not in trac-all but in the example config file, in the sense that $FREESURFER_HOME/trctrain/trainlist.txt is not actually the default. The default is $FREESURFER_HOME/trctrain/hcp/trainlist.txt. If you set your trainfile to that or, even better, leave that variable out of your config file entirely, trac-all should run fine. Let me know how that goes.

I'll fix the example file and make the documentation clearer on this point.

Thanks for bringing this to our attention,
Anastasia.




________________________________
From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of AmirHussein Abdolalizadeh <amirhussein.a@gmail.com>
Sent: Wednesday, July 21, 2021 2:54 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] dwi_orig_las issue trac-all -prep


        External Email - Use Caution

I used the default settings which is $FREESURFER_HOME/trctrain/trainlist.txt. I couldn't find a place to type in the pathlist.txt so I manually copied all the 42 paths into the config. I have also attached the config file.

Bests,
Amir

On Tue, Jul 20, 2021 at 11:37 PM Yendiki, Anastasia <AYENDIKI@mgh.harvard.edu<mailto:AYENDIKI@mgh.harvard.edu>> wrote:
Hi Amir - Glad the results were satisfying! I'm afraid that it's a bit hard to address issues before they are reported ?

About the second issue, was there something in your config file about where to find the training data, or did you just use the default?

Thanks,
Anastasia.

________________________________
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 AmirHussein Abdolalizadeh <amirhussein.a@gmail.com<mailto:amirhussein.a@gmail.com>>
Sent: Tuesday, July 20, 2021 2:17 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] dwi_orig_las issue trac-all -prep


        External Email - Use Caution

Hi Anastasia,

I installed the beta version and tried TRACULA on one of my subjects. The results were satisfying but there were a few issues that I had to address manually:

  *   I did thalamic segmentation using the T2 beside the T1 sequence, thus the thalamic segmentation had "*.T2.*" instead of T1 and I had to manually rename them.
  *   During trac-all -prep there were errors of pathlist and trclist; it was looking for them in $FREESURFER_HOME/trclist instead of trclist/hcp. So I copied them a directory above (into trclist).
  *   trac-all -bedp had an ubuntu-related issue: bedpostx_mgh errored with a syntax error, and I had to change the first line of bedpostx_mgh into /bin/bash.

I hope they've been addressed in the released 7.2 version.

Bests,
Amir

On Mon, Jul 19, 2021 at 6:06 AM Yendiki, Anastasia <AYENDIKI@mgh.harvard.edu<mailto:AYENDIKI@mgh.harvard.edu>> wrote:
Hi Amir - You can check the build stamp in your log file:

build-stamp.txt: freesurfer-linux-ubuntu18_x86_64-dev-20210207-440e8c2

You're using a development version of freesurfer that was built on Feb 7th, 2021 ("dev-20210207") . This is neither 7.1.1 (which was released on July 27th, 2020: MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://protect-au.mimecast.com/s/7NKRC2xZLrcpg8pZDHpZCCS?domain=surfer.nmr.mgh.harvard.edu<https://protect-au.mimecast.com/s/KnFyC3Q8MvCpO2p9rH99SLY?domain=secure-web.cisco.com>), nor 7.2 (which is about to be released). It's an unstable version somewhere in between.

I checked your trac-all output against the trac-all in 7.2, and I don't expect that you'll get this error in 7.2. You can try out the 7.2 beta here: MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://protect-au.mimecast.com/s/w10cC4QZNwCBqlB9wUo_aJe?domain=surfer.nmr.mgh.harvard.edu/<https://protect-au.mimecast.com/s/aXFhCWLJMvF5VD5XnSpreEt?domain=secure-web.cisco.com>

Let us know how it goes! ?

Anastasia.



