Re: [Freesurfer] bbregister dependencies recon-all

[Douglas N. Greve]

You pretty much have to run it through to the end. You can try using 
mri_coreg (this is the first step of bbregister). It does not need 
anything but two images and will  run in  a few min.

On 3/3/2022 5:24 AM, Guillem París wrote:
>  External Email - Use Caution
>
> Hello,
>
> I'm trying to run a Boundary-based registration by using bbregister. In
> the documentation, it is specified that the anatomical image has to be
> previously analysed in FreeSurfer. I assume that means to run the
> "recon-all" pipeline.
>
> Now, are all the stages of "recon-all -all" needed to perform this
> registration? Since I am time-constrained, I would like to run as few
> stages as possible, so I can use bbregister.
>
> If it matters, I'm trying to register a DWI to the same subject's T1-w.
>
> Thank you!
>
> Guillem
>
>
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[Freesurfer] bbregister dependencies recon-all

[Guillem París]

External Email - Use Caution

Hello,

I'm trying to run a Boundary-based registration by using bbregister. In 
the documentation, it is specified that the anatomical image has to be 
previously analysed in FreeSurfer. I assume that means to run the 
"recon-all" pipeline.

Now, are all the stages of "recon-all -all" needed to perform this 
registration? Since I am time-constrained, I would like to run as few 
stages as possible, so I can use bbregister.

If it matters, I'm trying to register a DWI to the same subject's T1-w.

Thank you!

Guillem


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continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
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Re: [Freesurfer] bbregister on DWI volumes using DOF 12 for epi distortions ?

[Douglas N. Greve]

Yea, I've tried that before. It does not work very well. You can 
proceed, but it will not be providing you with a very good correction.


On 8/9/2021 9:30 AM, Shane Schofield wrote:


External Email - Use Caution

Hi Freesurfer Experts,

I am trying to obtain coregister diffusion data b0 with T1.

One problem is that I do not have any means to correct for EPI 
distortions.


Because of this,  I am experimenting with DOF = 9 and DOF = 12. The 
mincost for 12 was consistently the lowest compared to 6 and 9 across 
my datasets [DOF 6 = 0.23, DOF 9 = 0.22, DOF 12 = 0.19]. However, it 
is hard to tell that DOF 12 is the best just by looking at the 
coregistered B0s overlaid on the brainmask.


Would it be fine to proceed with the DOF 12 option?

Thank you.

Best Wishes,
Shane

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continue to communicate over unencrypted e-mail. 

[Freesurfer] bbregister on DWI volumes using DOF 12 for epi distortions ?

[Shane Schofield]

External Email - Use Caution

Hi Freesurfer Experts,
I am trying to obtain coregister diffusion data b0 with T1. 
One problem is that I do not have any means to correct for EPI distortions.
Because of this,  I am experimenting with DOF = 9 and DOF = 12. The mincost for 
12 was consistently the lowest compared to 6 and 9 across my datasets [DOF 6 = 
0.23, DOF 9 = 0.22, DOF 12 = 0.19]. However, it is hard to tell that DOF 12 is 
the best just by looking at the coregistered B0s overlaid on the brainmask.
Would it be fine to proceed with the DOF 12 option?
Thank you.
Best Wishes,Shane___
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Re: [Freesurfer] bbregister using freesurfer v7

[Douglas N. Greve]

On 7/7/2020 3:14 AM, Ellen Ji wrote:


External Email - Use Caution

Dear experts,

I am running bbregister and have a couple questions:

1) I am using freesurfer version 7. My understanding is that I do not 
need any --init argument anymore, and without it, by default it uses 
init-coreg. Could you confirm this? (I tested the below and it seemed 
fine)


bbregister --s subject1 --mov $dtipath/subject1/data.nii.gz --dti 
--reg mri/register.dat

Correct, you do not need --init


2) A colleague performed recon-all using freesurfer v6. Is it ok if I 
use bbregister on these subjects using freesurfer v7 or should I 
install v6?

No, you can use v7 bbregister with v6 subjects


Many thanks for your input!


Ellen Ji, PhD
Postdoctoral researcher

*
Individual Differences in Psychosis (IDP) Lab
Psychiatric University Hospital
University of Zürich
ellen...@bli.uzh.ch


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[Freesurfer] bbregister using freesurfer v7

[Ellen Ji]

   External Email - Use Caution


Dear experts,

I am running bbregister and have a couple questions:

1) I am using freesurfer version 7. My understanding is that I do not 
need any --init argument anymore, and without it, by default it uses 
init-coreg. Could you confirm this? (I tested the below and it seemed fine)


bbregister --s subject1 --mov $dtipath/subject1/data.nii.gz --dti --reg 
mri/register.dat


2) A colleague performed recon-all using freesurfer v6. Is it ok if I 
use bbregister on these subjects using freesurfer v7 or should I install v6?


Many thanks for your input!


Ellen Ji, PhD
Postdoctoral researcher

*
Individual Differences in Psychosis (IDP) Lab
Psychiatric University Hospital
University of Zürich
ellen...@bli.uzh.ch

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Re: [Freesurfer] Bbregister misalignment {Disarmed}

[Douglas N. Greve]

You can ignore that warning. The source of the problem is that the 
whole-brain and the partial FoV are not in alignment. The idea here is 
that you acquire the whole head and the partial fov in the same scanning 
session so that they are more-or-less in alignment. When you register 
the whole brain to the structural, you can then get the partial fov to 
structural by concatenating the registrations. So, why is your whole 
brain out of alignment with the partial fov?


On 6/3/2020 12:31 PM, Mason Wells wrote:


External Email - Use Caution

Hi Doug,

Do you mean to raw partial epi and the whole brain? If so, I have ran:

tkregisterfv --mov 
/home/c1749990/data/PhD/Data/PMA_retinoScans/PPT_002/run1.nii.gz 
--targ 
/home//c1749990/data/PhD/Data/PMA_retinoScans/PPT_002/WholeEPI.nii.gz 
--regheader --reg partial-to-full.lta


but the once Freeview opens, the terminal states:

Warning: Transformation can only apply to volumes for now. If your 
data includes ROI/Surface/Way Points, please do not use this feature yet.


INFO: LTA input is not RAS to RAS...converting...

Also, in the freeview window, the whole brain and the raw epi are very 
misaligned as I click between displaying the two volumes in Freeview 
(attached). I should also add, of the 10 I have ran I did not use the 
whole brain –int flag as it appeared to make the registration a lot 
worse than just running:


bbregister --s PPT_002 --feat 
/cubric/data/c1749990/PhD/Data/PMA_retinoScans/PPT_002/run1.feat/ 
--init-coreg


Should I still try and register the whole epi to the T1 (structural)?

*Mason T Wells, MSc*

*PhD student*

School of Optometry and Vision Sciences

& Cardiff University Brain Research

Imaging Centre (CUBRIC), School of Psychology

Cardiff University

Cardiff

CF24 4HQ

UK

*/Email/*: wells...@cardiff.ac.uk <mailto:wells...@cardiff.ac.uk>

*/Tel/*: 02920 879628

*/Web/*: Cardiff University webpage 
<https://www.cardiff.ac.uk/people/research-students/view/974214->




*Mason T Wells, MSc*

*Myfyriwr PhD*

Yr Ysgol Optometreg a Gwyddorau’r Golwg

& Canolfan Ymchwil Delweddu’r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr 
Ysgol Seicoleg


Prifysgol Caerdydd

Heol Maindy

Caerdydd

CF24 4HQ

DU

*/E-bost/*: wells...@caerdydd.ac.uk <mailto:wells...@caerdydd.ac.uk>

*/Ffôn/*: 02920 879628

*From: * on behalf of "Douglas 
N. Greve" 

*Reply to: *Freesurfer support list 
*Date: *Wednesday, 3 June 2020 at 17:14
*To: *"freesurfer@nmr.mgh.harvard.edu" 
*Subject: *Re: [Freesurfer] Bbregister misalignment {Disarmed}


A couple of things to try:

First, make sure that the whole head and the partial FoV EPIs are in 
register without doing any registration
tkregisterfv --mov partialfovepi.nii.gz --targ wholeepi.nii.gz 
--regheader --reg partial-to-full.lta


Next, register the whole head EPI to the structural
bbregister --mov wholeepi.nii.gz --s subject --t2 --reg 
whole-to-struct.lta

View the result and make sure that it is in register

Let me know how that goes

On 6/3/2020 11:33 AM, Mason Wells wrote:

*External Email - Use Caution *

Sorry for yet another email on this, but 3/10 PPTs ended up with a
good reg from bbregister, all using the same command. The issue is
always when the epi orientation is like the attached. Have you any
idea what to do? It's almost like bbregister can't orientate the
brain so the epi is in the plane as the white matter. An epi slice
is diagonal and the structural slice is horizontal, and this is
where the issue is.

Cheers,

Mason

*Mason T Wells, MSc*

*PhD student*

School of Optometry and Vision Sciences

& Cardiff University Brain Research

Imaging Centre (CUBRIC), School of Psychology

Cardiff University

Cardiff

CF24 4HQ

UK

*/Email/*: wells...@cardiff.ac.uk <mailto:wells...@cardiff.ac.uk>

*/Tel/*: 02920 879628

*/Web/*: Cardiff University webpage
<https://www.cardiff.ac.uk/people/research-students/view/974214->



*Mason T Wells, MSc*

*Myfyriwr PhD*

Yr Ysgol Optometreg a Gwyddorau’r Golwg

& Canolfan Ymchwil Delweddu’r Ymennydd Prifysgol Caerdydd
(CUBRIC), Yr Ysgol Seicoleg

Prifysgol Caerdydd

Heol Maindy

Caerdydd

CF24 4HQ

DU

*/E-bost/*: wells...@caerdydd.ac.uk <mailto:wells...@caerdydd.ac.uk>

*/Ffôn/*: 02920 879628

*From: *
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Mason
Wells  <mailto:wells...@cardiff.ac.uk>
*Reply to: *Freesurfer support list

<mailto:freesurfer@nmr.mgh.harvard.edu>
*Date: *Wednesday, 3 June 2020 at 14:05
*To: *Freesurfer support list 
<mailto:freesurfer@nmr.mgh.harvard.edu>
*Subject: *Re: [Freesurfer] Bbregister misalignment {Disarmed}

*External Email - Use Caution *

Hi Doug,

Thanks for this. However, I can’t seem to access the ftp:

Re: [Freesurfer] Bbregister misalignment {Disarmed}

[Douglas N. Greve]

A couple of things to try:

First, make sure that the whole head and the partial FoV EPIs are in 
register without doing any registration
tkregisterfv --mov partialfovepi.nii.gz --targ wholeepi.nii.gz 
--regheader --reg partial-to-full.lta


Next, register the whole head EPI to the structural
bbregister --mov wholeepi.nii.gz --s subject --t2 --reg whole-to-struct.lta
View the result and make sure that it is in register

Let me know how that goes


On 6/3/2020 11:33 AM, Mason Wells wrote:


External Email - Use Caution

Sorry for yet another email on this, but 3/10 PPTs ended up with a 
good reg from bbregister, all using the same command. The issue is 
always when the epi orientation is like the attached. Have you any 
idea what to do? It's almost like bbregister can't orientate the brain 
so the epi is in the plane as the white matter. An epi slice is 
diagonal and the structural slice is horizontal, and this is where the 
issue is.


Cheers,

Mason

*Mason T Wells, MSc*

*PhD student*

School of Optometry and Vision Sciences

& Cardiff University Brain Research

Imaging Centre (CUBRIC), School of Psychology

Cardiff University

Cardiff

CF24 4HQ

UK

*/Email/*: wells...@cardiff.ac.uk <mailto:wells...@cardiff.ac.uk>

*/Tel/*: 02920 879628

*/Web/*: Cardiff University webpage 
<https://www.cardiff.ac.uk/people/research-students/view/974214->




*Mason T Wells, MSc*

*Myfyriwr PhD*

Yr Ysgol Optometreg a Gwyddorau’r Golwg

& Canolfan Ymchwil Delweddu’r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr 
Ysgol Seicoleg


Prifysgol Caerdydd

Heol Maindy

Caerdydd

CF24 4HQ

DU

*/E-bost/*: wells...@caerdydd.ac.uk <mailto:wells...@caerdydd.ac.uk>

*/Ffôn/*: 02920 879628

*From: * on behalf of Mason 
Wells 

*Reply to: *Freesurfer support list 
*Date: *Wednesday, 3 June 2020 at 14:05
*To: *Freesurfer support list 
*Subject: *Re: [Freesurfer] Bbregister misalignment {Disarmed}

*External Email - Use Caution *

Hi Doug,

Thanks for this. However, I can’t seem to access the ftp:

c1749990@l017:~/data/freesurfer/subjects$ ftp surfer.nmr.mgh.harvard.edu

bash: ftp: command not found...

Is there another way to do this?

Cheers,

Mason

*Mason T Wells, MSc*

*PhD student*

School of Optometry and Vision Sciences

& Cardiff University Brain Research

Imaging Centre (CUBRIC), School of Psychology

Cardiff University

Cardiff

CF24 4HQ

UK

*/Email/*: wells...@cardiff.ac.uk <mailto:wells...@cardiff.ac.uk>

*/Tel/*: 02920 879628

*/Web/*: Cardiff University webpage 
<https://www.cardiff.ac.uk/people/research-students/view/974214->




*Mason T Wells, MSc*

*Myfyriwr PhD*

Yr Ysgol Optometreg a Gwyddorau’r Golwg

& Canolfan Ymchwil Delweddu’r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr 
Ysgol Seicoleg


Prifysgol Caerdydd

Heol Maindy

Caerdydd

CF24 4HQ

DU

*/E-bost/*: wells...@caerdydd.ac.uk <mailto:wells...@caerdydd.ac.uk>

*/Ffôn/*: 02920 879628

*From: * on behalf of "Douglas 
N. Greve" 

*Reply to: *Freesurfer support list 
*Date: *Tuesday, 2 June 2020 at 18:39
*To: *"freesurfer@nmr.mgh.harvard.edu" 
*Subject: *Re: [Freesurfer] Bbregister misalignment {Disarmed}

If you upload the data, I'll take a look. Upload both the structural 
and the fMRI. See instructions below


From the linux command line,
Create the file you want to upload, eg,
cd $SUBJECTS_DIR
tar cvfz subject.tar.gz ./subject
Now log  into our anonymous FTP site:
ftp surfer.nmr.mgh.harvard.edu
It will ask you for a user name: use "anonymous" (no quotes)
It will ask you for a password: use "anonymous" (no quotes)
cd transfer/incoming
binary
put subject.tar.gz
Send an email that the file has been and the name of the file.



On 6/2/2020 9:14 AM, Mason Wells wrote:

*External Email - Use Caution *

Just a follow up here. I tried the command below on a machine with
v.6, and the flag was recognised, but the registration was still
off. No change to the output with the flag included.

*Mason T Wells, MSc*

*PhD student*

School of Optometry and Vision Sciences

& Cardiff University Brain Research

Imaging Centre (CUBRIC), School of Psychology

Cardiff University

Cardiff

CF24 4HQ

UK

*/Email/*: wells...@cardiff.ac.uk <mailto:wells...@cardiff.ac.uk>

*/Tel/*: 02920 879628

*/Web/*: Cardiff University webpage
<https://www.cardiff.ac.uk/people/research-students/view/974214->



*Mason T Wells, MSc*

*Myfyriwr PhD*

Yr Ysgol Optometreg a Gwyddorau’r Golwg

& Canolfan Ymchwil Delweddu’r Ymennydd Prifysgol Caerdydd
(CUBRIC), Yr Ysgol Seicoleg

Prifysgol Caerdydd

Heol Maindy

Caerdydd

CF24 4HQ

DU

*/E-bost/*: wells...@caerdydd.ac.uk <mailto:wells...@caerdydd.ac.uk>

*/Ffôn/*: 02920 879628

*From: *
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Mason
We

Re: [Freesurfer] Bbregister misalignment {Disarmed}

[Mason Wells]

External Email - Use Caution

Hi Doug,

Thanks for this. However, I can’t seem to access the ftp:

c1749990@l017:~/data/freesurfer/subjects$ ftp surfer.nmr.mgh.harvard.edu
bash: ftp: command not found...

Is there another way to do this?
Cheers,
Mason

Mason T Wells, MSc
PhD student
School of Optometry and Vision Sciences
& Cardiff University Brain Research
Imaging Centre (CUBRIC), School of Psychology
Cardiff University
Cardiff
CF24 4HQ
UK

Email: wells...@cardiff.ac.uk<mailto:wells...@cardiff.ac.uk>
Tel: 02920 879628
Web: Cardiff University 
webpage<https://www.cardiff.ac.uk/people/research-students/view/974214->
Mason T Wells, MSc
Myfyriwr PhD
Yr Ysgol Optometreg a Gwyddorau’r Golwg
& Canolfan Ymchwil Delweddu’r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr Ysgol 
Seicoleg
Prifysgol Caerdydd
Heol Maindy
Caerdydd
CF24 4HQ
DU

E-bost: wells...@caerdydd.ac.uk<mailto:wells...@caerdydd.ac.uk>
Ffôn: 02920 879628


From:  on behalf of "Douglas N. Greve" 

Reply to: Freesurfer support list 
Date: Tuesday, 2 June 2020 at 18:39
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: Re: [Freesurfer] Bbregister misalignment {Disarmed}

If you upload the data, I'll take a look. Upload both the structural and the 
fMRI. See instructions below

From the linux command line,
Create the file you want to upload, eg,
cd $SUBJECTS_DIR
tar cvfz subject.tar.gz ./subject
Now log  into our anonymous FTP site:
ftp surfer.nmr.mgh.harvard.edu
It will ask you for a user name: use "anonymous" (no quotes)
It will ask you for a password: use "anonymous" (no quotes)
cd transfer/incoming
binary
put subject.tar.gz
Send an email that the file has been and the name of the file.


On 6/2/2020 9:14 AM, Mason Wells wrote:

External Email - Use Caution
Just a follow up here. I tried the command below on a machine with v.6, and the 
flag was recognised, but the registration was still off. No change to the 
output with the flag included.

Mason T Wells, MSc
PhD student
School of Optometry and Vision Sciences
& Cardiff University Brain Research
Imaging Centre (CUBRIC), School of Psychology
Cardiff University
Cardiff
CF24 4HQ
UK

Email: wells...@cardiff.ac.uk<mailto:wells...@cardiff.ac.uk>
Tel: 02920 879628
Web: Cardiff University 
webpage<https://www.cardiff.ac.uk/people/research-students/view/974214->
Mason T Wells, MSc
Myfyriwr PhD
Yr Ysgol Optometreg a Gwyddorau’r Golwg
& Canolfan Ymchwil Delweddu’r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr Ysgol 
Seicoleg
Prifysgol Caerdydd
Heol Maindy
Caerdydd
CF24 4HQ
DU

E-bost: wells...@caerdydd.ac.uk<mailto:wells...@caerdydd.ac.uk>
Ffôn: 02920 879628


From: 
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 on behalf of Mason Wells 
<mailto:wells...@cardiff.ac.uk>
Reply to: Freesurfer support list 
<mailto:freesurfer@nmr.mgh.harvard.edu>
Date: Tuesday, 2 June 2020 at 14:06
To: Freesurfer support list 
<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Bbregister misalignment {Disarmed}


External Email - Use Caution
Hi Doug,

I have FS v6.0 and tried the following command:

ERROR: Flag --init-coreg unrecognized.
--s PPT_001 --feat 
/cubric/data/c1749990/PhD/Data/PMA_retinoScans/PPT_001/run1_pre_processed_functional.feat/
 --int /cubric/data/c1749990/PhD/Data/PMA_retinoScans/PPT_001/WholeEPI.nii.gz 
--init-header --init-coreg

Still get the error. Is this correct use of the flags?

Mason T Wells, MSc
PhD student
School of Optometry and Vision Sciences
& Cardiff University Brain Research
Imaging Centre (CUBRIC), School of Psychology
Cardiff University
Cardiff
CF24 4HQ
UK

Email: wells...@cardiff.ac.uk<mailto:wells...@cardiff.ac.uk>
Tel: 02920 879628
Web: Cardiff University 
webpage<https://www.cardiff.ac.uk/people/research-students/view/974214->
Mason T Wells, MSc
Myfyriwr PhD
Yr Ysgol Optometreg a Gwyddorau’r Golwg
& Canolfan Ymchwil Delweddu’r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr Ysgol 
Seicoleg
Prifysgol Caerdydd
Heol Maindy
Caerdydd
CF24 4HQ
DU

E-bost: wells...@caerdydd.ac.uk<mailto:wells...@caerdydd.ac.uk>
Ffôn: 02920 879628


From: 
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 on behalf of "Douglas N. Greve" 
<mailto:dgr...@mgh.harvard.edu>
Reply to: Freesurfer support list 
<mailto:freesurfer@nmr.mgh.harvard.edu>
Date: Tuesday, 2 June 2020 at 13:48
To: "freesurfer@nmr.mgh.harvard.edu"<mailto:freesurfer@nmr.mgh.harvard.edu> 
<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Bbregister misalignment {Disarmed}

Right now, I'm just guessing what the problem is (I'm speculating that it is 
FSL FLIRT). You could download just the new bbregister and mri_coreg to your VM 
and see if it works.




On 6/2/2020 6:40 AM, Mason Wells wrote:

External Email - Use Caution
I am using version 5.3, this is the version on the virtual machine I am working 
from.

Re: [Freesurfer] Bbregister misalignment {Disarmed}

[Douglas N. Greve]

If you upload the data, I'll take a look. Upload both the structural and 
the fMRI. See instructions below


From the linux command line,
Create the file you want to upload, eg,
cd $SUBJECTS_DIR
tar cvfz subject.tar.gz ./subject
Now log  into our anonymous FTP site:
ftp surfer.nmr.mgh.harvard.edu
It will ask you for a user name: use "anonymous" (no quotes)
It will ask you for a password: use "anonymous" (no quotes)
cd transfer/incoming
binary
put subject.tar.gz
Send an email that the file has been and the name of the file.



On 6/2/2020 9:14 AM, Mason Wells wrote:


External Email - Use Caution

Just a follow up here. I tried the command below on a machine with 
v.6, and the flag was recognised, but the registration was still off. 
No change to the output with the flag included.


*Mason T Wells, MSc*

*PhD student*

School of Optometry and Vision Sciences

& Cardiff University Brain Research

Imaging Centre (CUBRIC), School of Psychology

Cardiff University

Cardiff

CF24 4HQ

UK

*/Email/*: wells...@cardiff.ac.uk <mailto:wells...@cardiff.ac.uk>

*/Tel/*: 02920 879628

*/Web/*: Cardiff University webpage 
<https://www.cardiff.ac.uk/people/research-students/view/974214->




*Mason T Wells, MSc*

*Myfyriwr PhD*

Yr Ysgol Optometreg a Gwyddorau’r Golwg

& Canolfan Ymchwil Delweddu’r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr 
Ysgol Seicoleg


Prifysgol Caerdydd

Heol Maindy

Caerdydd

CF24 4HQ

DU

*/E-bost/*: wells...@caerdydd.ac.uk <mailto:wells...@caerdydd.ac.uk>

*/Ffôn/*: 02920 879628

*From: * on behalf of Mason 
Wells 

*Reply to: *Freesurfer support list 
*Date: *Tuesday, 2 June 2020 at 14:06
*To: *Freesurfer support list 
*Subject: *Re: [Freesurfer] Bbregister misalignment {Disarmed}

*External Email - Use Caution *

Hi Doug,

I have FS v6.0 and tried the following command:

ERROR: Flag --init-coreg unrecognized.

--s PPT_001 --feat 
/cubric/data/c1749990/PhD/Data/PMA_retinoScans/PPT_001/run1_pre_processed_functional.feat/ 
--int 
/cubric/data/c1749990/PhD/Data/PMA_retinoScans/PPT_001/WholeEPI.nii.gz 
--init-header --init-coreg


Still get the error. Is this correct use of the flags?

*Mason T Wells, MSc*

*PhD student*

School of Optometry and Vision Sciences

& Cardiff University Brain Research

Imaging Centre (CUBRIC), School of Psychology

Cardiff University

Cardiff

CF24 4HQ

UK

*/Email/*: wells...@cardiff.ac.uk <mailto:wells...@cardiff.ac.uk>

*/Tel/*: 02920 879628

*/Web/*: Cardiff University webpage 
<https://www.cardiff.ac.uk/people/research-students/view/974214->




*Mason T Wells, MSc*

*Myfyriwr PhD*

Yr Ysgol Optometreg a Gwyddorau’r Golwg

& Canolfan Ymchwil Delweddu’r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr 
Ysgol Seicoleg


Prifysgol Caerdydd

Heol Maindy

Caerdydd

CF24 4HQ

DU

*/E-bost/*: wells...@caerdydd.ac.uk <mailto:wells...@caerdydd.ac.uk>

*/Ffôn/*: 02920 879628

*From: * on behalf of "Douglas 
N. Greve" 

*Reply to: *Freesurfer support list 
*Date: *Tuesday, 2 June 2020 at 13:48
*To: *"freesurfer@nmr.mgh.harvard.edu" 
*Subject: *Re: [Freesurfer] Bbregister misalignment {Disarmed}

Right now, I'm just guessing what the problem is (I'm speculating that 
it is FSL FLIRT). You could download just the new bbregister and 
mri_coreg to your VM and see if it works.




On 6/2/2020 6:40 AM, Mason Wells wrote:

*External Email - Use Caution *

I am using version 5.3, this is the version on the virtual machine
I am working from. I can ask about an updated version, but is
there a way to fix this on v5.3 in the meantime?

*Mason T Wells, MSc*

*PhD student*

School of Optometry and Vision Sciences

& Cardiff University Brain Research

Imaging Centre (CUBRIC), School of Psychology

Cardiff University

Cardiff

CF24 4HQ

UK

*/Email/*: wells...@cardiff.ac.uk <mailto:wells...@cardiff.ac.uk>

*/Tel/*: 02920 879628

*/Web/*: Cardiff University webpage
<https://www.cardiff.ac.uk/people/research-students/view/974214->



*Mason T Wells, MSc*

*Myfyriwr PhD*

Yr Ysgol Optometreg a Gwyddorau’r Golwg

& Canolfan Ymchwil Delweddu’r Ymennydd Prifysgol Caerdydd
(CUBRIC), Yr Ysgol Seicoleg

Prifysgol Caerdydd

Heol Maindy

Caerdydd

CF24 4HQ

DU

*/E-bost/*: wells...@caerdydd.ac.uk <mailto:wells...@caerdydd.ac.uk>

*/Ffôn/*: 02920 879628

*From: *
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of
"Douglas N. Greve" 
<mailto:dgr...@mgh.harvard.edu>
*Reply to: *Freesurfer support list

<mailto:freesurfer@nmr.mgh.harvard.edu>
*Date: *Monday, 1 June 2020 at 18:02
*To: *"freesurfer@nmr.mgh.harvard.edu"
<mailto:freesurfer@nmr.mgh.harvard.edu>

<mailto:freesurfer@nmr.mgh.harvard.edu>
*Subject: *Re

Re: [Freesurfer] Bbregister misalignment {Disarmed}

[Mason Wells]

External Email - Use Caution

Just a follow up here. I tried the command below on a machine with v.6, and the 
flag was recognised, but the registration was still off. No change to the 
output with the flag included.

Mason T Wells, MSc
PhD student
School of Optometry and Vision Sciences
& Cardiff University Brain Research
Imaging Centre (CUBRIC), School of Psychology
Cardiff University
Cardiff
CF24 4HQ
UK

Email: wells...@cardiff.ac.uk<mailto:wells...@cardiff.ac.uk>
Tel: 02920 879628
Web: Cardiff University 
webpage<https://www.cardiff.ac.uk/people/research-students/view/974214->
Mason T Wells, MSc
Myfyriwr PhD
Yr Ysgol Optometreg a Gwyddorau’r Golwg
& Canolfan Ymchwil Delweddu’r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr Ysgol 
Seicoleg
Prifysgol Caerdydd
Heol Maindy
Caerdydd
CF24 4HQ
DU

E-bost: wells...@caerdydd.ac.uk<mailto:wells...@caerdydd.ac.uk>
Ffôn: 02920 879628


From:  on behalf of Mason Wells 

Reply to: Freesurfer support list 
Date: Tuesday, 2 June 2020 at 14:06
To: Freesurfer support list 
Subject: Re: [Freesurfer] Bbregister misalignment {Disarmed}


External Email - Use Caution
Hi Doug,

I have FS v6.0 and tried the following command:

ERROR: Flag --init-coreg unrecognized.
--s PPT_001 --feat 
/cubric/data/c1749990/PhD/Data/PMA_retinoScans/PPT_001/run1_pre_processed_functional.feat/
 --int /cubric/data/c1749990/PhD/Data/PMA_retinoScans/PPT_001/WholeEPI.nii.gz 
--init-header --init-coreg

Still get the error. Is this correct use of the flags?

