Re: [Freesurfer] T2 weighted images as input for recon-all command

[Iglesias Gonzalez, Eugenio]

External Email - Use Caution

Hola Miguel Ángel,
First, you need to run the T1 through recon-all normally, as you have already 
done. Next, you run the subfield module with the highres T2 as input - no 
recon-all on the T2 required, as it's used in a different way.
Cheers
Eugenio

Sent from my phone, please excuse brevity and typos


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Miguel Ángel Rivas 
Fernández 
Sent: Thursday, May 3, 2018 11:08:17 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] T2 weighted images as input for recon-all command


External Email - Use Caution

Hi Freesurfer developers,

I have executed the recon-all command using the T1 images but I would be 
interested in doing a reconstruction of the hippocampal subregions using for 
that purpose a higher resolution images (eg T2 or FLAIR) as input. I read here 
https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfields that is possible 
make hippocampal segmentation using the T2 images, but if T2 images cannot be 
used as input to execute the recon-all in consecuence I can´t do the 
segmentation of hippocampal subfields or on the contrary the recon-all and the 
hippocampal subfields segmentation are two operations that can be executed 
independently ?


I hope to have explained myself correctly

Thanks in advance.

Cheers


2018-05-03 18:28 GMT+02:00 Douglas N. Greve 
mailto:dgr...@mgh.harvard.edu>>:
No, not currently


On 05/03/2018 11:26 AM, M Janani wrote:
>
> Hi Team,
>
>I have one doubt. Can I input T2 weighted images for
> recon-all command?
>
> Regards,
>
> Janani
>
> ::DISCLAIMER::
> --
> The contents of this e-mail and any attachment(s) are confidential and
> intended for the named recipient(s) only. E-mail transmission is not
> guaranteed to be secure or error-free as information could be
> intercepted, corrupted, lost, destroyed, arrive late or incomplete, or
> may contain viruses in transmission. The e mail and its contents (with
> or without referred errors) shall therefore not attach any liability
> on the originator or HCL or its affiliates. Views or opinions, if any,
> presented in this email are solely those of the author and may not
> necessarily reflect the views or opinions of HCL or its affiliates.
> Any form of reproduction, dissemination, copying, disclosure,
> modification, distribution and / or publication of this message
> without the prior written consent of authorized representative of HCL
> is strictly prohibited. If you have received this email in error
> please delete it and notify the sender immediately. Before opening any
> email and/or attachments, please check them for viruses and other defects.
> --
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

___
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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 Partners Compliance HelpLine at
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dispose of the e-mail.




--
Miguel Ángel Rivas Fernández
___
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Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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 Partners Compliance HelpLine at
http://www.partners.org/complianceline . 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.

Re: [Freesurfer] T2 weighted images as input for recon-all command

[M Janani]

External Email - Use Caution

Thanks for your reply Eugenio.
You have mentioned like "No recon-all on the T2 required, as it's used in a 
different way". May I know the actual purpose of using T2 images for 
reconstruction process. Why we should not T2 images as input for recon-all 
command.
Regards,
Janani



From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Iglesias Gonzalez, 
Eugenio
Sent: 04 May 2018 12:50
To: Freesurfer support list ; Freesurfer 
support list 
Subject: Re: [Freesurfer] T2 weighted images as input for recon-all command


External Email - Use Caution
Hola Miguel Ángel,
First, you need to run the T1 through recon-all normally, as you have already 
done. Next, you run the subfield module with the highres T2 as input - no 
recon-all on the T2 required, as it's used in a different way.
Cheers
Eugenio
Sent from my phone, please excuse brevity and typos


From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Miguel Ángel Rivas Fernández 
mailto:miguelrivasf...@gmail.com>>
Sent: Thursday, May 3, 2018 11:08:17 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] T2 weighted images as input for recon-all command


External Email - Use Caution
Hi Freesurfer developers,
I have executed the recon-all command using the T1 images but I would be 
interested in doing a reconstruction of the hippocampal subregions using for 
that purpose a higher resolution images (eg T2 or FLAIR) as input. I read here 
https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfields
 that is possible make hippocampal segmentation using the T2 images, but if T2 
images cannot be used as input to execute the recon-all in consecuence I can´t 
do the segmentation of hippocampal subfields or on the contrary the recon-all 
and the hippocampal subfields segmentation are two operations that can be 
executed independently ?


I hope to have explained myself correctly


Thanks in advance.



Cheers



2018-05-03 18:28 GMT+02:00 Douglas N. Greve 
mailto:dgr...@mgh.harvard.edu>>:
No, not currently


On 05/03/2018 11:26 AM, M Janani wrote:
>
> Hi Team,
>
>I have one doubt. Can I input T2 weighted images for
> recon-all command?
>
> Regards,
>
> Janani
>
> ::DISCLAIMER::
> --
> The contents of this e-mail and any attachment(s) are confidential and
> intended for the named recipient(s) only. E-mail transmission is not
> guaranteed to be secure or error-free as information could be
> intercepted, corrupted, lost, destroyed, arrive late or incomplete, or
> may contain viruses in transmission. The e mail and its contents (with
> or without referred errors) shall therefore not attach any liability
> on the originator or HCL or its affiliates. Views or opinions, if any,
> presented in this email are solely those of the author and may not
> necessarily reflect the views or opinions of HCL or its affiliates.
> Any form of reproduction, dissemination, copying, disclosure,
> modification, distribution and / or publication of this message
> without the prior written consent of authorized representative of HCL
> is strictly prohibited. If you have received this email in error
> please delete it and notify the sender immediately. Before opening any
> email and/or attachments, please check them for viruses and other defects.
> --
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

