Re: [Freesurfer] Trac-All Error

[Hua, Jessica]

External Email - Use Caution

Hi Dr. Yendiki,

Thanks! That fixed the issue I was having.

Jessica

---

Jessica Hua, M.A.
Cognitive and Emotional Control Lab
Doctoral Candidate Clinical Psychology
University of Missouri
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[Freesurfer] eTIV vs. manual ICV

[Alexopoulos, Dimitrios]

External Email - Use Caution

I was just wondering if using the eTIV from FS 6.0 is a reliabile measure for 
intracanial volume normalization. Typically,  manual ICV includes extra-axial 
CSF which I don't think is included in the eTIV method, correct?

Our population is a control adoloscent cohort and we are interested in global 
GM and WM, and cortical aparc volumes.

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Re: [Freesurfer] -bash: segmentThalamicNuclei.sh: command not found

[Iglesias Gonzalez, Juan E.]

Hi Veronica
Did you source FreeSurfer?
After that, the command would be:
segmentThalamicNuclei.sh A7 /Users/vp/freesurfer/ANALISI_DATA/
Cheers,
/Eugenio

Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jeiglesias.com



From:  on behalf of Parisi Veronica 

Reply-To: Freesurfer support list 
Date: Friday, April 17, 2020 at 20:08
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: [Freesurfer] -bash: segmentThalamicNuclei.sh: command not found


External Email - Use Caution

Dear Freesurfer Support Team,



I'm trying to run the segmentThalamicNuclei.sh to segment the thalamic nuclei 
on a subject. I am using the latest Freesurfer dev version 
(https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev/). I previously ran 
recon-all to generate the required files for the thalamic segmentation tool 
using the version  
freesurfer-Darwin-OSX-stable-pub-v6.0.0.dmg.



After the download of the dev version, I followed the 
http://freesurfer.net/fswiki/ThalamicNuclei?action=fullsearch=180=linkto%3A%22ThalamicNuclei%22
 instruction as reported:

 - export FREESURFER_HOME=/Users/vp/freesurfer

 - cd $FREESURFER_HOME

 - curl 
"https://surfer.nmr.mgh.harvard.edu/fswiki/MatlabRuntime?action=AttachFile=get=runtime2014bMAC.tar.gz;
 -o "runtime.tar.gz"

 - tar xvf runtime.tar.gz

 - rm $FREESURFER_HOME/runtime.tar.gz

 - segmentThalamicNuclei.sh  bert  [SUBJECTS_DIR] =

segmentThalamicNuclei.sh A7 /Users/vp/freesurfer/ANALISI_DATA/A7/mri/norm.mgz



However, the program exits with the following error message:

-bash: segmentThalamicNuclei.sh: command not found



It doesn't seem to me that there are errors in the paths.



What can I do to fix the problem?



Thank you,

VP





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[Freesurfer] -bash: segmentThalamicNuclei.sh: command not found

[Parisi Veronica]

External Email - Use Caution

Dear Freesurfer Support Team,


I'm trying to run the segmentThalamicNuclei.sh to segment the thalamic nuclei 
on a subject. I am using the latest Freesurfer dev version 
(https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev/). I previously ran 
recon-all to generate the required files for the thalamic segmentation tool 
using the version  
freesurfer-Darwin-OSX-stable-pub-v6.0.0.dmg.


After the download of the dev version, I followed the 
http://freesurfer.net/fswiki/ThalamicNuclei?action=fullsearch=180=linkto%3A%22ThalamicNuclei%22
 instruction as reported:

 - export FREESURFER_HOME=/Users/vp/freesurfer

 - cd $FREESURFER_HOME

 - curl 
"https://surfer.nmr.mgh.harvard.edu/fswiki/MatlabRuntime?action=AttachFile=get=runtime2014bMAC.tar.gz;
 -o "runtime.tar.gz"

 - tar xvf runtime.tar.gz

 - rm $FREESURFER_HOME/runtime.tar.gz

 - segmentThalamicNuclei.sh  bert  [SUBJECTS_DIR] =

segmentThalamicNuclei.sh A7 /Users/vp/freesurfer/ANALISI_DATA/A7/mri/norm.mgz


However, the program exits with the following error message:

-bash: segmentThalamicNuclei.sh: command not found


It doesn't seem to me that there are errors in the paths.


What can I do to fix the problem?

Thank you,
VP




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Respect the environment: print this email only if necessary.
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Re: [Freesurfer] [External] Freesurfer Digest, Vol 194, Issue 24

[Soichi Hayashi]

External Email - Use Caution

Douglas,

I've uploaded my t1. It should be named "soichi-cw256.nii.gz".

I am running the freesurfer with -debug option set now. I will reply back
once I get the log.

Thank you!
Soichi



On Fri, Apr 17, 2020 at 12:38 PM freesurfer-requ...@nmr.mgh.harvard.edu <
freesurfer-requ...@nmr.mgh.harvard.edu> wrote:

> This message was sent from a non-IU address. Please exercise caution when
> clicking links or opening attachments from external sources.
> ---
>
> Send Freesurfer mailing list submissions to
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> or, via email, send a message with subject or body 'help' to
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>
> You can reach the person managing the list at
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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: cw256 option not working? (Douglas N. Greve)
>
>
> --
>
> Message: 1
> Date: Fri, 17 Apr 2020 12:37:10 -0400
> From: "Douglas N. Greve" 
> Subject: Re: [Freesurfer] cw256 option not working?
> To: 
> Message-ID: <92a8fb3b-7a8c-d31f-05c8-97983b590...@mgh.harvard.edu>
> Content-Type: text/plain; charset="utf-8"
>
> Can you run it with -debug as the first option and send me the (copious)
> terminal output? Even better if you can send me the data so I can try it
> out in the soon-to-be-released version 7. 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 4/17/2020 12:29 PM, Soichi Hayashi wrote:
> >
> > External Email - Use Caution
> >
> > Hello.
> >
> > I am trying to run recon-all on HCP7T data and seeing this error message.
> >
> > 
> > ERROR! FOV=268.800 > 256
> > Include the flag -cw256 with recon-all!
> > Inspect orig.mgz to ensure the head is fully visible.
> > 
> >
> > I've looked at orig.mgz, and it looks fine to me (screenshot attached).
> >
> > Anyway, I've added the -cw256 option to the command line.
> >
> > $ recon-all -i
> > ../5e977c0dfe00f4e4b4976207/5a052586eec2b300611abffc/t1.nii.gz
> > -subject output -all -parallel -openmp 8 -hippocampal-subfields-T1
> > -hires -cw256
> >
> > However, I am still seeing the same error message saying that I should
> > add the flag -cw256. Am I setting this option incorrectly? I am using
> > freesurfer version 6.0.0.
> >
> > Thank you!
> > Soichi Hayashi
> > Screenshot from 2020-04-17 12-28-01.png
> >
> >
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
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>
> End of Freesurfer Digest, Vol 194, Issue 24
> ***
>
>
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[Freesurfer] Which autorecon uses -hippocampal-subfields flags?

