[Freesurfer] T2 flair as additional scan in hippocampal subfields segmentation

[Rovai Antonin]

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Hello

I’d like to know if there is any advantage in having a T2 FLAIR as additional 
scan (in addition to our 1mm isotropic T1 scans) when using the hippocampal 
subfield segmentation tool. We do not have T2 nor PD available.

Thanks for you help

Antonin Rovai

Hôpital Erasme - ULB
Cliniques universitaires de Bruxelles
Route de Lennik 808 - B - 1070 Bruxelles
S www.erasme.ulb.ac.be

Disclaimer : http://www.erasme.ulb.ac.be/email-disclaimer

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[Freesurfer] Reconall with no-MPRAGE T1w image?

[Rovai Antonin]

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Hello,

From the ReconAllTable 
(https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllTableStableV6.0) I see that 
the mri_normalize step (producing the T1.mgz file) has the -mprage option.

I have two questions:
1. What is this option doing exactly? There is no description in the 
mri_normalize man page 
(https://surfer.nmr.mgh.harvard.edu/fswiki/mri_normalize); similarly, the CLI 
help doesn’t mention this option.
2. How do I change this when launching a ReconAll without re-writing a custom 
pipeline? (For context our T1 is not MPRAGE and we had some segmentation issues 
so this is an attempt to debug this).

Thanks for you help

AR

[Hôpital Erasme]

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Re: [Freesurfer] -conform option in mri_convert produces crazy artefacts

[Rovai Antonin]

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Hey

So opening only the conformed image in freeview, mricro and fsleyes constantly 
gives me crazy results. Also, the wm segmentation is completely wrong so I 
really think there something wrong in the file….

Best

Antonin

Hôpital Erasme - ULB
Cliniques universitaires de Bruxelles
Route de Lennik 808 - B - 1070 Bruxelles
S www.erasme.ulb.ac.be

Disclaimer : http://www.erasme.ulb.ac.be/email-disclaimer

> On 3 Sep 2019, at 15:55, Bruce Fischl  wrote:
>
> Hi Antonin
>
> hmmm. Can you try *only* loading the conformed image and seeing how it looks? 
> freeview will use one of the images as the basis for it's display 
> coordinates, which can cause apparent slicing artifacts that are only display 
> issues for other volumes.
>
> cheers
> Bruce
>
> On Tue, 3 Sep 2019, Rovai Antonin wrote:
>
>> External Email - Use Caution
>> Hello again
>> I have the following issue when running mri_convert. When using the option
>> -conform option (as in the reconall pipeline), the sag slices seems to be
>> shifted at some point (see attached pictures). What is happening?
>> By the way the option description is not super clear, could you please give
>> some extra details?
>> Best
>> Antonin
>> [IMAGE][IMAGE]
>> Hôpital Erasme
>> Lien vers Disclaimer
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Re: [Freesurfer] Reconall with no-MPRAGE T1w image?

[Rovai Antonin]

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Hi Bruce,

Thanks for your response. From what I read on the wiki 
(https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllTableStableV6.0) the switch 
in on by default since freesurfer6.0 (but that doesn’t seem to be the case in 
5.3).
At any rate we use the BRAVO sequence (on a GE MRI) and it also has an 
inversion pulse (also CNR isn’t as good as in a MPRAGE).

Best

Antonin

On 3 Sep 2019, at 15:44, Bruce Fischl 
mailto:fis...@nmr.mgh.harvard.edu>> wrote:

Hi AR

1. mprage in general has higher CNR and lower SNR than non inversion-prepared 
T1w sequences like FLASH. THe -mprage switch takes advantage of this to loosen 
the intensity gradient threshold in the region filling of the wm.

