Re: [Freesurfer] Building atlas by Xhemi: Segmentation fault (core dumped)

[Li-Zhen Chen]

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Not sure what is going wrong here. Try running
mri_annotation2label --subject myatlas.i3 --hemi lh --outdir 
/media/chenlz/Zixuans1/MRI_Data/Human_MRI/CCS_PrePro/myatlas.i3/make_cortex_label.tmp.8214
 
--annotation aparc.a2009s
Does it segfault in the same way?
Can you confirm that you are not running out of disk space?



On 4/15/2021 2:47 AM, Li-Zhen Chen wrote:
>
> External Email - Use Caution
>
> Hello Freesurfer Developer，
> I'm building my own symmetric atlas by Xhemi, something is wrong at 
> the final step(Make final iteration)
> Here is my code:
>
> make_average_subject --out myatlas.i3 --surf-reg myatlas.i2.sphere.reg 
> --subjects sub_01 sub_02 --xhemi --lh
>
> When I ran this code, a problem emerged. Here is part of the log:
>
> mris_seg2annot --seg 
> /media/chenlz/Zixuans1/MRI_Data/Human_MRI/CCS_PrePro/myatlas.i3/label/tmpdir.annot2std.8488/seg.vote.mgh
>  
> --ctab 
> /media/chenlz/Zixuans1/MRI_Data/Human_MRI/CCS_PrePro/myatlas.i3/label/tmpdir.annot2std.8488/seg.1.sub_01.xhemi.ctab
>  
> --s myatlas.i3 --hemi lh --o 
> /media/chenlz/Zixuans1/MRI_Data/Human_MRI/CCS_PrePro/myatlas.i3/label/lh.aparc.a2009s.annot
>
> $Id: mris_seg2annot.c,v 1.10 2014/11/15 00:07:19 greve Exp $
> cwd /media/chenlz/Zixuans1/MRI_Data/Human_MRI/CCS_PrePro/myatlas.i3
> cmdline mris_seg2annot --seg 
> /media/chenlz/Zixuans1/MRI_Data/Human_MRI/CCS_PrePro/myatlas.i3/label/tmpdir.annot2std.8488/seg.vote.mgh
>  
> --ctab 
> /media/chenlz/Zixuans1/MRI_Data/Human_MRI/CCS_PrePro/myatlas.i3/label/tmpdir.annot2std.8488/seg.1.sub_01.xhemi.ctab
>  
> --s myatlas.i3 --hemi lh --o 
> /media/chenlz/Zixuans1/MRI_Data/Human_MRI/CCS_PrePro/myatlas.i3/label/lh.aparc.a2009s.annot
>  
>
> sysname  Linux
> hostname chenlz-HP-ZHAN-99-Pro-G2-Microtower-PC
> machine  x86_64
> user     chenlz
> subject   myatlas.i3
> hemi      lh
> surfseg 
> /media/chenlz/Zixuans1/MRI_Data/Human_MRI/CCS_PrePro/myatlas.i3/label/tmpdir.annot2std.8488/seg.vote.mgh
> ctab 
>  
> /media/chenlz/Zixuans1/MRI_Data/Human_MRI/CCS_PrePro/myatlas.i3/label/tmpdir.annot2std.8488/seg.1.sub_01.xhemi.ctab
> annotfile 
> /media/chenlz/Zixuans1/MRI_Data/Human_MRI/CCS_PrePro/myatlas.i3/label/lh.aparc.a2009s.annot
> Reading surface seg 
> /media/chenlz/Zixuans1/MRI_Data/Human_MRI/CCS_PrePro/myatlas.i3/label/tmpdir.annot2std.8488/seg.vote.mgh
> Reading surface 
> /media/chenlz/Zixuans1/MRI_Data/Human_MRI/CCS_PrePro/myatlas.i3/surf/lh.white
> Reading ctab 
> /media/chenlz/Zixuans1/MRI_Data/Human_MRI/CCS_PrePro/myatlas.i3/label/tmpdir.annot2std.8488/seg.1.sub_01.xhemi.ctab
> Writing annot to 
> /media/chenlz/Zixuans1/MRI_Data/Human_MRI/CCS_PrePro/myatlas.i3/label/lh.aparc.a2009s.annot
>
> Annot2std-Run-Time-Sec 16
> annot2std Done
> mri_annotation2label --subject myatlas.i3 --hemi lh --outdir 
> /media/chenlz/Zixuans1/MRI_Data/Human_MRI/CCS_PrePro/myatlas.i3/make_cortex_label.tmp.8214
>  
> --annotation aparc.a2009s
> subject = myatlas.i3
> annotation = aparc.a2009s
> hemi = lh
> outdir = 
> /media/chenlz/Zixuans1/MRI_Data/Human_MRI/CCS_PrePro/myatlas.i3/make_cortex_label.tmp.8214
> surface   = white
>
> Reading surface
>  /media/chenlz/Zixuans1/MRI_Data/Human_MRI/CCS_PrePro/myatlas.i3/surf/lh.white
> Loading annotations from 
> /media/chenlz/Zixuans1/MRI_Data/Human_MRI/CCS_PrePro/myatlas.i3/label/lh.aparc.a2009s.annot
> reading colortable from annotation file...
> colortable with 11176 entries read (originally 
> /media/chenlz/Zixuans1/MRI_Data/Human_MRI/CCS_PrePro/myatlas.i3/label/tmpdir.annot2std.8488/seg.1.sub_01.xhemi.ctab)
> Segmentation fault (core dumped)
> ERROR: make_average_surface
>
> I run Freesurfer 6.0 on Ubuntu 18.04. I've tried to rerun my script 
> several times but I can't figure this problem out. What could be the 
> possible reasons? Any answer will be appreciated!
>
> Kind regards,
> Jewel
>
>
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Re: [Freesurfer] question about lesion segmentation using samseg