[Billah, Tashrif]

Douglas,

Let's try with an example. See the two 
ways T2 image can be 
integrated with recon-all

Altogether:

recon-all -subject subjectname -i /path/to/input_volume -T2 /path/to/T2_volume 
-T2pial -all

autorecon3 only:

recon-all -subject subjectname -T2 /path/to/T2_volume -T2pial -autorecon3

Similar to the former, 
-hippocampal-subfields-T1
 integrated with recon-all:

recon-all -all -s bert -hippocampal-subfields-T1

Now the question, compared to the latter, which autorecon[1/2/3] would accept 
-hippocampal-subfields-T1?

Does it make sense now?

-Tashrif
.
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Re: [Freesurfer] Data on the Freesurfer surface

[Mason Wells]

External Email - Use Caution

Please ignore my last email. I added --out_type mgh and also changed the --out 
to end with ?h.mgh and it's done the trick. Please do let me know if this isn’t 
correct though!

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
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
 

On 17/04/2020, 21:52, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of 
Mason Wells"  wrote:

External Email - Use Caution

Sorry, just to follow up on this. The surface based analysis needs the 
outputs in the format of MGH. I fear I may have missed a step here. Any advice 
would be great.

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
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
 

On 17/04/2020, 21:41, "Mason Wells"  wrote:

Great, thanks for this.
Am I right in thinking that the only outputs from this command are 
COR-.info and COR-001 and that neither of these should have which hemisphere it 
was created from in their name? I also notice the examples on the wiki page 
have more inputs/arguments, I assume these are not needed for what I am trying 
to do? E.g. resample filtered_func to the surface using the 
anat2exf.register.dat file?

Thanks again,
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
 

On 17/04/2020, 18:40, "Douglas N. Greve"  wrote:

That looks good. The only thing to change is to specify the 
projection 
fraction for vol2surf to --projfrac 0.5 (so that it samples in the 
middle of the cortical ribbon rather than at the white/gray 
boundary)

On 4/17/2020 1:36 PM, Mason Wells wrote:
>  External Email - Use Caution
>
> Hi,
>
> Can I just double check this seems correct to you experts? I am 
not 100% proficient in Freesurfer/FSL.
>
> I ran:
> bregister --s S1 --feat  
Data/Feat2/LM/scans/Preprocessed_functionals/6_CMRRMB_run1_.feat/
>
> Which seemed to give me what I needed, the white matter appears 
to be well aligned with the functional data when I ran:
> tkregisterfv --mov / 
Data/Feat2/S1/scans/Preprocessed_functionals/6_CMRRMB_run1_.feat//example_func.nii.gz
 --reg 
Data/Feat2/S1/scans/Preprocessed_functionals/6_CMRRMB_run1_.feat//reg/freesurfer/anat2exf.register.dat
 --surfs
>
> Now I believe I need to resample this to the surface with 
mri_vol2surf. Is the command as simple as:
>
> mri_vol2surf --src 
/scans/Preprocessed_functionals/6_CMRRMB_run1_.feat/filtered_func_data.nii.gz 
--out  /Preprocessed_functionals/ --srcreg 
/Preprocessed_functionals/6_CMRRMB_run1_.feat/reg/freesurfer/anat2exf.register.dat
 --hemi rh
>
> followed by the same command with lh instead for the other 
hemisphere? Or are the additional commands that you would recommend?
   

Re: [Freesurfer] Data on the Freesurfer surface

[Mason Wells]

External Email - Use Caution

Sorry, just to follow up on this. The surface based analysis needs the outputs 
in the format of MGH. I fear I may have missed a step here. Any advice would be 
great.

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
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
 

On 17/04/2020, 21:41, "Mason Wells"  wrote:

Great, thanks for this.
Am I right in thinking that the only outputs from this command are 
COR-.info and COR-001 and that neither of these should have which hemisphere it 
was created from in their name? I also notice the examples on the wiki page 
have more inputs/arguments, I assume these are not needed for what I am trying 
to do? E.g. resample filtered_func to the surface using the 
anat2exf.register.dat file?

Thanks again,
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
 

On 17/04/2020, 18:40, "Douglas N. Greve"  wrote:

That looks good. The only thing to change is to specify the projection 
fraction for vol2surf to --projfrac 0.5 (so that it samples in the 
middle of the cortical ribbon rather than at the white/gray boundary)

On 4/17/2020 1:36 PM, Mason Wells wrote:
>  External Email - Use Caution
>
> Hi,
>
> Can I just double check this seems correct to you experts? I am not 
100% proficient in Freesurfer/FSL.
>
> I ran:
> bregister --s S1 --feat  
Data/Feat2/LM/scans/Preprocessed_functionals/6_CMRRMB_run1_.feat/
>
> Which seemed to give me what I needed, the white matter appears to be 
well aligned with the functional data when I ran:
> tkregisterfv --mov / 
Data/Feat2/S1/scans/Preprocessed_functionals/6_CMRRMB_run1_.feat//example_func.nii.gz
 --reg 
Data/Feat2/S1/scans/Preprocessed_functionals/6_CMRRMB_run1_.feat//reg/freesurfer/anat2exf.register.dat
 --surfs
>
> Now I believe I need to resample this to the surface with 
mri_vol2surf. Is the command as simple as:
>
> mri_vol2surf --src 
/scans/Preprocessed_functionals/6_CMRRMB_run1_.feat/filtered_func_data.nii.gz 
--out  /Preprocessed_functionals/ --srcreg 
/Preprocessed_functionals/6_CMRRMB_run1_.feat/reg/freesurfer/anat2exf.register.dat
 --hemi rh
>
> followed by the same command with lh instead for the other 
hemisphere? Or are the additional commands that you would recommend?
>
> Thanks for all your help.
> 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
>   
>
> On 17/04/2020, 17:40, "freesurfer-boun...@nmr.mgh.harvard.edu on 
behalf of Douglas N. Greve"  wrote:
>
>  Yes, use the template.nii.gz as the registration target. A long 
time ago
>  we used to have some wrappers that would operate directly on feat
>  folders. Not sure if they still work but, check out
   

Re: [Freesurfer] Data on the Freesurfer surface

[Mason Wells]

External Email - Use Caution

Great, thanks for this.
Am I right in thinking that the only outputs from this command are COR-.info 
and COR-001 and that neither of these should have which hemisphere it was 
created from in their name? I also notice the examples on the wiki page have 
more inputs/arguments, I assume these are not needed for what I am trying to 
do? E.g. resample filtered_func to the surface using the anat2exf.register.dat 
file?