________________________________
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 AmirHussein Abdolalizadeh <amirhussein.a@gmail.com<mailto:amirhussein.a@gmail.com>>
Sent: Sunday, July 18, 2021 2:18 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: Re: [Freesurfer] dwi_orig_las issue trac-all -prep


        External Email - Use Caution

Hi Anastasia and thanks for your reply. Here I have attached trac-all.log. I think I installed the official FS 7.1.1 version and not the beta (not sure btw). Is there a way to get which one that I am using?
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
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The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://protect-au.mimecast.com/s/s1ioC5QZOxCZ26ZpriwibXr?domain=massgeneralbrigham.org<https://protect-au.mimecast.com/s/mayvCYWLOxhLwALpyIjy69G?domain=secure-web.cisco.com> . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
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Message: 14
Date: Wed, 21 Jul 2021 14:39:11 +0000
From: "Fischl, Bruce" <BFISCHL@mgh.harvard.edu>
Subject: Re: [Freesurfer] Intensity equalization
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
        <BL0PR04MB6609140BD84E516C157B71DFEFE39@BL0PR04MB6609.namprd04.prod.outlook.com>
       
Content-Type: text/plain; charset="utf-8"

Hi AJ

No, not easily. Maybe you can tell us your overall goal to see if we can help?

Cheers
Bruce

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of AJ
Sent: Wednesday, July 21, 2021 1:27 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Intensity equalization


        External Email - Use Caution
Hi,
I have 2 MRIs on different scanners. The tissue contrasts are slightly off and there is slight differences in the volumes of ROIs. Is there a way to make both MRIs have the same intensity? I.e., Im2's intensity follows Im1's intensity?
Many thanks
AJ
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Message: 15
Date: Wed, 21 Jul 2021 14:42:02 +0000
From: "Fischl, Bruce" <BFISCHL@mgh.harvard.edu>
Subject: Re: [Freesurfer] delineating gyral boundaries in native space
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Cc: Andrew Zalesky <andrewzalesky@gmail.com>
Message-ID:
        <BL0PR04MB6609782D58072F50E712ABF5EFE39@BL0PR04MB6609.namprd04.prod.outlook.com>
       
Content-Type: text/plain; charset="utf-8"

Hi Robin

If you run-recon-all you will get a map that we call ?sulc? for each subject. When we generated our original manual parcellations we used it to guide where to place the boundary between a sulcus and a gyrus. Essentially we used the zero-crossing of sulc. Load it on an white surface and see if that works for you.

Cheers
Bruce

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Robin Cash
Sent: Wednesday, July 21, 2021 1:35 AM
To: freesurfer@nmr.mgh.harvard.edu
Cc: Andrew Zalesky <andrewzalesky@gmail.com>
Subject: [Freesurfer] delineating gyral boundaries in native space


        External Email - Use Caution
Hi,
Is there a tool within freesurfer that can be used to delineate gyral boundaries (delineate sulci) from an individual's T1 scan in native space?
To be clear, the purpose wouldn't be to broadly identify or parcellate different gyri, but to delineate the boundary between gyri and sulci.
Many thanks,
Robin




Dr. Robin Cash (PhD) | ARC Senior Research Fellow

Department of Biomedical Engineering,

UNIVERSITY OF MELBOURNE
Melbourne Neuropsychiatry Centre,
Level 3,

Alan Gilbert Building,

161 Barry St,

Carlton VIC 3053 Australia


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Message: 16
Date: Wed, 21 Jul 2021 14:43:48 +0000
From: "Fischl, Bruce" <BFISCHL@mgh.harvard.edu>
Subject: Re: [Freesurfer] Control points and white matter segmentation
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
        <BL0PR04MB6609B5F4E4F831E1A70EAE79EFE39@BL0PR04MB6609.namprd04.prod.outlook.com>
       
Content-Type: text/plain; charset="utf-8"

Hi Rosie

Recon-all won?t delete edits unless you explicitly tell it to. That said, control points my affect the region you are working on (and possibly correct some defects!)

Cheers
Bruce

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Rosalia Dacosta Aguayo
Sent: Wednesday, July 21, 2021 5:10 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Control points and white matter segmentation


        External Email - Use Caution
Dear Freesurfer team,

Sorry for this basic question.

I wonder if once I have edited the white matter (topological defects), I can run control points without deleting what I have done to white matter segmentation.

Kind regards,
Rosie


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Message: 17
Date: Wed, 21 Jul 2021 16:49:06 +0200
From: Rosalia Dacosta Aguayo <rdacostaa@gmail.com>
Subject: Re: [Freesurfer] Control points and white matter segmentation
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
        <CAPBdvhiX5cfGFCfCYXU4HmBE77F6GZ_bLSerRWw+m4e9Q9GDLw@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"

        External Email - Use Caution       

Hi Bruce,

Thank you for answering my question.