[Iglesias Gonzalez, Juan E.]

Yes, it is possible, but the inferior contrasts of these sequences compared to 
FLAIR will likely yield noisier results.


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



From:  on behalf of Ritobrato Datta 

Reply-To: Freesurfer support list 
Date: Monday, April 19, 2021 at 16:54
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: [Freesurfer] question about lesion segmentation using samseg


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Hi All,

I have T1w MPRAGE, T2w and PD images but I dont have FLAIR images from a 
Multiple Sclerosis study. Can I use samseg to segment the lesions ?

Can you please suggest ?

Many thanks

Ri


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[Freesurfer] question about lesion segmentation using samseg

[Ritobrato Datta]

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Hi All,

I have T1w MPRAGE, T2w and PD images but I dont have FLAIR images from
a Multiple Sclerosis study. Can I use samseg to segment the lesions ?

Can you please suggest ?

Many thanks

Ri
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Re: [Freesurfer] problem running last step longitudinal analysis

[Zeng, Qi]

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Hi Douglas,

I found the aseg.presurf.mgz for all cross sessions and base using version
6.0.

Best,
Qi

On Sun, Apr 18, 2021 at 10:43 PM Douglas N. Greve 
wrote:

> Check each of your cross time points to make sure that all have an
> aseg.presurf.mgz.
>
> On 4/16/2021 4:35 PM, Zeng, Qi wrote:
>
> External Email - Use Caution
> Hi Experts,
>
> I am running the last step (-long) for a longitudinal analysis, However,
> encountering an error message saying: "error: ERROR: number of asegs and
> norm volumes do not match" for all the subjects I run this time. A similar
> problem has been reported before as the following link. The answer to the
> question is 'Freesufer version too old'. I have been following the exact
> same steps two months ago for my last cohort and it was fine. However, this
> time all the subjects reporting error messages (attaching error.log).
> *MailScanner has detected a possible fraud attempt from
> "secure-web.cisco.com" claiming to be* Re: [Freesurfer]
> mri_fuse_segmentations error in longitudinal stream (mail-archive.com)
> 
> My system: x86_64 GNU/Linux
> Freesufer version: freesurfer/6.0.0
> attached the error.log
>
> Best,
> Qi
>
>
>
>
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-- 

Ph.D. candidate
Icahn School of Medicine at Mount Sinai
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Re: [Freesurfer] Tracula group analysis in freesurfer

[Yendiki, Anastasia]

Hi Qi - This is documented here:
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TraculaStatistics

Anastasia.

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Zeng, Qi 

Sent: Monday, April 19, 2021 1:40 PM
To: Freesurfer support list 
Subject: [Freesurfer] Tracula group analysis in freesurfer


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Hi Experts,

I understand there is surface-based group analysis in Freesurfer, which is for 
thickness, curvature, volume and etc. Is there a group analysis for DTI tracula 
results? Any links to recommend to conduct the analysis?
Thank you so much!

Best,
Qi

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[Freesurfer] Tracula group analysis in freesurfer

[Zeng, Qi]

External Email - Use Caution

Hi Experts,

I understand there is surface-based group analysis in Freesurfer, which is
for thickness, curvature, volume and etc. Is there a group analysis for DTI
tracula results? Any links to recommend to conduct the analysis?
Thank you so much!