Thanks again,
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
 

On 17/04/2020, 18:40, "Douglas N. Greve"  wrote:

That looks good. The only thing to change is to specify the projection 
fraction for vol2surf to --projfrac 0.5 (so that it samples in the 
middle of the cortical ribbon rather than at the white/gray boundary)

On 4/17/2020 1:36 PM, Mason Wells wrote:
>  External Email - Use Caution
>
> Hi,
>
> Can I just double check this seems correct to you experts? I am not 100% 
proficient in Freesurfer/FSL.
>
> I ran:
> bregister --s S1 --feat  
Data/Feat2/LM/scans/Preprocessed_functionals/6_CMRRMB_run1_.feat/
>
> Which seemed to give me what I needed, the white matter appears to be 
well aligned with the functional data when I ran:
> tkregisterfv --mov / 
Data/Feat2/S1/scans/Preprocessed_functionals/6_CMRRMB_run1_.feat//example_func.nii.gz
 --reg 
Data/Feat2/S1/scans/Preprocessed_functionals/6_CMRRMB_run1_.feat//reg/freesurfer/anat2exf.register.dat
 --surfs
>
> Now I believe I need to resample this to the surface with mri_vol2surf. 
Is the command as simple as:
>
> mri_vol2surf --src 
/scans/Preprocessed_functionals/6_CMRRMB_run1_.feat/filtered_func_data.nii.gz 
--out  /Preprocessed_functionals/ --srcreg 
/Preprocessed_functionals/6_CMRRMB_run1_.feat/reg/freesurfer/anat2exf.register.dat
 --hemi rh
>
> followed by the same command with lh instead for the other hemisphere? Or 
are the additional commands that you would recommend?
>
> Thanks for all your help.
> 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
>   
>
> On 17/04/2020, 17:40, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf 
of Douglas N. Greve"  wrote:
>
>  Yes, use the template.nii.gz as the registration target. A long time 
ago
>  we used to have some wrappers that would operate directly on feat
>  folders. Not sure if they still work but, check out
>  
https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FFslFeatFreeSurferdata=02%7C01%7CWellsMT1%40cardiff.ac.uk%7Cd1f3f081039a4d49340808d7e2f660e9%7Cbdb74b3095684856bdbf06759778fcbc%7C1%7C0%7C637227420124409244sdata=lKy%2B8H9gAxvdLv8vKuqLp3kZ4FdMPlsRgx7AYmVqmvw%3Dreserved=0
>  
>  On 4/17/2020 10:43 AM, Mason Wells wrote:
>  >  External Email - Use Caution
>  >
>  > Great, thanks again Bruce.
>  > Doug, can you confirm this is the process for taking a 
filtered_func file and getting it onto the freesurfer surface ready for 
analysis?
>  >
>  > 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
>   

Re: [Freesurfer] Which autorecon uses -hippocampal-subfields flags?

[Douglas N. Greve]

I don't understand the question. To run recon-all through to the end 
implies that you have run all the -autorecons


On 4/17/2020 2:53 PM, Billah, Tashrif wrote:

Right, I understand the rule about the scripts.

However, my original question was about the subfields 
-hippocampal-subfields-T1/T2/T1T2
Again, can they be run with any of the autorecons separately? The 
example shown here 
 
integrates the subfileds with recon-all only but do no show 
combination with any autorecon commands.


-Tashrif
.

*From:* Billah, Tashrif
*Sent:* Friday, April 17, 2020 1:52 PM
*To:* freesurfer@nmr.mgh.harvard.edu 
*Subject:* Re: [Freesurfer] Which autorecon uses 
-hippocampal-subfields flags?

Douglas,

A little more elaboration would help. What is "it" and what are "them"?

-Tashrif

.



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Re: [Freesurfer] Does FS guarantee the same results if run several times?

[Tim Schäfer]

External Email - Use Caution

Hi Xiaojiang,

Given the precision of MRI scanners, I would say it's safe to assume that this 
difference can be ignored.

Best,

Tim

> On April 17, 2020 at 9:02 PM Xiaojiang Yang  wrote:
> 
> 
> External Email - Use Caution
> 
> Thank you Douglas! In my case, two runnings were from Centos7 and Redhat7
> respectively. Good thing is that the difference of the average thickness is
> small - it's 0.006 mm. Both lh and rh have 0.006 mm differences, but one's
> lh is thicker than the other's, while its rh is thinner than the other's. 
> 
>  
> 
> Xiaojiang
> 
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] Does FS guarantee the same results if run several times?

[Xiaojiang Yang]

External Email - Use Caution

Thank you Douglas! In my case, two runnings were from Centos7 and Redhat7
respectively. Good thing is that the difference of the average thickness is
small - it's 0.006 mm. Both lh and rh have 0.006 mm differences, but one's
lh is thicker than the other's, while its rh is thinner than the other's. 

 

Xiaojiang

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Re: [Freesurfer] Which autorecon uses -hippocampal-subfields flags?

[Billah, Tashrif]

Right, I understand the rule about the scripts.

However, my original question was about the subfields 
-hippocampal-subfields-T1/T2/T1T2

Again, can they be run with any of the autorecons separately? The example shown 
here integrates 
the subfileds with recon-all only but do no show combination with any autorecon 
commands.

-Tashrif
.

From: Billah, Tashrif
Sent: Friday, April 17, 2020 1:52 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] Which autorecon uses -hippocampal-subfields flags?

Douglas,

A little more elaboration would help. What is "it" and what are "them"?


-Tashrif

.

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Re: [Freesurfer] Does FS guarantee the same results if run several times?

[Douglas N. Greve]

I think recon-all should be deterministic for multiple threads. I know 
that different machines can give different answers (but usually this is 
a mac vs linux thing).


On 4/17/2020 2:34 PM, Xiaojiang Yang wrote:


External Email - Use Caution

Hi Douglas,

I checked the recon-all.log files for both, and found the difference – 
my mistake, one used FLAIR as extra input and the other did not.


I did find another case that has two different results in two 
runnings. Both runnings have MPRAGE and FLAIR as inputs, but one of 
the runnings has used the option “–openmp 16”, and the other did not.


Also, the two runnings were from two different machines. What do you 
think is the factor that has caused the different results, the openmp 
or different machine? The FS on two machines are the same version (V6).


Thanks!