___
Freesurfer mailing list
Freesurfer@n

Re: [Freesurfer] T2 weighted images as input for recon-all command

[Iglesias Gonzalez, Eugenio]

External Email - Use Caution

Sorry if I didn’t explain myself properly.
T2 scans of the whole head can be used by recon-all to improve the segmentation 
of the pial surface, but:  a) They are not required (you can use the T1 alone); 
and b) Cannot be run through recon-all independently from the T1.
For hippocampal subfields: the T2 scan is used in a separate stream. In fact, 
their field of view doesn’t even have to cover the whole head – just the 
hippocampi (this is what the ADNI highres T2 protocol does).
Cheers,
/Eugenio

--
Juan Eugenio Iglesias
ERC Senior Research Fellow
Translational Imaging Group
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/


From:  on behalf of M Janani 

Reply-To: Freesurfer support list 
Date: Friday, 4 May 2018 at 08:26
To: Freesurfer support list 
Subject: Re: [Freesurfer] T2 weighted images as input for recon-all command


External Email - Use Caution
Thanks for your reply Eugenio.
You have mentioned like “No recon-all on the T2 required, as it's used in a 
different way”. May I know the actual purpose of using T2 images for 
reconstruction process. Why we should not T2 images as input for recon-all 
command.
Regards,
Janani



From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Iglesias Gonzalez, 
Eugenio
Sent: 04 May 2018 12:50
To: Freesurfer support list ; Freesurfer 
support list 
Subject: Re: [Freesurfer] T2 weighted images as input for recon-all command


External Email - Use Caution
Hola Miguel Ángel,
First, you need to run the T1 through recon-all normally, as you have already 
done. Next, you run the subfield module with the highres T2 as input - no 
recon-all on the T2 required, as it's used in a different way.
Cheers
Eugenio
Sent from my phone, please excuse brevity and typos


From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Miguel Ángel Rivas Fernández 
mailto:miguelrivasf...@gmail.com>>
Sent: Thursday, May 3, 2018 11:08:17 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] T2 weighted images as input for recon-all command


External Email - Use Caution
Hi Freesurfer developers,
I have executed the recon-all command using the T1 images but I would be 
interested in doing a reconstruction of the hippocampal subregions using for 
that purpose a higher resolution images (eg T2 or FLAIR) as input. I read here 
https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfields
 that is possible make hippocampal segmentation using the T2 images, but if T2 
images cannot be used as input to execute the recon-all in consecuence I can´t 
do the segmentation of hippocampal subfields or on the contrary the recon-all 
and the hippocampal subfields segmentation are two operations that can be 
executed independently ?


I hope to have explained myself correctly



Thanks in advance.





Cheers




2018-05-03 18:28 GMT+02:00 Douglas N. Greve 
mailto:dgr...@mgh.harvard.edu>>:
No, not currently


On 05/03/2018 11:26 AM, M Janani wrote:
>
> Hi Team,
>
>I have one doubt. Can I input T2 weighted images for
> recon-all command?
>
> Regards,
>
> Janani
>
> ::DISCLAIMER::
> --
> The contents of this e-mail and any attachment(s) are confidential and
> intended for the named recipient(s) only. E-mail transmission is not
> guaranteed to be secure or error-free as information could be
> intercepted, corrupted, lost, destroyed, arrive late or incomplete, or
> may contain viruses in transmission. The e mail and its contents (with
> or without referred errors) shall therefore not attach any liability
> on the originator or HCL or its affiliates. Views or opinions, if any,
> presented in this email are solely those of the author and may not
> necessarily reflect the views or opinions of HCL or its affiliates.
> Any form of reproduction, dissemination, copying, disclosure,
> modification, distribution and / or publication of this message
> without the prior written consent of authorized representative of HCL
> is strictly prohibited. If you have received this email in error
> please delete it and notify the sender immediately. Before opening any
> email and/or attachments, please check them for viruses and other de

Re: [Freesurfer] T2 weighted images as input for recon-all command

[Miguel Ángel Rivas Fernández]

External Email - Use Caution

Hi,


What would be the command for hippocampal subfields using only the T2
images?

 This?

 recon-all -s  -hippocampal-subfields-T2  


I tried but obtained the following error


pcpb3846:~ lab1-rmn$ recon-all -s /Applications/freesurfer/subjects/4235_T2
-hippocampal-subfields-T2 T2 T2_3D_SAG

ERROR: cannot find T2

Darwin pcpb3846.inv.usc.es 15.6.0 Darwin Kernel Version 15.6.0: Tue Jan 30
11:45:51 PST 2018; root:xnu-3248.73.8~1/RELEASE_X86_64 x86_64


recon-all -s 4235_T2 exited with ERRORS at Fri May  4 10:43:04 CEST 2018




Thanks



cheers,

2018-05-04 10:00 GMT+02:00 Iglesias Gonzalez, Eugenio 
:

> External Email - Use Caution
>
> Sorry if I didn’t explain myself properly.
>
> T2 scans of the whole head can be used by recon-all to improve the
> segmentation of the pial surface, but:  a) They are not required (you can
> use the T1 alone); and b) Cannot be run through recon-all independently
> from the T1.
>
> For hippocampal subfields: the T2 scan is used in a separate stream. In
> fact, their field of view doesn’t even have to cover the whole head – just
> the hippocampi (this is what the ADNI highres T2 protocol does).
>
> Cheers,
>
> /Eugenio
>
>
>
> --
>
> Juan Eugenio Iglesias
>
> ERC Senior Research Fellow
>
> Translational Imaging Group
>
> University College London
>
> http://www.jeiglesias.com
>
> http://cmictig.cs.ucl.ac.uk/
>
>
>
>
>
> *From: * on behalf of M Janani <
> janan...@hcl.com>
> *Reply-To: *Freesurfer support list 
> *Date: *Friday, 4 May 2018 at 08:26
> *To: *Freesurfer support list 
> *Subject: *Re: [Freesurfer] T2 weighted images as input for recon-all
> command
>
>
>
> *External Email - Use Caution*
>
> Thanks for your reply Eugenio.
>
> You have mentioned like “No recon-all on the T2 required, as it's used in
> a different way”. May I know the actual purpose of using T2 images for
> reconstruction process. Why we should not T2 images as input for recon-all
> command.
>
> Regards,
>
> Janani
>
>
>
>
>
>
>
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@
> nmr.mgh.harvard.edu] *On Behalf Of *Iglesias Gonzalez, Eugenio
> *Sent:* 04 May 2018 12:50
> *To:* Freesurfer support list ;
> Freesurfer support list 
> *Subject:* Re: [Freesurfer] T2 weighted images as input for recon-all
> command
>
>
>
> *External Email - Use Caution*
>
> Hola Miguel Ángel,
>
> First, you need to run the T1 through recon-all normally, as you have
> already done. Next, you run the subfield module with the highres T2 as
> input - no recon-all on the T2 required, as it's used in a different way.
>
> Cheers
>
> Eugenio
>
> Sent from my phone, please excuse brevity and typos
>
>
> --
>
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Miguel Ángel Rivas
> Fernández 
> *Sent:* Thursday, May 3, 2018 11:08:17 PM
> *To:* Freesurfer support list
> *Subject:* Re: [Freesurfer] T2 weighted images as input for recon-all
> command
>
>
>
> *External Email - Use Caution*
>
> Hi Freesurfer developers,
>
> I have executed the recon-all command using the T1 images but I would be
> interested in doing a reconstruction of the hippocampal subregions using
> for that purpose a higher resolution images (eg T2 or FLAIR) as input. I
> read here https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfields
> 
> that is possible make hippocampal segmentation using the T2 images, but if
> T2 images cannot be used as input to execute the recon-all in consecuence I
> can´t do the segmentation of hippocampal subfields or on the contrary the
> recon-all and the hippocampal subfields segmentation are two operations
> that can be executed independently ?
>
>
> I hope to have explained myself correctly
>
>
>
> Thanks in advance.
>
>
>
>
>
> Cheers
>
>
>
>
>
>
> 2018-05-03 18:28 GMT+02:00 Douglas N. Greve :
>
> No, not currently
>
>
> On 05/03/2018 11:26 AM, M Janani wrote:
> >
> > Hi Team,
> >
> >I have one doubt. Can I input T2 weighted images for
> > recon-all command?
> >
> > Regards,
> >
> > Janani
> >
> > ::DISCLAIMER::
> > 
> 
> 
> 
> --
> > The contents of this e-mail and any attachment(s) are confidential and
> > intended for the named recipient(s) only. E-mail transmission is not
> > guaranteed to be secure 

Re: [Freesurfer] FSGD design for multi-centre study

[C.P.E. Rollins]

External Email - Use Caution

Hi,

Sorry for coming back to this, but I'm still confused about the issue of 
having unbalanced classes. I thought that I could not remove the class 
as you suggested since this would mean that the contrast positive and 
negative values would no longer add up to 0.  For instance if I remove 
only class "patient_centre2_female", then my contrast would have 11 (-1) 
and 12 (1) as opposed to 12 and 12. Could you please clarify?

Thanks again,
Colleen


On 2018-04-30 14:43, C.P.E. Rollins wrote:
> I thought that I could not remove the class since this would mean that
> the contrast positive and negative values would no longer add up to 0.
> For instance if I remove only class "patient_centre2_female", then my
> contrast would have 11 (-1) and 12 (1) as opposed to 12 and 12. Could
> you please clarify?
> 
> Thanks again,
> Colleen
> 
>  Original Message 
> Subject: Re: [Freesurfer] FSGD design for multi-centre study
> Date: 2018-04-20 11:19
> From: "C.P.E. Rollins" 
> To: Freesurfer 
> 
> Thanks a lot for the explanation. The issue is that I don't think
> Freesurfer will run a design for which there are no subjects for a
> given class. So if I keep the classes (24 classes since 6 centres x 2
> gender x 2 groups (patient vs. control), and have the contrast with 12
> (-1) and 12 (1),
> -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 1 1 1 1 1 1 1 1 1 1 1 1 0
> I get the error:
> 
> ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08
> 
> Possible problem with experimental design:
> Check for duplicate entries and/or lack of range of
> continuous variables within a class.
> 
> I'm assuming this is because there are no participants in, for
> example, patient_centre2_female
> Is there any way to get around this issue, or should I remove those
> centres from my analysis (since I can't only remove
> "patient_centre2_female", as this would make the contrast unbalanced
> (positives and negatives would not add to the same number). I hope
> this was clear but please let me know if it was not.
> 
> Thanks again,
> Colleen

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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 Partners Compliance HelpLine at
http://www.partners.org/complianceline . 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.