But the order matter, right? That is, first do control points and once
corrected, then do wm_segmentation edits, right?

Sorry for insisting, but this is very important to me.

Kind regards,
Rosie




On Wed, Jul 21, 2021 at 4:44 PM Fischl, Bruce <BFISCHL@mgh.harvard.edu>
wrote:

> Hi Rosie
>
>
>
> Recon-all won?t delete edits unless you explicitly tell it to. That said,
> control points my affect the region you are working on (and possibly
> correct some defects!)
>
>
>
> Cheers
>
> Bruce
>
>
>
> *From:* freesurfer-bounces@nmr.mgh.harvard.edu <
> freesurfer-bounces@nmr.mgh.harvard.edu> *On Behalf Of *Rosalia Dacosta
> Aguayo
> *Sent:* Wednesday, July 21, 2021 5:10 AM
> *To:* Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
> *Subject:* [Freesurfer] Control points and white matter segmentation
>
>
>
> *        External Email - Use Caution        *
>
> Dear Freesurfer team,
>
>
>
> Sorry for this basic question.
>
>
>
> I wonder if once I have edited the white matter (topological defects), I
> can run control points without deleting what I have done to white matter
> segmentation.
>
>
>
> Kind regards,
>
> Rosie
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://protect-au.mimecast.com/s/oiVQCJypvAfqVKqAjflw2gR?domain=secure-web.cisco.com
> The information in this e-mail is intended only for the person to whom it
> is addressed. If you believe this e-mail was sent to you in error and the
> e-mail contains patient information, please contact the Mass General
> Brigham Compliance HelpLine at
> MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://protect-au.mimecast.com/s/PPO-CK1qwBS2642MRuBGncQ?domain=secure-web.cisco.com . If the e-mail was sent
> to you in error but does not contain patient information, please contact
> the sender and properly dispose of the e-mail.
> 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 this message immediately.  Continuing to send or respond to
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> risk and wish to continue to communicate over unencrypted e-mail.
>
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Message: 18
Date: Wed, 21 Jul 2021 14:52:39 +0000
From: "Krieger, Donald N." <kriegerd@upmc.edu>
Subject: [Freesurfer] shortest distance between two points along the
        gray/white boundary
To: "'freesurfer@nmr.mgh.harvard.edu'"
        <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
        <DM6PR08MB517956D37113BCC3546BAA58AAE39@DM6PR08MB5179.namprd08.prod.outlook.com>
       
Content-Type: text/plain; charset="us-ascii"

        External Email - Use Caution       

Dear experts,

I would like to compute the shortest distance along the gray/white boundary between two points on the boundary, i.e. between points with "white" parcellation regions. The distance need not be guaranteed to be minimized and the path need not be unique. Can you suggest an approach using the freesurfer tools?

Thanks - Don

Department of Neurological Surgery
University of Pittsburgh

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Message: 19
Date: Wed, 21 Jul 2021 15:06:42 +0000
From: "Fischl, Bruce" <BFISCHL@mgh.harvard.edu>
Subject: Re: [Freesurfer] Control points and white matter segmentation
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
        <BL0PR04MB66091583C57718307B37B91EEFE39@BL0PR04MB6609.namprd04.prod.outlook.com>
       
Content-Type: text/plain; charset="utf-8"

Hi Rosie

The order in recon-all is fixed. In general control points can change a region of an image, while the wm segs are pointwise, so I guess it makes sense to do the cps first, particularly since they are a lot easier and may fix some of the seg errors

Cheers
Bruce

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Rosalia Dacosta Aguayo
Sent: Wednesday, July 21, 2021 10:49 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Control points and white matter segmentation


        External Email - Use Caution
Hi Bruce,

Thank you for answering my question.

But the order matter, right? That is, first do control points and once corrected, then do wm_segmentation edits, right?

Sorry for insisting, but this is very important to me.

Kind regards,
Rosie




On Wed, Jul 21, 2021 at 4:44 PM Fischl, Bruce <BFISCHL@mgh.harvard.edu<mailto:BFISCHL@mgh.harvard.edu>> wrote:
Hi Rosie

Recon-all won?t delete edits unless you explicitly tell it to. That said, control points my affect the region you are working on (and possibly correct some defects!)

