Re: [Freesurfer] mri_cvs_register using fsaverage

[Lilla Zollei]

Hi Noam,

Can you can use the --mni flag?

"Use the CVS atlas in MNI152 space as a target for registration (as 
opposed to the default CVS template)"


Lilla

On Wed, 1 Aug 2018, Peled, Noam wrote:



I need to transfer one of our patient's electrodes locations (depth electrodes, 
they aren't located on the cortical surface) to MNI305 space.
For that, I'm trying to use mri_cvs_register to register the patient to 
fsaverage. I'm using to the following command:


mri_cvs_register --mov subjid --template fsaverage --outdir output_name 
--nocleanup

And I'm getting the following error:
fsaverage : at least one mean and/or Gaussian curvature file is missing (.H, .K)

Indeed, fsaverage doesn't have the rh/lh.inflated.K/H files.
Any ideas?

Thanks,
Noam








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Re: [Freesurfer] Sag T1 3D post-contrast

[Bruce Fischl]

Hi John

I've pushed a lot of post-contrast scans through and haven't had many 
issues. Have you checked the talairach? If you upload the dataset we will 
take a look

cheers
Bruce


On Wed, 1 Aug 2018, John Absher wrote:



External Email - Use Caution

Has anyone else tried to do recon-all with Sagittal 3D T1 post-contrast volumes?

 

We’re getting hung in recon-all at the Talairach registration step, and I 
wonder if the vascular
enhancement at the pial surface might be throwing the algorithm off. About half 
the scans will run
smoothly, but the other half --- not so much.

 

Another question is whether a linear registration (e.g., using David 
MacDonald’s register program)
would allow us to do the recon-all … -notal option?

 

Thanks,

John

 

John R. Absher, MD, FAAN

GHS Neurosciences

jabs...@ghs.org

864-350-6655 (mobile)

 


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Re: [Freesurfer] Surface editing: recon-all exited with errors

[Rockers, Elijah D.]

External Email - Use Caution

Hi Andrew,


Looks like that cleared the errors.


Thank you both,

-Eli


From: Hoopes, Andrew 
Sent: Tuesday, July 31, 2018 3:09 PM
To: Freesurfer support list
Cc: Rockers, Elijah D.
Subject: Re: [Freesurfer] Surface editing: recon-all exited with errors

Hi Eli, the -make all flag contains a bug in the 6.0 release. This can be fixed 
if you download this script - 
https://urldefense.proofpoint.com/v2/url?u=ftp-3A__surfer.nmr.mgh.harvard.edu_pub_dist_freesurfer_dev-5Fbinaries_centos6-5Fx86-5F64_recon-2Dall.makefile&d=DwIGaQ&c=QmPtDiFixEjkMvDKaP3E2Vb9C2z4M0PdarxyAHQ2iDQ&r=xbyrBxm81l6mG_XEX66jgCNTXfK3eVo30T9sVQVTz1Q&m=NdmdZKAguIV8eXD4q6jw5Ub-tV1C8ZYAQonZaC5Moj4&s=OVTOQexQaYiTh7MsmChOewxSfa3PnCfztVjr2RDlnM8&e=
 - and overwrite the current $FREESURFER_HOME/bin/recon-all.makefile

Let me know if you still have issues

best,
Andrew


On 7/31/18, 3:15 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of 
Bruce Fischl"  wrote:

h, maybe -make all has changed (or my memory of what it does is
incorrect). I'll find someone else here to help you out

cheers
Bruce
On Tue, 31 Jul 2018,
Bruce Fischl wrote:

> did you run
>
> recon-all -s  -make all
>
> ?
>
>
> I don't see it in the log
> On Tue, 31 Jul 2018, Rockers, Elijah D. wrote:
>
>>
>>  External Email - Use Caution
>>
>>  Oh, yep, sorry about that. I copy the list on this e-mail, and attach 
the
>>  log. I think the list
>>  blocks attachments, but if anyone wants to see full log I can send it.
>>
>>
>>  Thanks to all,
>>
>>  -Eli
>>


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Re: [Freesurfer] Mixed Block Event-related Design Optseq Question