Xiaojiang


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Re: [Freesurfer] Which autorecon uses -hippocampal-subfields flags?

[Douglas N. Greve]

You have to run recon-all all the way through and then run the subfield 
scripts separately.


On 4/17/2020 12:21 PM, Douglas N. Greve wrote:
None! You have to run it all the way through to the end and then run 
them from the command line.


On 4/17/2020 11:40 AM, Billah, Tashrif wrote:

Hi all,

Which of the three autorecons makes use of 
https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfields flags?

autorecon1, 2 , or 3?

My goal is to use the flag specifically with one of the three and not 
with recon-all in general as shown in the above page.


I do understand that the new version of the commands are 
https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldsAndNucleiOfAmygdala


Best,
Tashrif


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Re: [Freesurfer] Does FS guarantee the same results if run several times?

[Xiaojiang Yang]

External Email - Use Caution

Hi Douglas,

 

I checked the recon-all.log files for both, and found the difference - my
mistake, one used FLAIR as extra input and the other did not.

 

I did find another case that has two different results in two runnings. Both
runnings have MPRAGE and FLAIR as inputs, but one of the runnings has used
the option "-openmp 16", and the other did not.

Also, the two runnings were from two different machines. What do you think
is the factor that has caused the different results, the openmp or different
machine? The FS on two machines are the same version (V6).

 

Thanks!

Xiaojiang

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Re: [Freesurfer] Which autorecon uses -hippocampal-subfields flags?

[Billah, Tashrif]

Douglas,

A little more elaboration would help. What is "it" and what are "them"?


-Tashrif

.

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Re: [Freesurfer] convert gii to mgh/nii.gz (freesurfer surface)

[Tim Schäfer]

External Email - Use Caution

You will need to convert it to FreeSurfer surface format (instead of MGH/NIFTI, 
which are volume formats), the standard one is the binary surface format. 
Assuming your file is 'lh.white.gii':

mris_convert lh.white.gii lh.white

or to use the less common ASCII version (I would not recommend that):

mris_convert lh.white.gii lh.white.asc

Best,

Tim

> On April 17, 2020 at 12:38 PM Marina Fernández 
>  wrote:
> 
> 
> External Email - Use Caution
> 
> Hi experts,
> 
> How can I convert a surface in .gii format to a surface in .mgh or nii.gz
> format?
> 
> I tried with mris_convert but it doesn't work.
> 
> 
> Best regards,
> Marina
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

--
Dr. Tim Schäfer
Postdoc Computational Neuroimaging
Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy
University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany

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Re: [Freesurfer] Data on the Freesurfer surface

[Douglas N. Greve]

That looks good. The only thing to change is to specify the projection 
fraction for vol2surf to --projfrac 0.5 (so that it samples in the 
middle of the cortical ribbon rather than at the white/gray boundary)

On 4/17/2020 1:36 PM, Mason Wells wrote:
>  External Email - Use Caution
>
> Hi,
>
> Can I just double check this seems correct to you experts? I am not 100% 
> proficient in Freesurfer/FSL.
>
> I ran:
> bregister --s S1 --feat  
> Data/Feat2/LM/scans/Preprocessed_functionals/6_CMRRMB_run1_.feat/
>
> Which seemed to give me what I needed, the white matter appears to be well 
> aligned with the functional data when I ran:
> tkregisterfv --mov / 
> Data/Feat2/S1/scans/Preprocessed_functionals/6_CMRRMB_run1_.feat//example_func.nii.gz
>  --reg 
> Data/Feat2/S1/scans/Preprocessed_functionals/6_CMRRMB_run1_.feat//reg/freesurfer/anat2exf.register.dat
>  --surfs
>
> Now I believe I need to resample this to the surface with mri_vol2surf. Is 
> the command as simple as:
>
> mri_vol2surf --src 
> /scans/Preprocessed_functionals/6_CMRRMB_run1_.feat/filtered_func_data.nii.gz 
> --out  /Preprocessed_functionals/ --srcreg 
> /Preprocessed_functionals/6_CMRRMB_run1_.feat/reg/freesurfer/anat2exf.register.dat
>  --hemi rh
>
> followed by the same command with lh instead for the other hemisphere? Or are 
> the additional commands that you would recommend?
>
> Thanks for all your help.
> 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
>   
>
> On 17/04/2020, 17:40, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of 
> Douglas N. Greve"  dgr...@mgh.harvard.edu> wrote:
>
>  Yes, use the template.nii.gz as the registration target. A long time ago
>  we used to have some wrappers that would operate directly on feat
>  folders. Not sure if they still work but, check out
>  
> https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FFslFeatFreeSurferdata=02%7C01%7CWellsMT1%40cardiff.ac.uk%7Caac15b24194e4daf083208d7e2ee1141%7Cbdb74b3095684856bdbf06759778fcbc%7C1%7C0%7C637227384425792122sdata=vRguHDB0RqsEAj8D0asSGOSzWzU4yORkEbtrhEknuvs%3Dreserved=0
>  
>  On 4/17/2020 10:43 AM, Mason Wells wrote:
>  >  External Email - Use Caution
>  >
>  > Great, thanks again Bruce.
>  > Doug, can you confirm this is the process for taking a filtered_func 
> file and getting it onto the freesurfer surface ready for analysis?
>  >
>  > 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
>  >
>  >
>  > On 17/04/2020, 15:32, "freesurfer-boun...@nmr.mgh.harvard.edu on 
> behalf of Bruce Fischl"  fis...@nmr.mgh.harvard.edu> wrote:
>  >
>  >  oh, then you probably want to use bbreg to register it and 
> mri_vol2surf
>  >  to sample it onto the surface. Doug is the expert on this and can
>  >  add/correct if this is not the whole story :)
>  >
>  >  cheers
>  >  Bruce
>  >  On Fri, 17 Apr 2020, Mason
>  >  Wells wrote:
>  >
>  >  >External Email - Use Caution
>  >  >
>  >  > Hi Bruce,
>  >  >
>  >  > The only pre-processing I have done is the motion correction, 
> high pass filtering and distortion correction. So, as far as I know it is 
> still in the volume and in the original functional space.
>  >  >
>  >  > Best wishes,
>  >  > Mason
>  >  >
>  >  > Mason T Wells, MSc
>  >  > PhD student
>  >  > School of Optometry and Vision Sciences
>  >  > & Cardiff University 

Re: [Freesurfer] Data on the Freesurfer surface

[Mason Wells]

External Email - Use Caution

Hi,

Can I just double check this seems correct to you experts? I am not 100% 
proficient in Freesurfer/FSL. 