Best,
Qi
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Re: [Freesurfer] recon_all subcortical volume adjuested eTIV

[Jaime Gomez]

External Email - Use Caution

Thank you Douglas for the answer. Could you be more explicit?
So, once you have the aseg.stats you need to run which command with --etiv-only?


On Mon, Apr 19, 2021 at 4:00 PM Douglas N. Greve 
wrote:

> It is not done. If you are running asegstats2table, you can have it
> perform the correction by adding --etiv to the command line
>
> On 4/19/2021 7:41 AM, Jaime Gomez wrote:
>
> External Email - Use Caution
>
> Hi,
>
> Does the asegs.stats produced by recon_all have the volume estimates of
> subcortical structures adjusted by the eTIV?
> I want to understand the effect of sex in the segmented structures. Should
> normalize the volumes of aseg.stats (Vol/eTIV) or is already done in
> recon_all?
> Thank you!
>
>
>
>
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Re: [Freesurfer] Native volume to fs_average surface

[Fischl, Bruce]

Hi Mason

Pretty much all surfaces of a single subject/hemi have the same topology 
(number of vertices/faces/etc...), so if you map to any of them you map to all 
of them.

As for the syntax for doing this in one step I defer to Doug. Doing it in 2 
steps I would use the white or pial surface to go vol->surf, then the 
sphere.reg to go surf->surf
Bruce

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Mason Wells
Sent: Monday, April 19, 2021 12:16 PM
To: Freesurfer support list ; Greve, Douglas 
N.,Ph.D. 
Subject: Re: [Freesurfer] Native volume to fs_average surface


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Hi Bruce,

No problem. I tried to run vol2surf using the following command, but it doesn't 
run.

  *   mri_vol2surf --mov filtered_func_data.nii.gz --hemi rh --reg 
/home/masontwells/Documents/freesurfer/subjects/sub-0006/surf/rh.sphere.reg 
--trgsubject fsaverage --projfrac 0.5 --o rh_func_fsa.mgh
I get the following error:

ltaReadRegisterDat: could not read 
/home/masontwells/Documents/freesurfer/subjects/sub-0006/surf/rh.sphere.reg
No such file or directory

Doug, am I missing something obvious here?

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


From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Fischl, Bruce 
mailto:bfis...@mgh.harvard.edu>>
Sent: Monday, April 19, 2021 5:06 PM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Native volume to fs_average surface


Hi Mason



I should have read to the end of my inbox before replying - Doug is the expert 
in this so I would definitely follow his advise over mine. In general the 
native->average surface transform is stored in the ?h.sphere.reg files



Cheers

Bruce



From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Mason Wells
Sent: Monday, April 19, 2021 11:50 AM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Native volume to fs_average surface



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Hi Bruce,



Thanks for the reply. Would you agree this is the optimal way to move from 
native vol to fs_average? I am confident with moving to native surface. My 
current pipeline for this is as follows. Anything here stick out that you think 
I should change?



bbregister to register the native functional volume data to the T1

  *   bbregister --s sub-0006 --feat 
/media/HDD/ICA_SSD_files/GroupICA/PPT6_PreProc.feat/ --init-coreg

Resampling to the native surface using the following command using the 
transformation matrix generated by bbregister:

  *   mri_vol2surf --src filtered_func_data.nii.gz --out 
rh_filtered_func_native.mgh --srcreg reg/freesurfer/anat2exf.register.dat 
--hemi rh --projfrac 0.5 --out_type mgh

I am not sure how to move from native surface to group average surface since I 
do not generate an appropriate transformation matrix to move from native 
surface to average surface in my pipeline. Can you offer any advice on this?



Cheers,

Mason





From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Fischl, Bruce 
mailto:bfis...@mgh.harvard.edu>>
Sent: Monday, April 19, 2021 4:38 PM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>; 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Native volume to fs_average surface



Hi Mason



Yes, you can use mri_vol2surf to go native vol->native surf, then mri_surf2surf 
to go native surf->group surf



Cheers

Bruce



From: 

Re: [Freesurfer] Native volume to fs_average surface

[Mason Wells]

External Email - Use Caution

Hi Bruce,

No problem. I tried to run vol2surf using the following command, but it doesn't 
run.