[Douglas N. Greve]

sorry, it does not do mixed block event related

On 07/31/2018 10:09 PM, Yu Han wrote:
>
> External Email - Use Caution
>
>
>   Hello experts,
>
>
>   We would like to use the optseq 2 to optimize a mixed block and
>   event-related design. Is it possible to use optseq for a mixed
>   design? We are specifically not sure how to specify block duration.
>   What commands shall I use in order to do that? Thank you in advance!
>
>   Best,
>   Yu
>   /
>   /
>   /Emotion Recognition Task. The emotion recognition and perceptual
>   control conditions developed by Greimel et al. have been adapted to
>   include surprise and embarrassment. The task requires participants
>   to either identify the emotions expressed in visually presented
>   faces (emotion recognition) or judge the gender (perceptual
>   control). The emotion recognition task will consist of interspersed
>   expressions of surprise and embarrassment. There will be four
>   blocks, one self-conscious emotion block (e.g., embarrassment and
>   surprise), one typical emotion block to distinguish brain areas of
>   self-conscious emotion to typical emotion (e.g., happy vs. sad), one
>   control block (ask participants to identify gender), one matching
>   shape block. Six images in each block. /
>
> /There are four blocks of 6 images each. /
>
>
>   /1) Surprise/Embarrassment faces/
>   /2) Happy/Sad faces/
>   /3) Identify gender of faces/
>   /4) Match shapes/
>   /We planned to have the Match shapes blocks to interleave all other
>   blocks./
>   /
>   /
>
> Yu Han
> Ph.D. Student, Prelock Lab
> Neuroscience Graduate Program
> University of Vermont
>
>
>
> ___
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Re: [Freesurfer] Fwd: vertex MNI305 (ruopeng)

[Douglas N. Greve]

Actually, I think this is a better question for Ruopeng (cc'ed)

On 07/31/2018 10:16 AM, Trisanna Sprung-Much wrote:
>
> External Email - Use Caution
>
> Hi there
>
> Still waiting for an answer to this!
>
> Thanks!
> Trisanna
> --
> Ph.D. Candidate
> McGill University
> Integrated Program in Neuroscience
> Psychology
>
>
> -- Forwarded message --
> From: *Trisanna Sprung-Much*  >
> Date: Thu, Jul 26, 2018 at 7:35 PM
> Subject: vertex MNI305
> To: Freesurfer support list  >
>
>
> Hi there
>
> This might be a very silly question but I actually cannot find the 
> answer in the email archive:
>
> Assuming I have loaded a label onto fsaverage in Freeview and want to 
> get the MNI305 coordinate of that labelled vertex, am I simply using 
> the x,y,z in brackets in the panel? I attach a photo of what I mean.
>
> Best wishes
> Trisanna
> --
> Ph.D. Candidate
> McGill University
> Integrated Program in Neuroscience
> Psychology
>
>
>
>
>
> ___
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[Freesurfer] (no subject)

[??????????]

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confirm 185a0e2daad6a81d7f3f1a9403d86009db538c35___
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Re: [Freesurfer] mri_cvs_register using fsaverage

[Peled, Noam]

Thanks Lilla!

Just to be sure, when using the --mni flag, should I remove the  --template 
flag?

Also, is there any way I can calculate the registration directly to MNI305 and 
not MNI152?


Thanks again,

Noam


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Lilla Zollei 

Sent: Wednesday, August 1, 2018 8:35:49 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] mri_cvs_register using fsaverage


Hi Noam,

Can you can use the --mni flag?

"Use the CVS atlas in MNI152 space as a target for registration (as
opposed to the default CVS template)"

Lilla

On Wed, 1 Aug 2018, Peled, Noam wrote:

>
> I need to transfer one of our patient's electrodes locations (depth 
> electrodes, they aren't located on the cortical surface) to MNI305 space.
> For that, I'm trying to use mri_cvs_register to register the patient to 
> fsaverage. I'm using to the following command:
>
>
> mri_cvs_register --mov subjid --template fsaverage --outdir output_name 
> --nocleanup
>
> And I'm getting the following error:
> fsaverage : at least one mean and/or Gaussian curvature file is missing (.H, 
> .K)
>
> Indeed, fsaverage doesn't have the rh/lh.inflated.K/H files.
> Any ideas?
>
> Thanks,
> Noam
>
>
>
>
>
>
>
>
>
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[Freesurfer] (no subject)

[??????????]