Mason T Wells, MSc
PhD student
School of Optometry and Vision Sciences
& Cardiff University Brain Research
Imaging Centre (CUBRIC), School of Psychology
Cardiff University
Cardiff
CF24 4HQ
UK

Email: wells...@cardiff.ac.uk<mailto:wells...@cardiff.ac.uk>
Tel: 02920 879628
Web: Cardiff University 
webpage<https://www.cardiff.ac.uk/people/research-students/view/974214->
Mason T Wells, MSc
Myfyriwr PhD
Yr Ysgol Optometreg a Gwyddorau’r Golwg
& Canolfan Ymchwil Delweddu’r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr Ysgol 
Seicoleg
Prifysgol Caerdydd
Heol Maindy
Caerdydd
CF24 4HQ
DU

E-bost: wells...@caerdydd.ac.uk<mailto:wells...@caerdydd.ac.uk>
Ffôn: 02920 879628


From:  on behalf of "Douglas N. Greve" 

Reply to: Freesurfer support list 
Date: Tuesday, 2 June 2020 at 13:48
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: Re: [Freesurfer] Bbregister misalignment {Disarmed}

Right now, I'm just guessing what the problem is (I'm speculating that it is 
FSL FLIRT). You could download just the new bbregister and mri_coreg to your VM 
and see if it works.



On 6/2/2020 6:40 AM, Mason Wells wrote:

External Email - Use Caution
I am using version 5.3, this is the version on the virtual machine I am working 
from. I can ask about an updated version, but is there a way to fix this on 
v5.3 in the meantime?

Mason T Wells, MSc
PhD student
School of Optometry and Vision Sciences
& Cardiff University Brain Research
Imaging Centre (CUBRIC), School of Psychology
Cardiff University
Cardiff
CF24 4HQ
UK

Email: wells...@cardiff.ac.uk<mailto:wells...@cardiff.ac.uk>
Tel: 02920 879628
Web: Cardiff University 
webpage<https://www.cardiff.ac.uk/people/research-students/view/974214->
Mason T Wells, MSc
Myfyriwr PhD
Yr Ysgol Optometreg a Gwyddorau’r Golwg
& Canolfan Ymchwil Delweddu’r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr Ysgol 
Seicoleg
Prifysgol Caerdydd
Heol Maindy
Caerdydd
CF24 4HQ
DU

E-bost: wells...@caerdydd.ac.uk<mailto:wells...@caerdydd.ac.uk>
Ffôn: 02920 879628


From: 
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 on behalf of "Douglas N. Greve" 
<mailto:dgr...@mgh.harvard.edu>
Reply to: Freesurfer support list 
<mailto:freesurfer@nmr.mgh.harvard.edu>
Date: Monday, 1 June 2020 at 18:02
To: "freesurfer@nmr.mgh.harvard.edu"<mailto:freesurfer@nmr.mgh.harvard.edu> 
<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Bbregister misalignment {Disarmed}

What version of FS are you running? That flag was introduced with v6
On 6/1/2020 12:57 PM, Mason Wells wrote:

External Email - Use Caution
Hi Doug,

That flag isn’t recognised in the terminal? Have I placed the flag in the wrong 
place? I tried it between the –feat and the directory, same outcome.

bbregister --s PPT_001 --feat 
/cubric/data/c1749990/PhD/Data/PMA_retinoScans/PPT_001/run1_pre_processed_functional.feat/
 --int /cubric/data/c1749990/PhD/Data/PMA_retinoScans/PPT_001/WholeEPI.nii.gz 
--init-header --init-coreg

ERROR: Flag --init-coreg unrecognized.
--s PPT_001 --feat 
/cubric/data/c1749990/PhD/Data/PMA_retinoScans/PPT_001/run1_pre_processed_

Mason T Wells, MSc
PhD student
School of Optometry and Vision Sciences
& Cardiff University Brain Research
Imaging Centre (CUBRIC), School of Psychology
Cardiff University
Cardiff
CF24 4HQ
UK

Email: wells...@cardiff.ac.uk<mailto:wells...@cardiff.ac.uk>

Re: [Freesurfer] Bbregister misalignment {Disarmed}

[Mason Wells]

External Email - Use Caution

Hi Doug,

I have FS v6.0 and tried the following command:

ERROR: Flag --init-coreg unrecognized.
--s PPT_001 --feat 
/cubric/data/c1749990/PhD/Data/PMA_retinoScans/PPT_001/run1_pre_processed_functional.feat/
 --int /cubric/data/c1749990/PhD/Data/PMA_retinoScans/PPT_001/WholeEPI.nii.gz 
--init-header --init-coreg

Still get the error. Is this correct use of the flags?

Mason T Wells, MSc
PhD student
School of Optometry and Vision Sciences
& Cardiff University Brain Research
Imaging Centre (CUBRIC), School of Psychology
Cardiff University
Cardiff
CF24 4HQ
UK

Email: wells...@cardiff.ac.uk<mailto:wells...@cardiff.ac.uk>
Tel: 02920 879628
Web: Cardiff University 
webpage<https://www.cardiff.ac.uk/people/research-students/view/974214->
Mason T Wells, MSc
Myfyriwr PhD
Yr Ysgol Optometreg a Gwyddorau’r Golwg
& Canolfan Ymchwil Delweddu’r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr Ysgol 
Seicoleg
Prifysgol Caerdydd
Heol Maindy
Caerdydd
CF24 4HQ
DU

E-bost: wells...@caerdydd.ac.uk<mailto:wells...@caerdydd.ac.uk>
Ffôn: 02920 879628


From:  on behalf of "Douglas N. Greve" 

Reply to: Freesurfer support list 
Date: Tuesday, 2 June 2020 at 13:48
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: Re: [Freesurfer] Bbregister misalignment {Disarmed}

Right now, I'm just guessing what the problem is (I'm speculating that it is 
FSL FLIRT). You could download just the new bbregister and mri_coreg to your VM 
and see if it works.


On 6/2/2020 6:40 AM, Mason Wells wrote:

External Email - Use Caution
I am using version 5.3, this is the version on the virtual machine I am working 
from. I can ask about an updated version, but is there a way to fix this on 
v5.3 in the meantime?

Mason T Wells, MSc
PhD student
School of Optometry and Vision Sciences
& Cardiff University Brain Research
Imaging Centre (CUBRIC), School of Psychology
Cardiff University
Cardiff
CF24 4HQ
UK

Email: wells...@cardiff.ac.uk<mailto:wells...@cardiff.ac.uk>
Tel: 02920 879628
Web: Cardiff University 
webpage<https://www.cardiff.ac.uk/people/research-students/view/974214->
Mason T Wells, MSc
Myfyriwr PhD
Yr Ysgol Optometreg a Gwyddorau’r Golwg
& Canolfan Ymchwil Delweddu’r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr Ysgol 
Seicoleg
Prifysgol Caerdydd
Heol Maindy
Caerdydd
CF24 4HQ
DU

E-bost: wells...@caerdydd.ac.uk<mailto:wells...@caerdydd.ac.uk>
Ffôn: 02920 879628


From: 
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 on behalf of "Douglas N. Greve" 
<mailto:dgr...@mgh.harvard.edu>
Reply to: Freesurfer support list 
<mailto:freesurfer@nmr.mgh.harvard.edu>
Date: Monday, 1 June 2020 at 18:02
To: "freesurfer@nmr.mgh.harvard.edu"<mailto:freesurfer@nmr.mgh.harvard.edu> 
<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Bbregister misalignment {Disarmed}

What version of FS are you running? That flag was introduced with v6
On 6/1/2020 12:57 PM, Mason Wells wrote:

External Email - Use Caution
Hi Doug,

That flag isn’t recognised in the terminal? Have I placed the flag in the wrong 
place? I tried it between the –feat and the directory, same outcome.

bbregister --s PPT_001 --feat 
/cubric/data/c1749990/PhD/Data/PMA_retinoScans/PPT_001/run1_pre_processed_functional.feat/
 --int /cubric/data/c1749990/PhD/Data/PMA_retinoScans/PPT_001/WholeEPI.nii.gz 
--init-header --init-coreg

ERROR: Flag --init-coreg unrecognized.
--s PPT_001 --feat 
/cubric/data/c1749990/PhD/Data/PMA_retinoScans/PPT_001/run1_pre_processed_

Mason T Wells, MSc
PhD student
School of Optometry and Vision Sciences
& Cardiff University Brain Research
Imaging Centre (CUBRIC), School of Psychology
Cardiff University
Cardiff
CF24 4HQ
UK

Email: wells...@cardiff.ac.uk<mailto:wells...@cardiff.ac.uk>
Tel: 02920 879628
Web: Cardiff University 
webpage<https://www.cardiff.ac.uk/people/research-students/view/974214->
Mason T Wells, MSc
Myfyriwr PhD
Yr Ysgol Optometreg a Gwyddorau’r Golwg
& Canolfan Ymchwil Delweddu’r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr Ysgol 
Seicoleg
Prifysgol Caerdydd
Heol Maindy
Caerdydd
CF24 4HQ
DU

E-bost: wells...@caerdydd.ac.uk<mailto:wells...@caerdydd.ac.uk>
Ffôn: 02920 879628


From: 
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 on behalf of "Douglas N. Greve" 
<mailto:dgr...@mgh.harvard.edu>
Reply to: Freesurfer support list 
<mailto:freesurfer@nmr.mgh.harvard.edu>
Date: Monday, 1 June 2020 at 17:38
To: "freesurfer@nmr.mgh.harvard.edu"<mailto:freesurfer@nmr.mgh.harvard.edu> 
<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Bbregister misalignment

Sorry for missing your first email. Can you try adding --init-coreg to your 
first bbregister command? Make sure to add it AFTER --feat
On 6/1/2020 12:06 PM, Mason Wells wrote:

External Email - Use Caution
Hi Experts,

I post

Re: [Freesurfer] Bbregister misalignment {Disarmed}

[Douglas N. Greve]

Right now, I'm just guessing what the problem is (I'm speculating that 
it is FSL FLIRT). You could download just the new bbregister and 
mri_coreg to your VM and see if it works.




On 6/2/2020 6:40 AM, Mason Wells wrote:


External Email - Use Caution

I am using version 5.3, this is the version on the virtual machine I 
am working from. I can ask about an updated version, but is there a 
way to fix this on v5.3 in the meantime?


*Mason T Wells, MSc*

*PhD student*

School of Optometry and Vision Sciences

& Cardiff University Brain Research

Imaging Centre (CUBRIC), School of Psychology

Cardiff University

Cardiff

CF24 4HQ

UK

*/Email/*: wells...@cardiff.ac.uk <mailto:wells...@cardiff.ac.uk>

*/Tel/*: 02920 879628

*/Web/*: Cardiff University webpage 
<https://www.cardiff.ac.uk/people/research-students/view/974214->




*Mason T Wells, MSc*

*Myfyriwr PhD*

Yr Ysgol Optometreg a Gwyddorau’r Golwg

& Canolfan Ymchwil Delweddu’r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr 
Ysgol Seicoleg


Prifysgol Caerdydd

Heol Maindy

Caerdydd

CF24 4HQ

DU

*/E-bost/*: wells...@caerdydd.ac.uk <mailto:wells...@caerdydd.ac.uk>

*/Ffôn/*: 02920 879628

*From: * on behalf of "Douglas 
N. Greve" 

*Reply to: *Freesurfer support list 
*Date: *Monday, 1 June 2020 at 18:02
*To: *"freesurfer@nmr.mgh.harvard.edu" 
*Subject: *Re: [Freesurfer] Bbregister misalignment {Disarmed}

What version of FS are you running? That flag was introduced with v6

On 6/1/2020 12:57 PM, Mason Wells wrote:

*External Email - Use Caution *

Hi Doug,

That flag isn’t recognised in the terminal? Have I placed the flag
in the wrong place? I tried it between the –feat and the
directory, same outcome.

bbregister --s PPT_001 --feat

/cubric/data/c1749990/PhD/Data/PMA_retinoScans/PPT_001/run1_pre_processed_functional.feat/
--int
/cubric/data/c1749990/PhD/Data/PMA_retinoScans/PPT_001/WholeEPI.nii.gz
--init-header --init-coreg

ERROR: Flag --init-coreg unrecognized.

--s PPT_001 --feat
/cubric/data/c1749990/PhD/Data/PMA_retinoScans/PPT_001/run1_pre_processed_

*Mason T Wells, MSc*

*PhD student*

School of Optometry and Vision Sciences

& Cardiff University Brain Research

Imaging Centre (CUBRIC), School of Psychology

Cardiff University

Cardiff

CF24 4HQ

UK

*/Email/*: wells...@cardiff.ac.uk <mailto:wells...@cardiff.ac.uk>

*/Tel/*: 02920 879628

*/Web/*: Cardiff University webpage
<https://www.cardiff.ac.uk/people/research-students/view/974214->



*Mason T Wells, MSc*

*Myfyriwr PhD*

Yr Ysgol Optometreg a Gwyddorau’r Golwg

& Canolfan Ymchwil Delweddu’r Ymennydd Prifysgol Caerdydd
(CUBRIC), Yr Ysgol Seicoleg

Prifysgol Caerdydd

Heol Maindy

Caerdydd

CF24 4HQ

DU

*/E-bost/*: wells...@caerdydd.ac.uk <mailto:wells...@caerdydd.ac.uk>

*/Ffôn/*: 02920 879628

*From: *
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of
"Douglas N. Greve" 
<mailto:dgr...@mgh.harvard.edu>
*Reply to: *Freesurfer support list

<mailto:freesurfer@nmr.mgh.harvard.edu>
*Date: *Monday, 1 June 2020 at 17:38
*To: *"freesurfer@nmr.mgh.harvard.edu"
    <mailto:freesurfer@nmr.mgh.harvard.edu>

<mailto:freesurfer@nmr.mgh.harvard.edu>
*Subject: *Re: [Freesurfer] Bbregister misalignment

Sorry for missing your first email. Can you try adding
--init-coreg to your first bbregister command? Make sure to add it
AFTER --feat

On 6/1/2020 12:06 PM, Mason Wells wrote:

*External Email - Use Caution *

Hi Experts,

I posted earlier, but I believe my message has not been posted
due to the size of attachments so I’ve removed them.

I am using bbregister to align functional data to anatomical
space. I have been using the bbregister command with a
combination of different flags. However, there appears to be
varying levels of poor registration.

The first command I used included flags for a whole brain ref
image and the --init-header flag. This leads to a misalignment.

bbregister --s PPT_1x --feat
 /Data/PMA_retinoScans/PPT_1x/run1_pre_processed_functional.feat/
--int  Data/PMA_retinoScans/PPT_1x/WholeEPI.nii.gz --init-header

I then removed the –int (whole brain reg image) flag. Again
the registration is massively misaligned.

bbregister --s PPT_1x --feat
 /Data/PMA_retinoScans/PPT_1x/run1_pre_processed_functional.feat
--init-header

I then removed the –init-header flag. Again poor registration.

Then I removed both flags. This was the best registration, but
even this still looks a little bit off to me. You can see that
around the

Re: [Freesurfer] Bbregister misalignment {Disarmed}

[Mason Wells]

External Email - Use Caution

I am using version 5.3, this is the version on the virtual machine I am working 
from. I can ask about an updated version, but is there a way to fix this on 
v5.3 in the meantime?

Mason T Wells, MSc
PhD student
School of Optometry and Vision Sciences
& Cardiff University Brain Research
Imaging Centre (CUBRIC), School of Psychology
Cardiff University
Cardiff
CF24 4HQ
UK

Email: wells...@cardiff.ac.uk<mailto:wells...@cardiff.ac.uk>
Tel: 02920 879628
Web: Cardiff University 
webpage<https://www.cardiff.ac.uk/people/research-students/view/974214->
Mason T Wells, MSc
Myfyriwr PhD
Yr Ysgol Optometreg a Gwyddorau’r Golwg
& Canolfan Ymchwil Delweddu’r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr Ysgol 
Seicoleg
Prifysgol Caerdydd
Heol Maindy
Caerdydd
CF24 4HQ
DU

E-bost: wells...@caerdydd.ac.uk<mailto:wells...@caerdydd.ac.uk>
Ffôn: 02920 879628


From:  on behalf of "Douglas N. Greve" 

Reply to: Freesurfer support list 
Date: Monday, 1 June 2020 at 18:02
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: Re: [Freesurfer] Bbregister misalignment {Disarmed}

What version of FS are you running? That flag was introduced with v6
On 6/1/2020 12:57 PM, Mason Wells wrote:

External Email - Use Caution
Hi Doug,

That flag isn’t recognised in the terminal? Have I placed the flag in the wrong 
place? I tried it between the –feat and the directory, same outcome.

bbregister --s PPT_001 --feat 
/cubric/data/c1749990/PhD/Data/PMA_retinoScans/PPT_001/run1_pre_processed_functional.feat/
 --int /cubric/data/c1749990/PhD/Data/PMA_retinoScans/PPT_001/WholeEPI.nii.gz 
--init-header --init-coreg

ERROR: Flag --init-coreg unrecognized.
--s PPT_001 --feat 
/cubric/data/c1749990/PhD/Data/PMA_retinoScans/PPT_001/run1_pre_processed_

Mason T Wells, MSc
PhD student
School of Optometry and Vision Sciences
& Cardiff University Brain Research
Imaging Centre (CUBRIC), School of Psychology
Cardiff University
Cardiff
CF24 4HQ
UK

Email: wells...@cardiff.ac.uk<mailto:wells...@cardiff.ac.uk>
Tel: 02920 879628
Web: Cardiff University 
webpage<https://www.cardiff.ac.uk/people/research-students/view/974214->
Mason T Wells, MSc
Myfyriwr PhD
Yr Ysgol Optometreg a Gwyddorau’r Golwg
& Canolfan Ymchwil Delweddu’r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr Ysgol 
Seicoleg
Prifysgol Caerdydd
Heol Maindy
Caerdydd
CF24 4HQ
DU

E-bost: wells...@caerdydd.ac.uk<mailto:wells...@caerdydd.ac.uk>
Ffôn: 02920 879628


From: 
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 on behalf of "Douglas N. Greve" 
<mailto:dgr...@mgh.harvard.edu>
Reply to: Freesurfer support list 
<mailto:freesurfer@nmr.mgh.harvard.edu>
Date: Monday, 1 June 2020 at 17:38
To: "freesurfer@nmr.mgh.harvard.edu"<mailto:freesurfer@nmr.mgh.harvard.edu> 
<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Bbregister misalignment

Sorry for missing your first email. Can you try adding --init-coreg to your 
first bbregister command? Make sure to add it AFTER --feat
On 6/1/2020 12:06 PM, Mason Wells wrote:

External Email - Use Caution
Hi Experts,

I posted earlier, but I believe my message has not been posted due to the size 
of attachments so I’ve removed them.

I am using bbregister to align functional data to anatomical space. I have been 
using the bbregister command with a combination of different flags. However, 
there appears to be varying levels of poor registration.

The first command I used included flags for a whole brain ref image and the 
--init-header flag. This leads to a misalignment.

bbregister --s PPT_1x --feat  
/Data/PMA_retinoScans/PPT_1x/run1_pre_processed_functional.feat/ --int  
Data/PMA_retinoScans/PPT_1x/WholeEPI.nii.gz --init-header

I then removed the –int (whole brain reg image) flag. Again the registration is 
massively misaligned.

bbregister --s PPT_1x --feat  
/Data/PMA_retinoScans/PPT_1x/run1_pre_processed_functional.feat --init-header

I then removed the –init-header flag. Again poor registration.

Then I removed both flags. This was the best registration, but even this still 
looks a little bit off to me. You can see that around the occipital lobe (reg3 
attached), there white matter isn't aligned very well.

bbregister --s PPT_1x --feat /Data/PPT_1x/run1_pre_processed_functional.feat/

Can anyone give me any advice on this? I really am unsure as to which why these 
flags failed to aid registration. I have 3 other participants from a different 
dataset for which the bbregister pointing to the feat directory and the 
–init-header flag worked perfectly. Have I missed an important step that could 
explain why no combination seems to register the data correctly?

Any advice would be great.
Thanks in advance,
Mason


Mason T Wells, MSc
PhD student
School of Optometry and Vision Sciences
& Cardiff University Brain Research
Imaging Centre (CUBRIC), School of Psychology
Cardi

Re: [Freesurfer] Bbregister misalignment {Disarmed}

[Douglas N. Greve]

What version of FS are you running? That flag was introduced with v6

On 6/1/2020 12:57 PM, Mason Wells wrote:


External Email - Use Caution

Hi Doug,

That flag isn’t recognised in the terminal? Have I placed the flag in 
the wrong place? I tried it between the –feat and the directory, same 
outcome.


bbregister --s PPT_001 --feat 
/cubric/data/c1749990/PhD/Data/PMA_retinoScans/PPT_001/run1_pre_processed_functional.feat/ 
--int 
/cubric/data/c1749990/PhD/Data/PMA_retinoScans/PPT_001/WholeEPI.nii.gz 
--init-header --init-coreg


ERROR: Flag --init-coreg unrecognized.

--s PPT_001 --feat 
/cubric/data/c1749990/PhD/Data/PMA_retinoScans/PPT_001/run1_pre_processed_


*Mason T Wells, MSc*

*PhD student*

School of Optometry and Vision Sciences

& Cardiff University Brain Research

Imaging Centre (CUBRIC), School of Psychology

Cardiff University

Cardiff

CF24 4HQ

UK

*/Email/*: wells...@cardiff.ac.uk <mailto:wells...@cardiff.ac.uk>

*/Tel/*: 02920 879628

*/Web/*: Cardiff University webpage 
<https://www.cardiff.ac.uk/people/research-students/view/974214->




*Mason T Wells, MSc*

*Myfyriwr PhD*

Yr Ysgol Optometreg a Gwyddorau’r Golwg

& Canolfan Ymchwil Delweddu’r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr 
Ysgol Seicoleg


Prifysgol Caerdydd

Heol Maindy

Caerdydd

CF24 4HQ

DU

*/E-bost/*: wells...@caerdydd.ac.uk <mailto:wells...@caerdydd.ac.uk>

*/Ffôn/*: 02920 879628

*From: * on behalf of "Douglas 
N. Greve" 

*Reply to: *Freesurfer support list 
*Date: *Monday, 1 June 2020 at 17:38
*To: *"freesurfer@nmr.mgh.harvard.edu" 
*Subject: *Re: [Freesurfer] Bbregister misalignment

Sorry for missing your first email. Can you try adding --init-coreg to 
your first bbregister command? Make sure to add it AFTER --feat


On 6/1/2020 12:06 PM, Mason Wells wrote:

*External Email - Use Caution *

Hi Experts,

I posted earlier, but I believe my message has not been posted due
to the size of attachments so I’ve removed them.

I am using bbregister to align functional data to anatomical
space. I have been using the bbregister command with a combination
of different flags. However, there appears to be varying levels of
poor registration.

The first command I used included flags for a whole brain ref
image and the --init-header flag. This leads to a misalignment.

bbregister --s PPT_1x --feat
 /Data/PMA_retinoScans/PPT_1x/run1_pre_processed_functional.feat/
--int  Data/PMA_retinoScans/PPT_1x/WholeEPI.nii.gz --init-header

I then removed the –int (whole brain reg image) flag. Again the
registration is massively misaligned.

bbregister --s PPT_1x --feat
 /Data/PMA_retinoScans/PPT_1x/run1_pre_processed_functional.feat
--init-header

I then removed the –init-header flag. Again poor registration.

Then I removed both flags. This was the best registration, but
even this still looks a little bit off to me. You can see that
around the occipital lobe (reg3 attached), there white matter
isn't aligned very well.

bbregister --s PPT_1x --feat
/Data/PPT_1x/run1_pre_processed_functional.feat/

Can anyone give me any advice on this? I really am unsure as to
which why these flags failed to aid registration. I have 3 other
participants from a different dataset for which the bbregister
pointing to the feat directory *and *the –init-header flag worked
perfectly. Have I missed an important step that could explain why
no combination seems to register the data correctly?

Any advice would be great.

Thanks in advance,

Mason

*Mason T Wells, MSc*

*PhD student*

School of Optometry and Vision Sciences

& Cardiff University Brain Research

Imaging Centre (CUBRIC), School of Psychology

Cardiff University

Cardiff

CF24 4HQ

UK

*/Email/*: wells...@cardiff.ac.uk <mailto:wells...@cardiff.ac.uk>

*/Tel/*: 02920 879628

*/Web/*: Cardiff University webpage
<https://www.cardiff.ac.uk/people/research-students/view/974214->



*Mason T Wells, MSc*

*Myfyriwr PhD*

Yr Ysgol Optometreg a Gwyddorau’r Golwg

& Canolfan Ymchwil Delweddu’r Ymennydd Prifysgol Caerdydd
(CUBRIC), Yr Ysgol Seicoleg

Prifysgol Caerdydd

Heol Maindy

Caerdydd

CF24 4HQ

DU

*/E-bost/*: wells...@caerdydd.ac.uk <mailto:wells...@caerdydd.ac.uk>

*/Ffôn/*: 02920 879628



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Re: [Freesurfer] Bbregister misalignment {Disarmed}

[Mason Wells]

External Email - Use Caution

Hi Doug,

That flag isn’t recognised in the terminal? Have I placed the flag in the wrong 
place? I tried it between the –feat and the directory, same outcome.

bbregister --s PPT_001 --feat 
/cubric/data/c1749990/PhD/Data/PMA_retinoScans/PPT_001/run1_pre_processed_functional.feat/
 --int /cubric/data/c1749990/PhD/Data/PMA_retinoScans/PPT_001/WholeEPI.nii.gz 
--init-header --init-coreg

ERROR: Flag --init-coreg unrecognized.
--s PPT_001 --feat 
/cubric/data/c1749990/PhD/Data/PMA_retinoScans/PPT_001/run1_pre_processed_

Mason T Wells, MSc
PhD student
School of Optometry and Vision Sciences
& Cardiff University Brain Research
Imaging Centre (CUBRIC), School of Psychology
Cardiff University
Cardiff
CF24 4HQ
UK

Email: wells...@cardiff.ac.uk<mailto:wells...@cardiff.ac.uk>
Tel: 02920 879628
Web: Cardiff University 
webpage<https://www.cardiff.ac.uk/people/research-students/view/974214->
Mason T Wells, MSc
Myfyriwr PhD
Yr Ysgol Optometreg a Gwyddorau’r Golwg
& Canolfan Ymchwil Delweddu’r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr Ysgol 
Seicoleg
Prifysgol Caerdydd
Heol Maindy
Caerdydd
CF24 4HQ
DU

E-bost: wells...@caerdydd.ac.uk<mailto:wells...@caerdydd.ac.uk>
Ffôn: 02920 879628


From:  on behalf of "Douglas N. Greve" 

Reply to: Freesurfer support list 
Date: Monday, 1 June 2020 at 17:38
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: Re: [Freesurfer] Bbregister misalignment

Sorry for missing your first email. Can you try adding --init-coreg to your 
first bbregister command? Make sure to add it AFTER --feat
On 6/1/2020 12:06 PM, Mason Wells wrote:

External Email - Use Caution
Hi Experts,

I posted earlier, but I believe my message has not been posted due to the size 
of attachments so I’ve removed them.

I am using bbregister to align functional data to anatomical space. I have been 
using the bbregister command with a combination of different flags. However, 
there appears to be varying levels of poor registration.

The first command I used included flags for a whole brain ref image and the 
--init-header flag. This leads to a misalignment.

bbregister --s PPT_1x --feat  
/Data/PMA_retinoScans/PPT_1x/run1_pre_processed_functional.feat/ --int  
Data/PMA_retinoScans/PPT_1x/WholeEPI.nii.gz --init-header

I then removed the –int (whole brain reg image) flag. Again the registration is 
massively misaligned.

bbregister --s PPT_1x --feat  
/Data/PMA_retinoScans/PPT_1x/run1_pre_processed_functional.feat --init-header

I then removed the –init-header flag. Again poor registration.