  *   mri_vol2surf --mov filtered_func_data.nii.gz --hemi rh --reg 
/home/masontwells/Documents/freesurfer/subjects/sub-0006/surf/rh.sphere.reg 
--trgsubject fsaverage --projfrac 0.5 --o rh_func_fsa.mgh

I get the following error:

ltaReadRegisterDat: could not read 
/home/masontwells/Documents/freesurfer/subjects/sub-0006/surf/rh.sphere.reg
No such file or directory

Doug, am I missing something obvious here?

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



From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Fischl, Bruce 

Sent: Monday, April 19, 2021 5:06 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Native volume to fs_average surface


Hi Mason



I should have read to the end of my inbox before replying – Doug is the expert 
in this so I would definitely follow his advise over mine. In general the 
native->average surface transform is stored in the ?h.sphere.reg files



Cheers

Bruce



From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Mason Wells
Sent: Monday, April 19, 2021 11:50 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Native volume to fs_average surface



External Email - Use Caution

External Email - Use Caution

Hi Bruce,



Thanks for the reply. Would you agree this is the optimal way to move from 
native vol to fs_average? I am confident with moving to native surface. My 
current pipeline for this is as follows. Anything here stick out that you think 
I should change?



bbregister to register the native functional volume data to the T1

  *   bbregister --s sub-0006 --feat 
/media/HDD/ICA_SSD_files/GroupICA/PPT6_PreProc.feat/ --init-coreg

Resampling to the native surface using the following command using the 
transformation matrix generated by bbregister:

  *   mri_vol2surf --src filtered_func_data.nii.gz --out 
rh_filtered_func_native.mgh --srcreg reg/freesurfer/anat2exf.register.dat 
--hemi rh --projfrac 0.5 --out_type mgh

I am not sure how to move from native surface to group average surface since I 
do not generate an appropriate transformation matrix to move from native 
surface to average surface in my pipeline. Can you offer any advice on this?



Cheers,

Mason





From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Fischl, Bruce 
mailto:bfis...@mgh.harvard.edu>>
Sent: Monday, April 19, 2021 4:38 PM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>; 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Native volume to fs_average surface



Hi Mason



Yes, you can use mri_vol2surf to go native vol->native surf, then mri_surf2surf 
to go native surf->group surf



Cheers

Bruce



From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Mason Wells
Sent: Monday, April 19, 2021 5:45 AM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>; 
freesurfer-boun...@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Native volume to fs_average surface



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HI Matt,



Thanks for the reply. Are you 

Re: [Freesurfer] Native volume to fs_average surface

[Fischl, Bruce]

Hi Mason

I should have read to the end of my inbox before replying - Doug is the expert 
in this so I would definitely follow his advise over mine. In general the 
native->average surface transform is stored in the ?h.sphere.reg files

Cheers
Bruce

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Mason Wells
Sent: Monday, April 19, 2021 11:50 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Native volume to fs_average surface


External Email - Use Caution

External Email - Use Caution
Hi Bruce,

Thanks for the reply. Would you agree this is the optimal way to move from 
native vol to fs_average? I am confident with moving to native surface. My 
current pipeline for this is as follows. Anything here stick out that you think 
I should change?

bbregister to register the native functional volume data to the T1

  *   bbregister --s sub-0006 --feat 
/media/HDD/ICA_SSD_files/GroupICA/PPT6_PreProc.feat/ --init-coreg
Resampling to the native surface using the following command using the 
transformation matrix generated by bbregister:

  *   mri_vol2surf --src filtered_func_data.nii.gz --out 
rh_filtered_func_native.mgh --srcreg reg/freesurfer/anat2exf.register.dat 
--hemi rh --projfrac 0.5 --out_type mgh
I am not sure how to move from native surface to group average surface since I 
do not generate an appropriate transformation matrix to move from native 
surface to average surface in my pipeline. Can you offer any advice on this?

Cheers,
Mason


From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Fischl, Bruce 
mailto:bfis...@mgh.harvard.edu>>
Sent: Monday, April 19, 2021 4:38 PM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>; 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Native volume to fs_average surface


Hi Mason



Yes, you can use mri_vol2surf to go native vol->native surf, then mri_surf2surf 
to go native surf->group surf



Cheers

Bruce



From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Mason Wells
Sent: Monday, April 19, 2021 5:45 AM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>; 
freesurfer-boun...@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Native volume to fs_average surface



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External Email - Use Caution

HI Matt,



Thanks for the reply. Are you suggesting I go native volume > native surface > 
fs_average? If so, can you recommend the best can I go from native to group 
average surface?