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Re: [Freesurfer] mri_cvs_register using fsaverage

[Douglas N. Greve]

FYI, fsaverage is already in MNI305 space

On 08/01/2018 11:14 AM, Peled, Noam wrote:
>
> Thanks Lilla!
>
> Just to be sure, when using the --mni flag, should I remove the  
> --template flag?
>
> Also, is there any way I can calculate the registration directly to 
> MNI305 and not MNI152?
>
>
> Thanks again,
>
> Noam
>
> 
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu 
>  on behalf of Lilla Zollei 
> 
> *Sent:* Wednesday, August 1, 2018 8:35:49 AM
> *To:* Freesurfer support list
> *Subject:* Re: [Freesurfer] mri_cvs_register using fsaverage
>
> Hi Noam,
>
> Can you can use the --mni flag?
>
> "Use the CVS atlas in MNI152 space as a target for registration (as
> opposed to the default CVS template)"
>
> Lilla
>
> On Wed, 1 Aug 2018, Peled, Noam wrote:
>
> >
> > I need to transfer one of our patient's electrodes locations (depth 
> electrodes, they aren't located on the cortical surface) to MNI305 space.
> > For that, I'm trying to use mri_cvs_register to register the patient 
> to fsaverage. I'm using to the following command:
> >
> >
> > mri_cvs_register --mov subjid --template fsaverage --outdir 
> output_name --nocleanup
> >
> > And I'm getting the following error:
> > fsaverage : at least one mean and/or Gaussian curvature file is 
> missing (.H, .K)
> >
> > Indeed, fsaverage doesn't have the rh/lh.inflated.K/H files.
> > Any ideas?
> >
> > Thanks,
> > Noam
> >
> >
> >
> >
> >
> >
> >
> >
> >
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
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[Freesurfer] Influence of control variables

[Kai Ohmstedt]

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Dear Freesurfers,

I am conducting a study on the link of cerebral structural measurements and
psychopathological dimensions.
At first, I investigated the link of structural markers and the respective
dimension while controlling for the patient's age and the other dimensions,
that are investigated in my study.
As I will maybe focus on only one of the dimensions, I ran exactly the same
analysis for this dimension again, while only controlling for age.
Suprisingly, this analysis does not show any significant correlations,
while the analysis which additionally controlled for the other dimensions
showed several clusters of significance in this dimension. I assumed the
analysis with less variables of control would rather find more clusters, as
less variables of control are used. Am I mistaken? Have any of you
encountered this problem before or can explain, why less variables of
control lead to fewer clusters with significant correlations?
Any help is appreciated!


Best regards

Kai Ohmstedt
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[Freesurfer] Thickness measurements.

[Nillo, Ryan Michael R]

External Email - Use Caution

Hello FreeSurfer experts,


I want to use FreeSurfer to generate thickness files using my own surfaces. Is 
there a way to use white and pial surfaces not generated from the 
mris_make_surfaces to create thickness files?


Mahalo,


Ryan M Nillo

Staff Research Associate I

UCSF Department of Radiology and Biomedical Imaging
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Re: [Freesurfer] mri_cvs_register using fsaverage

[Peled, Noam]

Thanks for the clarification, I'm asking that because in the mri_cvs_register 
docs it's written that the --mni flag will "use the CVS atlas in MNI152 space 
as a target for registration".


Thanks again,

Noam


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Douglas N. Greve 

Sent: Wednesday, August 1, 2018 11:19:16 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mri_cvs_register using fsaverage

FYI, fsaverage is already in MNI305 space

On 08/01/2018 11:14 AM, Peled, Noam wrote:
>
> Thanks Lilla!
>
> Just to be sure, when using the --mni flag, should I remove the
> --template flag?
>
> Also, is there any way I can calculate the registration directly to
> MNI305 and not MNI152?
>
>
> Thanks again,
>
> Noam
>
> 
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu
>  on behalf of Lilla Zollei
> 
> *Sent:* Wednesday, August 1, 2018 8:35:49 AM
> *To:* Freesurfer support list
> *Subject:* Re: [Freesurfer] mri_cvs_register using fsaverage
>
> Hi Noam,
>
> Can you can use the --mni flag?
>
> "Use the CVS atlas in MNI152 space as a target for registration (as
> opposed to the default CVS template)"
>
> Lilla
>
> On Wed, 1 Aug 2018, Peled, Noam wrote:
>
> >
> > I need to transfer one of our patient's electrodes locations (depth
> electrodes, they aren't located on the cortical surface) to MNI305 space.
> > For that, I'm trying to use mri_cvs_register to register the patient
> to fsaverage. I'm using to the following command:
> >
> >
> > mri_cvs_register --mov subjid --template fsaverage --outdir
> output_name --nocleanup
> >
> > And I'm getting the following error:
> > fsaverage : at least one mean and/or Gaussian curvature file is
> missing (.H, .K)
> >
> > Indeed, fsaverage doesn't have the rh/lh.inflated.K/H files.
> > Any ideas?
> >
> > Thanks,
> > Noam
> >
> >
> >
> >
> >
> >
> >
> >
> >
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
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Re: [Freesurfer] mri_cvs_register using fsaverage

[Lilla Zollei]

Yes, you can remove the template flag.