Then I removed both flags. This was the best registration, but even this still 
looks a little bit off to me. You can see that around the occipital lobe (reg3 
attached), there white matter isn't aligned very well.

bbregister --s PPT_1x --feat /Data/PPT_1x/run1_pre_processed_functional.feat/

Can anyone give me any advice on this? I really am unsure as to which why these 
flags failed to aid registration. I have 3 other participants from a different 
dataset for which the bbregister pointing to the feat directory and the 
–init-header flag worked perfectly. Have I missed an important step that could 
explain why no combination seems to register the data correctly?

Any advice would be great.
Thanks in advance,
Mason


Mason T Wells, MSc
PhD student
School of Optometry and Vision Sciences
& Cardiff University Brain Research
Imaging Centre (CUBRIC), School of Psychology
Cardiff University
Cardiff
CF24 4HQ
UK

Email: wells...@cardiff.ac.uk<mailto:wells...@cardiff.ac.uk>
Tel: 02920 879628
Web: Cardiff University 
webpage<https://www.cardiff.ac.uk/people/research-students/view/974214->
Mason T Wells, MSc
Myfyriwr PhD
Yr Ysgol Optometreg a Gwyddorau’r Golwg
& Canolfan Ymchwil Delweddu’r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr Ysgol 
Seicoleg
Prifysgol Caerdydd
Heol Maindy
Caerdydd
CF24 4HQ
DU

E-bost: wells...@caerdydd.ac.uk<mailto:wells...@caerdydd.ac.uk>
Ffôn: 02920 879628




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Re: [Freesurfer] Bbregister misalignment

[Douglas N. Greve]

Sorry for missing your first email. Can you try adding --init-coreg to 
your first bbregister command? Make sure to add it AFTER --feat


On 6/1/2020 12:06 PM, Mason Wells wrote:


External Email - Use Caution

Hi Experts,

I posted earlier, but I believe my message has not been posted due to 
the size of attachments so I’ve removed them.


I am using bbregister to align functional data to anatomical space. I 
have been using the bbregister command with a combination of different 
flags. However, there appears to be varying levels of poor registration.


The first command I used included flags for a whole brain ref image 
and the --init-header flag. This leads to a misalignment.


bbregister --s PPT_1x --feat 
 /Data/PMA_retinoScans/PPT_1x/run1_pre_processed_functional.feat/ 
--int  Data/PMA_retinoScans/PPT_1x/WholeEPI.nii.gz --init-header


I then removed the –int (whole brain reg image) flag. Again the 
registration is massively misaligned.


bbregister --s PPT_1x --feat 
 /Data/PMA_retinoScans/PPT_1x/run1_pre_processed_functional.feat 
--init-header


I then removed the –init-header flag. Again poor registration.

Then I removed both flags. This was the best registration, but even 
this still looks a little bit off to me. You can see that around the 
occipital lobe (reg3 attached), there white matter isn't aligned very 
well.


bbregister --s PPT_1x --feat 
/Data/PPT_1x/run1_pre_processed_functional.feat/


Can anyone give me any advice on this? I really am unsure as to which 
why these flags failed to aid registration. I have 3 other 
participants from a different dataset for which the bbregister 
pointing to the feat directory *and *the –init-header flag worked 
perfectly. Have I missed an important step that could explain why no 
combination seems to register the data correctly?


Any advice would be great.

Thanks in advance,

Mason

*Mason T Wells, MSc*

*PhD student*

School of Optometry and Vision Sciences

& Cardiff University Brain Research

Imaging Centre (CUBRIC), School of Psychology

Cardiff University

Cardiff

CF24 4HQ

UK

*/Email/*: wells...@cardiff.ac.uk 

*/Tel/*: 02920 879628

*/Web/*: Cardiff University webpage 





*Mason T Wells, MSc*

*Myfyriwr PhD*

Yr Ysgol Optometreg a Gwyddorau’r Golwg

& Canolfan Ymchwil Delweddu’r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr 
Ysgol Seicoleg


Prifysgol Caerdydd

Heol Maindy

Caerdydd

CF24 4HQ

DU

*/E-bost/*: wells...@caerdydd.ac.uk 

*/Ffôn/*: 02920 879628


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Re: [Freesurfer] bbregister & mri_convert

[Octavian Lie]

External Email - Use Caution

Thank you.  Can you please clarify, documentation for mri_convert states
default for resampling is -interpolate, does this mean trilinear? Also,
which method is preferable for bbregister (I am applying it for
intrasubject uni and multimodal registration), trilinear or cubic
interpolation? I assume trilinear if that is the default, but cubic is
listed in recon-all dev table in the -T2pial (multimodal) step, see below.
Thank you again, Octavian

bbregister --s  --mov mri/orig/T2raw.mgz --lta
mri/transforms/T2raw.lta --init-fsl --T2

transforms/T2raw.lta

orig/T2raw.mgz

mri_convert -odt short -at mri/transforms/T2raw.lta -rt *cubic* -ns 1 -rl
mri/orig.mgz mri/orig/T2raw.mgz mri/T2.prenorm.mgz

On Thu, Apr 30, 2020 at 1:16 PM Douglas N. Greve 
wrote:

> It will but, it will always be resampled with trilinear interpolation.
>
> On 4/30/2020 12:55 PM, Octavian Lie wrote:
>
> External Email - Use Caution
>
> Dear All,
>
> I have seen bbregister command lines using --o option to get the final
> output (say a .nii vol), and others where bbregister is used to get an lta
> transform, which is used in a follow-up step (mri_convert with -ns 1 (no
> scale), and -rl orig.mgz (reslice-like)
>
>
> Are these options equivalent? meaning
> when using bbregister with '--o x.nii' option, is the output volume x.nii
> resliced to orig.mgz, and without rescale?
>
> Thanks,
> Octavian
>
> ___
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>
>
> ___
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Re: [Freesurfer] bbregister & mri_convert

[Douglas N. Greve]

It will but, it will always be resampled with trilinear interpolation.

On 4/30/2020 12:55 PM, Octavian Lie wrote:


External Email - Use Caution


Dear All,

I have seen bbregister command lines using --o option to get the final 
output (say a .nii vol), and others where bbregister is used to get an 
lta transform, which is used in a follow-up step (mri_convert with -ns 
1 (no scale), and -rl orig.mgz (reslice-like)



Are these options equivalent? meaning
when using bbregister with '--o x.nii' option, is the output volume 
x.nii  resliced to orig.mgz, and without rescale?


Thanks,
Octavian

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[Freesurfer] bbregister & mri_convert

[Octavian Lie]

External Email - Use Caution

Dear All,

I have seen bbregister command lines using --o option to get the final
output (say a .nii vol), and others where bbregister is used to get an lta
transform, which is used in a follow-up step (mri_convert with -ns 1 (no
scale), and -rl orig.mgz (reslice-like)


Are these options equivalent? meaning
when using bbregister with '--o x.nii' option, is the output volume x.nii
resliced to orig.mgz, and without rescale?

Thanks,
Octavian
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Re: [Freesurfer] bbregister- switched coronal and axial views error

[Greve, Douglas N.,Ph.D.]

What version of FS are you using? If before 6.0 (eg, 5,3), then it may 
be an error with the initialization. This is much improved in version 6.

On 6/18/2019 5:38 PM, Wenzhen Zhao wrote:
>  External Email - Use Caution
>
> Dear list,
>
> After running preproc-sess on fmri data, bbr-sum was 0.94. After looking 
> through images of template.nii.gz with register.dof6.lta file, I found that 
> coronal and axial views of template(w/ registration applied) are switched.
>
> $preproc-sess -s sess01 -fsd rest -surface fsaverage lhrh -mni305 -fwhm 5 
> -per-run
>
> Is there any possible error that I might have made?
> or is there any way to fix it?
>
> I appreciate your help!
>
> Thanks,
> Wenzhen
>
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[Freesurfer] bbregister- switched coronal and axial views error

[Wenzhen Zhao]

External Email - Use Caution

Dear list,

After running preproc-sess on fmri data, bbr-sum was 0.94. After looking 
through images of template.nii.gz with register.dof6.lta file, I found that 
coronal and axial views of template(w/ registration applied) are switched. 

$preproc-sess -s sess01 -fsd rest -surface fsaverage lhrh -mni305 -fwhm 5 
-per-run

Is there any possible error that I might have made? 
or is there any way to fix it?

I appreciate your help! 

Thanks, 
Wenzhen

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Re: [Freesurfer] bbregister error

[Douglas N. Greve]

Can you send the terminal output and/or the log file?

On 08/22/2018 09:49 AM, Nada Naguib wrote:
>
> External Email - Use Caution
>
> Hello, thank you for your response, yes My terminal is in the tcsh 
> shell so I’m not sure why it’s not working
>
> Nada
>
>
> On Aug 22, 2018, at 3:22 PM, Adam Martersteck  > wrote:
>
>> External Email - Use Caution
>>
>> Are you sure you're terminal is setup in tcsh or csh? If you're using 
>> bash instead, you want "export SUBJECTS_DIR=/project/bil/Nada"
>> Take a look at: 
>> https://surfer.nmr.mgh.harvard.edu/fswiki/SetupConfiguration_Mac or 
>> https://surfer.nmr.mgh.harvard.edu/fswiki/SetupConfiguration_Linux to 
>> see if you may have missed something.
>>
>> On Wed, Aug 22, 2018 at 4:37 AM Nada Naguib > > wrote:
>>
>>   External Email - Use Caution
>>
>> Hello,
>>
>> I have been using bbregister in this format
>>
>> bbregister —mov dkti4d.nii —s NewT2out —init-fsl —bold —lea
>> register.lta
>>
>> NewT2out is the output of the free surfer processing on the T1
>> image and dkti4d.nii is the template file I want to use for the
>> registration.
>>
>> it has worked before but now there is a new error
>>
>> ERROR: cannot find NewT2out in
>> /project/iconic/apps/freesurfer/5.3.0/install/subjects
>>
>> even though I have already ran the command:
>>
>> setenv SUBJECTS_DIRECTORY /project/bil/Nada
>>
>>
>> This path is where both NewT2out and dkti4d.nii are located.
>>
>> I don’t understand what is going wrong
>>
>> Best
>> Nada
>>
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>>
>>
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>> 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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>> you in error
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>> and properly
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Re: [Freesurfer] bbregister error

[Nada Naguib]

External Email - Use Caution

Hello, thank you for your response, yes My terminal is in the tcsh shell so I’m 
not sure why it’s not working 

Nada 


> On Aug 22, 2018, at 3:22 PM, Adam Martersteck  wrote:
> 
> External Email - Use Caution
> 
> Are you sure you're terminal is setup in tcsh or csh? If you're using bash 
> instead, you want "export SUBJECTS_DIR=/project/bil/Nada"
> Take a look at: 
> https://surfer.nmr.mgh.harvard.edu/fswiki/SetupConfiguration_Mac or 
> https://surfer.nmr.mgh.harvard.edu/fswiki/SetupConfiguration_Linux to see if 
> you may have missed something.
> 
>> On Wed, Aug 22, 2018 at 4:37 AM Nada Naguib  wrote:
>> External Email - Use Caution
>> 
>> Hello,
>> 
>> I have been using bbregister in this format 
>> 
>> bbregister —mov dkti4d.nii —s NewT2out —init-fsl —bold —lea register.lta
>> 
>> NewT2out is the output of the free surfer processing on the T1 image and 
>> dkti4d.nii is the template file I want to use for the registration.
>> 
>> it has worked before but now there is a new error 
>> 
>> ERROR: cannot find NewT2out in 
>> /project/iconic/apps/freesurfer/5.3.0/install/subjects
>> 
>> even though I have already ran the command:
>> 
>> setenv SUBJECTS_DIRECTORY /project/bil/Nada
>> 
>> 
>> This path is where both NewT2out and dkti4d.nii are located. 
>> 
>> I don’t understand what is going wrong
>> 
>> Best
>> Nada
>> 
>> ___
>> Freesurfer mailing list
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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
>> 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.
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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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> error
> but does not contain patient information, please contact the sender and 
> properly
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Re: [Freesurfer] bbregister error

[Adam Martersteck]

External Email - Use Caution

Are you sure you're terminal is setup in tcsh or csh? If you're using bash
instead, you want "export SUBJECTS_DIR=/project/bil/Nada"
Take a look at:
https://surfer.nmr.mgh.harvard.edu/fswiki/SetupConfiguration_Mac or
https://surfer.nmr.mgh.harvard.edu/fswiki/SetupConfiguration_Linux to see
if you may have missed something.

On Wed, Aug 22, 2018 at 4:37 AM Nada Naguib  wrote:

> External Email - Use Caution
>
> Hello,
>
> I have been using bbregister in this format
>
> bbregister —mov dkti4d.nii —s NewT2out —init-fsl —bold —lea register.lta
>
> NewT2out is the output of the free surfer processing on the T1 image and
> dkti4d.nii is the template file I want to use for the registration.
>
> it has worked before but now there is a new error
>
> ERROR: cannot find NewT2out in
> /project/iconic/apps/freesurfer/5.3.0/install/subjects
>
> even though I have already ran the command:
>
> setenv SUBJECTS_DIRECTORY /project/bil/Nada
>
>
> This path is where both NewT2out and dkti4d.nii are located.
>
> I don’t understand what is going wrong
>
> Best
> Nada
>
> ___
> 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.
>
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[Freesurfer] bbregister error

[Nada Naguib]

External Email - Use Caution

Hello,

I have been using bbregister in this format 

bbregister —mov dkti4d.nii —s NewT2out —init-fsl —bold —lea register.lta

NewT2out is the output of the free surfer processing on the T1 image and 
dkti4d.nii is the template file I want to use for the registration.

it has worked before but now there is a new error 

ERROR: cannot find NewT2out in 
/project/iconic/apps/freesurfer/5.3.0/install/subjects

even though I have already ran the command:

setenv SUBJECTS_DIRECTORY /project/bil/Nada


This path is where both NewT2out and dkti4d.nii are located. 

I don’t understand what is going wrong

Best
Nada

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Re: [Freesurfer] bbregister aparc+aseg to diffusion space

[Yendiki, Anastasia]

Yes, same idea as in the tutorial. It doesn’t matter that you didn’t use 
dt_recon, if you had it would’ve just run bbregister for you.

From: 
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of "Michiko H." <michiko...@gmail.com<mailto:michiko...@gmail.com>>
Reply-To: Freesurfer support list 
<freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Friday, February 16, 2018 at 4:17 PM
To: Freesurfer support list 
<freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] bbregister aparc+aseg to diffusion space

Hi Anastasia,

Thank you for the quick response. I did not preprocess my diffusion data using 
dt_recon, so I suppose the way to do it would be to first run:
bbregister --s $subject --mov bo_brain.nii.gz --reg register2b0.dat --dti 
--init-fsl
and then:
mri_vol2vol --mov lowb.nii --targ $subject/mri/aparc+aseg.mgz  --inv --interp 
nearest --o $subjectj/mri/aparc+aseg2diff.mgz --reg register2b0.dat 
--no-save-reg

Does this look right?

Thank you very much,
M.

On Fri, Feb 16, 2018 at 4:08 PM, Yendiki, Anastasia 
<ayend...@mgh.harvard.edu<mailto:ayend...@mgh.harvard.edu>> wrote:
Hi M - You generally want to register the lower-res to the higher-res image. In 
this case, that’s diffusion to T1. Check the diffusion processing tutorial on 
the freesurfer wiki for how you can apply the inverse transform to the 
aparc+aseg to get it into diffusion space.

Best,
a.y

From: 
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of "Michiko H." <michiko...@gmail.com<mailto:michiko...@gmail.com>>
Reply-To: Freesurfer support list 
<freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Friday, February 16, 2018 at 3:57 PM
To: Freesurfer support list 
<freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] bbregister aparc+aseg to diffusion space

Hi,

I understand that bbregister can be used to register diffusion to T1 space but 
I'm a lot less certain how this can be done in the reverse way, i.e. 
registering the entire aparc+aseg file to diffusion B0? Do I also do: 
bbregister --s $subject --mov bo_brain.nii.gz --reg registration2b0.dat --dti 
--init-fsl

To follow up, I'm also unclear whether this method is inferior to registering 
diffusion to T1 - if so, why may this be so?

Thanks a lot in advance,
M.



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Re: [Freesurfer] bbregister aparc+aseg to diffusion space

[Michiko H.]

Hi Anastasia,

Thank you for the quick response. I did not preprocess my diffusion data
using dt_recon, so I suppose the way to do it would be to first run:
bbregister --s $subject --mov bo_brain.nii.gz --reg register2b0.dat --dti
--init-fsl
and then:
mri_vol2vol --mov lowb.nii --targ $subject/mri/aparc+aseg.mgz  --inv
--interp nearest --o $subjectj/mri/aparc+aseg2diff.mgz --reg
register2b0.dat --no-save-reg

Does this look right?

Thank you very much,
M.

On Fri, Feb 16, 2018 at 4:08 PM, Yendiki, Anastasia <
ayend...@mgh.harvard.edu> wrote:

> Hi M - You generally want to register the lower-res to the higher-res
> image. In this case, that’s diffusion to T1. Check the diffusion processing
> tutorial on the freesurfer wiki for how you can apply the inverse transform
> to the aparc+aseg to get it into diffusion space.
>
> Best,
> a.y
>
> From: <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of "Michiko H." <
> michiko...@gmail.com>
> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
> Date: Friday, February 16, 2018 at 3:57 PM
> To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
> Subject: [Freesurfer] bbregister aparc+aseg to diffusion space
>
> Hi,
>
> I understand that bbregister can be used to register diffusion to T1 space
> but I'm a lot less certain how this can be done in the reverse way, i.e.
> registering the entire aparc+aseg file to diffusion B0? Do I also do: 
> bbregister
> --s $subject --mov bo_brain.nii.gz --reg registration2b0.dat --dti
> --init-fsl
>
> To follow up, I'm also unclear whether this method is inferior to
> registering diffusion to T1 - if so, why may this be so?
>
> Thanks a lot in advance,
> M.
>
>
>
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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
> 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.
>
>
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Re: [Freesurfer] bbregister aparc+aseg to diffusion space

[Yendiki, Anastasia]

Hi M - You generally want to register the lower-res to the higher-res image. In 
this case, that’s diffusion to T1. Check the diffusion processing tutorial on 
the freesurfer wiki for how you can apply the inverse transform to the 
aparc+aseg to get it into diffusion space.

Best,
a.y

From: 
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of "Michiko H." <michiko...@gmail.com<mailto:michiko...@gmail.com>>
Reply-To: Freesurfer support list 
<freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Friday, February 16, 2018 at 3:57 PM
To: Freesurfer support list 
<freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] bbregister aparc+aseg to diffusion space

Hi,

I understand that bbregister can be used to register diffusion to T1 space but 
I'm a lot less certain how this can be done in the reverse way, i.e. 
registering the entire aparc+aseg file to diffusion B0? Do I also do: 
bbregister --s $subject --mov bo_brain.nii.gz --reg registration2b0.dat --dti 
--init-fsl

To follow up, I'm also unclear whether this method is inferior to registering 
diffusion to T1 - if so, why may this be so?

Thanks a lot in advance,
M.


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dispose of the e-mail.

[Freesurfer] bbregister aparc+aseg to diffusion space

[Michiko H.]

Hi,

I understand that bbregister can be used to register diffusion to T1 space
but I'm a lot less certain how this can be done in the reverse way, i.e.
registering the entire aparc+aseg file to diffusion B0? Do I also do:
bbregister
--s $subject --mov bo_brain.nii.gz --reg registration2b0.dat --dti
--init-fsl

To follow up, I'm also unclear whether this method is inferior to
registering diffusion to T1 - if so, why may this be so?

Thanks a lot in advance,
M.
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Re: [Freesurfer] bbregister error -- Human Connectome Project Data

[Matt Glasser]

There is a structural extended package that has the FreeSurfer folders.

Peace,

Matt.

From:  <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Lana Ruck
<lr...@umail.iu.edu>
Reply-To:  Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date:  Thursday, December 28, 2017 at 12:56 PM
To:  Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject:  Re: [Freesurfer] bbregister error -- Human Connectome Project Data

Okay so if I am going to try and run this option, recon-all must also be
done on the structural scans. I have the pre-processed structurals, and I
understand from y'all's 2013 paper
<http://linkinghub.elsevier.com/retrieve/pii/S1053811913005053>  that they
have already been through all of the steps in recon-all. First--is it
correct that all steps (1-31) have been done on the data? Second, as with my
original question, it seems that the HCP directories are quite different
than the defaults that would be created by a standard Freesurfer recon-all
run. Assuming that Freesurfer scripts will look for recon-all files in
directories not present in the HCP data as downloaded, (for example,
subjid/mri/... and subj/surf/... are not valid paths in the pre-processed
data), would it just be better to get the un-processed structurals and
re-run all of the recon-all steps myself?

I guess I'm just wondering what the value of the pre-processed data is if it
is re-organized as to be un-readable by Freesurfer defaults.

Lana

   
Lana Ruck, M.A.
Associate Instructor, Department of Anthropology
Graduate Scholars Fellow, Cognitive Science Program
Indiana University, Bloomington
Student Building 166
lr...@umail.iu.edu


On Wed, Dec 27, 2017 at 7:02 PM, Matt Glasser <m...@ma-tea.com> wrote:
> I wouldn¹t trust resting state data that have not been properly denoised.  You
> should only need the structural and FIX cleaned packages for what you are
> doing.  The link that I put below explains how to get HCP data onto the
> fsaverage4 surface.  You will need FreeSurfer and Connectome Workbench for
> this.  
> 
> Peace,
> 
> Matt.
> 
> From:  <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Lana Ruck
> <lr...@umail.iu.edu>
> Reply-To:  Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
> Date:  Wednesday, December 27, 2017 at 5:55 PM
> To:  Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
> 
> Subject:  Re: [Freesurfer] bbregister error -- Human Connectome Project Data
> 
> Matt,
> 
> Thanks for the quick reply! I'll check out that Wiki document and the 2016
> Nature paper first.
> 
> The reason I have the pre-processed (but not ICA-FIX'ed) rfMRI data is because
> I would like to use the iterative parcellation algorithm from the Liu Lab
> @Harvard (as described in Wang, D. et al. 2015: Parcellating Cortical
> Functional Networks in Individuals. Nat. Neurosci;
> http://nmr.mgh.harvard.edu/bid/DownLoad.html), but I am unsure if the ICA-FIX
> data are appropriate for this. I know that the minimally pre-processed rfMRI
> data just need to be smoothed and projected to fsaverage4 for the MATLAB
> algorithm to work, but I didn't see a clear way to get the ICA-FIX data in the
> right format, as per the specifications provided by the Lui Lab. I am also not
> using a local machine to do the processing (I am using my Uni's supercomputing
> infrastructure), so I don't know if I can get connectome workbench installed
> in order to pre-process CIFTI data. That's why I am working with standard
> formats (the supercomputer has freesurfer, fsl, etc.).
> 
> Assuming I can get cnm-wb installed by admins on the supercomputer, and that I
> can use it to get the ICA-FIX data appropriately formatted for parcellation
> with MATLAB, do you suggest I download the extended packages, or will the
> compact ones have everything I need?
> 
> Lana
> 
>  
> Lana Ruck, M.A.
> Associate Instructor, Department of Anthropology
> Graduate Scholars Fellow, Cognitive Science Program
> Indiana University, Bloomington
> Student Building 166
> lr...@umail.iu.edu
> 
> 
> On Wed, Dec 27, 2017 at 6:26 PM, Matt Glasser <m...@ma-tea.com> wrote:
>> You would be better off resampling the existing CIFTI data to the fsaverage4
>> surface rather than redoing the projection and smoothing in the volume.
>> Instructions for getting to fsaverage are available here:
>> 
>> https://wiki.humanconnectome.org/display/PublicData/HCP+Users+FAQ#HCPUsersFAQ
>> -9.HowdoImapdatabetweenFreeSurferandHCP?
>> 
>> Also I would recommend starting from the ICA+FIX cleaned data, not the
>> minimally preprocessed data.  If you must smooth the data, you can do that
>> with wb_command -cifti-smoothing before following the above steps.
>> 
>

Re: [Freesurfer] bbregister error -- Human Connectome Project Data

[Lana Ruck]

Okay so if I am going to try and run this option, recon-all must also be
done on the structural scans. I have the pre-processed structurals, and I
understand from y'all's 2013 paper
<http://linkinghub.elsevier.com/retrieve/pii/S1053811913005053> that they
have already been through all of the steps in recon-all. First--is it
correct that all steps (1-31) have been done on the data? Second, as with
my original question, it seems that the HCP directories are quite different
than the defaults that would be created by a standard Freesurfer recon-all
run. Assuming that Freesurfer scripts will look for recon-all files in
directories not present in the HCP data as downloaded, (for example,
subjid/mri/... and subj/surf/... are not valid paths in the pre-processed
data), would it just be better to get the un-processed structurals and
re-run all of the recon-all steps myself?

I guess I'm just wondering what the value of the pre-processed data is if
it is re-organized as to be un-readable by Freesurfer defaults.

Lana


Lana Ruck, M.A.
Associate Instructor, Department of Anthropology
Graduate Scholars Fellow, Cognitive Science Program
Indiana University, Bloomington
Student Building 166
lr...@umail.iu.edu


On Wed, Dec 27, 2017 at 7:02 PM, Matt Glasser <m...@ma-tea.com> wrote:

> I wouldn’t trust resting state data that have not been properly denoised.
> You should only need the structural and FIX cleaned packages for what you
> are doing.  The link that I put below explains how to get HCP data onto the
> fsaverage4 surface.  You will need FreeSurfer and Connectome Workbench for
> this.
>
> Peace,
>
> Matt.
>
> From: <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Lana Ruck <
> lr...@umail.iu.edu>
> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
> Date: Wednesday, December 27, 2017 at 5:55 PM
> To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
>
> Subject: Re: [Freesurfer] bbregister error -- Human Connectome Project
> Data
>
> Matt,
>
> Thanks for the quick reply! I'll check out that Wiki document and the 2016
> Nature paper first.
>
> The reason I have the pre-processed (but not ICA-FIX'ed) rfMRI data is
> because I would like to use the iterative parcellation algorithm from the
> Liu Lab @Harvard (as described in Wang, D. et al. 2015: Parcellating
> Cortical Functional Networks in Individuals. Nat. Neurosci;
> http://nmr.mgh.harvard.edu/bid/DownLoad.html), but I am unsure if the
> ICA-FIX data are appropriate for this. I know that the minimally
> pre-processed rfMRI data just need to be smoothed and projected to
> fsaverage4 for the MATLAB algorithm to work, but I didn't see a clear way
> to get the ICA-FIX data in the right format, as per the specifications
> provided by the Lui Lab. I am also not using a local machine to do the
> processing (I am using my Uni's supercomputing infrastructure), so I don't
> know if I can get connectome workbench installed in order to pre-process
> CIFTI data. That's why I am working with standard formats (the
> supercomputer has freesurfer, fsl, etc.).
>
> Assuming I can get cnm-wb installed by admins on the supercomputer, and
> that I can use it to get the ICA-FIX data appropriately formatted for
> parcellation with MATLAB, do you suggest I download the extended packages,
> or will the compact ones have everything I need?
>
> Lana
>
>
>
> Lana Ruck, M.A.
> Associate Instructor, Department of Anthropology
> Graduate Scholars Fellow, Cognitive Science Program
> Indiana University, Bloomington
> Student Building 166
> lr...@umail.iu.edu
>
>
> On Wed, Dec 27, 2017 at 6:26 PM, Matt Glasser <m...@ma-tea.com> wrote:
>
>> You would be better off resampling the existing CIFTI data to the
>> fsaverage4 surface rather than redoing the projection and smoothing in the
>> volume.  Instructions for getting to fsaverage are available here:
>>
>> https://wiki.humanconnectome.org/display/PublicData/HCP+User
>> s+FAQ#HCPUsersFAQ-9.HowdoImapdatabetweenFreeSurferandHCP?
>>
>> Also I would recommend starting from the ICA+FIX cleaned data, not the
>> minimally preprocessed data.  If you must smooth the data, you can do that
>> with wb_command -cifti-smoothing before following the above steps.
>>
>> Peace,
>>
>> Matt.
>>
>> From: <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Lana Ruck <
>> lr...@umail.iu.edu>
>> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
>> Date: Wednesday, December 27, 2017 at 4:41 PM
>> To: <freesurfer@nmr.mgh.harvard.edu>
>> Subject: Re: [Freesurfer] bbregister error -- Human Connectome Project
>> Data
>>
>> As a work-around t

Re: [Freesurfer] bbregister error -- Human Connectome Project Data

[Matt Glasser]

I wouldn¹t trust resting state data that have not been properly denoised.
You should only need the structural and FIX cleaned packages for what you
are doing.  The link that I put below explains how to get HCP data onto the
fsaverage4 surface.  You will need FreeSurfer and Connectome Workbench for
this.  