Cheers
Bruce

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 Rosalia Dacosta Aguayo
Sent: Wednesday, July 21, 2021 5:10 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] Control points and white matter segmentation


        External Email - Use Caution
Dear Freesurfer team,

Sorry for this basic question.

I wonder if once I have edited the white matter (topological defects), I can run control points without deleting what I have done to white matter segmentation.

Kind regards,
Rosie


_______________________________________________
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Message: 20
Date: Wed, 21 Jul 2021 15:08:18 +0000
From: "Fischl, Bruce" <BFISCHL@mgh.harvard.edu>
Subject: Re: [Freesurfer] shortest distance between two points along
        the     gray/white boundary
To: "'freesurfer@nmr.mgh.harvard.edu'"
        <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
        <BL0PR04MB660982DF4C96B298742A5C11EFE39@BL0PR04MB6609.namprd04.prod.outlook.com>
       
Content-Type: text/plain; charset="us-ascii"

Hi Don

By far the easiest way to do this is to find the locations of the points on the sphere then compute the length of the great circle arc connecting them, then correct by the ratio of the sqrt of the areas of the two surfaces.

Alternatively I think Rudolph may have had some tools for computing actual geodesics (the procedure about will give you like a 10% error)

Cheers
Bruce

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Krieger, Donald N.
Sent: Wednesday, July 21, 2021 10:53 AM
To: 'freesurfer@nmr.mgh.harvard.edu' <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] shortest distance between two points along the gray/white boundary


        External Email - Use Caution
Dear experts,

I would like to compute the shortest distance along the gray/white boundary between two points on the boundary, i.e. between points with "white" parcellation regions. The distance need not be guaranteed to be minimized and the path need not be unique. Can you suggest an approach using the freesurfer tools?

Thanks - Don

Department of Neurological Surgery
University of Pittsburgh

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

Message: 21
Date: Wed, 21 Jul 2021 16:19:46 +0100
From: Stephanie K <rklinden@gmail.com>
Subject: Re: [Freesurfer] (no subject)
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
        <CABwOaTX7Oy-R-MbEbN=a0v0TwZnyBycbSPxRTFDNxor1GOXiag@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"

        External Email - Use Caution       

Hello,

Can you please clarify the following:

Do we use subcortical QC rating for all subcortical measures such as
accumbens as well measures such as total white matter volume. We do not use
it for estimated total intracranial volume as this is accurately measured?

Do we use cortical QC rating for all regional cortical measures but not the
global measures (e.g. mean thickness/total surface area) as these are
accurately parcellated?

Sorry for my very basic questions. I am using already processed data and
only using the statistics for brain MRI data

Thanks,
Stephanie
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Message: 22
Date: Wed, 21 Jul 2021 15:22:35 +0000
From: "Krieger, Donald N." <kriegerd@upmc.edu>
Subject: Re: [Freesurfer] shortest distance between two points  along
        the     gray/white boundary
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
        <DM6PR08MB5179B7486FACB7096E66E33EAAE39@DM6PR08MB5179.namprd08.prod.outlook.com>
       
Content-Type: text/plain; charset="us-ascii"

        External Email - Use Caution       

Thanks, Bruce, and thanks for getting back so quickly.

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Fischl, Bruce
Sent: Wednesday, July 21, 2021 11:08 AM
To: 'freesurfer@nmr.mgh.harvard.edu' <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] shortest distance between two points along the gray/white boundary

Hi Don

By far the easiest way to do this is to find the locations of the points on the sphere then compute the length of the great circle arc connecting them, then correct by the ratio of the sqrt of the areas of the two surfaces.

Alternatively I think Rudolph may have had some tools for computing actual geodesics (the procedure about will give you like a 10% error)

Cheers
Bruce

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 Krieger, Donald N.
Sent: Wednesday, July 21, 2021 10:53 AM
To: 'freesurfer@nmr.mgh.harvard.edu' <freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] shortest distance between two points along the gray/white boundary


        External Email - Use Caution
Dear experts,

I would like to compute the shortest distance along the gray/white boundary between two points on the boundary, i.e. between points with "white" parcellation regions. The distance need not be guaranteed to be minimized and the path need not be unique. Can you suggest an approach using the freesurfer tools?

Thanks - Don

Department of Neurological Surgery
University of Pittsburgh

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End of Freesurfer Digest, Vol 209, Issue 33
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