And no, not at the moment.


Thanks Lilla!

Just to be sure, when using the --mni flag, should I remove the  --template 
flag?

Also, is there any way I can calculate the registration directly to MNI305 and 
not MNI152?


Thanks again,

Noam

__
From: freesurfer-boun...@nmr.mgh.harvard.edu  
on behalf of Lilla Zollei 
Sent: Wednesday, August 1, 2018 8:35:49 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] mri_cvs_register using fsaverage  

Hi Noam,

Can you can use the --mni flag?

"Use the CVS atlas in MNI152 space as a target for registration (as
opposed to the default CVS template)"

Lilla

On Wed, 1 Aug 2018, Peled, Noam wrote:

>
> I need to transfer one of our patient's electrodes locations (depth 
electrodes, they aren't located on the cortical surface) to MNI305 space.
> For that, I'm trying to use mri_cvs_register to register the patient to 
fsaverage. I'm using to the following command:
>
>
> mri_cvs_register --mov subjid --template fsaverage --outdir output_name 
--nocleanup
>
> And I'm getting the following error:
> fsaverage : at least one mean and/or Gaussian curvature file is missing (.H, 
.K)
>
> Indeed, fsaverage doesn't have the rh/lh.inflated.K/H files.
> Any ideas?
>
> Thanks,
> Noam
>
>
>
>
>
>
>
>
>

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Re: [Freesurfer] Thickness measurements.

[Bruce Fischl]

yes, you can use the binary mris_thickness to compute the thickness

cheers
Bruce
On Wed, 
1 Aug 2018, Nillo, Ryan Michael R wrote:




External Email - Use Caution

Hello FreeSurfer experts,


I want to use FreeSurfer to generate thickness files using my own surfaces. Is 
there a way to use
white and pial surfaces not generated from the mris_make_surfaces to create 
thickness files?


Mahalo,


Ryan M Nillo

Staff Research Associate I

UCSF Department of Radiology and Biomedical Imaging


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[Freesurfer] Problems associated segmentation results of hippocampal subfields

[Dev vasu]

External Email - Use Caution

Dear All,

I have a problem with the Freesurfer hippocampal longitudinal segmentation
results , when i have done segmentation using following algorithm (
https://github.com/CobraLab/antsRegistration-MAGeT) with no
anterior/posterior partitioning ( Head/body/tail ) , on my subject pool the
volumes that i have obtained for each subfield is very different from the
volumes of corresponding subfields that i am getting when i have done
subfield segmentation using freesurfer. I think algorithm does influence
the segmentation procedure, if this is the case then i am getting different
results for histology based segmentation using
https://github.com/CobraLab/antsRegistration-MAGeT and freesurfer.


When i compare the subfield volumes between healthy and disease patients
that i have obtained using first segmentation procedure using ANTS-MAGeT ,
i notice statistical significance   in subfields like CA1,CA2-CA3 but when
i do the same using freesurfer based algorithm i notice no statistical
significance in these subfields.

Do you think the algorithm has any influence on segmentation to such a
level that we get completely different results on two occasions.


Thanks
Vasudev
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[Freesurfer] PhD position avalaible in Torus, France : hisgh resolution Brainstem atlas

[Christophe Destrieux]

External Email - Use Caution

Dear all,

we have an open 3-year position for a PhD student in our lab in Tours, France 
beginning 2018, oct 1st.
This student will work on a brainstem atlas from 11.7T exvivo MRI data. 

Details are included here : 
https://ibrain.univ-tours.fr/actualites/scientifiques/offres-de-recrutement/phd-position-development-of-a-multiscale-mri-atlas-of-the-human-brainstem-638411.kjsp?RH=1381307896713
 


Do not hesitate to distribute 

Christophe Destrieux, 
Unité iBrain UMRS INSERM U1253, Université de Tours 
http://www.u930.tours.inserm.fr/  

Service de Neurochirurgie 
et Laboratoire d'Anatomie - Faculté de Médecine - 10 Bd Tonnellé - 37032 Tours 
- France 
tel (33) 2 47 36 61 36 - fax (33) 2 47 36 62 07 





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