Peace,

Matt.

From:  <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Lana Ruck
<lr...@umail.iu.edu>
Reply-To:  Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date:  Wednesday, December 27, 2017 at 5:55 PM
To:  Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject:  Re: [Freesurfer] bbregister error -- Human Connectome Project Data

Matt,

Thanks for the quick reply! I'll check out that Wiki document and the 2016
Nature paper first.

The reason I have the pre-processed (but not ICA-FIX'ed) rfMRI data is
because I would like to use the iterative parcellation algorithm from the
Liu Lab @Harvard (as described in Wang, D. et al. 2015: Parcellating
Cortical Functional Networks in Individuals. Nat. Neurosci;
http://nmr.mgh.harvard.edu/bid/DownLoad.html), but I am unsure if the
ICA-FIX data are appropriate for this. I know that the minimally
pre-processed rfMRI data just need to be smoothed and projected to
fsaverage4 for the MATLAB algorithm to work, but I didn't see a clear way to
get the ICA-FIX data in the right format, as per the specifications provided
by the Lui Lab. I am also not using a local machine to do the processing (I
am using my Uni's supercomputing infrastructure), so I don't know if I can
get connectome workbench installed in order to pre-process CIFTI data.
That's why I am working with standard formats (the supercomputer has
freesurfer, fsl, etc.).

Assuming I can get cnm-wb installed by admins on the supercomputer, and that
I can use it to get the ICA-FIX data appropriately formatted for
parcellation with MATLAB, do you suggest I download the extended packages,
or will the compact ones have everything I need?

Lana

   
Lana Ruck, M.A.
Associate Instructor, Department of Anthropology
Graduate Scholars Fellow, Cognitive Science Program
Indiana University, Bloomington
Student Building 166
lr...@umail.iu.edu


On Wed, Dec 27, 2017 at 6:26 PM, Matt Glasser <m...@ma-tea.com> wrote:
> You would be better off resampling the existing CIFTI data to the fsaverage4
> surface rather than redoing the projection and smoothing in the volume.
> Instructions for getting to fsaverage are available here:
> 
> https://wiki.humanconnectome.org/display/PublicData/HCP+Users+FAQ#HCPUsersFAQ-
> 9.HowdoImapdatabetweenFreeSurferandHCP?
> 
> Also I would recommend starting from the ICA+FIX cleaned data, not the
> minimally preprocessed data.  If you must smooth the data, you can do that
> with wb_command -cifti-smoothing before following the above steps.
> 
> Peace,
> 
> Matt.
> 
> From:  <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Lana Ruck
> <lr...@umail.iu.edu>
> Reply-To:  Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
> Date:  Wednesday, December 27, 2017 at 4:41 PM
> To:  <freesurfer@nmr.mgh.harvard.edu>
> Subject:  Re: [Freesurfer] bbregister error -- Human Connectome Project Data
> 
> As a work-around to the above issue, I did the registrations directly in FSL
> using FLIRT, and then converted the resultant fsl reg.mat files to freesurfer
> reg.dat files (using tkregister2; they all look fine). Now, all I need is to
> project these rfMRI data to fsaverage4, and I thought mri_vol2surf was the
> right way to do this.
> 
> Unfortunately, I am now having the same directory issue with mri_vol2surf (new
> error log below), where it can't find /surf/lh.white for my subject. The HCP
> pre-processed data has already been through recon-all, so there are several
> *white*surf* files to choose from for each subject, but they are not in the
> directory specified by default in MRISread (subjid/surf/).
> 
> I thought I could fix this by specifying the right target subject
> (--trgsubject fsaverage4, which I have manually copied, along with the other
> $FREESURFER_HOME/subjects, to my own $SUBJECTS_DIR as per the message boards),
> or specifying the right directory (I've tried the --surf command with both the
> fsaverage4 path, and to multiple [subject]?h.white paths, but it just appends
> them to the non-existent default path--see below). Thus, regardless of what I
> specify, I keep getting the same error related to a default search in
> subjid/surf/.
> 
> Is there a way to point MRISread to the correct surf files, without re-doing
> recon-all or moving the pre-processed surfaces to a "surf" folder for all 40
> subjects?
> 
> Lana
> 
>> [lruck@c5 LH_all]$ mri_vol2surf --mov
>> /N/dc2/scratch/lruck/LH_all/101915/MNINonLinear/Results/rfMRI_REST1_

Re: [Freesurfer] bbregister error -- Human Connectome Project Data

[Lana Ruck]

Matt,

Thanks for the quick reply! I'll check out that Wiki document and the 2016
Nature paper first.

The reason I have the pre-processed (but not ICA-FIX'ed) rfMRI data is
because I would like to use the iterative parcellation algorithm from the
Liu Lab @Harvard (as described in Wang, D. et al. 2015: Parcellating
Cortical Functional Networks in Individuals. Nat. Neurosci;
http://nmr.mgh.harvard.edu/bid/DownLoad.html), but I am unsure if the
ICA-FIX data are appropriate for this. I know that the minimally
pre-processed rfMRI data just need to be smoothed and projected to
fsaverage4 for the MATLAB algorithm to work, but I didn't see a clear way
to get the ICA-FIX data in the right format, as per the specifications
provided by the Lui Lab. I am also not using a local machine to do the
processing (I am using my Uni's supercomputing infrastructure), so I don't
know if I can get connectome workbench installed in order to pre-process
CIFTI data. That's why I am working with standard formats (the
supercomputer has freesurfer, fsl, etc.).

Assuming I can get cnm-wb installed by admins on the supercomputer, and
that I can use it to get the ICA-FIX data appropriately formatted for
parcellation with MATLAB, do you suggest I download the extended packages,
or will the compact ones have everything I need?

Lana


Lana Ruck, M.A.
Associate Instructor, Department of Anthropology
Graduate Scholars Fellow, Cognitive Science Program
Indiana University, Bloomington
Student Building 166
lr...@umail.iu.edu


On Wed, Dec 27, 2017 at 6:26 PM, Matt Glasser <m...@ma-tea.com> wrote:

> You would be better off resampling the existing CIFTI data to the
> fsaverage4 surface rather than redoing the projection and smoothing in the
> volume.  Instructions for getting to fsaverage are available here:
>
> https://wiki.humanconnectome.org/display/PublicData/HCP+
> Users+FAQ#HCPUsersFAQ-9.HowdoImapdatabetweenFreeSurferandHCP?
>
> Also I would recommend starting from the ICA+FIX cleaned data, not the
> minimally preprocessed data.  If you must smooth the data, you can do that
> with wb_command -cifti-smoothing before following the above steps.
>
> Peace,
>
> Matt.
>
> From: <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Lana Ruck <
> lr...@umail.iu.edu>
> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
> Date: Wednesday, December 27, 2017 at 4:41 PM
> To: <freesurfer@nmr.mgh.harvard.edu>
> Subject: Re: [Freesurfer] bbregister error -- Human Connectome Project
> Data
>
> As a work-around to the above issue, I did the registrations directly in
> FSL using FLIRT, and then converted the resultant fsl reg.mat files to
> freesurfer reg.dat files (using tkregister2; they all look fine). Now, all
> I need is to project these rfMRI data to fsaverage4, and I thought
> mri_vol2surf was the right way to do this.
>
> Unfortunately, I am now having the same directory issue with mri_vol2surf
> (new error log below), where it can't find /surf/lh.white for my subject.
> The HCP pre-processed data has already been through recon-all, so there are
> several *white*surf* files to choose from for each subject, but they are
> not in the directory specified by default in MRISread (subjid/surf/).
>
> I thought I could fix this by specifying the right target subject
> (--trgsubject fsaverage4, which I have manually copied, along with the
> other $FREESURFER_HOME/subjects, to my own $SUBJECTS_DIR as per the message
> boards), or specifying the right directory (I've tried the --surf command
> with both the fsaverage4 path, and to multiple [subject]?h.white paths, but
> it just appends them to the non-existent default path--see below). Thus,
> regardless of what I specify, I keep getting the same error related to a
> default search in subjid/surf/.
>
> Is there a way to point MRISread to the correct surf files, without
> re-doing recon-all or moving the pre-processed surfaces to a "surf" folder
> for all 40 subjects?
>
> Lana
>
> [lruck@c5 LH_all]$ mri_vol2surf --mov /N/dc2/scratch/lruck/LH_all/
> 101915/MNINonLinear/Results/rfMRI_REST1_LR/REST1LR.img --src_type analyze
> --reg /N/dc2/scratch/lruck/LH_all/101915/MNINonLinear/Results/
> rfMRI_REST1_LR/REST1LR_register.dat --hemi lh --fwhm 6 --trgsubject
> fsaverage4 --surf /N/dc2/scratch/lruck/LH_all/fsaverage4/surf/lh.white
> --out /N/dc2/scratch/lruck/LH_all/101915/MNINonLinear/Results/
> rfMRI_REST1_LR/
> srcvol = /N/dc2/scratch/lruck/LH_all/101915/MNINonLinear/Results/
> rfMRI_REST1_LR/REST1LR.img
> srctype = analyze
> srcreg = /N/dc2/scratch/lruck/LH_all/101915/MNINonLinear/Results/
> rfMRI_REST1_LR/REST1LR_register.dat
> srcregold = 0
> srcwarp unspecified
> surf = /N/dc2/scratch/lruck/LEH_all/fsaverage4/surf/lh.white
> hemi = lh
> trgsubject = fsa

Re: [Freesurfer] bbregister error -- Human Connectome Project Data

[Matt Glasser]

You would be better off resampling the existing CIFTI data to the fsaverage4
surface rather than redoing the projection and smoothing in the volume.
Instructions for getting to fsaverage are available here:

https://wiki.humanconnectome.org/display/PublicData/HCP+Users+FAQ#HCPUsersFA
Q-9.HowdoImapdatabetweenFreeSurferandHCP?

Also I would recommend starting from the ICA+FIX cleaned data, not the
minimally preprocessed data.  If you must smooth the data, you can do that
with wb_command -cifti-smoothing before following the above steps.

Peace,

Matt.

From:  <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Lana Ruck
<lr...@umail.iu.edu>
Reply-To:  Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date:  Wednesday, December 27, 2017 at 4:41 PM
To:  <freesurfer@nmr.mgh.harvard.edu>
Subject:  Re: [Freesurfer] bbregister error -- Human Connectome Project Data

As a work-around to the above issue, I did the registrations directly in FSL
using FLIRT, and then converted the resultant fsl reg.mat files to
freesurfer reg.dat files (using tkregister2; they all look fine). Now, all I
need is to project these rfMRI data to fsaverage4, and I thought
mri_vol2surf was the right way to do this.

Unfortunately, I am now having the same directory issue with mri_vol2surf
(new error log below), where it can't find /surf/lh.white for my subject.
The HCP pre-processed data has already been through recon-all, so there are
several *white*surf* files to choose from for each subject, but they are not
in the directory specified by default in MRISread (subjid/surf/).

I thought I could fix this by specifying the right target subject
(--trgsubject fsaverage4, which I have manually copied, along with the other
$FREESURFER_HOME/subjects, to my own $SUBJECTS_DIR as per the message
boards), or specifying the right directory (I've tried the --surf command
with both the fsaverage4 path, and to multiple [subject]?h.white paths, but
it just appends them to the non-existent default path--see below). Thus,
regardless of what I specify, I keep getting the same error related to a
default search in subjid/surf/.

Is there a way to point MRISread to the correct surf files, without re-doing
recon-all or moving the pre-processed surfaces to a "surf" folder for all 40
subjects?

Lana

> [lruck@c5 LH_all]$ mri_vol2surf --mov
> /N/dc2/scratch/lruck/LH_all/101915/MNINonLinear/Results/rfMRI_REST1_LR/REST1LR
> .img --src_type analyze --reg
> /N/dc2/scratch/lruck/LH_all/101915/MNINonLinear/Results/rfMRI_REST1_LR/REST1LR
> _register.dat --hemi lh --fwhm 6 --trgsubject fsaverage4 --surf
> /N/dc2/scratch/lruck/LH_all/fsaverage4/surf/lh.white --out
> /N/dc2/scratch/lruck/LH_all/101915/MNINonLinear/Results/rfMRI_REST1_LR/
> srcvol = 
> /N/dc2/scratch/lruck/LH_all/101915/MNINonLinear/Results/rfMRI_REST1_LR/REST1LR
> .img
> srctype = analyze
> srcreg = 
> /N/dc2/scratch/lruck/LH_all/101915/MNINonLinear/Results/rfMRI_REST1_LR/REST1LR
> _register.dat
> srcregold = 0
> srcwarp unspecified
> surf = /N/dc2/scratch/lruck/LEH_all/fsaverage4/surf/lh.white
> hemi = lh
> trgsubject = fsaverage4
> surfreg = sphere.reg
> reshape = 0
> interp = nearest
> float2int = round
> GetProjMax = 0
> INFO: float2int code = 0
>   analyzeRead() roi_scale   0.0
> Done loading volume
> INFO: This REGISTER_DAT transform is valid only for volumes between  COR types
> with c_(r,a,s) = 0.
> Input reg is register.dat
>  original matrix ---
>  0.96607   0.00120   0.00047  -0.78994;
>  0.01685   0.96915  -0.00899   2.16005;
> -0.00580  -0.00642   0.98726  -0.56166;
>  0.0   0.0   0.0   1.0;
>  original matrix ---
> INFO: smoothing volume at fwhm = 6 mm (std = 2.54797)
> Reading surface 
> /N/dc2/scratch/lruck/LH_all//101915/surf/lh./N/dc2/scratch/lruck/LH_all/fsaver
> age4/surf/lh.white
> MRISread(/N/dc2/scratch/lruck/LH_all//101915/surf/lh./N/dc2/scratch/lruck/LH_a
> ll/fsaverage4/surf/lh.white): could not open file
> No such file or directory
> mri_vol2surf: could not read surface
> /N/dc2/scratch/lruck/LH_all//101915/surf/lh./N/dc2/scratch/lruck/LH_all/fsaver
> age4/surf/lh.white
> No such file or directory


   
Lana Ruck, M.A.
Associate Instructor, Department of Anthropology
Graduate Scholars Fellow, Cognitive Science Program
Indiana University, Bloomington
Student Building 166
lr...@umail.iu.edu


On Wed, Dec 27, 2017 at 1:43 PM, Lana Ruck <lr...@umail.iu.edu> wrote:
> Hello, 
> 
> I am currently starting a project with the minimally pre-processed rfMRI from
> the Human Connectome Project, but I need to do some additional processing
> first. This includes smoothing at 6mm FWHM and projection onto the fsaverage4
> surface. I have smoothed the pre-processed rfMRI data using mri_convert (and
> have also conver

Re: [Freesurfer] bbregister error -- Human Connectome Project Data

[Lana Ruck]

As a work-around to the above issue, I did the registrations directly in
FSL using FLIRT, and then converted the resultant fsl reg.mat files to
freesurfer reg.dat files (using tkregister2; they all look fine). Now, all
I need is to project these rfMRI data to fsaverage4, and I thought
mri_vol2surf was the right way to do this.

Unfortunately, I am now having the same directory issue with mri_vol2surf
(new error log below), where it can't find /surf/lh.white for my subject.
The HCP pre-processed data has already been through recon-all, so there are
several *white*surf* files to choose from for each subject, but they are
not in the directory specified by default in MRISread (subjid/surf/).

I thought I could fix this by specifying the right target subject
(--trgsubject fsaverage4, which I have manually copied, along with the
other $FREESURFER_HOME/subjects, to my own $SUBJECTS_DIR as per the message
boards), or specifying the right directory (I've tried the --surf command
with both the fsaverage4 path, and to multiple [subject]?h.white paths, but
it just appends them to the non-existent default path--see below). Thus,
regardless of what I specify, I keep getting the same error related to a
default search in subjid/surf/.

Is there a way to point MRISread to the correct surf files, without
re-doing recon-all or moving the pre-processed surfaces to a "surf" folder
for all 40 subjects?

Lana

[lruck@c5 LH_all]$ mri_vol2surf --mov
/N/dc2/scratch/lruck/LH_all/101915/MNINonLinear/Results/rfMRI_REST1_LR/REST1LR.img
--src_type analyze --reg
/N/dc2/scratch/lruck/LH_all/101915/MNINonLinear/Results/rfMRI_REST1_LR/REST1LR_register.dat
--hemi lh --fwhm 6 --trgsubject fsaverage4 --surf
/N/dc2/scratch/lruck/LH_all/fsaverage4/surf/lh.white --out
/N/dc2/scratch/lruck/LH_all/101915/MNINonLinear/Results/rfMRI_REST1_LR/
srcvol =
/N/dc2/scratch/lruck/LH_all/101915/MNINonLinear/Results/rfMRI_REST1_LR/REST1LR.img
srctype = analyze
srcreg =
/N/dc2/scratch/lruck/LH_all/101915/MNINonLinear/Results/rfMRI_REST1_LR/REST1LR_register.dat
srcregold = 0
srcwarp unspecified
surf = /N/dc2/scratch/lruck/LEH_all/fsaverage4/surf/lh.white
hemi = lh
trgsubject = fsaverage4
surfreg = sphere.reg
reshape = 0
interp = nearest
float2int = round
GetProjMax = 0
INFO: float2int code = 0
  analyzeRead() roi_scale   0.0
Done loading volume
INFO: This REGISTER_DAT transform is valid only for volumes between  COR
types with c_(r,a,s) = 0.
Input reg is register.dat
 original matrix ---
 0.96607   0.00120   0.00047  -0.78994;
 0.01685   0.96915  -0.00899   2.16005;
-0.00580  -0.00642   0.98726  -0.56166;
 0.0   0.0   0.0   1.0;
 original matrix ---
INFO: smoothing volume at fwhm = 6 mm (std = 2.54797)
*Reading surface
/N/dc2/scratch/lruck/LH_all//101915/surf/lh./N/dc2/scratch/lruck/LH_all/fsaverage4/surf/lh.white*
*MRISread(/N/dc2/scratch/lruck/LH_all//101915/surf/lh./N/dc2/scratch/lruck/LH_all/fsaverage4/surf/lh.white):
could not open file*
*No such file or directory*
*mri_vol2surf: could not read surface
/N/dc2/scratch/lruck/LH_all//101915/surf/lh./N/dc2/scratch/lruck/LH_all/fsaverage4/surf/lh.white*
*No such file or directory*




Lana Ruck, M.A.
Associate Instructor, Department of Anthropology
Graduate Scholars Fellow, Cognitive Science Program
Indiana University, Bloomington
Student Building 166
lr...@umail.iu.edu


On Wed, Dec 27, 2017 at 1:43 PM, Lana Ruck  wrote:

> Hello,
>
> I am currently starting a project with the minimally pre-processed rfMRI
> from the Human Connectome Project, but I need to do some additional
> processing first. This includes smoothing at 6mm FWHM and projection onto
> the fsaverage4 surface. I have smoothed the pre-processed rfMRI data using
> mri_convert (and have also converted the provided brain-extracted
> anatomical), but I am having issues registering the smoothed rfMRI volumes,
> and I understand that I need these register.dat files for mri_vol2surf.
>
> I have tried bbregister --init-fsl; bbregister --init-spm; and manual
> registration using tkregister2. All of them give me the same error--I think
> it is a path error looking for a subject-specific brain mask (see detailed
> console errors below).
>
> After reading through others' problems with bbregister, I made sure I am
> running the updated versions of bb- and fsl-register, below:
>
> fslregister,v 1.40 2016/02/12 21:43:15 zkaufman
> bbregister,v 1.75 2016/05/10 20:02:28 greve
> freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
>
> I also made sure these files had the edits recommended to others, so I
> don't think this is an previously-addressed issue.
>
> That // in all my errors suggests to me that this is a path problem with
> my HCP data? I am new to FreeSurfer, but I would think that the
> HCP-pre-determined path organization should be compatible with FSL and
> FreeSurfer, since their pipelines use both. Is this a compatibility issue
> with FreeSurfer 6.0?
>
> Anyways, I 

[Freesurfer] bbregister error -- Human Connectome Project Data

[Lana Ruck]

Hello,

I am currently starting a project with the minimally pre-processed rfMRI
from the Human Connectome Project, but I need to do some additional
processing first. This includes smoothing at 6mm FWHM and projection onto
the fsaverage4 surface. I have smoothed the pre-processed rfMRI data using
mri_convert (and have also converted the provided brain-extracted
anatomical), but I am having issues registering the smoothed rfMRI volumes,
and I understand that I need these register.dat files for mri_vol2surf.

I have tried bbregister --init-fsl; bbregister --init-spm; and manual
registration using tkregister2. All of them give me the same error--I think
it is a path error looking for a subject-specific brain mask (see detailed
console errors below).

After reading through others' problems with bbregister, I made sure I am
running the updated versions of bb- and fsl-register, below:

fslregister,v 1.40 2016/02/12 21:43:15 zkaufman
bbregister,v 1.75 2016/05/10 20:02:28 greve
freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c

I also made sure these files had the edits recommended to others, so I
don't think this is an previously-addressed issue.

That // in all my errors suggests to me that this is a path problem with my
HCP data? I am new to FreeSurfer, but I would think that the
HCP-pre-determined path organization should be compatible with FSL and
FreeSurfer, since their pipelines use both. Is this a compatibility issue
with FreeSurfer 6.0?

Anyways, I would prefer to use bbregister --init-fsl, but do not know how
to point it to the right directory for a brainmask. There is no information
provided in any of the --help menus or Wiki pages regarding how to specify
brain masks for registration, and the HCP pre-processed data provides
multiple 'mask.nii.gz' files that I suppose are not being recognized by
bbregister (perhaps because they are not .mgz? I tried converting one to
mgz and also got an error from mghWrite). Either way, I have 4 rfMRI runs
per subject and over 40 subjects to process, so any advice on this error
would be greatly appreciated.

Thanks in advance!
Lana Ruck


Console errors (bolded and underlined) for bbregister --init-fsl,
bbregister --init-spm, and tkregister2:

[lruck@c5 MNINonLinear]$ bbregister --mov
./Results/rfMRI_REST1_LR/REST1LR.img --bold --s 101915 --init-fsl --reg
/N/dc2/scratch/lruck/LH_all/101915/MNINonLinear/Results/rfMRI_REST1_LR/REST1LR_register.dat
tmp
/N/dc2/scratch/lruck/LH_all/101915/MNINonLinear/Results/rfMRI_REST1_LR/tmp.bbregister.26127
Log file is
/N/dc2/scratch/lruck/LH_all/101915/MNINonLinear/Results/rfMRI_REST1_LR/REST1LR_register.dat.log
Wed Dec 27 12:51:51 EST 2017

setenv SUBJECTS_DIR /N/dc2/scratch/lruck/LH_all/
cd /N/dc2/scratch/lruck/LH_all/101915/MNINonLinear
/N/soft/rhel6/freesurfer/6.0.0/freesurfer/bin/bbregister --mov
./Results/rfMRI_REST1_LR/REST1LR.img --bold --s 101915 --init-fsl --reg
/N/dc2/scratch/lruck/LH_all/101915/MNINonLinear/Results/rfMRI_REST1_LR/REST1LR_register.dat

$Id: bbregister,v 1.75 2016/05/10 20:02:28 greve Exp $
Linux c5.karst.uits.iu.edu 2.6.32-696.16.1.el6.x86_64 #1 SMP Sun Oct 8
09:45:56 EDT 2017 x86_64 x86_64 x86_64 GNU/Linux
FREESURFER_HOME /N/soft/rhel6/freesurfer/6.0.0/freesurfer
mri_convert ./Results/rfMRI_REST1_LR/REST1LR.img
/N/dc2/scratch/lruck/LH_all/101915/MNINonLinear/Results/rfMRI_REST1_LR/tmp.bbregister.26127/template.nii
mri_convert.bin ./Results/rfMRI_REST1_LR/REST1LR.img
/N/dc2/scratch/lruck/LH_all/101915/MNINonLinear/Results/rfMRI_REST1_LR/tmp.bbregister.26127/template.nii
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from ./Results/rfMRI_REST1_LR/REST1LR.img...
  analyzeRead() roi_scale   0.0
TR=720.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, 0)
j_ras = (0, 1, 0)
k_ras = (0, 0, 1)
writing to
/N/dc2/scratch/lruck/LH_all/101915/MNINonLinear/Results/rfMRI_REST1_LR/tmp.bbregister.26127/template.nii...
fslregister --s 101915 --mov
/N/dc2/scratch/lruck/LH_all/101915/MNINonLinear/Results/rfMRI_REST1_LR/tmp.bbregister.26127/template.nii
--reg
/N/dc2/scratch/lruck/LH_all/101915/MNINonLinear/Results/rfMRI_REST1_LR/tmp.bbregister.26127/reg.init.dat
--niters 1 --maxangle 90 --tmp
/N/dc2/scratch/lruck/LH_all/101915/MNINonLinear/Results/rfMRI_REST1_LR/tmp.bbregister.26127/fslregister
--dof 6 --fsvol brainmask.mgz --nobetmov

Log file is
/N/dc2/scratch/lruck/LH_all/101915/MNINonLinear/Results/rfMRI_REST1_LR/tmp.bbregister.26127/reg.init.dat.fslregister.log

Wed Dec 27 12:51:52 EST 2017
--s 101915 --mov
/N/dc2/scratch/lruck/LH_all/101915/MNINonLinear/Results/rfMRI_REST1_LR/tmp.bbregister.26127/template.nii
--reg
/N/dc2/scratch/lruck/LH_all/101915/MNINonLinear/Results/rfMRI_REST1_LR/tmp.bbregister.26127/reg.init.dat
--niters 1 --maxangle 90 --tmp
/N/dc2/scratch/lruck/LH_all/101915/MNINonLinear/Results/rfMRI_REST1_LR/tmp.bbregister.26127/fslregister
--dof 6 --fsvol brainmask.mgz --nobetmov
$Id: fslregister,v 1.40 2016/02/12 21:43:15 zkaufman Exp $
c5.karst.uits.iu.edu
Linux 

Re: [Freesurfer] bbregister issues with ?h.only

[Douglas N Greve]

Hi Dorit, I'm suspecting that the initial registration is off. Can you 
upload the data to somewhere I can get at it?

doug


On 12/18/2017 03:08 PM, Dorit Kliemann wrote:
> Hi,
>
> I’m having some troubles with using bbregister on hemispherectomy 
> brains (i.e only one hemisphere; data is successfully processed with 
> recon-all dev version - thanks to Bruce).
>
> I use bbregister to create a register.dat for the functional 
> (preprocessed with fmriprep and registered -but not resampled- to 
> standard space with fmriprep) to structural. Goal is to use the aparc+aseg
> with mri_label2vol to transform to functional volume space. Ultimate 
> goal is then to extract time series with mrisegstats. And this seems 
> to work fine for 3 out of 5 subjects with hemispherectomy.
>
> However for two subjects the bbregister steps produced a bad output 
> (as in the input tilts vertically, see screenshot overlaid on T1). One 
> reason might be that for those subjects two heads are in a bid of a 
> ‘funky tilted’ position, which maybe causes the automatic registration 
> in bbregister to fail?
> Regardless of the reason, I was just wondering if any of you (Doug?) 
> have further suggestions?
>
> One issue I noticed in the log is its suggested to use the T1 flag 
> (not the bold) but its a bold input, just weird intensities probably 
> bc of the ‘empty’ hemisphere. I also tried to run it with the T1 
> flag..same issue
>
> Thank you,
> Dorit
>
>
> Here is the command I use for bbregister
> bbregister --s subjx --mov func.nii.gz --init-fsl --reg 
> subjx_register.dat --bold --lh-only
>
> Also happy to upload the relevant data or paste the whole log.
> I use Fs 6.0 to run bbregister,mri_label2vol and mri_segstats.
>
>
>
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> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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[Freesurfer] bbregister issues with ?h.only

[Dorit Kliemann]

Hi,

I’m having some troubles with using bbregister on hemispherectomy brains (i.e 
only one hemisphere; data is successfully processed with recon-all dev version 
- thanks to Bruce). 