Re: [Freesurfer] T2 weighted images as input for recon-all command

[Iglesias Gonzalez, Eugenio]

External Email - Use Caution

It depends on the version, but yes, in 6.0 it’d be that command.
The file name of the additional scan should be an existing nii/nii.gz/mgz file, 
though (right now you just have “T2”).
Cheers,
/E

--
Juan Eugenio Iglesias
ERC Senior Research Fellow
Translational Imaging Group
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/


From:  on behalf of Miguel Ángel Rivas 
Fernández 
Reply-To: Freesurfer support list 
Date: Friday, 4 May 2018 at 09:46
To: Freesurfer support list 
Subject: Re: [Freesurfer] T2 weighted images as input for recon-all command


External Email - Use Caution
Hi,


What would be the command for hippocampal subfields using only the T2 images?

 This?

 recon-all -s  -hippocampal-subfields-T2  




I tried but obtained the following error



pcpb3846:~ lab1-rmn$ recon-all -s /Applications/freesurfer/subjects/4235_T2 
-hippocampal-subfields-T2 T2 T2_3D_SAG

ERROR: cannot find T2

Darwin pcpb3846.inv.usc.es 15.6.0 Darwin Kernel 
Version 15.6.0: Tue Jan 30 11:45:51 PST 2018; 
root:xnu-3248.73.8~1/RELEASE_X86_64 x86_64



recon-all -s 4235_T2 exited with ERRORS at Fri May  4 10:43:04 CEST 2018







Thanks





cheers,

2018-05-04 10:00 GMT+02:00 Iglesias Gonzalez, Eugenio 
mailto:e.igles...@ucl.ac.uk>>:

External Email - Use Caution
Sorry if I didn’t explain myself properly.
T2 scans of the whole head can be used by recon-all to improve the segmentation 
of the pial surface, but:  a) They are not required (you can use the T1 alone); 
and b) Cannot be run through recon-all independently from the T1.
For hippocampal subfields: the T2 scan is used in a separate stream. In fact, 
their field of view doesn’t even have to cover the whole head – just the 
hippocampi (this is what the ADNI highres T2 protocol does).
Cheers,
/Eugenio

--
Juan Eugenio Iglesias
ERC Senior Research Fellow
Translational Imaging Group
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/


From: 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of M Janani mailto:janan...@hcl.com>>
Reply-To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Friday, 4 May 2018 at 08:26
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] T2 weighted images as input for recon-all command


External Email - Use Caution
Thanks for your reply Eugenio.
You have mentioned like “No recon-all on the T2 required, as it's used in a 
different way”. May I know the actual purpose of using T2 images for 
reconstruction process. Why we should not T2 images as input for recon-all 
command.
Regards,
Janani



From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu]
 On Behalf Of Iglesias Gonzalez, Eugenio
Sent: 04 May 2018 12:50
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>; 
Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] T2 weighted images as input for recon-all command


External Email - Use Caution
Hola Miguel Ángel,
First, you need to run the T1 through recon-all normally, as you have already 
done. Next, you run the subfield module with the highres T2 as input - no 
recon-all on the T2 required, as it's used in a different way.
Cheers
Eugenio
Sent from my phone, please excuse brevity and typos


From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Miguel Ángel Rivas Fernández 
mailto:miguelrivasf...@gmail.com>>
Sent: Thursday, May 3, 2018 11:08:17 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] T2 weighted images as input for recon-all command


External Email - Use Caution
Hi Freesurfer developers,
I have executed the recon-all command using the T1 images but I would be 
interested in doing a reconstruction of the hippocampal subregions using for 
that purpose a higher resolution images (eg T2 or FLAIR) as input. I read here 
https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfields
 that is possible make hippocampal segmentation using the T2 images, but if T2 
images cannot be used as input to execute the recon-all in consecuence I can´t 
do the segmentation of hippocampal subfields or on the contrary the recon-all 
and the hippocampal subfields segmentation are two operations that can be 
executed independently ?


I hope to have explained 

Re: [Freesurfer] T2 weighted images as input for recon-all command

[Miguel Ángel Rivas Fernández]

External Email - Use Caution

Hi Eugenio,


In my error free surfer say that cannot find the file, It´s necessary put
the additional scan in a specific folder? I have this organization in the
free surfer subjects directory

4235_T2 (main folder)

   mri (subfolder)

   orig (subfolder)

 Inside the subfolder orig i have two files T2.nii and T2.mgz
(T2.mgz was previously generated using mir_convert command)


Why don´t find the file?