I ran:
bregister --s S1 --feat  
Data/Feat2/LM/scans/Preprocessed_functionals/6_CMRRMB_run1_.feat/

Which seemed to give me what I needed, the white matter appears to be well 
aligned with the functional data when I ran:
tkregisterfv --mov / 
Data/Feat2/S1/scans/Preprocessed_functionals/6_CMRRMB_run1_.feat//example_func.nii.gz
 --reg 
Data/Feat2/S1/scans/Preprocessed_functionals/6_CMRRMB_run1_.feat//reg/freesurfer/anat2exf.register.dat
 --surfs

Now I believe I need to resample this to the surface with mri_vol2surf. Is the 
command as simple as:

mri_vol2surf --src 
/scans/Preprocessed_functionals/6_CMRRMB_run1_.feat/filtered_func_data.nii.gz 
--out  /Preprocessed_functionals/ --srcreg 
/Preprocessed_functionals/6_CMRRMB_run1_.feat/reg/freesurfer/anat2exf.register.dat
 --hemi rh

followed by the same command with lh instead for the other hemisphere? Or are 
the additional commands that you would recommend?

Thanks for all your help.
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
 

On 17/04/2020, 17:40, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of 
Douglas N. Greve"  wrote:

Yes, use the template.nii.gz as the registration target. A long time ago 
we used to have some wrappers that would operate directly on feat 
folders. Not sure if they still work but, check out 

https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FFslFeatFreeSurferdata=02%7C01%7CWellsMT1%40cardiff.ac.uk%7Caac15b24194e4daf083208d7e2ee1141%7Cbdb74b3095684856bdbf06759778fcbc%7C1%7C0%7C637227384425792122sdata=vRguHDB0RqsEAj8D0asSGOSzWzU4yORkEbtrhEknuvs%3Dreserved=0

On 4/17/2020 10:43 AM, Mason Wells wrote:
>  External Email - Use Caution
>
> Great, thanks again Bruce.
> Doug, can you confirm this is the process for taking a filtered_func file 
and getting it onto the freesurfer surface ready for analysis?
>
> 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
>   
>
> On 17/04/2020, 15:32, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf 
of Bruce Fischl"  wrote:
>
>  oh, then you probably want to use bbreg to register it and 
mri_vol2surf
>  to sample it onto the surface. Doug is the expert on this and can
>  add/correct if this is not the whole story :)
>  
>  cheers
>  Bruce
>  On Fri, 17 Apr 2020, Mason
>  Wells wrote:
>  
>  >External Email - Use Caution
>  >
>  > Hi Bruce,
>  >
>  > The only pre-processing I have done is the motion correction, high 
pass filtering and distortion correction. So, as far as I know it is still in 
the volume and in the original functional space.
>  >
>  > Best wishes,
>  > 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
>  > 

Re: [Freesurfer] on Ubuntu (was FreeSurfer V 7.0 on Centos 8) {Disarmed}

[TRISTAN J PAUTSCH]

External Email - Use Caution

Just a quick follow up, I've now been able to find my issue in the wild as well 
(not just on my own machines).

I use Arch Linux personally and on a small handful of workstations 
professionally, and when investigating using FS on Arch, I stumbled upon an AUR 
build someone had done. While I didn't intend to use this buildfile (still 
version 6.x), the top comment on the below link alludes to the same PETSC error 
message with FS as I'm experiencing on my Ubuntu machines:

https://aur.archlinux.org/packages/freesurfer-bin/

T


From: TRISTAN J PAUTSCH 
Sent: Monday, April 6, 2020 1:32 PM
To: freesurfer@nmr.mgh.harvard.edu 
Cc: ts...@rcmd.org 
Subject: Re: [Freesurfer] on Ubuntu (was FreeSurfer V 7.0 on Centos 8) 
{Disarmed}

Apologies for the late reply, hectic times.

Please find the requested files here:
https://uwmadison.box.com/s/vod1t4vlycd9baom42qqqwkc6unj9aui

Let me know how else I can help!
T


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of fsbu...@contbay.com 

Sent: Tuesday, March 31, 2020 6:20 PM
To: freesurfer@nmr.mgh.harvard.edu 
Cc: ts...@rcmd.org 
Subject: Re: [Freesurfer] on Ubuntu (was FreeSurfer V 7.0 on Centos 8) 
{Disarmed}


External Email - Use Caution

Hello Tristan,

Going back to that thread, I’d like to try the command you uploaded data for as 
freesurfer_data.tar.gz on a couple of Ubuntu systems, but either I’m looking in 
the wrong place or it’s not there anymore.  Is there a shared google drive link 
or something you point me to for a download link?


> freeview -v brainmask.mgz T1.mgz -f lh.white:edgecolor=yellow
> lh.pial:edgecolor=magenta rh.white:edgecolor=yellow rh.pial:edgecolor=magenta
>
> We can also replicate the error by opening freeview and opening all the above
> files sequentially through the GUI.


- R.

On Mar 31, 2020, at 13:41, TRISTAN J PAUTSCH  wrote:

External Email - Use Caution
Thanks for the reply, all.

The issues I'm having are the same as they were in my prior thread, found here:
MailScanner has detected a possible fraud attempt from "www..mail-archive.com" 
claiming to be 
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg63458.html

I tried everything up to and including compiling everything from scratch 
(including FS itself, missing libs, PETSC, etc.). The main takeaway is that I 
pretty convincingly narrowed the issue down to PETSC+Ubuntu 18.04, the most 
pertinent details for that being in the following post:
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg63702.html

Back when I was active in that thread, I emailed the PETSC mailing list and got 
no response, and at the time I was pretty busy with other projects so I had to 
let it go for the time being; I maintained my old RHEL6 server so people could 
continue to use FS. Now with everyone in quarantine (and RHEL6 entering ELS 
this November), it's a decent time to look back into this issue.

I wouldn't have reached back out to the FS list, however when I saw that a 
focus was being placed on Ubuntu (and that there was a working Ubuntu VM), I 
became hopeful that maybe this issue was resolved?

T

From: fsbu...@contbay.com 
mailto:fsbu...@contbay.com>>
Sent: Tuesday, March 31, 2020 3:57 AM
To: freesurfer@nmr.mgh.harvard.edu 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Cc: ts...@rcmd.org 
mailto:ts...@rcmd.org>>; TRISTAN J PAUTSCH 
mailto:tpaut...@wisc.edu>>
Subject: Re: [Freesurfer] on Ubuntu (was FreeSurfer V 7.0 on Centos 8)

We would also like to know about any issues you are seeing on Ubuntu.