2. If you just leave out the -mprage switch it will revert to the default 
behavior

cheers
Bruce



On Tue, 3 Sep 2019, Rovai Antonin wrote:

External Email - Use Caution
Hello,
From the ReconAllTable
(https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllTableStableV6.0) I see
that the mri_normalize step (producing the T1.mgz file) has the -mprage
option.
I have two questions:
1. What is this option doing exactly? There is no description in the
mri_normalize man page
(https://surfer.nmr.mgh.harvard.edu/fswiki/mri_normalize); similarly, the CLI
help doesn’t mention this option.
2. How do I change this when launching a ReconAll without re-writing a custom
pipeline? (For context our T1 is not MPRAGE and we had some segmentation
issues so this is an attempt to debug this).
Thanks for you help
AR
Hôpital Erasme
Lien vers Disclaimer

[Hôpital Erasme]

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Re: [Freesurfer] Reconall with no-MPRAGE T1w image?

[Rovai Antonin]

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(Continued)

Of course I meant using the recon-all command!

On 3 Sep 2019, at 15:48, Rovai Antonin 
mailto:antonin.ro...@erasme.ulb.ac.be>> wrote:


External Email - Use Caution

Hi Bruce,

Thanks for your response. From what I read on the wiki 
(https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllTableStableV6.0) the switch 
in on by default since freesurfer6.0 (but that doesn’t seem to be the case in 
5.3).
At any rate we use the BRAVO sequence (on a GE MRI) and it also has an 
inversion pulse (also CNR isn’t as good as in a MPRAGE).

Best

Antonin

On 3 Sep 2019, at 15:44, Bruce Fischl 
mailto:fis...@nmr.mgh.harvard.edu>> wrote:

Hi AR

1. mprage in general has higher CNR and lower SNR than non inversion-prepared 
T1w sequences like FLASH. THe -mprage switch takes advantage of this to loosen 
the intensity gradient threshold in the region filling of the wm.

2. If you just leave out the -mprage switch it will revert to the default 
behavior

cheers
Bruce



On Tue, 3 Sep 2019, Rovai Antonin wrote:

External Email - Use Caution
Hello,
From the ReconAllTable
(https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllTableStableV6.0) I see
that the mri_normalize step (producing the T1.mgz file) has the -mprage
option.
I have two questions:
1. What is this option doing exactly? There is no description in the
mri_normalize man page
(https://surfer.nmr.mgh.harvard.edu/fswiki/mri_normalize); similarly, the CLI
help doesn’t mention this option.
2. How do I change this when launching a ReconAll without re-writing a custom
pipeline? (For context our T1 is not MPRAGE and we had some segmentation
issues so this is an attempt to debug this).
Thanks for you help
AR
Hôpital Erasme
Lien vers Disclaimer


Lien vers Disclaimer<http://www.erasme.ulb.ac.be/email-disclaimer>

[Hôpital Erasme]

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Re: [Freesurfer] Additional scans in hippocampal subfields segmentation

[Rovai Antonin]

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I’m resending this request as I really would like to know what you think :-)

Best

Antonin

Hôpital Erasme - ULB
Cliniques universitaires de Bruxelles
Route de Lennik 808 - B - 1070 Bruxelles
S www.erasme.ulb.ac.be

Disclaimer : http://www.erasme.ulb.ac.be/email-disclaimer

> On 30 Aug 2019, at 11:00, Rovai Antonin  
> wrote:
>
> Hello
>
> I’d like to know if there is any advantage in having a T2 FLAIR as additional 
> scan (in addition to our 1mm isotropic T1 scans) when using the hippocampal 
> subfield segmentation tool. We do not have T2 nor PD available.
>
> Thanks for you help
>
> Antonin Rovai


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Re: [Freesurfer] -conform option in mri_convert produces crazy artefacts

[Rovai Antonin]

External Email - Use Caution

Hello

I think there is a problem with the dicom files. I could not see it on the 
images before mri_convert -conform but there’s definitely something weird in 
there. I suspect it comes from some software that misexported the data.
Running reconall on properly imported dicom data show not problem at all…

Never mind then!