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





From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Glasser, Matthew mailto:glass...@wustl.edu>>
Sent: Monday, April 19, 2021 10:27 AM
To: Freesurfer support list 

Re: [Freesurfer] Abormally high foldind index

[Fischl, Bruce]

Hi Ellen
The folding index is pretty sensitive to kmax, which can be huge for tiny 
antennae and such. It may not be the right measure for what you are trying to 
capture.  You can always compute the curvatures with mris_curvature then 
overlay them and see if there are outlier values, or find the max in matlab or 
something, but in the end you may want to quantify things differently. 

Cheers
Bruce

-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Ellen Ji
Sent: Monday, April 19, 2021 9:06 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Abormally high foldind index

External Email - Use Caution

Hi Bruce,

I looked at the pial surfaces and WM by running this for the outlier
subjects:

freeview -v subject1/mri/T1.mgz \
subject1/mri/brainmask.mgz \
-f subject1/surf/lh.white:edgecolor=yellow \ 
subject1/surf/lh.pial:edgecolor=red \ subject1/surf/rh.white:edgecolor=yellow \ 
subject1/surf/rh.pial:edgecolor=red

Nothing stood out to me. Is there anything else you suggest I investigate? What 
could explain a negative folding index?

Best,
Ellen



On 3/31/2021 12:18 AM, Fischl, Bruce wrote:
> Hi Ellen
>
> It is certainly possible. Have you looked at the surfaces for those subjects?
>
> Cheers
> Bruce
>
> -Original Message-
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>  On Behalf Of Ellen Ji
> Sent: Tuesday, March 30, 2021 5:44 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: [Freesurfer] Abormally high foldind index
>
>  External Email - Use Caution
>
> Dear Experts,
>
> While the majority of our subjects have a folding index between 5-30, there 
> are a couple of *extreme* outliers in the thousands or even negative.
>
> Could this hint that a particular part of recon-all failed and should be 
> rerun?
>
> Thank you for your interpretation and advice!
>
> -Ellen
>
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> wC4XlmxiH5LNWhX43zib-VJ7Mr-bW9V9ppd-SPmpku_6426YUSHSdKGVDd9A2lLYMsb6wW
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Re: [Freesurfer] Autorecon1 failure

[Abdollahi, Shervin (NIH/NINDS) [C]]

External Email - Use Caution

What is your advice for me now? Should I abandon the approach or is there 
anyway to dig deeper into it and solve the error?

From: "Douglas N. Greve" 
Reply-To: Freesurfer support list 
Date: Sunday, April 18, 2021 at 10:21 PM
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: Re: [Freesurfer] Autorecon1 failure

No, we have not talked
On 4/16/2021 12:20 PM, Abdollahi, Shervin (NIH/NINDS) [C] wrote:

External Email - Use Caution
So yes running it from scratch would work. But I was trying to implement 
fmriprep approach in which they have chosen the optimal approaches for 
skull-stripping or intensity normalization via other applications like ANTs or 
FSL and they imported those to be used in Freesurfer instead of internally 
calculated skull-strip brain mask (brainmask.mgz).  The last step of 
autorecon-1 is where the skull stripping needs to be off and that’s where it 
fails, cause its waiting for that brainmask.mgz and cant find it. Has there 
been any collaboration between freesurfer and fmriprep people on this matter?

Thanks
Shervin

From: "Douglas N. Greve" 
Reply-To: Freesurfer support list 

Date: Friday, April 16, 2021 at 11:08 AM
To: "freesurfer@nmr.mgh.harvard.edu" 

Subject: Re: [Freesurfer] Autorecon1 failure

If you run it from scratch (recon-all -s subject -all), does it work? If you 
are going to pick and chose which options to apply, then there is a high risk 
of missing steps
On 4/14/2021 2:23 PM, Abdollahi, Shervin (NIH/NINDS) [C] wrote:

External Email - Use Caution
Hi Douglas, Sure, here is the copy of recon-all.log

From: "Douglas N. Greve" 
Reply-To: Freesurfer support list 

Date: Wednesday, April 14, 2021 at 10:32 AM
To: "freesurfer@nmr.mgh.harvard.edu" 

Subject: Re: [Freesurfer] Autorecon1 failure

Sorry, can you resend the recon-all.log file?
On 4/7/2021 8:45 AM, Abdollahi, Shervin (NIH/NINDS) [C] wrote:

External Email - Use Caution


From: "Abdollahi, Shervin (NIH/NINDS) [C]" 

Date: Thursday, March 18, 2021 at 12:42 PM
To: "freesurfer@nmr.mgh.harvard.edu" 