I use bbregister to create a register.dat for the functional (preprocessed with 
fmriprep and registered -but not resampled- to standard space with fmriprep) to 
structural. Goal is to use the aparc+aseg
with mri_label2vol to transform to functional volume space. Ultimate goal is 
then to extract time series with mrisegstats. And this seems to work fine for 3 
out of 5 subjects with hemispherectomy.

However for two subjects the bbregister steps produced a bad output (as in the 
input tilts vertically, see screenshot overlaid on T1). One reason might be 
that for those subjects two heads are in a bid of a ‘funky tilted’ position, 
which maybe causes the automatic registration in bbregister to fail? 
Regardless of the reason, I was just wondering if any of you (Doug?) have 
further suggestions? 

One issue I noticed in the log is its suggested to use the T1 flag (not the 
bold) but its a bold input, just weird intensities probably bc of the ‘empty’ 
hemisphere. I also tried to run it with the T1 flag..same issue

Thank you,
Dorit


Here is the command I use for bbregister
bbregister --s subjx --mov func.nii.gz --init-fsl --reg subjx_register.dat 
--bold --lh-only 

Also happy to upload the relevant data or paste the whole log.
I use Fs 6.0 to run bbregister,mri_label2vol and mri_segstats.



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Re: [Freesurfer] bbregister + mri_vol2vol different results

[Douglas N Greve]

Have you tried passing the fs registration matrix to mri_vol2vol instead 
of the fsl matrix?


On 07/13/2017 05:02 PM, Paul Glad Mihai wrote:
> Hello,
>
> I'm getting two different results from the coregistration step. When I run 
> bbregister on the mean epi it coregisters properly and writes out _bbreg.nii. 
> The next step involves registering the realigned epi time series to the T1 
> image using the same transform matrix calculated from the mean image. But the 
> results fail miserably. I've attached some sample images.
>
> I came across the same result after transforming the matrix it to ITK space 
> and applying the transform using ANTs' applyTransform, which tells me that 
> the ITK conversion works, but this registration goes wrong. Or I may not 
> really understand what I'm doing, lol.
>
> Here are the commands:
>
> bbregister --t2 --epi-mask --init-header --fslmat 
> /data/pt_nmc002/TDMGB_FMRI_coreg/tmp/preproc/_subject_id_sub-01/bbreg/mapflow/_bbreg0/meanusub-01_task-spespk_run-01_bold_bbreg_sub-01.mat
>  --reg 
> /data/pt_nmc002/TDMGB_FMRI_coreg/tmp/preproc/_subject_id_sub-01/bbreg/mapflow/_bbreg0/meanusub-01_task-spespk_run-01_bold_bbreg_sub-01.dat
>  --o 
> /data/pt_nmc002/TDMGB_FMRI_coreg/tmp/preproc/_subject_id_sub-01/bbreg/mapflow/_bbreg0/meanusub-01_task-spespk_run-01_bold_bbreg.nii
>  --mov 
> /data/pt_nmc002/TDMGB_FMRI_coreg/tmp/preproc/_subject_id_sub-01/bbreg/mapflow/_bbreg0/meanusub-01_task-spespk_run-01_bold.nii
>  --s sub-01
>
> mri_vol2vol --fsl 
> /data/pt_nmc002/TDMGB_FMRI_coreg/tmp/preproc/_subject_id_sub-01/bbreg/mapflow/_bbreg0/meanusub-01_task-spespk_run-01_bold_bbreg_sub-01.mat
>  --mov 
> /data/pt_nmc002/TDMGB_FMRI_coreg/tmp/preproc/_subject_id_sub-01/coreg_func/mapflow/_coreg_func0/usub-01_task-spespk_run-01_bold.nii
>  --targ 
> /data/pt_nmc002/TDMGB_FMRI_coreg/tmp/preproc/_subject_id_sub-01/brainextract/sub-01_acq-T1w_brain.nii.gz
>  --o 
> /data/pt_nmc002/TDMGB_FMRI_coreg/tmp/preproc/_subject_id_sub-01/coreg_func/mapflow/_coreg_func0/usub-01_task-spespk_run-01_bold_warped.nii
>
> Regards,
> Glad
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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Re: [Freesurfer] bbregister + mri_vol2vol different results

[Bruce Fischl]

glad it worked out
Bruce
On Mon, 17 Jul 2017, Paul Glad Mihai wrote:

> Hello again,
>
> I've found my mistake! Instead of using the brainmask from reconall for
> the target, I used the brain from the fsl ouput of BET. This is a
> mistake, since the two brains aren't aligned. I've corrected the mistake
> and now it works.
>
> Regards,
> Glad
>
> On 07/13/2017 11:02 PM, Paul Glad Mihai wrote:
>> Hello,
>>
>> I'm getting two different results from the coregistration step. When I run 
>> bbregister on the mean epi it coregisters properly and writes out 
>> _bbreg.nii. The next step involves registering the realigned epi time series 
>> to the T1 image using the same transform matrix calculated from the mean 
>> image. But the results fail miserably. I've attached some sample images.
>>
>> I came across the same result after transforming the matrix it to ITK space 
>> and applying the transform using ANTs' applyTransform, which tells me that 
>> the ITK conversion works, but this registration goes wrong. Or I may not 
>> really understand what I'm doing, lol.
>>
>> Here are the commands:
>>
>> bbregister --t2 --epi-mask --init-header --fslmat 
>> /data/pt_nmc002/TDMGB_FMRI_coreg/tmp/preproc/_subject_id_sub-01/bbreg/mapflow/_bbreg0/meanusub-01_task-spespk_run-01_bold_bbreg_sub-01.mat
>>  --reg 
>> /data/pt_nmc002/TDMGB_FMRI_coreg/tmp/preproc/_subject_id_sub-01/bbreg/mapflow/_bbreg0/meanusub-01_task-spespk_run-01_bold_bbreg_sub-01.dat
>>  --o 
>> /data/pt_nmc002/TDMGB_FMRI_coreg/tmp/preproc/_subject_id_sub-01/bbreg/mapflow/_bbreg0/meanusub-01_task-spespk_run-01_bold_bbreg.nii
>>  --mov 
>> /data/pt_nmc002/TDMGB_FMRI_coreg/tmp/preproc/_subject_id_sub-01/bbreg/mapflow/_bbreg0/meanusub-01_task-spespk_run-01_bold.nii
>>  --s sub-01
>>
>> mri_vol2vol --fsl 
>> /data/pt_nmc002/TDMGB_FMRI_coreg/tmp/preproc/_subject_id_sub-01/bbreg/mapflow/_bbreg0/meanusub-01_task-spespk_run-01_bold_bbreg_sub-01.mat
>>  --mov 
>> /data/pt_nmc002/TDMGB_FMRI_coreg/tmp/preproc/_subject_id_sub-01/coreg_func/mapflow/_coreg_func0/usub-01_task-spespk_run-01_bold.nii
>>  --targ 
>> /data/pt_nmc002/TDMGB_FMRI_coreg/tmp/preproc/_subject_id_sub-01/brainextract/sub-01_acq-T1w_brain.nii.gz
>>  --o 
>> /data/pt_nmc002/TDMGB_FMRI_coreg/tmp/preproc/_subject_id_sub-01/coreg_func/mapflow/_coreg_func0/usub-01_task-spespk_run-01_bold_warped.nii
>>
>> Regards,
>> Glad
>>
>>
>>
>> ___
>> 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.
>>
>
>
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Re: [Freesurfer] bbregister + mri_vol2vol different results

[Paul Glad Mihai]

Hello again,

I've found my mistake! Instead of using the brainmask from reconall for
the target, I used the brain from the fsl ouput of BET. This is a
mistake, since the two brains aren't aligned. I've corrected the mistake
and now it works.

Regards,
Glad

On 07/13/2017 11:02 PM, Paul Glad Mihai wrote:
> Hello,
> 
> I'm getting two different results from the coregistration step. When I run 
> bbregister on the mean epi it coregisters properly and writes out _bbreg.nii. 
> The next step involves registering the realigned epi time series to the T1 
> image using the same transform matrix calculated from the mean image. But the 
> results fail miserably. I've attached some sample images. 
> 
> I came across the same result after transforming the matrix it to ITK space 
> and applying the transform using ANTs' applyTransform, which tells me that 
> the ITK conversion works, but this registration goes wrong. Or I may not 
> really understand what I'm doing, lol.
> 
> Here are the commands:
> 
> bbregister --t2 --epi-mask --init-header --fslmat 
> /data/pt_nmc002/TDMGB_FMRI_coreg/tmp/preproc/_subject_id_sub-01/bbreg/mapflow/_bbreg0/meanusub-01_task-spespk_run-01_bold_bbreg_sub-01.mat
>  --reg 
> /data/pt_nmc002/TDMGB_FMRI_coreg/tmp/preproc/_subject_id_sub-01/bbreg/mapflow/_bbreg0/meanusub-01_task-spespk_run-01_bold_bbreg_sub-01.dat
>  --o 
> /data/pt_nmc002/TDMGB_FMRI_coreg/tmp/preproc/_subject_id_sub-01/bbreg/mapflow/_bbreg0/meanusub-01_task-spespk_run-01_bold_bbreg.nii
>  --mov 
> /data/pt_nmc002/TDMGB_FMRI_coreg/tmp/preproc/_subject_id_sub-01/bbreg/mapflow/_bbreg0/meanusub-01_task-spespk_run-01_bold.nii
>  --s sub-01
> 
> mri_vol2vol --fsl 
> /data/pt_nmc002/TDMGB_FMRI_coreg/tmp/preproc/_subject_id_sub-01/bbreg/mapflow/_bbreg0/meanusub-01_task-spespk_run-01_bold_bbreg_sub-01.mat
>  --mov 
> /data/pt_nmc002/TDMGB_FMRI_coreg/tmp/preproc/_subject_id_sub-01/coreg_func/mapflow/_coreg_func0/usub-01_task-spespk_run-01_bold.nii
>  --targ 
> /data/pt_nmc002/TDMGB_FMRI_coreg/tmp/preproc/_subject_id_sub-01/brainextract/sub-01_acq-T1w_brain.nii.gz
>  --o 
> /data/pt_nmc002/TDMGB_FMRI_coreg/tmp/preproc/_subject_id_sub-01/coreg_func/mapflow/_coreg_func0/usub-01_task-spespk_run-01_bold_warped.nii
> 
> Regards,
> Glad
> 
> 
> 
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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
> 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.
> 

-- 
Paul Glad Mihai, PhD

Independent Research Group "Neural Mechanisms of Human Communication"
Max Planck Institute for Human Cognitive and Brain Sciences
Stephanstraße 1A, 04103 Leipzig, Germany

Phone:   +49 (0) 341-9940-2478
E-mail:  mi...@cbs.mpg.de

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Re: [Freesurfer] bbregister + mri_vol2vol different results

[Paul Glad Mihai]

Hello Experts,

Just to follow up on my previous posting, here is the information from
the headrs of the different nifti files after the steps performed.

  * First, the header of the mean original nifti after realignment:
qto_xyz:1  -1.099422  0.024665  0.025745  65.286888
qto_xyz:2  -0.021598  -1.092710  0.124570  38.997047
qto_xyz:3  0.028368  0.123999  1.092621  -26.324900
qto_xyz:4  0.00  0.00  0.00  1.00
qform_xorient  Right-to-Left
qform_yorient  Anterior-to-Posterior
qform_zorient  Inferior-to-Superior
sform_name Aligned Anat
sform_code 2
sto_xyz:1  -1.099422  0.024662  0.025746  65.286888
sto_xyz:2  -0.021594  -1.092710  0.124570  38.997047
sto_xyz:3  0.028368  0.123999  1.092621  -26.324900
sto_xyz:4  0.00  0.00  0.00  1.00
sform_xorient  Right-to-Left
sform_yorient  Anterior-to-Posterior
sform_zorient  Inferior-to-Superior

  * Second, the header of the nifti after bbregister with the write
output option enabled:
qto_xyz:1  -1.00  0.00  -0.00  126.995163
qto_xyz:2  0.00  0.00  1.00  -135.546768
qto_xyz:3  -0.00  -1.00  -0.00  109.658028
qto_xyz:4  0.00  0.00  0.00  1.00
qform_xorient  Right-to-Left
qform_yorient  Superior-to-Inferior
qform_zorient  Posterior-to-Anterior
sform_name Scanner Anat
sform_code 1
sto_xyz:1  -1.00  0.00  0.00  126.995163
sto_xyz:2  0.00  0.00  1.00  -135.546768
sto_xyz:3  0.00  -1.00  0.00  109.658028
sto_xyz:4  0.00  0.00  0.00  1.00
sform_xorient  Right-to-Left
sform_yorient  Superior-to-Inferior
sform_zorient  Posterior-to-Anterior

  * This is the matrix (.mat) resulting from the bbregister step:
  -0.69660.00760214   -0.00178158  192.10556030
   0.00103370   -0.09726234   -0.99525851  135.02107239
  -0.00773941   -0.995229780.09725130  173.68141174
   0.0.0.1.


  * Third, the header of the nifti after mri_vol2vol using the matrix
from the bbregister step:
qto_xyz:1  0.00  0.00  0.70  -85.004837
qto_xyz:2  -0.70  0.00  0.00  104.453209
qto_xyz:3  0.00  -0.70  0.00  93.658028
qto_xyz:4  0.00  0.00  0.00  1.00
qform_xorient  Anterior-to-Posterior
qform_yorient  Superior-to-Inferior
qform_zorient  Left-to-Right
sform_name Scanner Anat
sform_code 1
sto_xyz:1  0.00  0.00  0.70  -85.004837
sto_xyz:2  -0.70  0.00  0.00  104.453209
sto_xyz:3  0.00  -0.70  0.00  93.658028
sto_xyz:4  0.00  0.00  0.00  1.00
sform_xorient  Anterior-to-Posterior
sform_yorient  Superior-to-Inferior
sform_zorient  Left-to-Right

Regards,
Glad

On 07/13/2017 11:02 PM, Paul Glad Mihai wrote:
> Hello,
> 
> I'm getting two different results from the coregistration step. When I run 
> bbregister on the mean epi it coregisters properly and writes out _bbreg.nii. 
> The next step involves registering the realigned epi time series to the T1 
> image using the same transform matrix calculated from the mean image. But the 
> results fail miserably. I've attached some sample images. 
> 
> I came across the same result after transforming the matrix it to ITK space 
> and applying the transform using ANTs' applyTransform, which tells me that 
> the ITK conversion works, but this registration goes wrong. Or I may not 
> really understand what I'm doing, lol.
> 
> Here are the commands:
> 
> bbregister --t2 --epi-mask --init-header --fslmat 
> /data/pt_nmc002/TDMGB_FMRI_coreg/tmp/preproc/_subject_id_sub-01/bbreg/mapflow/_bbreg0/meanusub-01_task-spespk_run-01_bold_bbreg_sub-01.mat
>  --reg 
> /data/pt_nmc002/TDMGB_FMRI_coreg/tmp/preproc/_subject_id_sub-01/bbreg/mapflow/_bbreg0/meanusub-01_task-spespk_run-01_bold_bbreg_sub-01.dat
>  --o 
> /data/pt_nmc002/TDMGB_FMRI_coreg/tmp/preproc/_subject_id_sub-01/bbreg/mapflow/_bbreg0/meanusub-01_task-spespk_run-01_bold_bbreg.nii
>  --mov 
> /data/pt_nmc002/TDMGB_FMRI_coreg/tmp/preproc/_subject_id_sub-01/bbreg/mapflow/_bbreg0/meanusub-01_task-spespk_run-01_bold.nii
>  --s sub-01
> 
> mri_vol2vol --fsl 
> /data/pt_nmc002/TDMGB_FMRI_coreg/tmp/preproc/_subject_id_sub-01/bbreg/mapflow/_bbreg0/meanusub-01_task-spespk_run-01_bold_bbreg_sub-01.mat
>  --mov 
> /data/pt_nmc002/TDMGB_FMRI_coreg/tmp/preproc/_subject_id_sub-01/coreg_func/mapflow/_coreg_func0/usub-01_task-spespk_run-01_bold.nii
>  --targ 
> /data/pt_nmc002/TDMGB_FMRI_coreg/tmp/preproc/_subject_id_sub-01/brainextract/sub-01_acq-T1w_brain.nii.gz
>  --o 
> /data/pt_nmc002/TDMGB_FMRI_coreg/tmp/preproc/_subject_id_sub-01/coreg_func/mapflow/_coreg_func0/usub-01_task-spespk_run-01_bold_warped.nii
> 
> Regards,
> Glad
> 
> 
> 
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> 
> 
> The information 

Re: [Freesurfer] BBRegister + partial FoV fail

[Paul Glad Mihai]

So far it isn't anymore. It's more of a problem with ANTs now.
BBRegister works with --init-header for partial FoV T1 and mean EPI are
more or less in alignment. But if they wouldn't be then one would have a
problem with registration.

On 07/13/2017 12:35 AM, Douglas N Greve wrote:
> Is this still a problem?
> 
> On 07/11/2017 09:51 AM, Paul Glad Mihai wrote:
>> Hi Bruce,
>>
>> Thanks for the quick reply. I've just finished rerunning it with spm,
>> fsl and header init and the latter seemed to work if I write out a
>> _bbreg.nii file. The former two failed, however. Apparently using the
>> header seems to work for this one subject and one run. I'm testing the
>> rest of the runs.
>>
>> This is an example from the FSL init. Please note that I'm running it
>> through nipype, hence the jumbled subdirectory strucutre.
>>
>> bbregister --t2 --epi-mask --init-fsl --fslmat
>> /data/pt_nmc002/TDMGB_FMRI_coreg/tmp/preproc/_subject_id_sub-01/_init_fsl/bbreg/mapflow/_bbreg0/meanusub-01_task-spespk_run-01_bold_bbreg_sub-01.mat
>> --reg
>> /data/pt_nmc002/TDMGB_FMRI_coreg/tmp/preproc/_subject_id_sub-01/_init_fsl/bbreg/mapflow/_bbreg0/meanusub-01_task-spespk_run-01_bold_bbreg_sub-01.dat
>> --o
>> /data/pt_nmc002/TDMGB_FMRI_coreg/tmp/preproc/_subject_id_sub-01/_init_fsl/bbreg/mapflow/_bbreg0/meanusub-01_task-spespk_run-01_bold_bbreg.nii
>> --mov
>> /data/pt_nmc002/TDMGB_FMRI_coreg/tmp/preproc/_subject_id_sub-01/_init_fsl/bbreg/mapflow/_bbreg0/meanusub-01_task-spespk_run-01_bold.nii
>> --s sub-01
>>
>> The output is attached. Details are under the heading 'Terminal output'.
>> I'm also attaching a screenshot of the T2 with a white overlay for the
>> header init. It seems to be alright. The output from the header init is
>> also attached. The difference in the command line is --init-header
>> instead of --init-fsl.
>>
>> Downstream, however, the registration to MNI through ANTs seems to fail,
>> even though I've converted the transformation matrices to ITK through
>> C3D. H... I just had a revelation. I may have used the wrong T1 to
>> calculate the registration matrix through ANTs. Instead of using the T1
>> from the ReconAll output, I used the one from the fsl.bet. I'll make
>> sure to use the ReconAll T1 and get back to you.
>>
>> I would appreciate a comment, however, on how to get better registration
>> of partial FoV T2 images to T1 images through BBRegister. It seems that
>> the easiest option is a full head EPI at the time of the experiment.
>>
>> Regards,
>> Glad
>>
>>
>>
>> On 07/11/2017 03:33 PM, Bruce Fischl wrote:
>>> Hi Glad
>>>
>>> can you send us the full command line you are using and screen output?
>>>
>>> thanks
>>>
>>> Bruce
>>> On
>>> Tue, 11 Jul 2017, Paul Glad Mihai wrote:
>>>
 Dear List,

 I've been quite frustrated with the BBRegister results when trying to
 register a partial field of view EPI mean functional image to a T1 scan.
 I've tried different init arguments (fsl, spm, header) and none really
 work. I've found that the initial registration is causing the problem,
 since the T1 and mean EPi are in reasonable alignment, but not perfect.
 As soon as it passes the initial alignment it's totally off and
 obviously fails in the BBR step. I have no full head EPI, unfortunately.
 I have a full head scout which seems to be a T1 image with really poor
 contrast. If I try to register this to the T1 through BBRegister it
 works. But if I use it as an intermediate file it still fails. What can
 I do? How does the intermediate file come into play? Will it get
 registered to the T1 initially and then the resulting matrix is used
 further? I also tried to feed the resulting registration matrix as
 init-reg but that didn't work either.

 Is there a way to skip the initial registration?

 Can I mask the T1 image with the FoV of the functional scan if they are
 initially in reasonable alignment? Would that work? Would that mean that
 I have to re-run ReconAll with the masked T1?

 Would love to hear back from someone.

 Regards,
 Glad

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

-- 
Paul Glad Mihai, PhD

Re: [Freesurfer] BBRegister + partial FoV fail

[Douglas N Greve]

Is this still a problem?

On 07/11/2017 09:51 AM, Paul Glad Mihai wrote:
> Hi Bruce,
>
> Thanks for the quick reply. I've just finished rerunning it with spm,
> fsl and header init and the latter seemed to work if I write out a
> _bbreg.nii file. The former two failed, however. Apparently using the
> header seems to work for this one subject and one run. I'm testing the
> rest of the runs.
>
> This is an example from the FSL init. Please note that I'm running it
> through nipype, hence the jumbled subdirectory strucutre.
>
> bbregister --t2 --epi-mask --init-fsl --fslmat
> /data/pt_nmc002/TDMGB_FMRI_coreg/tmp/preproc/_subject_id_sub-01/_init_fsl/bbreg/mapflow/_bbreg0/meanusub-01_task-spespk_run-01_bold_bbreg_sub-01.mat
> --reg
> /data/pt_nmc002/TDMGB_FMRI_coreg/tmp/preproc/_subject_id_sub-01/_init_fsl/bbreg/mapflow/_bbreg0/meanusub-01_task-spespk_run-01_bold_bbreg_sub-01.dat
> --o
> /data/pt_nmc002/TDMGB_FMRI_coreg/tmp/preproc/_subject_id_sub-01/_init_fsl/bbreg/mapflow/_bbreg0/meanusub-01_task-spespk_run-01_bold_bbreg.nii
> --mov
> /data/pt_nmc002/TDMGB_FMRI_coreg/tmp/preproc/_subject_id_sub-01/_init_fsl/bbreg/mapflow/_bbreg0/meanusub-01_task-spespk_run-01_bold.nii
> --s sub-01
>
> The output is attached. Details are under the heading 'Terminal output'.
> I'm also attaching a screenshot of the T2 with a white overlay for the
> header init. It seems to be alright. The output from the header init is
> also attached. The difference in the command line is --init-header
> instead of --init-fsl.
>
> Downstream, however, the registration to MNI through ANTs seems to fail,
> even though I've converted the transformation matrices to ITK through
> C3D. H... I just had a revelation. I may have used the wrong T1 to
> calculate the registration matrix through ANTs. Instead of using the T1
> from the ReconAll output, I used the one from the fsl.bet. I'll make
> sure to use the ReconAll T1 and get back to you.
>
> I would appreciate a comment, however, on how to get better registration
> of partial FoV T2 images to T1 images through BBRegister. It seems that
> the easiest option is a full head EPI at the time of the experiment.
>
> Regards,
> Glad
>
>
>
> On 07/11/2017 03:33 PM, Bruce Fischl wrote:
>> Hi Glad
>>
>> can you send us the full command line you are using and screen output?
>>
>> thanks
>>
>> Bruce
>> On
>> Tue, 11 Jul 2017, Paul Glad Mihai wrote:
>>
>>> Dear List,
>>>
>>> I've been quite frustrated with the BBRegister results when trying to
>>> register a partial field of view EPI mean functional image to a T1 scan.
>>> I've tried different init arguments (fsl, spm, header) and none really
>>> work. I've found that the initial registration is causing the problem,
>>> since the T1 and mean EPi are in reasonable alignment, but not perfect.
>>> As soon as it passes the initial alignment it's totally off and
>>> obviously fails in the BBR step. I have no full head EPI, unfortunately.
>>> I have a full head scout which seems to be a T1 image with really poor
>>> contrast. If I try to register this to the T1 through BBRegister it
>>> works. But if I use it as an intermediate file it still fails. What can
>>> I do? How does the intermediate file come into play? Will it get
>>> registered to the T1 initially and then the resulting matrix is used
>>> further? I also tried to feed the resulting registration matrix as
>>> init-reg but that didn't work either.
>>>
>>> Is there a way to skip the initial registration?
>>>
>>> Can I mask the T1 image with the FoV of the functional scan if they are
>>> initially in reasonable alignment? Would that work? Would that mean that
>>> I have to re-run ReconAll with the masked T1?
>>>
>>> Would love to hear back from someone.
>>>
>>> Regards,
>>> Glad
>>>
>> ___
>> 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.
>>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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Re: [Freesurfer] BBRegister + partial FoV fail

[Bruce Fischl]

sure. I'll leave the rest to Doug except to say that a full head EPI is a 
pretty cheap and useful thing to get, and that it is not surprising the 
using the header (assuming they are same session) works better than 
anything else

cheers
Bruce

On Tue, 11 Jul 2017, Paul Glad Mihai wrote:

> Hi Bruce,
>
> Thanks for the quick reply. I've just finished rerunning it with spm,
> fsl and header init and the latter seemed to work if I write out a
> _bbreg.nii file. The former two failed, however. Apparently using the
> header seems to work for this one subject and one run. I'm testing the
> rest of the runs.
>
> This is an example from the FSL init. Please note that I'm running it
> through nipype, hence the jumbled subdirectory strucutre.
>
> bbregister --t2 --epi-mask --init-fsl --fslmat
> /data/pt_nmc002/TDMGB_FMRI_coreg/tmp/preproc/_subject_id_sub-01/_init_fsl/bbreg/mapflow/_bbreg0/meanusub-01_task-spespk_run-01_bold_bbreg_sub-01.mat
> --reg
> /data/pt_nmc002/TDMGB_FMRI_coreg/tmp/preproc/_subject_id_sub-01/_init_fsl/bbreg/mapflow/_bbreg0/meanusub-01_task-spespk_run-01_bold_bbreg_sub-01.dat
> --o
> /data/pt_nmc002/TDMGB_FMRI_coreg/tmp/preproc/_subject_id_sub-01/_init_fsl/bbreg/mapflow/_bbreg0/meanusub-01_task-spespk_run-01_bold_bbreg.nii
> --mov
> /data/pt_nmc002/TDMGB_FMRI_coreg/tmp/preproc/_subject_id_sub-01/_init_fsl/bbreg/mapflow/_bbreg0/meanusub-01_task-spespk_run-01_bold.nii
> --s sub-01
>
> The output is attached. Details are under the heading 'Terminal output'.
> I'm also attaching a screenshot of the T2 with a white overlay for the
> header init. It seems to be alright. The output from the header init is
> also attached. The difference in the command line is --init-header
> instead of --init-fsl.
>
> Downstream, however, the registration to MNI through ANTs seems to fail,
> even though I've converted the transformation matrices to ITK through
> C3D. H... I just had a revelation. I may have used the wrong T1 to
> calculate the registration matrix through ANTs. Instead of using the T1
> from the ReconAll output, I used the one from the fsl.bet. I'll make
> sure to use the ReconAll T1 and get back to you.
>
> I would appreciate a comment, however, on how to get better registration
> of partial FoV T2 images to T1 images through BBRegister. It seems that
> the easiest option is a full head EPI at the time of the experiment.
>
> Regards,
> Glad
>
>
>
> On 07/11/2017 03:33 PM, Bruce Fischl wrote:
>> Hi Glad
>>
>> can you send us the full command line you are using and screen output?
>>
>> thanks
>>
>> Bruce
>> On
>> Tue, 11 Jul 2017, Paul Glad Mihai wrote:
>>
>>> Dear List,
>>>
>>> I've been quite frustrated with the BBRegister results when trying to
>>> register a partial field of view EPI mean functional image to a T1 scan.
>>> I've tried different init arguments (fsl, spm, header) and none really
>>> work. I've found that the initial registration is causing the problem,
>>> since the T1 and mean EPi are in reasonable alignment, but not perfect.
>>> As soon as it passes the initial alignment it's totally off and
>>> obviously fails in the BBR step. I have no full head EPI, unfortunately.
>>> I have a full head scout which seems to be a T1 image with really poor
>>> contrast. If I try to register this to the T1 through BBRegister it
>>> works. But if I use it as an intermediate file it still fails. What can
>>> I do? How does the intermediate file come into play? Will it get
>>> registered to the T1 initially and then the resulting matrix is used
>>> further? I also tried to feed the resulting registration matrix as
>>> init-reg but that didn't work either.
>>>
>>> Is there a way to skip the initial registration?
>>>
>>> Can I mask the T1 image with the FoV of the functional scan if they are
>>> initially in reasonable alignment? Would that work? Would that mean that
>>> I have to re-run ReconAll with the masked T1?
>>>
>>> Would love to hear back from someone.
>>>
>>> Regards,
>>> Glad
>>>
>> ___
>> 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.
>>
>
>
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Re: [Freesurfer] BBRegister + partial FoV fail

[Bruce Fischl]

Hi Glad

can you send us the full command line you are using and screen output?

thanks

Bruce
On 
Tue, 11 Jul 2017, Paul Glad Mihai wrote:

> Dear List,
>
> I've been quite frustrated with the BBRegister results when trying to
> register a partial field of view EPI mean functional image to a T1 scan.
> I've tried different init arguments (fsl, spm, header) and none really
> work. I've found that the initial registration is causing the problem,
> since the T1 and mean EPi are in reasonable alignment, but not perfect.
> As soon as it passes the initial alignment it's totally off and
> obviously fails in the BBR step. I have no full head EPI, unfortunately.
> I have a full head scout which seems to be a T1 image with really poor
> contrast. If I try to register this to the T1 through BBRegister it
> works. But if I use it as an intermediate file it still fails. What can
> I do? How does the intermediate file come into play? Will it get
> registered to the T1 initially and then the resulting matrix is used
> further? I also tried to feed the resulting registration matrix as
> init-reg but that didn't work either.
>
> Is there a way to skip the initial registration?
>
> Can I mask the T1 image with the FoV of the functional scan if they are
> initially in reasonable alignment? Would that work? Would that mean that
> I have to re-run ReconAll with the masked T1?
>
> Would love to hear back from someone.
>
> Regards,
> Glad
>
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contains patient information, please contact the Partners Compliance HelpLine at
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[Freesurfer] BBRegister + partial FoV fail

[Paul Glad Mihai]

Dear List,

I've been quite frustrated with the BBRegister results when trying to
register a partial field of view EPI mean functional image to a T1 scan.
I've tried different init arguments (fsl, spm, header) and none really
work. I've found that the initial registration is causing the problem,
since the T1 and mean EPi are in reasonable alignment, but not perfect.
As soon as it passes the initial alignment it's totally off and
obviously fails in the BBR step. I have no full head EPI, unfortunately.
I have a full head scout which seems to be a T1 image with really poor
contrast. If I try to register this to the T1 through BBRegister it
works. But if I use it as an intermediate file it still fails. What can
I do? How does the intermediate file come into play? Will it get
registered to the T1 initially and then the resulting matrix is used
further? I also tried to feed the resulting registration matrix as
init-reg but that didn't work either.