Best

Antonin

Hôpital Erasme - ULB
Cliniques universitaires de Bruxelles
Route de Lennik 808 - B - 1070 Bruxelles
S www.erasme.ulb.ac.be

Disclaimer : http://www.erasme.ulb.ac.be/email-disclaimer

> On 3 Sep 2019, at 16:57, Bruce Fischl  wrote:
>
> hmmm. Can you tar and gzip the whole subject dir and upload it to our ftp 
> site?
> On Tue, 3 Sep 2019, Rovai Antonin wrote:
>
>>   External Email - Use Caution
>>
>> Hey
>>
>> So opening only the conformed image in freeview, mricro and fsleyes 
>> constantly gives me crazy results. Also, the wm segmentation is completely 
>> wrong so I really think there something wrong in the file….
>>
>> Best
>>
>> Antonin
>>
>> Hôpital Erasme - ULB
>> Cliniques universitaires de Bruxelles
>> Route de Lennik 808 - B - 1070 Bruxelles
>> S www.erasme.ulb.ac.be
>>
>> Disclaimer : http://www.erasme.ulb.ac.be/email-disclaimer
>>
>>> On 3 Sep 2019, at 15:55, Bruce Fischl  wrote:
>>>
>>> Hi Antonin
>>>
>>> hmmm. Can you try *only* loading the conformed image and seeing how it 
>>> looks? freeview will use one of the images as the basis for it's display 
>>> coordinates, which can cause apparent slicing artifacts that are only 
>>> display issues for other volumes.
>>>
>>> cheers
>>> Bruce
>>>
>>> On Tue, 3 Sep 2019, Rovai Antonin wrote:
>>>
>>>>External Email - Use Caution
>>>> Hello again
>>>> I have the following issue when running mri_convert. When using the option
>>>> -conform option (as in the reconall pipeline), the sag slices seems to be
>>>> shifted at some point (see attached pictures). What is happening?
>>>> By the way the option description is not super clear, could you please give
>>>> some extra details?
>>>> Best
>>>> Antonin
>>>> [IMAGE][IMAGE]
>>>> Hôpital Erasme
>>>> Lien vers Disclaimer
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>>
>>
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>>
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Re: [Freesurfer] Additional scans in hippocampal subfields segmentation

[Rovai Antonin]

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Hi Bruce,

What are the relevant parameters you need? It’s a pretty standard T2FLAIR with 
spacing 0.7mm x 1mm x 1mm with inversion time 2247ms, TR of 8502ms and TE of 
137ms.

Thanks for you help

Antonin

Hôpital Erasme - ULB
Cliniques universitaires de Bruxelles
Route de Lennik 808 - B - 1070 Bruxelles
S www.erasme.ulb.ac.be

Disclaimer : http://www.erasme.ulb.ac.be/email-disclaimer

> On 5 Sep 2019, at 15:53, Bruce Fischl  wrote:
>
> Hi Antonin
>
> can you give us the details of your T2-FLAIR? Certainly it helps us generate 
> more accurate pial surfaces by avoiding dura. For the subfields I defer to 
> Eugenio
>
> cheers
> Bruce
> On Thu, 5 Sep 2019, Rovai Antonin wrote:
>
>>   External Email - Use Caution
>>
>> I’m resending this request as I really would like to know what you think :-)
>>
>> Best
>>
>> Antonin
>>
>> Hôpital Erasme - ULB
>> Cliniques universitaires de Bruxelles
>> Route de Lennik 808 - B - 1070 Bruxelles
>> S www.erasme.ulb.ac.be
>>
>> Disclaimer : http://www.erasme.ulb.ac.be/email-disclaimer
>>
>>> On 30 Aug 2019, at 11:00, Rovai Antonin  
>>> wrote:
>>>
>>> Hello
>>>
>>> I’d like to know if there is any advantage in having a T2 FLAIR as 
>>> additional scan (in addition to our 1mm isotropic T1 scans) when using the 
>>> hippocampal subfield segmentation tool. We do not have T2 nor PD available.
>>>
>>> Thanks for you help
>>>
>>> Antonin Rovai
>>
>>
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[Freesurfer] remark regarding tcsh with bad locale

[Rovai Antonin]

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Hi,

this is not really a question but rather a comment that, hopefully,
will help those running into the issue I ran into today.

I was using mri_glm-sim with --mczsim 2 option, and got an error saying
that "2,0 must be 1.3, 2.0 ...".
The issue is that printf (used in the mri_glm-sim script) refers to the
LC_NUMERIC locale which, in my unfortunate case, has instructed printf
%2.1f to replace the dot by a comma.