Thanks for your help


Cheers,


2018-05-04 10:50 GMT+02:00 Iglesias Gonzalez, Eugenio 
:

> External Email - Use Caution
>
> It depends on the version, but yes, in 6.0 it’d be that command.
>
> The file name of the additional scan should be an existing nii/nii.gz/mgz
> file, though (right now you just have “T2”).
>
> Cheers,
>
> /E
>
>
>
> --
>
> Juan Eugenio Iglesias
>
> ERC Senior Research Fellow
>
> Translational Imaging Group
>
> University College London
>
> http://www.jeiglesias.com
>
> http://cmictig.cs.ucl.ac.uk/
>
>
>
>
>
> *From: * on behalf of Miguel
> Ángel Rivas Fernández 
> *Reply-To: *Freesurfer support list 
> *Date: *Friday, 4 May 2018 at 09:46
>
> *To: *Freesurfer support list 
> *Subject: *Re: [Freesurfer] T2 weighted images as input for recon-all
> command
>
>
>
> *External Email - Use Caution*
>
> Hi,
>
>
>
>
>
> What would be the command for hippocampal subfields using only the T2
> images?
>
>
>
>  This?
>
>
>
>  recon-all -s  -hippocampal-subfields-T2  additional scan> 
>
>
>
>
>
> I tried but obtained the following error
>
>
>
>
>
> pcpb3846:~ lab1-rmn$ recon-all -s /Applications/freesurfer/subjects/4235_T2
> -hippocampal-subfields-T2 T2 T2_3D_SAG
>
> ERROR: cannot find T2
>
> Darwin pcpb3846.inv.usc.es 15.6.0 Darwin Kernel Version 15.6.0: Tue Jan
> 30 11:45:51 PST 2018; root:xnu-3248.73.8~1/RELEASE_X86_64 x86_64
>
>
>
> recon-all -s 4235_T2 exited with ERRORS at Fri May  4 10:43:04 CEST 2018
>
>
>
>
>
>
>
> Thanks
>
>
>
>
>
> cheers,
>
>
>
> 2018-05-04 10:00 GMT+02:00 Iglesias Gonzalez, Eugenio <
> e.igles...@ucl.ac.uk>:
>
> *External Email - Use Caution*
>
> Sorry if I didn’t explain myself properly.
>
> T2 scans of the whole head can be used by recon-all to improve the
> segmentation of the pial surface, but:  a) They are not required (you can
> use the T1 alone); and b) Cannot be run through recon-all independently
> from the T1.
>
> For hippocampal subfields: the T2 scan is used in a separate stream. In
> fact, their field of view doesn’t even have to cover the whole head – just
> the hippocampi (this is what the ADNI highres T2 protocol does).
>
> Cheers,
>
> /Eugenio
>
>
>
> --
>
> Juan Eugenio Iglesias
>
> ERC Senior Research Fellow
>
> Translational Imaging Group
>
> University College London
>
> http://www.jeiglesias.com
>
> http://cmictig.cs.ucl.ac.uk/
>
>
>
>
>
> *From: * on behalf of M Janani <
> janan...@hcl.com>
> *Reply-To: *Freesurfer support list 
> *Date: *Friday, 4 May 2018 at 08:26
> *To: *Freesurfer support list 
>
> *Subject: *Re: [Freesurfer] T2 weighted images as input for recon-all
> command
>
>
>
> *External Email - Use Caution*
>
> Thanks for your reply Eugenio.
>
> You have mentioned like “No recon-all on the T2 required, as it's used in
> a different way”. May I know the actual purpose of using T2 images for
> reconstruction process. Why we should not T2 images as input for recon-all
> command.
>
> Regards,
>
> Janani
>
>
>
>
>
>
>
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@
> nmr.mgh.harvard.edu] *On Behalf Of *Iglesias Gonzalez, Eugenio
> *Sent:* 04 May 2018 12:50
> *To:* Freesurfer support list ;
> Freesurfer support list 
> *Subject:* Re: [Freesurfer] T2 weighted images as input for recon-all
> command
>
>
>
> *External Email - Use Caution*
>
> Hola Miguel Ángel,
>
> First, you need to run the T1 through recon-all normally, as you have
> already done. Next, you run the subfield module with the highres T2 as
> input - no recon-all on the T2 required, as it's used in a different way.
>
> Cheers
>
> Eugenio
>
> Sent from my phone, please excuse brevity and typos
>
>
> --
>
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Miguel Ángel Rivas
> Fernández 
> *Sent:* Thursday, May 3, 2018 11:08:17 PM
> *To:* Freesurfer support list
> *Subject:* Re: [Freesurfer] T2 weighted images as input for recon-all
> command
>
>
>
> *External Email - Use Caution*
>
> Hi Freesurfer developers,
>
> I have executed the recon-all command using the T1 images but I would be
> interested in doing a reconstruction of the hippocampal subregions using
> for that purpose a higher resolution images (eg T2 or FLAIR) as input. I
> read here https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfields
> 

Re: [Freesurfer] T2 weighted images as input for recon-all command

[Iglesias Gonzalez, Eugenio]

External Email - Use Caution

recon-all –sd /Applications/freesurfer/subjects  -s  4235_T2 
-hippocampal-subfields-T2   
/Applications/freesurfer/subjects/4235_T2/mri/orig/T2.mgz T2_3D_SAG


--
Juan Eugenio Iglesias
ERC Senior Research Fellow
Translational Imaging Group
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/


From:  on behalf of Miguel Ángel Rivas 
Fernández 
Reply-To: Freesurfer support list 
Date: Friday, 4 May 2018 at 10:09
To: Freesurfer support list 
Subject: Re: [Freesurfer] T2 weighted images as input for recon-all command


External Email - Use Caution
Hi Eugenio,


In my error free surfer say that cannot find the file, It´s necessary put the 
additional scan in a specific folder? I have this organization in the free 
surfer subjects directory

4235_T2 (main folder)

   mri (subfolder)

   orig (subfolder)

 Inside the subfolder orig i have two files T2.nii and T2.mgz 
(T2.mgz was previously generated using mir_convert command)


Why don´t find the file?