Is there a way to skip the initial registration?

Can I mask the T1 image with the FoV of the functional scan if they are
initially in reasonable alignment? Would that work? Would that mean that
I have to re-run ReconAll with the masked T1?

Would love to hear back from someone.

Regards,
Glad
-- 
Paul Glad Mihai, PhD

Independent Research Group "Neural Mechanisms of Human Communication"
Max Planck Institute for Human Cognitive and Brain Sciences
Stephanstraße 1A, 04103 Leipzig, Germany

Phone:   +49 (0) 341-9940-2478
E-mail:  mi...@cbs.mpg.de

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Re: [Freesurfer] bbregister vs spmregister vs mri_coreg

[Douglas Greve]

there is not an mri_spmregister (there is spmregister). If you have an 
FA map, then I would use bbregister



On 2/25/17 8:03 PM, John Anderson wrote:

Hi Doug, thank you for the detailed response. Highly appreciated!
Kindly. I want to register FA map to structural T1 image using the 
command mri_spmregister as follow:


mri_spmregister move FA.nii --s subj1 --reg reg dat --o FA_2_T1.nii.gz

Is this correct?






 Original Message 
Subject: bbregister vs spmregister vs mri_coreg
Local Time: February 25, 2017 8:49 AM
UTC Time: February 25, 2017 1:49 PM
From: john.ande...@protonmail.com
To: freesurfer@nmr.mgh.harvard.edu 

mri_coreg is the FS implementation of spm_coreg (spmregister) both of 
which use normalized mutual info. bbregister uses the BBR cost 
function and is preferred for all MRI. For registration to MNI space, 
we usually use mni152reg (a wrapper around fsl's flirt)



On 2/25/17 8:49 AM, John Anderson wrote:

Dear Freesurfer experts,

I see that the tool "mri_coreg" has been implemented recently in Free 
Surfer 6 and I really wanted to know what are the differences between 
the registration tools "bbregister", " spmregister" and "mri_coreg"! 
Kindly:


1. Are these tools similar? if not what are the differences ?

2. Is there any preference of using a tool over the others for 
specific type of data. For example:


 A. If I want to register FA map to T1 image which tool is 
more robust?


 B. if I want to register FA map to MNI space which tool is 
more robust?




I highly appreciate your input on this!


John t?e�?�Z�׮
Dear Freesurfer experts,
I see that the tool "mri_coreg" has been implemented recently in Free 
Surfer 6 and I really wanted to know what are the differences between 
the registration tools "bbregister", " spmregister" and "mri_coreg"! 
Kindly:

1. Are these tools similar? if not what are the differences ?
2. Is there any preference of using a tool over the others for 
specific type of data. For example:
   A. If I want to register FA map to T1 image which tool is 
more robust?
   B. if I want to register FA map to MNI space which tool is 
more robust?



I highly appreciate your input on this!

John




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Re: [Freesurfer] bbregister problem with --init-best

[Feilong Ma]

In those cases the cost of coreg is quite close to the optimal, for
example, 0.366088 vs 0.366089.  I guess the final results won't differ much
if I used --init-coreg instead of --init-best.

Best,
Feilong

On Fri, Mar 17, 2017 at 10:04 PM, Douglas Greve 
wrote:

> what happened in the ones that coreg was not the best? what is the nature
> of the data?
>
> On 3/17/17 6:39 PM, Feilong Ma wrote:
>
> Thanks, Doug!  I've run bbregister with --init-best on my data comparing
> coreg, fsl, rr, and header; most of the times the choice is coreg as you
> said (59 out of 88 total runs).
>
> Best,
> Feilong
>
> On Fri, Mar 17, 2017 at 4:11 PM, Douglas N Greve <
> gr...@nmr.mgh.harvard.edu> wrote:
>
>> Hi Feilong, you do not need to use --init-best with bbregister anymore.
>> It automatically uses --init-coreg (a remake of the spm coreg) which is
>> the best as far a I can tell
>>
>>
>> On 03/17/2017 02:47 PM, Feilong Ma wrote:
>> > Hi FreeSurfer Developers,
>> >
>> > I'm having trouble using bbregister with the `--init-best` flag, a
>> > minimal example and error message is like this:
>> > $> bbregister --s ag00 --mov data/ag00/align/raiders/run00_ref.nii.gz
>> > --init-best --bold --lta data/ag00/align/raiders/run00_ref_to_anat.lta
>> > ERROR: cannot spec an init method with --init-best
>> >
>> > It seems `InitCoreg` is set to 1 by default in the code of bbregister.
>> > Therefore, when `--init-best` is also set, it would always trigger the
>> > conflict detection and exit with the error message.
>> >
>> > Here are some related version information:
>> > - FreeSurfer version:
>> > freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
>> > - bbregister version: $Id: bbregister,v 1.75 2016/05/10 20:02:28 greve
>> > Exp $
>> > - OS: CentOS Linux release 7.3.1611 (Core)
>> >
>> > Best,
>> > Feilong
>> >
>> >
>> >
>> > ___
>> > Freesurfer mailing list
>> > Freesurfer@nmr.mgh.harvard.edu
>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>> --
>> Douglas N. Greve, Ph.D.
>> MGH-NMR Center
>> gr...@nmr.mgh.harvard.edu
>> Phone Number: 617-724-2358
>> Fax: 617-726-7422
>>
>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>>
>> ___
>> 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.
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>
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Re: [Freesurfer] bbregister problem with --init-best

[Douglas Greve]

what happened in the ones that coreg was not the best? what is the 
nature of the data?



On 3/17/17 6:39 PM, Feilong Ma wrote:
Thanks, Doug!  I've run bbregister with --init-best on my data 
comparing coreg, fsl, rr, and header; most of the times the choice is 
coreg as you said (59 out of 88 total runs).


Best,
Feilong

On Fri, Mar 17, 2017 at 4:11 PM, Douglas N Greve 
> wrote:


Hi Feilong, you do not need to use --init-best with bbregister
anymore.
It automatically uses --init-coreg (a remake of the spm coreg)
which is
the best as far a I can tell


On 03/17/2017 02:47 PM, Feilong Ma wrote:
> Hi FreeSurfer Developers,
>
> I'm having trouble using bbregister with the `--init-best` flag, a
> minimal example and error message is like this:
> $> bbregister --s ag00 --mov
data/ag00/align/raiders/run00_ref.nii.gz
> --init-best --bold --lta
data/ag00/align/raiders/run00_ref_to_anat.lta
> ERROR: cannot spec an init method with --init-best
>
> It seems `InitCoreg` is set to 1 by default in the code of
bbregister.
> Therefore, when `--init-best` is also set, it would always
trigger the
> conflict detection and exit with the error message.
>
> Here are some related version information:
> - FreeSurfer version:
> freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
> - bbregister version: $Id: bbregister,v 1.75 2016/05/10 20:02:28
greve
> Exp $
> - OS: CentOS Linux release 7.3.1611 (Core)
>
> Best,
> Feilong
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu

> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu 
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2

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Re: [Freesurfer] bbregister problem with --init-best

[Feilong Ma]

Thanks, Doug!  I've run bbregister with --init-best on my data comparing
coreg, fsl, rr, and header; most of the times the choice is coreg as you
said (59 out of 88 total runs).

Best,
Feilong

On Fri, Mar 17, 2017 at 4:11 PM, Douglas N Greve 
wrote:

> Hi Feilong, you do not need to use --init-best with bbregister anymore.
> It automatically uses --init-coreg (a remake of the spm coreg) which is
> the best as far a I can tell
>
>
> On 03/17/2017 02:47 PM, Feilong Ma wrote:
> > Hi FreeSurfer Developers,
> >
> > I'm having trouble using bbregister with the `--init-best` flag, a
> > minimal example and error message is like this:
> > $> bbregister --s ag00 --mov data/ag00/align/raiders/run00_ref.nii.gz
> > --init-best --bold --lta data/ag00/align/raiders/run00_ref_to_anat.lta
> > ERROR: cannot spec an init method with --init-best
> >
> > It seems `InitCoreg` is set to 1 by default in the code of bbregister.
> > Therefore, when `--init-best` is also set, it would always trigger the
> > conflict detection and exit with the error message.
> >
> > Here are some related version information:
> > - FreeSurfer version:
> > freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
> > - bbregister version: $Id: bbregister,v 1.75 2016/05/10 20:02:28 greve
> > Exp $
> > - OS: CentOS Linux release 7.3.1611 (Core)
> >
> > Best,
> > Feilong
> >
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
> ___
> Freesurfer mailing list
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> 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.
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Re: [Freesurfer] bbregister problem with --init-best

[Douglas N Greve]

Hi Feilong, you do not need to use --init-best with bbregister anymore. 
It automatically uses --init-coreg (a remake of the spm coreg) which is 
the best as far a I can tell


On 03/17/2017 02:47 PM, Feilong Ma wrote:
> Hi FreeSurfer Developers,
>
> I'm having trouble using bbregister with the `--init-best` flag, a 
> minimal example and error message is like this:
> $> bbregister --s ag00 --mov data/ag00/align/raiders/run00_ref.nii.gz 
> --init-best --bold --lta data/ag00/align/raiders/run00_ref_to_anat.lta
> ERROR: cannot spec an init method with --init-best
>
> It seems `InitCoreg` is set to 1 by default in the code of bbregister.
> Therefore, when `--init-best` is also set, it would always trigger the 
> conflict detection and exit with the error message.
>
> Here are some related version information:
> - FreeSurfer version: 
> freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
> - bbregister version: $Id: bbregister,v 1.75 2016/05/10 20:02:28 greve 
> Exp $
> - OS: CentOS Linux release 7.3.1611 (Core)
>
> Best,
> Feilong
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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Re: [Freesurfer] bbregister problem with --init-best

[Feilong Ma]

Awesome!  Thanks for your help!

Best,
Feilong

On Fri, Mar 17, 2017 at 2:57 PM, Z K  wrote:

> It seems that a freesurfer user just submitted a pull request yesterday
> that fixes this bug:
>
>   https://github.com/freesurfer/freesurfer/pull/24
>
> Feel free to download the fixed version:
>
>   https://github.com/freesurfer/freesurfer/blob/dev/scripts/bbregister
>
>
>
>
> On 03/17/2017 02:47 PM, Feilong Ma wrote:
>
>> Hi FreeSurfer Developers,
>>
>> I'm having trouble using bbregister with the `--init-best` flag, a
>> minimal example and error message is like this:
>> $> bbregister --s ag00 --mov data/ag00/align/raiders/run00_ref.nii.gz
>> --init-best --bold --lta data/ag00/align/raiders/run00_ref_to_anat.lta
>> ERROR: cannot spec an init method with --init-best
>>
>> It seems `InitCoreg` is set to 1 by default in the code of bbregister.
>> Therefore, when `--init-best` is also set, it would always trigger the
>> conflict detection and exit with the error message.
>>
>> Here are some related version information:
>> - FreeSurfer version:
>> freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
>> - bbregister version: $Id: bbregister,v 1.75 2016/05/10 20:02:28 greve
>> Exp $
>> - OS: CentOS Linux release 7.3.1611 (Core)
>>
>> Best,
>> Feilong
>>
>>
>>
>> ___
>> 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
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Re: [Freesurfer] bbregister problem with --init-best

[Z K]

It seems that a freesurfer user just submitted a pull request yesterday 
that fixes this bug:

   https://github.com/freesurfer/freesurfer/pull/24

Feel free to download the fixed version:

   https://github.com/freesurfer/freesurfer/blob/dev/scripts/bbregister



On 03/17/2017 02:47 PM, Feilong Ma wrote:
> Hi FreeSurfer Developers,
>
> I'm having trouble using bbregister with the `--init-best` flag, a
> minimal example and error message is like this:
> $> bbregister --s ag00 --mov data/ag00/align/raiders/run00_ref.nii.gz
> --init-best --bold --lta data/ag00/align/raiders/run00_ref_to_anat.lta
> ERROR: cannot spec an init method with --init-best
>
> It seems `InitCoreg` is set to 1 by default in the code of bbregister.
> Therefore, when `--init-best` is also set, it would always trigger the
> conflict detection and exit with the error message.
>
> Here are some related version information:
> - FreeSurfer version:
> freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
> - bbregister version: $Id: bbregister,v 1.75 2016/05/10 20:02:28 greve Exp $
> - OS: CentOS Linux release 7.3.1611 (Core)
>
> Best,
> Feilong
>
>
>
> ___
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> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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[Freesurfer] bbregister problem with --init-best

[Feilong Ma]

Hi FreeSurfer Developers,

I'm having trouble using bbregister with the `--init-best` flag, a minimal
example and error message is like this:
$> bbregister --s ag00 --mov data/ag00/align/raiders/run00_ref.nii.gz
--init-best --bold --lta data/ag00/align/raiders/run00_ref_to_anat.lta
ERROR: cannot spec an init method with --init-best

It seems `InitCoreg` is set to 1 by default in the code of bbregister.
Therefore, when `--init-best` is also set, it would always trigger the
conflict detection and exit with the error message.

Here are some related version information:
- FreeSurfer version:
freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
- bbregister version: $Id: bbregister,v 1.75 2016/05/10 20:02:28 greve Exp $
- OS: CentOS Linux release 7.3.1611 (Core)

Best,
Feilong
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Re: [Freesurfer] bbregister vs spmregister vs mri_coreg

[Douglas N Greve]

Hi Antonin,

mni152reg was just meant to replicate the affine registration used by 
other software and to provide users with a fast-and-easy way to do 
volume-based (subcortical) analysis in FS. I would prefer to use CVS for 
everything, but, as you mention, it does have a huge computational 
footprint.

doug


On 02/27/2017 11:42 AM, Antonin Skoch wrote:
> Dear Doug,
>
> thank you for the feedback. In this context I would like to ask you to 
> share your opinion on the mri_cvs_register. This tool should be far 
> the most accurate for the registration to MNI, than any of 
> affine-based registration tools, shouldn't be? Are there any 
> pitfalls/disadvantages (apart from huge demand on computing resources) 
> of using this tool? Since you mentioned that you usually use 
> mni152reg, could you share the reason why do not use mri_cvs_register 
> as the preferential tool for registration to MNI?
>
> Regards,
>
> Antonin
>
>
> I have not actually tested it on the mni152 reg. It might (probably 
> does) work fine.
> On 2/25/17 5:33 PM, Antonin Skoch wrote:
>
> Dear Doug,
>
> I was wondering, why do you prefer mni152reg to mri_coreg for
> gregistration to MNI? According to help, mri_coreg is also able to
> do 12 DOF registration.
>
> Antonin
>
>
>
> mri_coreg is the FS implementation of spm_coreg (spmregister) both
> of which use normalized mutual info. bbregister uses the BBR cost
> function and is preferred for all MRI. For registration to MNI
> space, we usually use mni152reg (a wrapper around fsl's flirt)
>
> On 2/25/17 8:49 AM, John Anderson wrote:
> Dear Freesurfer experts,
>
> I see that the tool "mri_coreg" has been implemented recently in
> Free Surfer 6 and I really wanted to know what are the differences
> between the registration tools "bbregister", " spmregister" and
> "mri_coreg"! Kindly:
>
> 1. Are these tools similar? if not what are the differences ?
>
> 2. Is there any preference of using a tool over the others for
> specific type of data. For example: A. If I want to register FA
> map to T1 image which tool is more robust? B. if I want to
> register FA map to MNI space which tool is more robust?
>
> I highly appreciate your input on this!
>
> John
>
>
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>
>
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-- 
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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
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Re: [Freesurfer] bbregister vs spmregister vs mri_coreg

[Antonin Skoch]

Dear Doug,

thank you for the feedback. In this context I would like to ask you to share 
your opinion on the mri_cvs_register. This tool should be far the most accurate 
for the registration to MNI, than any of affine-based registration tools, 
shouldn't be? Are there any pitfalls/disadvantages (apart from huge demand on 
computing resources) of using this tool? Since you mentioned that you usually 
use mni152reg, could you share the reason why do not use mri_cvs_register as 
the preferential tool for registration to MNI?

Regards,

Antonin


I have not actually tested it on the mni152 reg. It might (probably  does) work 
fine. On 2/25/17 5:33 PM, Antonin Skoch wrote:
Dear Doug,

I was wondering, why do you prefer mni152reg to mri_coreg for  gregistration to 
MNI? According to help, mri_coreg is also able to do  12 DOF registration. 
Antonin



mri_coreg is the FS implementation of spm_coreg (spmregister) both of  which 
use normalized mutual info. bbregister uses the BBR cost  function and is 
preferred for all MRI. For registration to MNI space,  we usually use mni152reg 
(a wrapper around fsl's flirt) On 2/25/17 8:49 AM, John Anderson wrote:
Dear Freesurfer experts,
I see that the tool "mri_coreg" has been implemented recently in Free  Surfer 6 
and I really wanted to know what are the differences between  the registration 
tools "bbregister", " spmregister" and "mri_coreg"!  Kindly: 1. Are these tools 
similar? if not what are the differences ?
2. Is there any preference of using a tool over the others for  specific type 
of data. For example: A. If I want to register FA map to  T1 image which tool 
is more robust? B. if I want to register FA map to  MNI space which tool is 
more robust? I highly appreciate your input on this!

John


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Re: [Freesurfer] bbregister vs spmregister vs mri_coreg

[Douglas Greve]

You can do the masking with mri_mask


On 2/26/17 7:04 AM, Shane Schofield wrote:

Dear Doug,

If I want to create a new volume that is registered to the MNIspace 
(using mni1525reg), can I mask out other voxels that are not part of 
the mni template brain? It is a PET volume (already in individual 
space using bbregister) that has noisy signals in non-brain regions.


Thank you.

S


On 25 February 2017 at 22:33:35, Antonin Skoch (a...@ikem.cz 
) wrote:



Dear Doug,

I was wondering, why do you prefer mni152reg to mri_coreg for 
gregistration to MNI? According to help, mri_coreg is also able to do 
12 DOF registration.


Antonin



mri_coreg is the FS implementation of spm_coreg (spmregister) both 
ofwhich use normalized mutual info. bbregister uses the BBR cost 
functionand is preferred for all MRI. For registration to MNI space, 
we usuallyuse mni152reg (a wrapper around fsl's flirt)

On 2/25/17 8:49 AM , John 
Anderson wrote:
Dear Freesurfer experts,
I see that the tool "mri_coreg" has been implemented recently in 
FreeSurfer 6 and I really wanted to know what are the differences 
betweenthe registration tools "bbregister", " spmregister" and 
"mri_coreg"!Kindly:

1. Are these tools similar? if not what are the differences ?
2. Is there any preference of using a tool over the others 
forspecific type of data. For example:A. If I want to register FA map 
to T1 image which tool ismore robust?B. if I want to register FA map 
to MNI space which tool ismore robust?

I highly appreciate your input on this!

John
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Re: [Freesurfer] bbregister vs spmregister vs mri_coreg

[Douglas Greve]

I have not actually tested it on the mni152 reg. It might (probably 
does) work fine.



On 2/25/17 5:33 PM, Antonin Skoch wrote:

Dear Doug,

I was wondering, why do you prefer mni152reg to mri_coreg for 
gregistration to MNI? According to help, mri_coreg is also able to do 
12 DOF registration.


Antonin



mri_coreg is the FS implementation of spm_coreg (spmregister) both of 
which use normalized mutual info. bbregister uses the BBR cost 
function and is preferred for all MRI. For registration to MNI space, 
we usually use mni152reg (a wrapper around fsl's flirt)

On 2/25/17 8:49 AM, John Anderson wrote:
Dear Freesurfer experts,
I see that the tool "mri_coreg" has been implemented recently in Free 
Surfer 6 and I really wanted to know what are the differences between 
the registration tools "bbregister", " spmregister" and "mri_coreg"! 
Kindly:

1. Are these tools similar? if not what are the differences ?
2. Is there any preference of using a tool over the others for 
specific type of data. For example: A. If I want to register FA map to 
T1 image which tool is more robust? B. if I want to register FA map to 
MNI space which tool is more robust?

I highly appreciate your input on this!

John


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Re: [Freesurfer] bbregister vs spmregister vs mri_coreg

[Shane Schofield]

Dear Doug,

If I want to create a new volume that is registered to the MNIspace (using 
mni1525reg), can I mask out other voxels that are not part of the mni template 
brain? It is a PET volume (already in individual space using bbregister) that 
has noisy signals in non-brain regions.

Thank you.

S


On 25 February 2017 at 22:33:35, Antonin Skoch (a...@ikem.cz) wrote:

Dear Doug,

I was wondering, why do you prefer mni152reg to mri_coreg for gregistration to 
MNI? According to help, mri_coreg is also able to do 12 DOF registration.

Antonin



mri_coreg is the FS implementation of spm_coreg (spmregister) both of which use 
normalized mutual info. bbregister uses the BBR cost function and is preferred 
for all MRI. For registration to MNI space, we usually use mni152reg (a wrapper 
around fsl's flirt)
On 2/25/17 8:49 AM, John Anderson wrote:
Dear Freesurfer experts,
I see that the tool "mri_coreg" has been implemented recently in Free Surfer 6 
and I really wanted to know what are the differences between the registration 
tools "bbregister", " spmregister" and "mri_coreg"! Kindly:
1. Are these tools similar? if not what are the differences ?
2. Is there any preference of using a tool over the others for specific type of 
data. For example: A. If I want to register FA map to T1 image which tool 
ismore robust? B. if I want to register FA map to MNI space which tool is more 
robust?
I highly appreciate your input on this!

John
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Re: [Freesurfer] bbregister vs spmregister vs mri_coreg

[John Anderson]

Hi Doug, thank you for the detailed response. Highly appreciated!
Kindly. I want to register FA map to structural T1 image using the command 
mri_spmregister as follow:

mri_spmregister move FA.nii --s subj1 --reg reg dat --o FA_2_T1.nii.gz

Is this correct?







 Original Message 
Subject: bbregister vs spmregister vs mri_coreg
Local Time: February 25, 2017 8:49 AM
UTC Time: February 25, 2017 1:49 PM
From: john.ande...@protonmail.com
To: freesurfer@nmr.mgh.harvard.edu 

mri_coreg is the FS implementation of spm_coreg (spmregister) both of which use 
normalized mutual info. bbregister uses the BBR cost function and is preferred 
for all MRI. For registration to MNI space, we usually use mni152reg (a wrapper 
around fsl's flirt)





On 2/25/17 8:49 AM, John Anderson wrote:


Dear Freesurfer experts,


I see that the tool "mri_coreg" has been implemented recently in Free Surfer 6 
and I really wanted to know what are the differences between the registration 
tools "bbregister", " spmregister" and "mri_coreg"! Kindly:


1. Are these tools similar? if not what are the differences ?


2. Is there any preference of using a tool over the others for specific type of 
data. For example:


A. If I want to register FA map to T1 image which tool is more robust?


B. if I want to register FA map to MNI space which tool is more robust?








I highly appreciate your input on this!




John t?e�?�Z�׮
Dear Freesurfer experts,
I see that the tool "mri_coreg" has been implemented recently in Free Surfer 6 
and I really wanted to know what are the differences between the registration 
tools "bbregister", " spmregister" and "mri_coreg"! Kindly:
1. Are these tools similar? if not what are the differences ?
2. Is there any preference of using a tool over the others for specific type of 
data. For example:
A. If I want to register FA map to T1 image which tool is more robust?
B. if I want to register FA map to MNI space which tool is more robust?


I highly appreciate your input on this!

John___
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Re: [Freesurfer] bbregister vs spmregister vs mri_coreg

[Antonin Skoch]

Dear Doug,

I was wondering, why do you prefer mni152reg to mri_coreg for gregistration to 
MNI? According to help, mri_coreg is also able to do 12 DOF registration.

Antonin



mri_coreg is the FS implementation of spm_coreg (spmregister) both of  which 
use normalized mutual info. bbregister uses the BBR cost function  and is 
preferred for all MRI. For registration to MNI space, we usually  use mni152reg 
(a wrapper around fsl's flirt) On 2/25/17 8:49 AM, John Anderson wrote:
Dear Freesurfer experts,
I see that the tool "mri_coreg" has been implemented recently in Free  Surfer 6 
and I really wanted to know what are the differences between  the registration 
tools "bbregister", " spmregister" and "mri_coreg"!  Kindly: 1. Are these tools 
similar? if not what are the differences ?
2. Is there any preference of using a tool over the others for  specific type 
of data. For example:A. If I want to register FA map to T1 image 
which tool is  more robust?B. if I want to register FA map to MNI 
space which tool is  more robust? 
I highly appreciate your input on this!

John
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Re: [Freesurfer] bbregister vs spmregister vs mri_coreg

[Douglas Greve]

mri_coreg is the FS implementation of spm_coreg (spmregister) both of 
which use normalized mutual info. bbregister uses the BBR cost function 
and is preferred for all MRI. For registration to MNI space, we usually 
use mni152reg (a wrapper around fsl's flirt)



On 2/25/17 8:49 AM, John Anderson wrote:

Dear Freesurfer experts,
I see that the tool "mri_coreg" has been implemented recently in Free 
Surfer 6 and I really wanted to know what are the differences between 
the registration tools "bbregister", " spmregister" and "mri_coreg"! 
Kindly:

1. Are these tools similar? if not what are the differences ?
2. Is there any preference of using a tool over the others for 
specific type of data. For example:
   A. If I want to register FA map to T1 image which tool is 
more robust?
   B. if I want to register FA map to MNI space which tool is 
more robust?