You can check this by typing locale in a terminal.
If, like me, you live in an undercivilized part of the world, then you
may update your locale using e.g.

sudo update-locale LC_NUMERIC=en_US.UTF-8

Log in and out and you'll be back on the right side of the force.

It would be great if a future release of FS could include a locale
check :-)

Hope this help someone, someday.

Best

AR

Hôpital Erasme - ULB
Cliniques universitaires de Bruxelles
Route de Lennik 808 - B - 1070 Bruxelles
S www.erasme.ulb.ac.be

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[Freesurfer] asegstats2table error with options --etiv and --no-vol-extras

[Rovai Antonin]

External Email - Use Caution

Hello,

when using asegstats2table with the two flags --etiv and --no-vol-
extras, I get the following error:

ERROR: --etiv, cannot find EstimatedTotalIntraCranialVol in list

It seems computing the ratio of volumes to etiv needs etiv to be
included in the list (which by the way is not very useful because it is
100% by definition), but is there a way to get the ratios without
including all the "extra" volumes?

For instance using

asegstats2table --tablefile "output.txt" --no-vol-extras --etiv --segno
225

I would expect to get the volume of CC_Anterior in % of etiv.

Thanks for your help

Antonin

Hôpital Erasme - ULB
Cliniques universitaires de Bruxelles
Route de Lennik 808 - B - 1070 Bruxelles
S www.erasme.ulb.ac.be

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Re: [Freesurfer] freeview Core Dumped Error after upgrade in ubuntu

[Rovai Antonin]

External Email - Use Caution

Hi there!

thanks for the answer and your searches.

Actually I solved my issue, basically the last upgrade created a
circular depency issue in my nvidia driver packages, causing issues
with graphical applications. I think this, in the end, is unrelated to
the kernel upgrade.

Thanks again for your time!

Best

Antonin


Hôpital Erasme - ULB
Cliniques universitaires de Bruxelles
Route de Lennik 808 - B - 1070 Bruxelles
S www.erasme.ulb.ac.be

Disclaimer : http://www.erasme.ulb.ac.be/email-disclaimer
On Mon, 2020-10-26 at 19:50 +0100, fsbuild wrote:
> Hello Antonin,
>
> I’ve found a few posts that seem to indicate you can upgrade as well
> as downgrade the kernel (and its dependent packages) by editing the
> /etc/apt/sources.list to point to the Ubuntu distribution you want
> (and then running update, upgrade, dist-upgrade commands).   Not sure
> what the previous Ubuntu distribution name was for you, but this
> post, https://sypalo.com/how-to-upgrade-ubuntu, lists the
> distributions as,
>
> 18.04 - bionic
> 18.10 - cosmic
> 19.04 - disco
> 19.10 - eoan
> 20.04 - focal
> 20.10 - groovy
>
> While that post gives the example of *upgrading*, this post gives the
> example of *downgrading*,
> https://linuxconfig.org/how-to-downgrade-ubuntu-linux-system-to-its-previous-version
> , but I think they are essentially doing the same thing, i.e. it’s a
> function of the distribution name listed in /etc/apt/sources.list.
>
> Note that even if you are downgrading the kernel, as far as the apt
> package manager is concerned you still have to run the various
> “upgrade” commands to change the distribution to a different one even
> if it is older.
>
> - R.
>
>
> > On Oct 26, 2020, at 11:00, Rovai Antonin <
> > antonin.ro...@erasme.ulb.ac.be> wrote:
> >
> >External Email - Use Caution
> >
> > Dear experts,
> >
> > I use to have a perfectly working freesurfer installation on my
> > Ubuntu
> > 18.04 LTS machine, until that doomsday where I installed updates as
> > recommended by ubuntu itself.
> >
> > Now, each time I run freeview, I get the following error:
> >
> > Aborted (core dumped)
> >
> > I reinstalled freesurfer from scratch, fixing nothing.
> >
> > I think Ubuntu did a kernel upgrade; now I have a uname -r output =
> > 5.4.0-52-generic
> > I think it used to be 49 instead of 52 before the upgrade, but I am
> > not
> > sure.
> >
> > Do you know of any patch fixing this, by any chance?
> >
> > Thanks for your lights
> >
> > Antonin Rovai
> >
> > Hôpital Erasme - ULB
> > Cliniques universitaires de Bruxelles
> > Route de Lennik 808 - B - 1070 Bruxelles
> > S www.erasme.ulb.ac.be
> >
> > Disclaimer : http://www.erasme.ulb.ac.be/email-disclaimer
> >
> > ___
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> > Freesurfer@nmr.mgh.harvard.edu
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>
>