Subject: Autorecon1 failure

Hello Freesurfer Developers,

am trying to use run freesurfer that is configured inside 
smriprep.workflow.anatomical.py under init_anat_preproc_wf pipeline. this 
workflow, does the following:


  1.  T1w reference: realigning and then averaging T1w images
  2.  Brain Extraction and INU (bias field) correction (antsBrainExtraction.sh)
  3.  Brian tissue segmentation (@fsl_fast)
  4.  Spatial normalization to standard space (antsRegistration)
  5.  Surface reconstruction with Freesurfer

When it gets to step 5, it takes skull-stripped t1, ants_segm, and 
bias_corrected image to use in freesurfer recon-all command. In the surface 
reconstruction section, it starts by running the following command:

recon-all -autorecon1
-i /path-to /sub-03_ses-20140624_T1w.nii
-T2 /path-to/sub-03_ses-20140624_T2w.nii
-noskullstrip
-hires
-openmp 1
-subjid sub-03
-sd /Users/abdollahis2/Desktop/fcd_nipype/derivatives/freesurfer
-expert 
/Users/abdollahis2/Desktop/fcd_nipype/single_subject_03/anat_preproc_wf/surface_recon_wf/_subject_id_03/autorecon1/expert.opts

And surely soon, it gives me an error that it can not read mgh file 
(brainmask.mgz). looking into freesurfer/sub-03/mri directory I can see that 
brainmask.mgz is not created and I am not sure if this is because the option 
-noskullstrip was used? I have attached the recon-all.log file. I would 
appreciate any suggestion on how to debug this problem.


  1.  Freesurfer version: 7.1.1 (freesurfer-darwin-macOS-7.1.1-20200811-8b40551)
  2.  Platform: macOS Catalina, Version 10.15.7
  3.  uname -a: Darwin ndsd-eeg-cedar 19.6.0 Darwin Kernel Version 19.6.0: Tue 
Jan 12 22:13:05 PST 2021; root:xnu-6153.141.16~1/RELEASE_X86_64 x86_64
  4.  Recon-all.log: see attached







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Re: [Freesurfer] Native volume to fs_average surface

[Mason Wells]

External Email - Use Caution

Hi Bruce,

Thanks for the reply. Would you agree this is the optimal way to move from 
native vol to fs_average? I am confident with moving to native surface. My 
current pipeline for this is as follows. Anything here stick out that you think 
I should change?

bbregister to register the native functional volume data to the T1

  *   bbregister --s sub-0006 --feat 
/media/HDD/ICA_SSD_files/GroupICA/PPT6_PreProc.feat/ --init-coreg

Resampling to the native surface using the following command using the 
transformation matrix generated by bbregister:

  *   mri_vol2surf --src filtered_func_data.nii.gz --out 
rh_filtered_func_native.mgh --srcreg reg/freesurfer/anat2exf.register.dat 
--hemi rh --projfrac 0.5 --out_type mgh

I am not sure how to move from native surface to group average surface since I 
do not generate an appropriate transformation matrix to move from native 
surface to average surface in my pipeline. Can you offer any advice on this?

Cheers,
Mason


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Fischl, Bruce 

Sent: Monday, April 19, 2021 4:38 PM
To: Freesurfer support list ; 
freesurfer-boun...@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] Native volume to fs_average surface


Hi Mason



Yes, you can use mri_vol2surf to go native vol->native surf, then mri_surf2surf 
to go native surf->group surf



Cheers

Bruce



From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Mason Wells
Sent: Monday, April 19, 2021 5:45 AM
To: Freesurfer support list ; 
freesurfer-boun...@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Native volume to fs_average surface



External Email - Use Caution

External Email - Use Caution

HI Matt,



Thanks for the reply. Are you suggesting I go native volume > native surface > 
fs_average? If so, can you recommend the best can I go from native to group 
average surface?



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





From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Glasser, Matthew mailto:glass...@wustl.edu>>
Sent: Monday, April 19, 2021 10:27 AM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>; 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Native volume to fs_average surface



External email to Cardiff University - Take care when replying/opening 
attachments or links.

Nid ebost mewnol o Brifysgol Caerdydd yw hwn - Cymerwch ofal wrth ateb/agor 
atodiadau neu ddolenni.



External Email - Use Caution

You would do that through the subject’s own surface.  It does not work very 
well to map data directly from the volume onto group average surfaces (see e.g. 
Coalson et al., 2018 PNAS).



Matt.