Thanks for your help


Cheers,


2018-05-04 10:50 GMT+02:00 Iglesias Gonzalez, Eugenio 
mailto:e.igles...@ucl.ac.uk>>:

External Email - Use Caution
It depends on the version, but yes, in 6.0 it’d be that command.
The file name of the additional scan should be an existing nii/nii.gz/mgz file, 
though (right now you just have “T2”).
Cheers,
/E

--
Juan Eugenio Iglesias
ERC Senior Research Fellow
Translational Imaging Group
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/


From: 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Miguel Ángel Rivas Fernández 
mailto:miguelrivasf...@gmail.com>>
Reply-To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Friday, 4 May 2018 at 09:46

To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] T2 weighted images as input for recon-all command


External Email - Use Caution
Hi,


What would be the command for hippocampal subfields using only the T2 images?

 This?

 recon-all -s  -hippocampal-subfields-T2  


I tried but obtained the following error



pcpb3846:~ lab1-rmn$ recon-all -s /Applications/freesurfer/subjects/4235_T2 
-hippocampal-subfields-T2 T2 T2_3D_SAG

ERROR: cannot find T2

Darwin pcpb3846.inv.usc.es 15.6.0 Darwin Kernel 
Version 15.6.0: Tue Jan 30 11:45:51 PST 2018; 
root:xnu-3248.73.8~1/RELEASE_X86_64 x86_64



recon-all -s 4235_T2 exited with ERRORS at Fri May  4 10:43:04 CEST 2018







Thanks





cheers,

2018-05-04 10:00 GMT+02:00 Iglesias Gonzalez, Eugenio 
mailto:e.igles...@ucl.ac.uk>>:

External Email - Use Caution
Sorry if I didn’t explain myself properly.
T2 scans of the whole head can be used by recon-all to improve the segmentation 
of the pial surface, but:  a) They are not required (you can use the T1 alone); 
and b) Cannot be run through recon-all independently from the T1.
For hippocampal subfields: the T2 scan is used in a separate stream. In fact, 
their field of view doesn’t even have to cover the whole head – just the 
hippocampi (this is what the ADNI highres T2 protocol does).
Cheers,
/Eugenio

--
Juan Eugenio Iglesias
ERC Senior Research Fellow
Translational Imaging Group
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/


From: 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of M Janani mailto:janan...@hcl.com>>
Reply-To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Friday, 4 May 2018 at 08:26
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] T2 weighted images as input for recon-all command


External Email - Use Caution
Thanks for your reply Eugenio.
You have mentioned like “No recon-all on the T2 required, as it's used in a 
different way”. May I know the actual purpose of using T2 images for 
reconstruction process. Why we should not T2 images as input for recon-all 
command.
Regards,
Janani



From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu]
 On Behalf Of Iglesias Gonzalez, Eugenio
Sent: 04 May 2018 12:50
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>; 
Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] T2 weighted images as input for recon-all command


External Email - Use Caution
Hola Miguel Ángel,
First, you need to run the T1 through recon-all normally, as you have already 
done. Next, you run the subfield module with the highres T2 as input - no 
recon-all on the T2 required, as it's used in a different way.
Cheers
Eugenio
Sent from my phone, please excuse brevity and typos


From: 
freesurfer-boun...@nmr.mgh.harvard.edu

[Freesurfer] Register individual functional volume to MNI152

[Anna Mynick]

External Email - Use Caution

Hi all,

I’m having some trouble getting an an accurate registration between an 
individual functional volume and MNI152 space. Presently, I’m using the 
commands:

bbregister --s MNI152_FS --mov volumeInFunctional  --reg 
mniDir/filename2mni.lta --init-fsl --bold
mri_vol2vol --mov volumeInFunctional  --reg  mniDir/filename2mni.lta --fstarg 
--o ‘ mniDir/filename.nii --no-resample

I’ve also tried using the strategy detailed 
here,
 without much luck (the registration was very distorted).

Is there a different method for registration to MNI152  that yields more 
accurate results?

Thanks very much for any suggestions!

Best,
Anna

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Re: [Freesurfer] Longitudinal data from different sequences and scanners

[James Gullickson]

External Email - Use Caution

Martin,

Thanks for the feedback. Given our data set (1mm^3 timepoint1 and 0.8mm^3
timepoint 2), what would be the best way to salvage this data and look for
longitudinal changes? Would it be possible to upsample/downsample the
images so that they are the same resolution (i.e. using mriconvert)? Also,
would a normalized measure like ventricle-brain-ratio theoretically be
resistant to these scanner/acquisition induced biases?

Thanks,

James

On Mon, Apr 16, 2018 at 5:15 AM, Martin Reuter 
wrote:

> Hi,
>
> never switch hardware or protocols in a longitudinal study. This is a good
> example for what happens: you will find effects that are caused by
> different acquisition rather than anatomical differences. It will be
> impossible to disentangle true change from scanner/acquisition induced
> changes, especially with only a few time points and no or little subjects
> scanned on both scanners or with both protocols.
>
> Also 5mm resolution is too low for freesurfer and anything can come out of
> that. It won’t be reliable.
>
> Best, Martin
>
>
> On 6. Apr 2018, at 21:21, Matthew Grecsek  wrote:
>
> Here are some statistics I generated for one of my subjects processed
> through the longitudinal stream with T0 as the initial scan and T1 18 mos
> later. (not sure if the inline tables will be properly formatted so I
> attached text files of them).
>
> Unfortunately the only initial scan I had was a 5mm resolution for T0
> versus 1mm for T1. I understand FS recommends a resolution not exceeding
> 1.5mm, but we gave it a try anyway to see if there was anything useful. My
> expectation was that the stats would be off by a consistent ratio due to
> the different resolutions, however I was surprised by the variability.
>
> In particular, as James found, for some ROIs there are net increases in
> cortical thickness and brain volume over time.
>
> Is this simply a factor that the algorithms are confused by the different
> image resolutions and therefore no possible longitudinal study can reliably
> be presumed in this circumstance?
>
> Should we expect similar anomalies in cross-sectional studies, such as if
> my subjects have 1mm resolutions and a collaborating institution has 0.8mm
> subjects?
>
> Cheers,
>
> -Matt
>
> Aseg Stats
> Measure:volume T0 T1 Base T0.long.base T1.long.base
> Left-Lateral-Ventricle 9,455.2   13,085.8
> 12,344.2   10,928.1   13,268.0
> Left-Inf-Lat-Vent   61.8 174.1
> 171.7   90.3 303.3
> Left-Cerebellum-White-Matter   26,892.5   18,563.1
>   17,066.4   23,905.6   17,597.8
> Left-Cerebellum-Cortex   57,390.8   66,458.7
> 64,631.3   60,374.1   65,898.6
> Left-Thalamus-Proper   10,757.3 9,094.2
> 9,918.5   10,350.8 9,588.3
> Left-Caudate 3,619.4 3,673.8
> 3,608.8 3,588.7 3,872.7
> Left-Putamen 5,463.7 5,439.2
> 5,171.0 5,602.0 5,721.7
> Left-Pallidum 2,380.9 2,208.6
> 1,897.1 2,270.8 2,147.9
> 3rd-Ventricle 1,181.8 1,174.6
> 1,328.7 1,432.2 1,416.9
> 4th-Ventricle 1,209.1 1,602.0
> 1,547.7 1,322.4 1,981.1
> Brain-Stem   25,154.2   26,141.3   
> 25,890.7
>   25,988.7   25,954.6
> Left-Hippocampus 4,205.3 4,335.6
> 4,378.0 4,478.2 4,407.2
> Left-Amygdala 1,488.1 1,725.9
> 1,588.6 1,531.3 1,638.0
> CSF 1,440.9 1,321.0 1,551.0
> 1,910.1 1,394.7
> Left-Accumbens-area 295.0 273.2
> 327.7 274.9 380.0
> Left-VentralDC 5,086.1 4,935.5
> 5,429.6 5,106.9 5,041.7
> Left-vessel- 16.6
> 7.7- 48.5
> Left-choroid-plexus 221.6 419.4
> 271.7 429.5 734.2
> Right-Lateral-Ventricle 6,465.1 9,581.5
> 8,695.5 6,893.5 9,713.9
> Right-Inf-Lat-Vent 360.0 333.7
> 408.5 400.5 518.0
> Right-Cerebellum-White-Matter   21,673.2 

[Freesurfer] Freeview surface annotation outline line thickness

[Kayle Sawyer]

External Email - Use Caution

The freeview flag "annot_outline=1" is great for viewing results for
significant clusters from mri_glmfit-sim. Is there a way to make the
outlines thicker?

With the default thickness, the outlines are difficult to make out in a
multipanel figure. (The "edgethickness=" flag specifies the slice
intersection crosshair with the surface, not the annotation outline
thickness.)
Thanks,
-Kayle
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Re: [Freesurfer] transforming functional volumes to MNI without resampling

[David Beeler]

External Email - Use Caution

Hi Doug,

funcVol is an individual functional resting state scan. We are doing some 
clustering analyses and trying to visually compare the clustering across 
subjects (I would be a bit sketched out trying to quantify the overlap between 
subjects due to individual differences in anatomy, etc, but just looking at it 
might give us a clue on what is going on). We do all our analyses in the 
individual subject's native space, but it's hard to see what the similarities / 
differences are.

If not bbregister, what would be the correct way to align all subjects to a 
common space?

Thanks,
DB



Douglas N. Greve wrote:


What is funcVol? An individual functional? If so, then use --12 (12 dof
to account for scaling). In general, we don't recommend doing cross
subject registration with BBR as it is really not appropriate for that
kind of thing.




On 05/03/2018 01:30 PM, David Beeler wrote:

Hi,

I'm trying to register and transform some raw functional data (108x108x72x175, 
2mm iso voxels) to MNI space, while keeping the low res dimensions.

I have tried:
bbregister --s MNI152_FS --mov funcVol --reg func2mni.lta --init-fsl --bold
mri_vol2vol --mov funcVol --reg func2mni.lta --o funcVolMNI --fstarg 
--no-resample --nearest
mri_vol2vol --mov funcVol --reg func2mni.lta --o funcVolMNI --fstarg 
--no-resample

And this looks pretty good, but not perfect... the functional data is oriented 
correctly but the brain seems to be a centimeter or two smaller in multiple 
dimensions, see:

http://web.mit.edu/dsbeeler/www/images/bbregister-mni.png

I'm not too surprised since the MNI brain is blurry and oddly round, but 
presumably there is a way to do this transformation more accurately. I've run 
mri_cvs_register for this subject using the --mni flag:

mri_cvs_register --openmp 8 --mni --mov $subjID --outdir $mniDir

And for other applications I use this m3z file to transform volumes between MNI 
orig.mgz and individual subject orig.mgz, but is there a way to use it to 
transform functional data to MNI space while keeping the functional dimensions?