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[Freesurfer] freeview Core Dumped Error after upgrade in ubuntu

[Rovai Antonin]

External Email - Use Caution

Dear experts,

I use to have a perfectly working freesurfer installation on my Ubuntu
18.04 LTS machine, until that doomsday where I installed updates as
recommended by ubuntu itself.

Now, each time I run freeview, I get the following error:

Aborted (core dumped)

I reinstalled freesurfer from scratch, fixing nothing.

I think Ubuntu did a kernel upgrade; now I have a uname -r output =
5.4.0-52-generic
I think it used to be 49 instead of 52 before the upgrade, but I am not
sure.

Do you know of any patch fixing this, by any chance?

Thanks for your lights

Antonin Rovai

Hôpital Erasme - ULB
Cliniques universitaires de Bruxelles
Route de Lennik 808 - B - 1070 Bruxelles
S www.erasme.ulb.ac.be

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Re: [Freesurfer] aparcstats2table error

[Rovai Antonin]

External Email - Use Caution

Hi Devika,
I ran into the same issue and in case you don’t want to change your PATH (like 
me), another option is to edit aparcstats2table script and simply replace the 
shebang from “#!/usr/bin/env python” to e.g. “#!/usr/bin/env python2” (please 
make sure “which python2” returns something in a terminal).
Cheers
Antonin

On 19 Jan 2020, at 20:35, Hoopes, Andrew 
mailto:ahoo...@mgh.harvard.edu>> wrote:

Hi Devika, the python scripts (like aparcstats2table) in 6.0 unfortunately must 
be run with python2. Your error implies that the python in your PATH points to 
python3. You should make sure python points to a python2 version before running 
freesurfer. Sorry for the inconvenience.
Andrew


From: 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Devika K mailto:devikakutt...@gmail.com>>
Reply-To: FS Help 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Sunday, January 19, 2020 at 9:09 AM
To: FS Help 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] aparcstats2table error


External Email - Use Caution

I tried doing cortical parcellation using Destrieux atlas.  I ran the 
aparcstats2table command from the SUBJECTS_DIR directory containing all of the 
output from recon-all.
But I got an error, PFA. Do I need to run any other commands before running 
aparcstats2table command, I would be grateful if anyone could  help me to 
resolve this issue.

Many thanks in advance.
[Image removed by sender.]
Regards
Devika K
Research Scholar, Dept of EEE
e: k_dev...@cb.students.amrita.edu
Amrita Vishwa Vidyapeetham
Coimbatore, India


[Hôpital Erasme]

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[Freesurfer] color and sign of sig.mgh data

[Rovai Antonin]

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Hello,

I am creating sig.mgh overlays in a group analysis. On this map, I can
see some blue and red vertices, corresponding to negative and positive
values (respectively) on the map.

On the other hand, I read in the documentation that sig.mgh is a map
created by computing -log(p) (base 10, whatever).

That cannot be true, since 00.

After some exploration I came up with the following guess: sig.mgh is
actually -sign(z)*log(p). (That is of course very useful to quickly
interpret the maps.)

Question 1: is this guess correct?
Question 2: where is the piece of documentation I missed where this is
explained? (I am asking this because I feel like I am missing a lot on
the details on the machinery behind FS commands...)

Cheers
Antonin

Hôpital Erasme - ULB
Cliniques universitaires de Bruxelles
Route de Lennik 808 - B - 1070 Bruxelles
S 
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