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: Monday, April 19, 2021 at 4:23 AM
To: Freesurfer support list 

Re: [Freesurfer] Native volume to fs_average surface

[Fischl, Bruce]

Hi Mason

Yes, you can use mri_vol2surf to go native vol->native surf, then mri_surf2surf 
to go native surf->group surf

Cheers
Bruce

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Mason Wells
Sent: Monday, April 19, 2021 5:45 AM
To: Freesurfer support list ; 
freesurfer-boun...@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Native volume to fs_average surface


External Email - Use Caution

External Email - Use Caution
HI Matt,

Thanks for the reply. Are you suggesting I go native volume > native surface > 
fs_average? If so, can you recommend the best can I go from native to group 
average surface?


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


From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Glasser, Matthew mailto:glass...@wustl.edu>>
Sent: Monday, April 19, 2021 10:27 AM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>; 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Native volume to fs_average surface

External email to Cardiff University - Take care when replying/opening 
attachments or links.
Nid ebost mewnol o Brifysgol Caerdydd yw hwn - Cymerwch ofal wrth ateb/agor 
atodiadau neu ddolenni.


External Email - Use Caution

You would do that through the subject's own surface.  It does not work very 
well to map data directly from the volume onto group average surfaces (see e.g. 
Coalson et al., 2018 PNAS).



Matt.



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: Monday, April 19, 2021 at 4:23 AM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>, 
"freesurfer-boun...@nmr.mgh.harvard.edu"
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] Native volume to fs_average surface





External Email - Use Caution

Hi experts,



I have some fMRI data that I have pre-processed in Feat. I want to resample a 
single subject's data to the fs_average surface but unsure of the most optimal 
way of doing this. At present I am warping the functional data to the MNI brain 
in the volume (using FSL's applywarp) and then resampling to fs_average using 
the following command.

  *   mri_vol2surf --src filtered_func_MNI.nii --out filtered_func_surf.mgh 
--hemi rh --mni152reg



My question is whether you think this is the most appropriate approach, and/or 
if there is way to move directly from native volume to fs_average surface 
without needing to go via MNI volume?



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 

Re: [Freesurfer] Native volume to fs_average surface

[Mason Wells]

External Email - Use Caution

Hi Doug,

I have the data both in its native functional space (e.g. filtered_func_data). 
I also run bbregister so have the transformation matrix to register it to the 
T1 (e.g. anat2exf.register.dat). Do you suggest running vol2surf on the 
filtered_func_data file? Also is reg.lta generated by FreeSurfer during 
recon-all or do I need to generate this file? I would like to end up with the 
filtered_func_data file on the fs_average surrface, which would require the 
file format to be .mgh to load this an overlay on Freeview, right?


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



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

Sent: Monday, April 19, 2021 2:57 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] Native volume to fs_average surface

External email to Cardiff University - Take care when replying/opening 
attachments or links.
Nid ebost mewnol o Brifysgol Caerdydd yw hwn - Cymerwch ofal wrth ateb/agor 
atodiadau neu ddolenni.


If you have the data in the native functional space, then just
mri_vol2surf --mov func.nii --hemi rh --reg reg.lta --trgsubject fsaverage 
--projfrac 0.5 --o rh.func.fsa.mgz


On 4/19/2021 5:23 AM, Mason Wells wrote:

External Email - Use Caution

External Email - Use Caution

Hi experts,

I have some fMRI data that I have pre-processed in Feat. I want to resample a 
single subject's data to the fs_average surface but unsure of the most optimal 
way of doing this. At present I am warping the functional data to the MNI brain 
in the volume (using FSL's applywarp) and then resampling to fs_average using 
the following command.

  *   mri_vol2surf --src filtered_func_MNI.nii --out filtered_func_surf.mgh 
--hemi rh --mni152reg

My question is whether you think this is the most appropriate approach, and/or 
if there is way to move directly from native volume to fs_average surface 
without needing to go via MNI volume?

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 

Re: [Freesurfer] Native volume to fs_average surface

[Mason Wells]

External Email - Use Caution

I am using FreeSurfer formatted data, yes. I believe I am mapping to the 
individual surface correctly, but can I double check you agree?

I am running bbregister to register the functional data to the T1 which appears 
to do a good job:

  *   bbregister --s sub-0006 --feat 
/media/HDD/ICA_SSD_files/GroupICA/PPT6_PreProc.feat/ --init-coreg

I then resampling to the surface using the following command using the 
transformation matrix generated by bbregister:

  *   mri_vol2surf --src filtered_func_data.nii.gz --out 
rh_filtered_func_native.mgh --srcreg reg/freesurfer/anat2exf.register.dat 
--hemi rh --projfrac 0.5 --out_type mgh

If suggest a different route to do this, I would appreciate your advice.