I think Ubuntu eliminated some jpeg/png packages from their repos.  Those can 
be downloaded and installed manually,e.g., 
libpng12-0_1.2.54-1ubuntu1.1_amd64.deb, libjpeg62_6b2-3_amd64.deb.  That is 
part of the reason we made an Ubuntu 18 VM available with everything 
pre-installed.

The VM is essentially what has been used for the freesurfer course which runs 
mostly freeview commands with some mri* commands (though I believe a recon-all 
also works).  The VM is running binaries built on CentOS7 - as the reference 
platforms for freesurfer dev are currently CentOS and MacOS.  We are looking at 
making a .deb installer for freesurfer on Ubuntu though.

There is some info on the wiki about packages required to compile the source on 
Ubuntu - but you don’t need all of these to run (even the CentOS) binaries.

MailScanner has detected a possible fraud attempt from 
"surfer..nmr.mgh.harvard.edu" claiming to 
behttps://surfer.nmr.mgh.harvard.edu/fswiki/BuildRequirements

- R.

On Mar 31, 2020, at 02:50, Tim Schäfer  wrote:

   External Email - Use Caution

Hi Tristan,

I'm about to 

Re: [Freesurfer] Data on the Freesurfer surface

[Douglas N. Greve]

Yes, use the template.nii.gz as the registration target. A long time ago 
we used to have some wrappers that would operate directly on feat 
folders. Not sure if they still work but, check out 
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/FslFeatFreeSurfer

On 4/17/2020 10:43 AM, Mason Wells wrote:
>  External Email - Use Caution
>
> Great, thanks again Bruce.
> Doug, can you confirm this is the process for taking a filtered_func file and 
> getting it onto the freesurfer surface ready for analysis?
>
> 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
>   
>
> On 17/04/2020, 15:32, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of 
> Bruce Fischl"  fis...@nmr.mgh.harvard.edu> wrote:
>
>  oh, then you probably want to use bbreg to register it and mri_vol2surf
>  to sample it onto the surface. Doug is the expert on this and can
>  add/correct if this is not the whole story :)
>  
>  cheers
>  Bruce
>  On Fri, 17 Apr 2020, Mason
>  Wells wrote:
>  
>  >External Email - Use Caution
>  >
>  > Hi Bruce,
>  >
>  > The only pre-processing I have done is the motion correction, high 
> pass filtering and distortion correction. So, as far as I know it is still in 
> the volume and in the original functional space.
>  >
>  > Best wishes,
>  > 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
>  >
>  >
>  > On 17/04/2020, 15:11, "freesurfer-boun...@nmr.mgh.harvard.edu on 
> behalf of Bruce Fischl"  fis...@nmr.mgh.harvard.edu> wrote:
>  >
>  >Hi Mason
>  >
>  >is your filtered_func file already sampled onto the surface or is 
> it a
>  >volume?
>  >
>  >cheers
>  >Bruce
>  >On Fri, 17 Apr 2020, Mason Wells wrote:
>  >
>  >>
>  >> External Email - Use Caution
>  >>
>  >> Hi all,
>  >>
>  >>
>  >>
>  >> I am trying to use an analysis package that works on surface 
> based data
>  >> (SamSrf). I have ran Feat and have a filtered_func file which is 
> of course
>  >> the motion corrected/unwarped version of my EPI. However, I need 
> some advice
>  >> on how to get these data onto the Freesurfer surface. I have 
> found this
>  >> page, but I wanted to double check this is the most up-to-date 
> pipeline. On
>  >> the page it suggests using the same DOF as used in Feat, I use 
> BBR so this
>  >> seems a little redundant. Has anyone on these lists got any 
> experience of
>  >> getting filtered_func onto the Freesurfer surface?
>  >>
>  >>
>  >>
>  >> 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 

Re: [Freesurfer] Does FS guarantee the same results if run several times?

[Douglas N. Greve]

No, it should be giving the same result every time

On 4/17/2020 12:03 PM, Xiaojiang Yang wrote:


External Email - Use Caution

Thank you Douglas and Tashrif!

Does this mean I should run recon-all for each subject several times, 
and compute the average to get the more reliable thickness?


Can anyone else confirm this?  Thanks!

Xiaojiang

Billah, Tashrif 
<https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu=from:%22Billah%2C+Tashrif%22>Fri, 
17 Apr 2020 08:34:14 -0700 
<https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu=date:20200417>


Hi Xiaojiang and Douglas,
I think it is the attribute of having random initialization in the 
registration

steps. This slight discrepancy can also be observed with antsRegistration.
I don't know the exact algorithm FreeSurfer uses for registration though.
Best,
Tashrif


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Re: [Freesurfer] Which autorecon uses -hippocampal-subfields flags?

[Douglas N. Greve]

None! You have to run it all the way through to the end and then run 
them from the command line.


On 4/17/2020 11:40 AM, Billah, Tashrif wrote:

Hi all,

Which of the three autorecons makes use of 
https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfields flags?

autorecon1, 2 , or 3?

My goal is to use the flag specifically with one of the three and not 
with recon-all in general as shown in the above page.


I do understand that the new version of the commands are 
https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldsAndNucleiOfAmygdala


Best,
Tashrif


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Re: [Freesurfer] Does FS guarantee the same results if run several times?

[Douglas N. Greve]

When we run repeated analyses on the same data on the same system, we 
always get the same results

doug


On 4/17/2020 11:32 AM, Billah, Tashrif wrote:

Hi Xiaojiang and Douglas,
I think it is the attribute of having random initialization in the 
registration steps. This slight discrepancy can also be observed with 
antsRegistration.

I don't know the exact algorithm FreeSurfer uses for registration though.

Best,
Tashrif


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Re: [Freesurfer] Does FS guarantee the same results if run several times?

[Douglas N. Greve]

Can you send the recon-all.log files for two of the runs that should be 
identical?


On 4/17/2020 11:15 AM, Xiaojiang Yang wrote:


External Email - Use Caution

No. I just checked, they are not identical. Although some of numbers 
are the same, many are different.


Xiaojiang

Are the other results identical? Eg, lh.aparc.stats?

On 4/17/2020 10:49 AM, Xiaojiang Yang wrote:

External Email - Use Caution

Dear Freeserfer developers,

I have run recon-all for a bunch of subjects on the same machine 
forseveral times. When I use the “mris_anatomical_stats”to calculate 
thestatistics (specifically, I am interested in average 
corticalthickness), I found that for the same subject I got different 
results,as shown below:


$ mris_anatomical_stats -b QEN001 lh

…

128449862392433752.588 0.8760.1230.026 
1496133.3/xxx…/subjects/QEN001/surf/lh.white


$

$ mris_anatomical_stats -b QEN001_old lh

…

128449862412295542.404 0.8350.1230.026 
1496133.3/xxx…/subjects/QEN001_old/surf/lh.white


The results shows that some of the stats numbers ( such as the 
numberof vertices) are the same, but the “average cortical thickness 
+-standard deviation (mm)”are different, and they differ quite a lot.