I could do:

mri_vol2vol --mov funcVol --targ $SUBJECTS_DIR/$subjID/mri/orig.mgz --reg 
register.dof6.lta --nearest --o template-in-anat.nii.gz

mri_vol2vol --noDefM3zPath --targ $SUBJECTS_DIR/$subjID/mri/orig.mgz --mov 
template-in-anat.nii.gz --m3z $mniDir/final_CVSmorph_tocvs_avg35_inMNI152.m3z 
--o template-in-MNI-m3z.nii.gz --nearest

But not only is this unideal because it requires upsampling the functional data 
to 256x256x256, it also gets these funky wavy distortions:

http://web.mit.edu/dsbeeler/www/images/m3z-mni.png


Any thoughts are appreciated, thanks!

-DB
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Re: [Freesurfer] Freeview surface annotation outline line thickness

[Ruopeng Wang]

Hi Kayle,

There is no such option. I'll put it on my list for future improvement.

Best,
Ruopeng


On 05/04/2018 01:09 PM, Kayle Sawyer wrote:
The freeview flag "annot_outline=1" is great for viewing results for 
significant clusters from mri_glmfit-sim. Is there a way to make the 
outlines thicker?


With the default thickness, the outlines are difficult to make out in 
a multipanel figure. (The "edgethickness=" flag specifies the slice 
intersection crosshair with the surface, not the annotation outline 
thickness.)

Thanks,
-Kayle




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but does not contain patient information, please contact the sender and properly
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Re: [Freesurfer] fmriprep to fsfast interface

[Boggess, Matthew Jozsef]

Hello,


I just wanted to follow up on this again. Is there any way to transform 
functional data (already in T1 space) to tal space directly? Something like 
passing an identity registration matrix to mri_vol2vol or another command that 
would apply the tal transform without a registration?


If not, I will just try re-registering as you suggested, but I am hoping to 
minimize the extra processing steps.


Thanks,

Matt


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Boggess, Matthew Jozsef 

Sent: Friday, April 20, 2018 8:13:11 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] fmriprep to fsfast interface


Thank you for the response!


I'm interested primarily in tal space, but potentially native as well. For tal 
space, is there no easy way to just directly transform the data into tal space 
or provide an identity matrix for the registration?


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

Sent: Tuesday, April 17, 2018 12:01:46 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] fmriprep to fsfast interface


sorry for the delay, see below

On 4/14/18 10:00 AM, Boggess, Matthew Jozsef wrote:

Hello,


I just wanted to follow up to see if anyone could help with any of my 
questions, particularly # 1.


Thank you!

Matt Boggess


From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 

 on behalf of Boggess, Matthew Jozsef 

Sent: Thursday, April 5, 2018 8:02:07 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] fmriprep to fsfast interface

Hello,

I've been working on taking the outputs of the fmriprep BOLD preprocessing tool 
(https://fmriprep.readthedocs.io/en/latest/index.html) and coercing them into 
the fsfast structure so that first levels can be run with mkanalysis-sess and 
selxavg3b-sess. It's been a bit trickier than anticipated and I was hoping to 
get some help verifying my current approach (attached to this email).

Question 1:

fmriprep outputs the preprocessed BOLD data in the T1 space (mni305 is not an 
option). However, the typical spatial normalization workflow uses a 
registration matrix from the bold to T1 to transform to talairach. Is there a 
way to do this transformation without having to specify a registration matrix 
given the functional data is already in the T1 space? My current approach is to 
use mri_convert with the --apply_transform flag pointing to the talairach.xfm 
registration matrix in the subject's recon folder, but I am not sure if this is 
a reasonable workaround.
Do you want to analyze it in the native T1 space or in talairach space? If 
native, then when you run mkanalysis-sess you can bypass the preprocessing by 
directly specifying the stem of the functional data you want to process 
(-funcstem). If tal space, then I think it should work out of the box (it would 
recalc the registration, but that should  be ok).

Question 2:

fsfast normally calculates the global mean value of the raw data to be used for 
intensity normalization. However, with fmriprep I only have access to the 
preprocessed data in T1 space. Would extracting the global mean value for 
intensity normalization from the preprocessed BOLD in T1 space be valid?
Yes

Question 3:

Is there a way to do first levels in the native subcortical space? If so, what 
is the filename structure expected (maybe mni305.2mm gets replaced with the 
subject name as with the surface data)? I've only seen examples transforming to 
mni305 space, but ideally an option would be to just transfer the preprocessed 
BOLD in T1 space and run first levels staying in the native T1 space.
See above.

Thanks for your help!

Matt






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[Freesurfer] Problems at exporting recon-all outputs

[Miguel Ángel Rivas Fernández]

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Hi Freesurfer developers,


After having executed the recon-all in several subjects I tried to export
all measures of the Destrieux atlas (area, volume, curvind, foldind,
gauscurv, meancurv, thickness and thicknesstd) but I got an error because
in some variables only zeros appear and however, in the other variables I
did obtain values when doing the export. I had the same error in some
variables when exported the subcortical segmentation (aseg.stats) and the
wm (wmparc.stats).

Why do some variables appear without any value?


Thanks in advance,



Cheers,

-- 
*Miguel Ángel Rivas Fernández*
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