I highly appreciate your input on this!

John


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[Freesurfer] bbregister vs spmregister vs mri_coreg

[John Anderson]

Dear Freesurfer experts,
I see that the tool "mri_coreg" has been implemented recently in Free Surfer 6 
and I really wanted to know what are the differences between the registration 
tools "bbregister", " spmregister" and "mri_coreg"! Kindly:
1. Are these tools similar? if not what are the differences ?
2. Is there any preference of using a tool over the others for specific type of 
data. For example:
A. If I want to register FA map to T1 image which tool is more robust?
B. if I want to register FA map to MNI space which tool is more robust?


I highly appreciate your input on this!

John___
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[Freesurfer] bbregister

[John Anderson]

Thank you very much!






Kindly, I have one follow up question:

 

I have VOI 20X20X20 mm have been created during an MR spectroscopy session. This VOI was placed in specific loacation on the T1 image. I have created this VOI using the command "mri_volsynth"  and I want to move it from native space (T1) to Freesurfer space (e.g. wmparc.mgz) so I can generrat somestatistics using the command "mri_segstats".

 

I ran the following commands:

bbregister  --t1 --mov T1.nii --init-fsl --reg t1.reg.dat --s subj
tkregister2 --mov VOI.nii --int T1.nii t1.reg.dat --reg VOI.reg.dat --noedit --subject subj 

mri_vol2vol --mov VOI.nii --reg t1.reg.dat --fstarg --interp nearest --o VOI.anat.nii

 

Are these stpes correct?

When I open T1.nii and the VOI.nii in  freeview, I can see the VOI in it is correct position. But when I open "wmparc.mgz" and "VOI.anat.nii" then VOI is not showing in the correct position. I suspet that I am doing something wrong in the previous steps and I highly appreciate any feedback!

 

 

Best,
John 

 

 

For version 6, it should not matter.




Sent: Friday, February 10, 2017 at 4:03 PM
From: "Bruce Fischl" <fis...@nmr.mgh.harvard.edu>
To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] bbregister

Hi John

one of the many nice things about bbregister is that it is quite
resistant to non-brain tissue, since it's just trying to place the
gray/white (and optionally the pial surface) at a reasonable spot in the
volume. I guess it might make the initialization less robust, not sure, but
I expect it works pretty well without doing brain extraction

cheers
Bruce

On Fri, 10 Feb 2017, John Anderson wrote:

> Hi FS experts,
> I want to register T1 image to its freesurfer space (i.e. wmparc.mgz) using
> the command 
> bbregister  --t1 --mov T1.nii --init-fsl --reg t1.reg.dat --s subj
>  
> do I need to apply brain extraction tools before this step or bb register
> can accept non-brain extracted images?
>  
> Best,
> John
>
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Re: [Freesurfer] bbregister

[Douglas Greve]

For version 6, it should not matter.


On 2/10/17 3:59 PM, John Anderson wrote:

Hi FS experts,
I want to register T1 image to its freesurfer space (i.e. wmparc.mgz) 
using the command

bbregister  --t1 --mov T1.nii --init-fsl --reg t1.reg.dat --s subj
do I need to apply brain extraction tools before this step or bb 
register can accept non-brain extracted images?

Best,
John


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Re: [Freesurfer] bbregister

[Bruce Fischl]

Hi John

one of the many nice things about bbregister is that it is quite 
resistant to non-brain tissue, since it's just trying to place the 
gray/white (and optionally the pial surface) at a reasonable spot in the 
volume. I guess it might make the initialization less robust, not sure, but 
I expect it works pretty well without doing brain extraction


cheers
Bruce

On Fri, 10 Feb 2017, John Anderson wrote:


Hi FS experts,
I want to register T1 image to its freesurfer space (i.e. wmparc.mgz) using
the command 
bbregister  --t1 --mov T1.nii --init-fsl --reg t1.reg.dat --s subj
 
do I need to apply brain extraction tools before this step or bb register
can accept non-brain extracted images?
 
Best,
John

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[Freesurfer] bbregister

[John Anderson]

Hi FS experts,

I want to register T1 image to its freesurfer space (i.e. wmparc.mgz) using the command 

bbregister  --t1 --mov T1.nii --init-fsl --reg t1.reg.dat --s subj

 

do I need to apply brain extraction tools before this step or bb register can accept non-brain extracted images?

 

Best,
John
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Re: [Freesurfer] bbregister surfaces

[Douglas N Greve]

the pial surface is not currently used. It is possible in the current 
version to use pial surface if you want to


On 01/12/2017 04:35 PM, Christopher Markiewicz wrote:
> Hi all,
>
> According to 
> https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg25476.html, 
> bbregister uses the white matter surface and cortical thickness 
> measures to perform its registrations, though there was some 
> possibility of using the pial surface in further releases. I just want 
> to verify that this is still the case, and the pial surface is not 
> currently being used.
>
> Thanks,
> Chris Markiewicz
>
>
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-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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[Freesurfer] bbregister surfaces

[Christopher Markiewicz]

Hi all,

According to
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg25476.html,
bbregister uses the white matter surface and cortical thickness measures to
perform its registrations, though there was some possibility of using the
pial surface in further releases. I just want to verify that this is still
the case, and the pial surface is not currently being used.

Thanks,
Chris Markiewicz
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Re: [Freesurfer] bbregister --init-reg not working (reg2subject --r returning empty string)

[Antonin Skoch]

Dear Doug, 

yes, the point is, that my_initial_lta.lta does not have subject name in it.

Your suggestion to rearrange parameters in bbregister indeed helped to get 
further, however, later ended with error in bbregister execution in call of 
mri_segreg, which does not pass the subject parameter and reads it from the 
.reg file:

mri_segreg --mov 
/hydradb/hydra_io/vypocty/skoch/20160609_HCENAT_DWI/proc/HCE_C00573_20160524_1456_2/reg/tmp.bbregister.5112/template.nii
 --init-reg 
/hydradb/hydra_io/vypocty/skoch/20160609_HCENAT_DWI/proc/HCE_C00573_20160524_1456_2/reg/tmp.bbregister.5112/init.reg.5112.dat
 --out-reg 
/hydradb/hydra_io/vypocty/skoch/20160609_HCENAT_DWI/proc/HCE_C00573_20160524_1456_2/reg/tmp.bbregister.5112/bbr.pass1.dat
 --subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4 
--surf white --gm-proj-frac 0.5 --gm-gt-wm 0.5

The error is:
mghRead(/hydradb/hydra_io/vypocty/skoch/20161008_HCENAT_struct/A_HCP_w_FS_dev_long/subject-unknown/mri/orig.mgz,
 -1): could not open file

I solved the issue by additional appending subject id into my_initial_lta.lta 
file. It seems to work OK, bbregister finishes without error.

Antonin



does my_initial_lta.lta have the subject name in it? If not, then put 
that argument before the --s
On 12/05/2016 10:34 AM, Antonin Skoch wrote:
> Dear experts,
>
> I am having trouble using --init-reg option in bbregister (FreeSurfer 
> v6 beta version).  It exits with error: must supply subject id.
>
> My command line is:
> bbregister --mov my_moveable.nii.gz --s my_subject_id --lta 
> my_lta_out.lta --dti --init-reg my_initial_lta.lta
>
> I traced the problem to reg2subject --r my_initial_lta.lta which is 
> executed inside bbregister. This script returns empty string. By 
> examining reg2subject code, it in case of .lta searches for string 
> "subject" in lta file. However there is no such string in my .lta.
>
> My .lta file was created by tkregister2 by conversion from fsl .mat 
> file (without specification of subject) by command:
>
> tkregister2 --mov mov.nii.gz --targ targ.nii.gz --ltaout mov2targ.lta 
> --fsl mov2targ.mat --reg /tmp/junk --noedit
>
> where mov2targ.mat is vox2vox fsl-style matrix encoding transformation 
> from mov.nii.gz to targ.nii.gz. I checked validity of produced .lta 
> file by tkregister2 and it looks OK.
>
> The straightforward remedy in my case possibly would be to remove 
> reg2subject invocation from bbregister (since I am already providing 
> the subject by --s option), or add subject id to .lta.
>
> General solution in bbregister code would possibly be to provide test 
> whether subject id is specified and in case it is not, then read the 
> subject id from registration file. Or read both and in case of 
> non-empty return of reg2subject, then compare obtained subject id with 
> subject id supplied by --s and  in case of different strings, produce 
> a warning and use one of them (--s would take precedence?).
>
> My second inquiry is following: My idea was to do the registration in 
> 3 stages: provide rough alignment with .lta, then mri_coreg (or 
> fsl-flirt) and then bb-registration. My experience is, that in some 
> situations when the images are very differently aligned, the 
> --init-fsl totally fails.
>
> Is it possible to realize it by supplying both --init-reg and 
> --init-coreg (or even combination of --init-reg --init-best to try 
> both mri_coreg and flirt)?
>
> Regards,
>
> Antonin Skoch
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Re: [Freesurfer] bbregister --init-reg not working (reg2subject --r returning empty string)

[Douglas N Greve]

does my_initial_lta.lta have the subject name in it? If not, then put 
that argument before the --s


On 12/05/2016 10:34 AM, Antonin Skoch wrote:
> Dear experts,
>
> I am having trouble using --init-reg option in bbregister (FreeSurfer 
> v6 beta version).  It exits with error: must supply subject id.
>
> My command line is:
> bbregister --mov my_moveable.nii.gz --s my_subject_id --lta 
> my_lta_out.lta --dti --init-reg my_initial_lta.lta
>
> I traced the problem to reg2subject --r my_initial_lta.lta which is 
> executed inside bbregister. This script returns empty string. By 
> examining reg2subject code, it in case of .lta searches for string 
> "subject" in lta file. However there is no such string in my .lta.
>
> My .lta file was created by tkregister2 by conversion from fsl .mat 
> file (without specification of subject) by command:
>
> tkregister2 --mov mov.nii.gz --targ targ.nii.gz --ltaout mov2targ.lta 
> --fsl mov2targ.mat --reg /tmp/junk --noedit
>
> where mov2targ.mat is vox2vox fsl-style matrix encoding transformation 
> from mov.nii.gz to targ.nii.gz. I checked validity of produced .lta 
> file by tkregister2 and it looks OK.
>
> The straightforward remedy in my case possibly would be to remove 
> reg2subject invocation from bbregister (since I am already providing 
> the subject by --s option), or add subject id to .lta.
>
> General solution in bbregister code would possibly be to provide test 
> whether subject id is specified and in case it is not, then read the 
> subject id from registration file. Or read both and in case of 
> non-empty return of reg2subject, then compare obtained subject id with 
> subject id supplied by --s and  in case of different strings, produce 
> a warning and use one of them (--s would take precedence?).
>
> My second inquiry is following: My idea was to do the registration in 
> 3 stages: provide rough alignment with .lta, then mri_coreg (or 
> fsl-flirt) and then bb-registration. My experience is, that in some 
> situations when the images are very differently aligned, the 
> --init-fsl totally fails.
>
> Is it possible to realize it by supplying both --init-reg and 
> --init-coreg (or even combination of --init-reg --init-best to try 
> both mri_coreg and flirt)?
>
> Regards,
>
> Antonin Skoch
>
>
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-- 
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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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[Freesurfer] bbregister --init-reg not working (reg2subject --r returning empty string)

[Antonin Skoch]

Dear experts,

I am having trouble using --init-reg option in bbregister (FreeSurfer v6 beta 
version).  It exits with error: must supply subject id.

My command line is:
bbregister --mov my_moveable.nii.gz --s my_subject_id --lta my_lta_out.lta 
--dti --init-reg my_initial_lta.lta 

I traced the problem to reg2subject --r my_initial_lta.lta which is executed 
inside bbregister. This script returns empty string. By examining reg2subject 
code, it in case of .lta searches for string "subject" in lta file. However 
there is no such string in my .lta. 

My .lta file was created by tkregister2 by conversion from fsl .mat file 
(without specification of subject) by command:

tkregister2 --mov mov.nii.gz --targ targ.nii.gz --ltaout mov2targ.lta --fsl 
mov2targ.mat --reg /tmp/junk --noedit

where mov2targ.mat is vox2vox fsl-style matrix encoding transformation from 
mov.nii.gz to targ.nii.gz. I checked validity of produced .lta file by 
tkregister2 and it looks OK.

The straightforward remedy in my case possibly would be to remove reg2subject 
invocation from bbregister (since I am already providing the subject by --s 
option), or add subject id to .lta.

General solution in bbregister code would possibly be to provide test whether 
subject id is specified and in case it is not, then read the subject id from 
registration file. Or read both and in case of non-empty return of reg2subject, 
then compare obtained subject id with subject id supplied by --s and  in case 
of different strings, produce a warning and use one of them (--s would take 
precedence?).

My second inquiry is following: My idea was to do the registration in 3 stages: 
provide rough alignment with .lta, then mri_coreg (or fsl-flirt) and then 
bb-registration. My experience is, that in some situations when the images are 
very differently aligned, the --init-fsl totally fails.

Is it possible to realize it by supplying both --init-reg and  --init-coreg (or 
even combination of --init-reg --init-best to try both mri_coreg and flirt)?

Regards,

Antonin Skoch
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Re: [Freesurfer] bbregister problem in FS5.1

[Douglas N Greve]

I have no idea. You can try copying the 5.3 version of mri_segreg to 5.1

On 07/28/2016 04:10 AM, Fred Sampedro wrote:
> Hi Douglas,
>
>
> Thanks a lot for your help, I understand. I tried replacing the 
> mri_convert in 5.1 from the 5.3 and the bbregister command went a 
> little bit further. Unfortunately, it segfaulted again when computing 
> the relative costs.
>
> I'm attaching the output of the same command in 5.3 and in 5.1. Until 
> the "Loading mov" in line 210, the output is actually the same. Could 
> it be related to errors regarding the reading of the PET image?
>
> If anyone could help me figuring out which instruction is failing so I 
> could try to replace it with the 5.3 version I would be very grateful.
>
> Thanks a lot in advance,
>
> Fred
>
> On Tue, Jul 26, 2016 at 1:30 AM, Douglas Greve 
> > wrote:
>
> Sorry, I have no idea and I'm not going to try to dig in to 5.1 to
> see. You can just copy mri_convert from 5.3 into 5.1 (make a
> backup first)
>
>
> On 7/25/16 12:31 PM, Fred Sampedro wrote:
>> Hi Douglas,
>>
>> Thank you very much for answering. Unfortunately, I can read all
>> the files without any problem in FSL/SPM, and I still have more
>> than 40GB of free space. In fact, running the exact same
>> instruction in freesurfer 5.3 works fine.
>>
>> :(
>>
>>
>>
>> On Mon, Jul 25, 2016 at 5:21 PM, Douglas Greve
>> > wrote:
>>
>> It looks like one of two things:
>>
>> 1. The files SUBJ_ID.nii.gz is corrupted. See if another tool
>> (FSL, SPM, AFNI) can read the file
>>
>> 2. You have run out of disk space
>>
>>
>> On 7/24/16 10:52 AM, Fred Sampedro wrote:
>>> Dear FS experts,
>>>
>>> I've installed
>>> freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 and I'm
>>> trying to run bbregister to register a AV45-PET image to its
>>> corresponding FS processed T1 image. For that, I'm trying to
>>> run:
>>>
>>> bbregister --s SUBJ_ID --mov SUBJ_PET --reg register.dat
>>> --init-fsl --t1
>>>
>>> And I keep getting segfaults:
>>>
>>> Log file is register.dat.log
>>> dom jul 24 16:44:19 CEST 2016
>>>
>>> $Id: bbregister,v 1.49 2011/03/06 23:38:41 greve Exp $
>>> Linux fredlab 3.16.0-30-generic #40~14.04.1-Ubuntu SMP Thu
>>> Jan 15 17:43:14 UTC 2015 x86_64 x86_64 x86_64 GNU/Linux
>>> FREESURFER_HOME /usr/local/freesurfer
>>> mri_convert ./allpets/SUBJ_ID/SUBJ_ID.nii.gz
>>> ./tmp.bbregister.5353/template.nii
>>> mri_convert ./allpets/SUBJ_ID/SUBJ_ID.nii.gz
>>> ./tmp.bbregister.5353/template.nii
>>> Segmentation fault (core dumped)
>>>
>>>
>>> I have tried the same installation and command in two
>>> different computers and obtained the same segfault. I have
>>> also tried the same pipeline using instead the FS version
>>> freesurfer-Linux-centos4-stable-pub-v5.1.0.tar.gz and get
>>> the same result. I didn't have this issue using freesurfer
>>> 5.3, but I need to use 5.1 for an ongoing project.
>>>
>>> I'm in an Ubuntu 14.04 LTS with 3.6GB of Memory, Processor
>>> Intel Core 2 Duo 3.0GHz, Graphics Intel Q45/Q43 OS type 64 bits.
>>>
>>> Any help would be much appreciated,
>>>
>>> Thanks a lot in advance,
>>>
>>> Fred Sampedro
>>>
>>>
>>> ___
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> 
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>> ___
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>> 
>> 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.
>>
>>
>>
>>
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Re: [Freesurfer] bbregister problem in FS5.1

[Fred Sampedro]

Hi Douglas,


Thanks a lot for your help, I understand. I tried replacing the mri_convert
in 5.1 from the 5.3 and the bbregister command went a little bit further.
Unfortunately, it segfaulted again when computing the relative costs.

I'm attaching the output of the same command in 5.3 and in 5.1. Until the
"Loading mov" in line 210, the output is actually the same. Could it be
related to errors regarding the reading of the PET image?

If anyone could help me figuring out which instruction is failing so I
could try to replace it with the 5.3 version I would be very grateful.

Thanks a lot in advance,

Fred

On Tue, Jul 26, 2016 at 1:30 AM, Douglas Greve 
wrote:

> Sorry, I have no idea and I'm not going to try to dig in to 5.1 to see.
> You can just copy mri_convert from 5.3 into 5.1 (make a backup first)
>
> On 7/25/16 12:31 PM, Fred Sampedro wrote:
>
> Hi Douglas,
>
> Thank you very much for answering. Unfortunately, I can read all the files
> without any problem in FSL/SPM, and I still have more than 40GB of free
> space. In fact, running the exact same instruction in freesurfer 5.3 works
> fine.
>
> :(
>
>
>
> On Mon, Jul 25, 2016 at 5:21 PM, Douglas Greve 
> wrote:
>
>> It looks like one of two things:
>>
>> 1. The files SUBJ_ID.nii.gz is corrupted. See if another tool (FSL, SPM,
>> AFNI) can read the file
>>
>> 2. You have run out of disk space
>>
>> On 7/24/16 10:52 AM, Fred Sampedro wrote:
>>
>> Dear FS experts,
>>
>> I've installed freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 and I'm
>> trying to run bbregister to register a AV45-PET image to its corresponding
>> FS processed T1 image. For that, I'm trying to run:
>>
>> bbregister --s SUBJ_ID --mov SUBJ_PET --reg register.dat --init-fsl --t1
>>
>> And I keep getting segfaults:
>>
>> Log file is register.dat.log
>> dom jul 24 16:44:19 CEST 2016
>>
>> $Id: bbregister,v 1.49 2011/03/06 23:38:41 greve Exp $
>> Linux fredlab 3.16.0-30-generic #40~14.04.1-Ubuntu SMP Thu Jan 15
>> 17:43:14 UTC 2015 x86_64 x86_64 x86_64 GNU/Linux
>> FREESURFER_HOME /usr/local/freesurfer
>> mri_convert ./allpets/SUBJ_ID/SUBJ_ID.nii.gz
>> ./tmp.bbregister.5353/template.nii
>> mri_convert ./allpets/SUBJ_ID/SUBJ_ID.nii.gz
>> ./tmp.bbregister.5353/template.nii
>> Segmentation fault (core dumped)
>>
>>
>> I have tried the same installation and command in two different computers
>> and obtained the same segfault. I have also tried the same pipeline using
>> instead the FS version freesurfer-Linux-centos4-stable-pub-v5.1.0.tar.gz
>> and get the same result. I didn't have this issue using freesurfer 5.3, but
>> I need to use 5.1 for an ongoing project.
>>
>> I'm in an Ubuntu 14.04 LTS with 3.6GB of Memory, Processor Intel Core 2
>> Duo 3.0GHz, Graphics Intel Q45/Q43 OS type 64 bits.
>>
>> Any help would be much appreciated,
>>
>> Thanks a lot in advance,
>>
>> Fred Sampedro
>>
>>
>> ___
>> Freesurfer mailing 
>> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>>
>> ___
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>> 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.
>>
>>
>
>
> ___
> Freesurfer mailing 
> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
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>
>
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> 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
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>
Log file is provantreg.dat.log
jue jul 28 09:47:50 CEST 2016

setenv SUBJECTS_DIR ./lesresos
cd /home/fred/Desktop/SurfaceFBP/PET_Surface_analysis
/usr/local/freesurfer/bin/bbregister --s SUBJ_ID --mov 
./allpets/SUBJ_ID/SUBJ_ID_PETFBP.nii.gz --reg provantreg.dat --init-fsl --t1

$Id: bbregister,v 1.49 2011/03/06 23:38:41 greve Exp $
Linux fredlab 3.16.0-30-generic #40~14.04.1-Ubuntu SMP Thu Jan 15 17:43:14 UTC 
2015 x86_64 x86_64 x86_64 GNU/Linux

Re: [Freesurfer] bbregister problem in FS5.1

[Douglas Greve]

Sorry, I have no idea and I'm not going to try to dig in to 5.1 to see. 
You can just copy mri_convert from 5.3 into 5.1 (make a backup first)



On 7/25/16 12:31 PM, Fred Sampedro wrote:

Hi Douglas,

Thank you very much for answering. Unfortunately, I can read all the 
files without any problem in FSL/SPM, and I still have more than 40GB 
of free space. In fact, running the exact same instruction in 
freesurfer 5.3 works fine.


:(



On Mon, Jul 25, 2016 at 5:21 PM, Douglas Greve 
> wrote:


It looks like one of two things:

1. The files SUBJ_ID.nii.gz is corrupted. See if another tool
(FSL, SPM, AFNI) can read the file

2. You have run out of disk space


On 7/24/16 10:52 AM, Fred Sampedro wrote:

Dear FS experts,

I've installed freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0
and I'm trying to run bbregister to register a AV45-PET image to
its corresponding FS processed T1 image. For that, I'm trying to run:

bbregister --s SUBJ_ID --mov SUBJ_PET --reg register.dat
--init-fsl --t1

And I keep getting segfaults:

Log file is register.dat.log
dom jul 24 16:44:19 CEST 2016

$Id: bbregister,v 1.49 2011/03/06 23:38:41 greve Exp $
Linux fredlab 3.16.0-30-generic #40~14.04.1-Ubuntu SMP Thu Jan 15
17:43:14 UTC 2015 x86_64 x86_64 x86_64 GNU/Linux
FREESURFER_HOME /usr/local/freesurfer
mri_convert ./allpets/SUBJ_ID/SUBJ_ID.nii.gz
./tmp.bbregister.5353/template.nii
mri_convert ./allpets/SUBJ_ID/SUBJ_ID.nii.gz
./tmp.bbregister.5353/template.nii
Segmentation fault (core dumped)


I have tried the same installation and command in two different
computers and obtained the same segfault. I have also tried the
same pipeline using instead the FS version
freesurfer-Linux-centos4-stable-pub-v5.1.0.tar.gz and get the
same result. I didn't have this issue using freesurfer 5.3, but I
need to use 5.1 for an ongoing project.

I'm in an Ubuntu 14.04 LTS with 3.6GB of Memory, Processor Intel
Core 2 Duo 3.0GHz, Graphics Intel Q45/Q43 OS type 64 bits.

Any help would be much appreciated,

Thanks a lot in advance,

Fred Sampedro


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Re: [Freesurfer] bbregister problem in FS5.1

[Fred Sampedro]

Hi Douglas,

Thank you very much for answering. Unfortunately, I can read all the files
without any problem in FSL/SPM, and I still have more than 40GB of free
space. In fact, running the exact same instruction in freesurfer 5.3 works
fine.

:(



On Mon, Jul 25, 2016 at 5:21 PM, Douglas Greve 
wrote:

> It looks like one of two things:
>
> 1. The files SUBJ_ID.nii.gz is corrupted. See if another tool (FSL, SPM,
> AFNI) can read the file
>
> 2. You have run out of disk space
>
> On 7/24/16 10:52 AM, Fred Sampedro wrote:
>
> Dear FS experts,
>
> I've installed freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 and I'm
> trying to run bbregister to register a AV45-PET image to its corresponding
> FS processed T1 image. For that, I'm trying to run:
>
> bbregister --s SUBJ_ID --mov SUBJ_PET --reg register.dat --init-fsl --t1
>
> And I keep getting segfaults:
>
> Log file is register.dat.log
> dom jul 24 16:44:19 CEST 2016
>
> $Id: bbregister,v 1.49 2011/03/06 23:38:41 greve Exp $
> Linux fredlab 3.16.0-30-generic #40~14.04.1-Ubuntu SMP Thu Jan 15 17:43:14
> UTC 2015 x86_64 x86_64 x86_64 GNU/Linux
> FREESURFER_HOME /usr/local/freesurfer
> mri_convert ./allpets/SUBJ_ID/SUBJ_ID.nii.gz
> ./tmp.bbregister.5353/template.nii
> mri_convert ./allpets/SUBJ_ID/SUBJ_ID.nii.gz
> ./tmp.bbregister.5353/template.nii
> Segmentation fault (core dumped)
>
>
> I have tried the same installation and command in two different computers
> and obtained the same segfault. I have also tried the same pipeline using
> instead the FS version freesurfer-Linux-centos4-stable-pub-v5.1.0.tar.gz
> and get the same result. I didn't have this issue using freesurfer 5.3, but
> I need to use 5.1 for an ongoing project.
>
> I'm in an Ubuntu 14.04 LTS with 3.6GB of Memory, Processor Intel Core 2
> Duo 3.0GHz, Graphics Intel Q45/Q43 OS type 64 bits.
>
> Any help would be much appreciated,
>
> Thanks a lot in advance,
>
> Fred Sampedro
>
>
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Re: [Freesurfer] bbregister problem in FS5.1

[Douglas Greve]

It looks like one of two things:

1. The files SUBJ_ID.nii.gz is corrupted. See if another tool (FSL, SPM, 
AFNI) can read the file


2. You have run out of disk space


On 7/24/16 10:52 AM, Fred Sampedro wrote:

Dear FS experts,

I've installed freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 and 
I'm trying to run bbregister to register a AV45-PET image to its 
corresponding FS processed T1 image. For that, I'm trying to run:


bbregister --s SUBJ_ID --mov SUBJ_PET --reg register.dat --init-fsl --t1

And I keep getting segfaults:

Log file is register.dat.log
dom jul 24 16:44:19 CEST 2016

$Id: bbregister,v 1.49 2011/03/06 23:38:41 greve Exp $
Linux fredlab 3.16.0-30-generic #40~14.04.1-Ubuntu SMP Thu Jan 15 
17:43:14 UTC 2015 x86_64 x86_64 x86_64 GNU/Linux

FREESURFER_HOME /usr/local/freesurfer
mri_convert ./allpets/SUBJ_ID/SUBJ_ID.nii.gz 
./tmp.bbregister.5353/template.nii
mri_convert ./allpets/SUBJ_ID/SUBJ_ID.nii.gz 
./tmp.bbregister.5353/template.nii

Segmentation fault (core dumped)


I have tried the same installation and command in two different 
computers and obtained the same segfault. I have also tried the same 
pipeline using instead the FS version 
freesurfer-Linux-centos4-stable-pub-v5.1.0.tar.gz and get the same 
result. I didn't have this issue using freesurfer 5.3, but I need to 
use 5.1 for an ongoing project.


I'm in an Ubuntu 14.04 LTS with 3.6GB of Memory, Processor Intel Core 
2 Duo 3.0GHz, Graphics Intel Q45/Q43 OS type 64 bits.