I have tried several subjects; some of them get the 
all-the-sameresults, some of them not.


I am sure the subjects and the corresponding images are the same. 
Arethese expected results?


Thanks!

Xiaojiang


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Re: [Freesurfer] Does FS guarantee the same results if run several times?

[Xiaojiang Yang]

External Email - Use Caution

Thank you Douglas and Tashrif!

 

Does this mean I should run recon-all for each subject several times, and
compute the average to get the more reliable thickness?

 

Can anyone else confirm this?  Thanks!

 

Xiaojiang

 

 

 
<https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu=from
:%22Billah%2C+Tashrif%22> Billah, Tashrif
<https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu=date
:20200417> Fri, 17 Apr 2020 08:34:14 -0700

Hi Xiaojiang and Douglas,
 
I think it is the attribute of having random initialization in the
registration 
steps. This slight discrepancy can also be observed with antsRegistration.
 
I don't know the exact algorithm FreeSurfer uses for registration though.
 
Best,
Tashrif

 

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[Freesurfer] Which autorecon uses -hippocampal-subfields flags?

[Billah, Tashrif]

Hi all,

Which of the three autorecons makes use of 
https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfields flags?
autorecon1, 2 , or 3?

My goal is to use the flag specifically with one of the three and not with 
recon-all in general as shown in the above page.

I do understand that the new version of the commands are 
https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldsAndNucleiOfAmygdala

Best,
Tashrif

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Re: [Freesurfer] Does FS guarantee the same results if run several times?

[Billah, Tashrif]

Hi Xiaojiang and Douglas,


I think it is the attribute of having random initialization in the registration 
steps. This slight discrepancy can also be observed with antsRegistration.

I don't know the exact algorithm FreeSurfer uses for registration though.

Best,
Tashrif

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Re: [Freesurfer] Does FS guarantee the same results if run several times?

[Xiaojiang Yang]

External Email - Use Caution

No. I just checked, they are not identical. Although some of numbers are the
same, many are different.

 

Xiaojiang

 

 

Are the other results identical? Eg, lh.aparc.stats?

 

On 4/17/2020 10:49 AM, Xiaojiang Yang wrote:

 

External Email - Use Caution

 

Dear Freeserfer developers,

 

I have run recon-all for a bunch of subjects on the same machine for several
times. When I use the "mris_anatomical_stats" to calculate the statistics
(specifically, I am interested in average cortical thickness), I found that
for the same subject I got different results, as shown below:

 

  $ mris_anatomical_stats -b QEN001 lh

 

.

 

  128449  86239  243375  2.588 0.876 0.123 0.026 1496   133.3
/xxx./subjects/QEN001/surf/lh.white

 

$

 

$ mris_anatomical_stats -b QEN001_old lh

 

   .

 

  128449  86241  229554  2.404 0.835 0.123 0.026 1496   133.3
/xxx./subjects/QEN001_old/surf/lh.white

 

The results shows that some of the stats numbers ( such as the number of
vertices) are the same, but the "average cortical thickness +- standard
deviation (mm)" are different, and they differ quite a lot.

 

I have tried several subjects; some of them get the all-the-same results,
some of them not.

 

I am sure the subjects and the corresponding images are the same. Are these
expected results?

 

Thanks!

 

Xiaojiang

 

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Re: [Freesurfer] Does FS guarantee the same results if run several times?

[Douglas N. Greve]

Are the other results identical? Eg, lh.aparc.stats?

On 4/17/2020 10:49 AM, Xiaojiang Yang wrote:


External Email - Use Caution

Dear Freeserfer developers,

I have run recon-all for a bunch of subjects on the same machine for 
several times. When I use the “mris_anatomical_stats” to calculate the 
statistics (specifically, I am interested in average cortical 
thickness), I found that for the same subject I got different results, 
as shown below:


  $ mris_anatomical_stats -b QEN001 lh

…

  128449  86239  243375  2.588 0.876 0.123 0.026 1496   133.3  
/xxx…/subjects/QEN001/surf/lh.white


$

$ mris_anatomical_stats -b QEN001_old lh

   …

  128449  86241  229554  2.404 0.835 0.123 0.026 1496   133.3 
/xxx…/subjects/QEN001_old/surf/lh.white


The results shows that some of the stats numbers ( such as the number 
of vertices) are the same, but the “average cortical thickness +- 
standard deviation (mm)” are different, and they differ quite a lot.


I have tried several subjects; some of them get the all-the-same 
results, some of them not.


I am sure the subjects and the corresponding images are the same. Are 
these expected results?


Thanks!

Xiaojiang


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Re: [Freesurfer] concatenate transformations

[Douglas N. Greve]

If these are tkregister style .dat files, you can try mri_matrix_multiply


On 4/16/2020 11:27 PM, Sam W wrote:


External Email - Use Caution

Hello!

I performed two registrations: diffusion-to-orig.dat and 
orig-to-rawavg.dat. Now I would like to concatenate the two 
transformation matrices into a diffusion-to-rawavg.dat. Is there a 
command in freesurfer that allows me to do that?


Best regards,
Sam

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[Freesurfer] Does FS guarantee the same results if run several times?

[Xiaojiang Yang]

External Email - Use Caution

Dear Freeserfer developers,

 

I have run recon-all for a bunch of subjects on the same machine for several
times. When I use the "mris_anatomical_stats" to calculate the statistics
(specifically, I am interested in average cortical thickness), I found that
for the same subject I got different results, as shown below:

 

$ mris_anatomical_stats -b QEN001 lh

  .

  128449  86239  243375  2.588 0.876 0.123 0.026 1496
133.3  /xxx./subjects/QEN001/surf/lh.white

$

$ mris_anatomical_stats -b QEN001_old lh

  .

  128449  86241  229554  2.404 0.835 0.123 0.026 1496
133.3 /xxx./subjects/QEN001_old/surf/lh.white

 

The results shows that some of the stats numbers ( such as the number of
vertices) are the same, but the "average cortical thickness +- standard
deviation (mm)" are different, and they differ quite a lot.

 

I have tried several subjects; some of them get the all-the-same results,
some of them not. 

 

I am sure the subjects and the corresponding images are the same. Are these
expected results?

 

Thanks!

Xiaojiang

 

 

 

 

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Re: [Freesurfer] Data on the Freesurfer surface

[Mason Wells]

External Email - Use Caution

Great, thanks again Bruce.
Doug, can you confirm this is the process for taking a filtered_func file and 
getting it onto the freesurfer surface ready for analysis?

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
 

On 17/04/2020, 15:32, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of 
Bruce Fischl"  wrote:

oh, then you probably want to use bbreg to register it and mri_vol2surf 
to sample it onto the surface. Doug is the expert on this and can 
add/correct if this is not the whole story :)

cheers
Bruce
On Fri, 17 Apr 2020, Mason 
Wells wrote:

>External Email - Use Caution
>
> Hi Bruce,
>
> The only pre-processing I have done is the motion correction, high pass 
filtering and distortion correction. So, as far as I know it is still in the 
volume and in the original functional space.
>
> Best wishes,
> 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
>
>
> On 17/04/2020, 15:11, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf 
of Bruce Fischl"  wrote:
>
>Hi Mason
>
>is your filtered_func file already sampled onto the surface or is it a
>volume?
>
>cheers
>Bruce
>On Fri, 17 Apr 2020, Mason Wells wrote:
>
>>
>> External Email - Use Caution
>>
>> Hi all,
>>
>>
>>
>> I am trying to use an analysis package that works on surface based 
data
>> (SamSrf). I have ran Feat and have a filtered_func file which is of 
course
>> the motion corrected/unwarped version of my EPI. However, I need 
some advice
>> on how to get these data onto the Freesurfer surface. I have found 
this
>> page, but I wanted to double check this is the most up-to-date 
pipeline. On
>> the page it suggests using the same DOF as used in Feat, I use BBR 
so this
>> seems a little redundant. Has anyone on these lists got any 
experience of
>> getting filtered_func onto the Freesurfer surface?
>>
>>
>>
>> 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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> Freesurfer@nmr.mgh.harvard.edu
> 

Re: [Freesurfer] Data on the Freesurfer surface

[Bruce Fischl]

oh, then you probably want to use bbreg to register it and mri_vol2surf 
to sample it onto the surface. Doug is the expert on this and can 
add/correct if this is not the whole story :)


cheers
Bruce
On Fri, 17 Apr 2020, Mason 
Wells wrote:



   External Email - Use Caution

Hi Bruce,

The only pre-processing I have done is the motion correction, high pass 
filtering and distortion correction. So, as far as I know it is still in the 
volume and in the original functional space.

Best wishes,
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


On 17/04/2020, 15:11, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Bruce 
Fischl"  wrote:

   Hi Mason

   is your filtered_func file already sampled onto the surface or is it a
   volume?

   cheers
   Bruce
   On Fri, 17 Apr 2020, Mason Wells wrote:

   >
   > External Email - Use Caution
   >
   > Hi all,
   >
   >
   >
   > I am trying to use an analysis package that works on surface based data
   > (SamSrf). I have ran Feat and have a filtered_func file which is of course
   > the motion corrected/unwarped version of my EPI. However, I need some 
advice
   > on how to get these data onto the Freesurfer surface. I have found this
   > page, but I wanted to double check this is the most up-to-date pipeline. On
   > the page it suggests using the same DOF as used in Feat, I use BBR so this
   > seems a little redundant. Has anyone on these lists got any experience of
   > getting filtered_func onto the Freesurfer surface?
   >
   >
   >
   > 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] Data on the Freesurfer surface

[Mason Wells]

External Email - Use Caution

Hi Bruce,

The only pre-processing I have done is the motion correction, high pass 
filtering and distortion correction. So, as far as I know it is still in the 
volume and in the original functional space.

Best wishes,
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
 

On 17/04/2020, 15:11, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of 
Bruce Fischl"  wrote:

Hi Mason

is your filtered_func file already sampled onto the surface or is it a 
volume?

cheers
Bruce
On Fri, 17 Apr 2020, Mason Wells wrote:

> 
> External Email - Use Caution
> 
> Hi all,
> 
>   
> 
> I am trying to use an analysis package that works on surface based data
> (SamSrf). I have ran Feat and have a filtered_func file which is of course
> the motion corrected/unwarped version of my EPI. However, I need some 
advice
> on how to get these data onto the Freesurfer surface. I have found this
> page, but I wanted to double check this is the most up-to-date pipeline. 
On
> the page it suggests using the same DOF as used in Feat, I use BBR so this
> seems a little redundant. Has anyone on these lists got any experience of
> getting filtered_func onto the Freesurfer surface?
> 
>  
> 
> 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] Data on the Freesurfer surface

[Bruce Fischl]

Hi Mason

is your filtered_func file already sampled onto the surface or is it a 
volume?


cheers
Bruce
On Fri, 17 Apr 2020, Mason Wells wrote:



External Email - Use Caution

Hi all,

  

I am trying to use an analysis package that works on surface based data
(SamSrf). I have ran Feat and have a filtered_func file which is of course
the motion corrected/unwarped version of my EPI. However, I need some advice
on how to get these data onto the Freesurfer surface. I have found this
page, but I wanted to double check this is the most up-to-date pipeline. On
the page it suggests using the same DOF as used in Feat, I use BBR so this
seems a little redundant. Has anyone on these lists got any experience of
getting filtered_func onto the Freesurfer surface?

 

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] convert gii to mgh/nii.gz (freesurfer surface)

[Bruce Fischl]

Hi Marina

can you include command line and full screen output (in text!) so we can 
understand what you mean by "it doesn't work". Also, note that 
.mgh/.nii.gz are volume formats, not surface ones, so you can't convert a 
surface to them. You will need to use our surface format


cheers
Bruce
On Fri, 17 Apr 
2020, Marina Fernández wrote:




External Email - Use Caution

Hi experts,
How can I convert a surface in .gii format to a surface in .mgh or nii.gz
format?

I tried with mris_convert but it doesn't work.


Best regards,
Marina

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[Freesurfer] Data on the Freesurfer surface

[Mason Wells]

External Email - Use Caution

Hi all,

I am trying to use an analysis package that works on surface based data 
(SamSrf). I have ran Feat and have a filtered_func file which is of course the 
motion corrected/unwarped version of my EPI. However, I need some advice on how 
to get these data onto the Freesurfer surface. I have found this 
page, but I wanted to double 
check this is the most up-to-date pipeline. On the page it suggests using the 
same DOF as used in Feat, I use BBR so this seems a little redundant. Has 
anyone on these lists got any experience of getting filtered_func onto the 
Freesurfer surface?

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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[Freesurfer] convert gii to mgh/nii.gz (freesurfer surface)

[Marina Fernández]

External Email - Use Caution

Hi experts,

How can I convert a surface in .gii format to a surface in .mgh or nii.gz
format?

I tried with mris_convert but it doesn't work.


Best regards,
Marina
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