Any help would be much appreciated,

Thanks a lot in advance,

Fred Sampedro


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[Freesurfer] bbregister problem in FS5.1

[Fred Sampedro]

Dear FS experts,

I've installed freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 and I'm
trying to run bbregister to register a AV45-PET image to its corresponding
FS processed T1 image. For that, I'm trying to run:

bbregister --s SUBJ_ID --mov SUBJ_PET --reg register.dat --init-fsl --t1

And I keep getting segfaults:

Log file is register.dat.log
dom jul 24 16:44:19 CEST 2016

$Id: bbregister,v 1.49 2011/03/06 23:38:41 greve Exp $
Linux fredlab 3.16.0-30-generic #40~14.04.1-Ubuntu SMP Thu Jan 15 17:43:14
UTC 2015 x86_64 x86_64 x86_64 GNU/Linux
FREESURFER_HOME /usr/local/freesurfer
mri_convert ./allpets/SUBJ_ID/SUBJ_ID.nii.gz
./tmp.bbregister.5353/template.nii
mri_convert ./allpets/SUBJ_ID/SUBJ_ID.nii.gz
./tmp.bbregister.5353/template.nii
Segmentation fault (core dumped)


I have tried the same installation and command in two different computers
and obtained the same segfault. I have also tried the same pipeline using
instead the FS version freesurfer-Linux-centos4-stable-pub-v5.1.0.tar.gz
and get the same result. I didn't have this issue using freesurfer 5.3, but
I need to use 5.1 for an ongoing project.

I'm in an Ubuntu 14.04 LTS with 3.6GB of Memory, Processor Intel Core 2 Duo
3.0GHz, Graphics Intel Q45/Q43 OS type 64 bits.

Any help would be much appreciated,

Thanks a lot in advance,

Fred Sampedro
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Re: [Freesurfer] bbregister --init-spm with Freesurfer 6.0

[Ajay Kurani]

Thanks for the follow up about the new tool you developed!  I look forward
to using it and I will remove the --init-spm option.

Just as a follow up I did add the pathway for freesurfer/matlab and it ran
properly for hippocampal subfields, so I do not think that is the issue.

Thanks,
Ajay



On Wed, Apr 6, 2016 at 12:59 PM, Ajay Kurani 
wrote:

> Hello Freesurfer Experts,
>As a follow up question for bbregister, I used the --tmp and --epi-mask
> options, but I did not see a mask in the directory.  I wanted to  see if
> there is any way to output the B0/edge excluded epi-mask used in bbregister?
>
> Thanks,
> Ajay
>
> On Tue, Apr 5, 2016 at 11:03 PM, Ajay Kurani 
> wrote:
>
>> Hi Freesurfer Experts,
>>I was running bbregister and came across an issue.  I have used
>> previous versions of bbregister (FS 5.3.0 with spm8) with the --init-spm at
>> it worked perfectly for a specific subject.
>>
>> I recently installed FS dev 6.0 with SPM12b and ran bbregister --init-spm
>> option with the same resting state scan, and it did not move at all.  When
>> looking at the terminal I saw that when matlab started up within
>> bbregister, the command fs_spmreg was not found.  I also installed spm8 and
>> reran the subject with the same issue.  When I changed the option to
>> --init-fsl everything worked. I checked the matlab installation and
>> everything looks fine, so I think the issue may be the fs_spmreg function
>> not being found.  I am not sure if there is an easy fix for this, but any
>> help would be appreciated.
>>
>> Thanks,
>> Ajay
>>
>>
>
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Re: [Freesurfer] bbregister --init-spm with Freesurfer 6.0

[Douglas Greve]

 --epi-mask is a simple flag without any options. It tells bbregsiter 
to exclude certain regions from the surface-based parcellation 
(?h.aparc.annot). The regions can be gleened from the code below


  B0Annots[0] = CTABentryNameToAnnotation("middletemporal",lhwm->ct);
  B0Annots[1] = CTABentryNameToAnnotation("inferiortemporal",lhwm->ct);
  B0Annots[2] = CTABentryNameToAnnotation("temporalpole",lhwm->ct);
  B0Annots[3] = CTABentryNameToAnnotation("fusiform",lhwm->ct);
  B0Annots[4] = CTABentryNameToAnnotation("entorhinal",lhwm->ct);
  B0Annots[5] = 
CTABentryNameToAnnotation("medialorbitofrontal",lhwm->ct);
  B0Annots[6] = 
CTABentryNameToAnnotation("caudalanteriorcingulate",lhwm->ct);
  B0Annots[7] = 
CTABentryNameToAnnotation("rostralanteriorcingulate",lhwm->ct);

  B0Annots[8] = CTABentryNameToAnnotation("unknown",lhwm->ct);
  B0Annots[9] = CTABentryNameToAnnotation("corpuscallosum",lhwm->ct);


On 4/6/16 1:59 PM, Ajay Kurani wrote:

Hello Freesurfer Experts,
   As a follow up question for bbregister, I used the --tmp and 
--epi-mask options, but I did not see a mask in the directory.  I 
wanted to  see if there is any way to output the B0/edge excluded 
epi-mask used in bbregister?


Thanks,
Ajay

On Tue, Apr 5, 2016 at 11:03 PM, Ajay Kurani > wrote:


Hi Freesurfer Experts,
   I was running bbregister and came across an issue.  I have used
previous versions of bbregister (FS 5.3.0 with spm8) with the
--init-spm at it worked perfectly for a specific subject.

I recently installed FS dev 6.0 with SPM12b and ran bbregister
--init-spm option with the same resting state scan, and it did not
move at all.  When looking at the terminal I saw that when matlab
started up within bbregister, the command fs_spmreg was not
found.  I also installed spm8 and reran the subject with the same
issue.  When I changed the option to --init-fsl everything worked.
I checked the matlab installation and everything looks fine, so I
think the issue may be the fs_spmreg function not being found.  I
am not sure if there is an easy fix for this, but any help would
be appreciated.

Thanks,
Ajay




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Re: [Freesurfer] bbregister --init-spm with Freesurfer 6.0

[Douglas Greve]

Is $FREESURFER_HOME/matlab in your matlab path? Also, I wrote a new 
program called mri_coreg that replicates the functionality of 
spmregister. This is now the default (no need to spec an init method), 
and I encourage you to use it.


On 4/6/16 12:03 AM, Ajay Kurani wrote:

Hi Freesurfer Experts,
   I was running bbregister and came across an issue.  I have used 
previous versions of bbregister (FS 5.3.0 with spm8) with the 
--init-spm at it worked perfectly for a specific subject.


I recently installed FS dev 6.0 with SPM12b and ran bbregister 
--init-spm option with the same resting state scan, and it did not 
move at all.  When looking at the terminal I saw that when matlab 
started up within bbregister, the command fs_spmreg was not found.  I 
also installed spm8 and reran the subject with the same issue.  When I 
changed the option to --init-fsl everything worked. I checked the 
matlab installation and everything looks fine, so I think the issue 
may be the fs_spmreg function not being found.  I am not sure if there 
is an easy fix for this, but any help would be appreciated.


Thanks,
Ajay



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Re: [Freesurfer] bbregister --init-spm with Freesurfer 6.0

[Ajay Kurani]

Hello Freesurfer Experts,
   As a follow up question for bbregister, I used the --tmp and --epi-mask
options, but I did not see a mask in the directory.  I wanted to  see if
there is any way to output the B0/edge excluded epi-mask used in bbregister?

Thanks,
Ajay

On Tue, Apr 5, 2016 at 11:03 PM, Ajay Kurani 
wrote:

> Hi Freesurfer Experts,
>I was running bbregister and came across an issue.  I have used
> previous versions of bbregister (FS 5.3.0 with spm8) with the --init-spm at
> it worked perfectly for a specific subject.
>
> I recently installed FS dev 6.0 with SPM12b and ran bbregister --init-spm
> option with the same resting state scan, and it did not move at all.  When
> looking at the terminal I saw that when matlab started up within
> bbregister, the command fs_spmreg was not found.  I also installed spm8 and
> reran the subject with the same issue.  When I changed the option to
> --init-fsl everything worked. I checked the matlab installation and
> everything looks fine, so I think the issue may be the fs_spmreg function
> not being found.  I am not sure if there is an easy fix for this, but any
> help would be appreciated.
>
> Thanks,
> Ajay
>
>
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[Freesurfer] bbregister --init-spm with Freesurfer 6.0

[Ajay Kurani]

Hi Freesurfer Experts,
   I was running bbregister and came across an issue.  I have used previous
versions of bbregister (FS 5.3.0 with spm8) with the --init-spm at it
worked perfectly for a specific subject.

I recently installed FS dev 6.0 with SPM12b and ran bbregister --init-spm
option with the same resting state scan, and it did not move at all.  When
looking at the terminal I saw that when matlab started up within
bbregister, the command fs_spmreg was not found.  I also installed spm8 and
reran the subject with the same issue.  When I changed the option to
--init-fsl everything worked. I checked the matlab installation and
everything looks fine, so I think the issue may be the fs_spmreg function
not being found.  I am not sure if there is an easy fix for this, but any
help would be appreciated.

Thanks,
Ajay
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Re: [Freesurfer] bbregister problems with PET data

[Adam Martersteck]

Thanks Martin and Doug,

I'll give both robust_register with robent and mri_coreg a try.

RE: Doug
The PET tracer is Avid's amyloid compound -- F18-florbetapir (aka amyvid,
aka AV45).
The asymmetric signal is a result of the population -- individuals with a
non-amnestic language dementia with underlying Alzheimer's pathology. I
realize the focal left lateralized atrophy could play a role in partial
voluming, next step is PVC.

Thanks again,
Adam

On Thu, Mar 31, 2016 at 12:13 PM, Douglas N Greve  wrote:

> btw, what tracer is this? And the asymmetry you are talking about is
> between the hemispheres? Is that typical for this tracer or is this a
> phenomena with this subject (or population)?
>
> On 03/30/2016 03:41 PM, Adam Martersteck wrote:
> > Hi Freesurfer team,
> >
> > I’m encountering a problem using bbregister on PET data:
> >
> > -- When I attempt to register a PET volume to T1-space the asymmetric
> > tracer uptake of the PET throws off proper registration. (Treating the
> > PET as a T1 because of the non-specific white matter uptake > grey
> > matter signal).
> >
> > -- You can really see the bbregister mis-registration in this gif
> > here: https://goo.gl/iM6yrT
> >
> > -- It (expectedly) attempts to find the best match between signal
> > intensities on both the left and right surfaces, but is inherently
> > biased by the asymmetric uptake shifts the entire volume to the right.
> >
> > -- Are there any suggestions for dealing with asymmetric scans like
> > this? Stick with just a simple FLIRT? It doesn't seem to do that great
> > a job for everyone.
> >
> > Cutting left and right hemispheres apart and register separately?
> >
> > Using Martin’s new robust register for multi-modal data? Any
> > suggestions on the parameters of ROBENT?
> >
> > Thanks,
> > Adam
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
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>
>
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> 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.
>
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Re: [Freesurfer] bbregister problems with PET data

[Douglas N Greve]

btw, what tracer is this? And the asymmetry you are talking about is 
between the hemispheres? Is that typical for this tracer or is this a 
phenomena with this subject (or population)?

On 03/30/2016 03:41 PM, Adam Martersteck wrote:
> Hi Freesurfer team,
>
> I’m encountering a problem using bbregister on PET data:
>
> -- When I attempt to register a PET volume to T1-space the asymmetric 
> tracer uptake of the PET throws off proper registration. (Treating the 
> PET as a T1 because of the non-specific white matter uptake > grey 
> matter signal).
>
> -- You can really see the bbregister mis-registration in this gif 
> here: https://goo.gl/iM6yrT
>
> -- It (expectedly) attempts to find the best match between signal 
> intensities on both the left and right surfaces, but is inherently 
> biased by the asymmetric uptake shifts the entire volume to the right.
>
> -- Are there any suggestions for dealing with asymmetric scans like 
> this? Stick with just a simple FLIRT? It doesn't seem to do that great 
> a job for everyone.
>
> Cutting left and right hemispheres apart and register separately?
>
> Using Martin’s new robust register for multi-modal data? Any 
> suggestions on the parameters of ROBENT?
>
> Thanks,
> Adam
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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Re: [Freesurfer] bbregister problems with PET data

[Douglas N Greve]

Try using mri_coreg
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_coreg


On 03/30/2016 04:20 PM, Martin Reuter wrote:
> Hi Adam,
>
> not sure robust_register robent will work on this type of stuff (never 
> tested it). I would recommend to keep the radius small (2,or 3), but 
> switch on --entcorrection.
>
> You can also try robust_register with normalized mutual information 
> (NMI) or simple MI to see how that works.
>
> You will probably be able to tell if a registration is completely off, 
> but if you get something that looks similar to FLIRT it will be hard 
> to judge which one is better.
>
> Good luck, Martin
>
>
> On 03/30/2016 03:41 PM, Adam Martersteck wrote:
>> Hi Freesurfer team,
>>
>> I’m encountering a problem using bbregister on PET data:
>>
>> -- When I attempt to register a PET volume to T1-space the asymmetric 
>> tracer uptake of the PET throws off proper registration. (Treating 
>> the PET as a T1 because of the non-specific white matter uptake > 
>> grey matter signal).
>>
>> -- You can really see the bbregister mis-registration in this gif 
>> here: https://goo.gl/iM6yrT
>>
>> -- It (expectedly) attempts to find the best match between signal 
>> intensities on both the left and right surfaces, but is inherently 
>> biased by the asymmetric uptake shifts the entire volume to the right.
>>
>> -- Are there any suggestions for dealing with asymmetric scans like 
>> this? Stick with just a simple FLIRT? It doesn't seem to do that 
>> great a job for everyone.
>>
>> Cutting left and right hemispheres apart and register separately?
>>
>> Using Martin’s new robust register for multi-modal data? Any 
>> suggestions on the parameters of ROBENT?
>>
>> Thanks,
>> Adam
>>
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> -- 
> Martin Reuter, PhD
> Assistant Professor of Radiology, Harvard Medical School
> Assistant Professor of Neurology, Harvard Medical School
> A.A.Martinos Center for Biomedical Imaging
> Massachusetts General Hospital
> Research Affiliate, CSAIL, MIT
> Phone: +1-617-724-5652
> Web  :http://reuter.mit.edu  
>
>
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Re: [Freesurfer] bbregister problems with PET data

[Martin Reuter]

Hi Adam,

not sure robust_register robent will work on this type of stuff (never 
tested it). I would recommend to keep the radius small (2,or 3), but 
switch on --entcorrection.


You can also try robust_register with normalized mutual information 
(NMI) or simple MI to see how that works.


You will probably be able to tell if a registration is completely off, 
but if you get something that looks similar to FLIRT it will be hard to 
judge which one is better.


Good luck, Martin


On 03/30/2016 03:41 PM, Adam Martersteck wrote:

Hi Freesurfer team,

I’m encountering a problem using bbregister on PET data:

-- When I attempt to register a PET volume to T1-space the asymmetric 
tracer uptake of the PET throws off proper registration. (Treating the 
PET as a T1 because of the non-specific white matter uptake > grey 
matter signal).


-- You can really see the bbregister mis-registration in this gif 
here: https://goo.gl/iM6yrT


-- It (expectedly) attempts to find the best match between signal 
intensities on both the left and right surfaces, but is inherently 
biased by the asymmetric uptake shifts the entire volume to the right.


-- Are there any suggestions for dealing with asymmetric scans like 
this? Stick with just a simple FLIRT? It doesn't seem to do that great 
a job for everyone.


Cutting left and right hemispheres apart and register separately?

Using Martin’s new robust register for multi-modal data? Any 
suggestions on the parameters of ROBENT?


Thanks,
Adam


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Assistant Professor of Neurology, Harvard Medical School
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Massachusetts General Hospital
Research Affiliate, CSAIL, MIT
Phone: +1-617-724-5652
Web  : http://reuter.mit.edu

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[Freesurfer] bbregister problems with PET data

[Adam Martersteck]

 Hi Freesurfer team,

I’m encountering a problem using bbregister on PET data:

-- When I attempt to register a PET volume to T1-space the asymmetric
tracer uptake of the PET throws off proper registration. (Treating the PET
as a T1 because of the non-specific white matter uptake > grey matter
signal).

-- You can really see the bbregister mis-registration in this gif here:
https://goo.gl/iM6yrT

-- It (expectedly) attempts to find the best match between signal
intensities on both the left and right surfaces, but is inherently biased
by the asymmetric uptake shifts the entire volume to the right.

-- Are there any suggestions for dealing with asymmetric scans like this?
Stick with just a simple FLIRT? It doesn't seem to do that great a job for
everyone.

Cutting left and right hemispheres apart and register separately?

Using Martin’s new robust register for multi-modal data? Any suggestions on
the parameters of ROBENT?

Thanks,
Adam
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Re: [Freesurfer] bbregister problems

[Pradeep]

Thank you Douglas!
mri_coreg did an awesome job and the registration look good.


On Mon, Feb 22, 2016 at 7:51 PM, Douglas Greve 
wrote:

> If you have spm, you can use --init-spm. Alternatively, you can use
> mri_coreg instead of bbr (bbr is not as effective on blurry data)
>
> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_coreg
>
> mri_coreg --s $fs --mov  ${pet_ext}_LIA.nii --lta output.lta
>
> Also, why is the top of the head cut off? That makes it much more
> difficult to register.
>
> doug
>
>
>
>
> On 2/22/16 8:02 PM, Pradeep wrote:
>
> Hello All,
>
> I am trying to map pet scans to MRI  using bbregister and quite a few
> subjects were improperly registered.
>
> Here are my steps:
> bbregister --s $fs --mov  ${pet_ext}_LIA.nii --init-fsl --t1 --lta
> output.lta
> tkregister2 --mov summed_LIA.nii --reg output.dat --surf
>
>
> [ mri]$ more output.dat.mincost
> 0.860663 0.000513 0.000492 -11.863233
> The first value is quite close to 1 so its bad
>
> I have attached a screen shot of the image and the log file generated
> after bbregister.
> Please let me know if there are any parameters that I could tweak to make
> the registration better.
>
> Thank you for your help,
> -Pradeep
>
>
>
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Re: [Freesurfer] bbregister problems

[Douglas Greve]

If you have spm, you can use --init-spm. Alternatively, you can use 
mri_coreg instead of bbr (bbr is not as effective on blurry data)


ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_coreg

mri_coreg --s $fs --mov  ${pet_ext}_LIA.nii --lta output.lta

Also, why is the top of the head cut off? That makes it much more 
difficult to register.


doug



On 2/22/16 8:02 PM, Pradeep wrote:

Hello All,

I am trying to map pet scans to MRI  using bbregister and quite a few 
subjects were improperly registered.


Here are my steps:
bbregister --s $fs --mov  ${pet_ext}_LIA.nii --init-fsl --t1 --lta 
output.lta

tkregister2 --mov summed_LIA.nii --reg output.dat --surf


[ mri]$ more output.dat.mincost
0.860663 0.000513 0.000492 -11.863233
The first value is quite close to 1 so its bad

I have attached a screen shot of the image and the log file generated 
after bbregister.
Please let me know if there are any parameters that I could tweak to 
make the registration better.


Thank you for your help,
-Pradeep



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Re: [Freesurfer] bbregister with label

[Douglas N Greve]

It is masked in, ie, it only uses the vertices that are in the label.

On 09/03/2015 04:26 PM, Sebastien Proulx wrote:
>
> Quick question :
>
> When using --label with bbregister, does the specified label file mask 
> in or out (is the the voxels that are out or in of the label file that 
> are excluded from the analysis)?
>
> Thanks a lot!!
>
> Sebastien
>
>
>
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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
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[Freesurfer] bbregister with label

[Sebastien Proulx]

Quick question :

When using --label with bbregister, does the specified label file mask in or 
out (is the the voxels that are out or in of the label file that are excluded 
from the analysis)?

Thanks a lot!!
Sebastien
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Re: [Freesurfer] bbregister --12?

[Douglas N Greve]

Yes, it is for 12dof. It is not hidden for any particular purpose 
(except maybe that I'm lazy). In general, I don't think it is a good 
idea to use 12 or 9 dof unless you have an explicit reason to.

On 08/04/2015 01:54 PM, Perea Camargo, Rodrigo Dennis wrote:
 Hi all,
 I am using a previous script to update a pipeline for pre-processing 
 diffusion data. My objective related to this question is  the (what I 
 think is a hidden) argument “- -12” when using bbregister (v. 1.49.2.3 
 FreeSurfer 5.3). Will this denote 12 degrees of freedom for my 
 registration? If so, why is this argument hidden (not in the manual or 
 --help) and what are your insights when registering diffusion data to 
 the Freesurfer T1 image? Should I keep 12dof or just do a simple rigid 
 body registraion (e.g. 6 dof)

 Thanks in advance for your response,
 Rodrigo


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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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[Freesurfer] bbregister --12?

[Perea Camargo, Rodrigo Dennis]

Hi all,
I am using a previous script to update a pipeline for pre-processing diffusion 
data. My objective related to this question is  the (what I think is a hidden) 
argument “- -12” when using bbregister (v. 1.49.2.3 FreeSurfer 5.3). Will this 
denote 12 degrees of freedom for my registration? If so, why is this argument 
hidden (not in the manual or --help) and what are your insights when 
registering diffusion data to the Freesurfer T1 image? Should I keep 12dof or 
just do a simple rigid body registraion (e.g. 6 dof)

Thanks in advance for your response,
Rodrigo
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Re: [Freesurfer] bbregister --12?

[Perea Camargo, Rodrigo Dennis]

Great, thank you for your help!

On 8/4/15, 2:36 PM, freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
Douglas N Greve freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
gr...@nmr.mgh.harvard.edu wrote:

Yes, it is for 12dof. It is not hidden for any particular purpose
(except maybe that I'm lazy). In general, I don't think it is a good
idea to use 12 or 9 dof unless you have an explicit reason to.

On 08/04/2015 01:54 PM, Perea Camargo, Rodrigo Dennis wrote:
 Hi all,
 I am using a previous script to update a pipeline for pre-processing
 diffusion data. My objective related to this question is  the (what I
 think is a hidden) argument ³- -12² when using bbregister (v. 1.49.2.3
 FreeSurfer 5.3). Will this denote 12 degrees of freedom for my
 registration? If so, why is this argument hidden (not in the manual or
 --help) and what are your insights when registering diffusion data to
 the Freesurfer T1 image? Should I keep 12dof or just do a simple rigid
 body registraion (e.g. 6 dof)

 Thanks in advance for your response,
 Rodrigo


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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- 
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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
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Re: [Freesurfer] bbregister error

[Z K]

Hello,

Stefani,

 export FREESURFER_HOME=/usr/local/apps/freesurfer/5.1.0/
 source $FREESURFER_HOME/SetUpFreeSurfer.sh

 It says SUBJECTS_DIR/usr/local/apps/freesurfer/5.1.0/subjects

This looks good. At this point if you type the following:

$ ls -l $SUBJECTS_DIR/001ER

you should see the various folders containing your subjects data (label, 
mri, stats, etc). If this is the case than you should be able to type 
the bbregister command.

 I then went into the directorycontaining 001ER and set environment with
 following command:
 setenv FREESURFER_HOME ${PWD}

Do not perform this step. You shouldnt be setting the FREESURFER_HOME 
environment variable twice.

-Zeke







 I'm still getting errors running the command, so I must be setting this
 up incorrectly.


 Thanks,

 Stefani

 On Tue, May 19, 2015 at 8:41 PM, freesurfer-requ...@nmr.mgh.harvard.edu
 mailto:freesurfer-requ...@nmr.mgh.harvard.edu wrote:

 Send Freesurfer mailing list submissions to
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 To subscribe or unsubscribe via the World Wide Web, visit
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 or, via email, send a message with subject or body 'help' to
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 When replying, please edit your Subject line so it is more specific
 than Re: Contents of Freesurfer digest...


 Today's Topics:

 1. Re: bbregister error (Z K)
 2. Longitudinal difference... (Gonzalo Rojas Costa)
 3. Re: error in atlas creation (Anthony Dick)
 4. Re: funcroi-table-sess error, \set: variable name must begin
with a letter\ (Joseph Andreano)


 --

 Message: 1
 Date: Tue, 19 May 2015 12:00:32 -0400
 From: Z K zkauf...@nmr.mgh.harvard.edu
 mailto:zkauf...@nmr.mgh.harvard.edu
 Subject: Re: [Freesurfer] bbregister error
 To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu
 mailto:freesurfer@nmr.mgh.harvard.edu
 Message-ID: 555b5e20.6000...@nmr.mgh.harvard.edu
 mailto:555b5e20.6000...@nmr.mgh.harvard.edu
 Content-Type: text/plain; charset=windows-1252; format=flowed

 It looks like the SUBJECTS_DIR environment variable is probably set
 incorrectly.

 Does /usr/local/apps/freesurfer/5.1.0/subject/001ER exist? What is
 SUBJECTS_DIR set to?

 SUBJECTS_DIR should be set to the directory containing 001ER.

 -Zeke

 On 05/19/2015 11:48 AM, Stefani O'Donoghue wrote:
   Hi Freesurfer users,
  
   I'm trying to run the bbregister command on the brain.mgz file.
  
   Here is the command line and resulting error:
  
   [12239012@psych2 ~/001ER]$ bbregister --s 001ER --mov mri/brain.mgz
   --reg register.dat
   ERROR: cannot find 001ER in /usr/local/apps/freesurfer/5.1.0/subjects
  
   I need to co-register the Freesurfer ROIs to the skull-stripped
   brain.mgz file. Is this an environment error or am I calling on the
   subject file and volume file incorrectly?
  
   Any help would be greatly appreciated!
  
  
   Thanks,
  
  
   Stefani
  
  
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 --

 Message: 2
 Date: Tue, 19 May 2015 15:36:00 -0300
 From: Gonzalo Rojas Costa gonzalo.rojas.co...@gmail.com
 mailto:gonzalo.rojas.co...@gmail.com
 Subject: [Freesurfer] Longitudinal difference...
 To: freesurfer@nmr.mgh.harvard.edu
 mailto:freesurfer@nmr.mgh.harvard.edu
 freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu
 Message-ID:

 CAHPHMw6WPSrpKJp1+4jbPqV=XRGQz=d1r5v31q9s6c+84ac...@mail.gmail.com
 mailto:d1r5v31q9s6c%2b84ac...@mail.gmail.com
 Content-Type: text/plain; charset=utf-8

 Hi:
 We have GE 1.5T MRI fspgr volumetric acquisition of a MS patient (39
 years
 old) and a Siemens 3T MRI mprage acquisition of the same patient three
 years after (42 years old)... we processed that images to got the
 volume of
 some structures that we need and compare... but, we found that multiple
 brain structures are bigger in the 42 year old images: right hypocampus
 (3187-3755), right cerebral white matter (151164-172448), right
 Cerebellum-White-Matter (12652-14902), right Cerebellum-Cortex
 (48812-51935), etc... And a similar situation occurs in left
 hemisphere...
 The Intracranial volumen in both cases is: 1348899,976

[Freesurfer] bbregister error

[Stefani O'Donoghue]

Hi Freesurfer users,

I'm trying to run the bbregister command on the brain.mgz file.

Here is the command line and resulting error:

[12239012@psych2 ~/001ER]$ bbregister --s 001ER --mov mri/brain.mgz --reg
register.dat
ERROR: cannot find 001ER in /usr/local/apps/freesurfer/5.1.0/subjects

I need to co-register the Freesurfer ROIs to the skull-stripped brain.mgz
file. Is this an environment error or am I calling on the subject file and
volume file incorrectly?

Any help would be greatly appreciated!


Thanks,


Stefani
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Re: [Freesurfer] bbregister error

[Z K]

It looks like the SUBJECTS_DIR environment variable is probably set 
incorrectly.

Does /usr/local/apps/freesurfer/5.1.0/subject/001ER exist? What is 
SUBJECTS_DIR set to?

SUBJECTS_DIR should be set to the directory containing 001ER.

-Zeke

On 05/19/2015 11:48 AM, Stefani O'Donoghue wrote:
 Hi Freesurfer users,

 I'm trying to run the bbregister command on the brain.mgz file.

 Here is the command line and resulting error:

 [12239012@psych2 ~/001ER]$ bbregister --s 001ER --mov mri/brain.mgz
 --reg register.dat
 ERROR: cannot find 001ER in /usr/local/apps/freesurfer/5.1.0/subjects

 I need to co-register the Freesurfer ROIs to the skull-stripped
 brain.mgz file. Is this an environment error or am I calling on the
 subject file and volume file incorrectly?

 Any help would be greatly appreciated!


 Thanks,


 Stefani


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