And if anyone else on the list can offer some advice on how to move from native 
surface to fs_average surface that would be great. I assume it will be via 
mri_surf2surf, but unsure as to correct flags to use to do this correctly.



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



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

Sent: Monday, April 19, 2021 10:51 AM
To: Freesurfer support list ; 
freesurfer-boun...@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] Native volume to fs_average surface


External Email - Use Caution

What is most important is that you map to your individual’s surface (whether 
that is in subject’s physical space or MNI space doesn’t matter so much).  If 
you are using FreeSurfer formatted data, others can suggest how to do this.  
With NIFTI/GIFTI/CIFTI, it can be accomplished with wb_command 
-volume-to-surface-mapping and wb_command -metric-resampling among other things 
(e.g. see MailScanner has detected a possible fraud attempt from 
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Matt.



From:  on behalf of Mason Wells 

Reply-To: Freesurfer support list 
Date: Monday, April 19, 2021 at 4:45 AM
To: 

[Freesurfer] FLAIR image analysis

[Jindal, Saurabh]

External Email - Use Caution

Hi experts,

Could we analyze FLAIR images using freesurfer without having T1 images?

Saurabh


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Re: [Freesurfer] Autorecon1 failure

[Douglas N. Greve]

You should talk to them

On 4/19/2021 7:52 AM, Abdollahi, Shervin (NIH/NINDS) [C] wrote:


External Email - Use Caution

What is your advice for me now? Should I abandon the approach or is 
there anyway to dig deeper into it and solve the error?


*From: *"Douglas N. Greve" 
*Reply-To: *Freesurfer support list 
*Date: *Sunday, April 18, 2021 at 10:21 PM
*To: *"freesurfer@nmr.mgh.harvard.edu" 
*Subject: *Re: [Freesurfer] Autorecon1 failure

No, we have not talked

On 4/16/2021 12:20 PM, Abdollahi, Shervin (NIH/NINDS) [C] wrote:

*External Email - Use Caution *

So yes running it from scratch would work. But I was trying to
implement fmriprep approach in which they have chosen the optimal
approaches for skull-stripping or intensity normalization via
other applications like ANTs or FSL and they imported those to be
used in Freesurfer instead of internally calculated skull-strip
brain mask (brainmask.mgz).  The last step of autorecon-1 is where
the skull stripping needs to be off and that’s where it fails,
cause its waiting for that brainmask.mgz and cant find it. Has
there been any collaboration between freesurfer and fmriprep
people on this matter?

Thanks

Shervin

*From: *"Douglas N. Greve" 

*Reply-To: *Freesurfer support list


*Date: *Friday, April 16, 2021 at 11:08 AM
*To: *"freesurfer@nmr.mgh.harvard.edu"



*Subject: *Re: [Freesurfer] Autorecon1 failure

If you run it from scratch (recon-all -s subject -all), does it
work? If you are going to pick and chose which options to apply,
then there is a high risk of missing steps

On 4/14/2021 2:23 PM, Abdollahi, Shervin (NIH/NINDS) [C] wrote:

*External Email - Use Caution *

Hi Douglas, Sure, here is the copy of recon-all.log

*From: *"Douglas N. Greve" 

*Reply-To: *Freesurfer support list


*Date: *Wednesday, April 14, 2021 at 10:32 AM
*To: *"freesurfer@nmr.mgh.harvard.edu"



*Subject: *Re: [Freesurfer] Autorecon1 failure

Sorry, can you resend the recon-all.log file?

On 4/7/2021 8:45 AM, Abdollahi, Shervin (NIH/NINDS) [C] wrote:

*External Email - Use Caution *

*From: *"Abdollahi, Shervin (NIH/NINDS) [C]"
 
*Date: *Thursday, March 18, 2021 at 12:42 PM
*To: *"freesurfer@nmr.mgh.harvard.edu"



*Subject: *Autorecon1 failure

Hello Freesurfer Developers,

am trying to use run freesurfer that is configured inside
smriprep.workflow.anatomical.py under init_anat_preproc_wf
pipeline. this workflow, does the following:

 1. T1w reference: realigning and then averaging T1w images
 2. Brain Extraction and INU (bias field) correction
(antsBrainExtraction.sh)
 3. Brian tissue segmentation (@fsl_fast)
 4. Spatial normalization to standard space (antsRegistration)
 5. Surface reconstruction with Freesurfer

When it gets to step 5, it takes skull-stripped t1,
ants_segm, and bias_corrected image to use in freesurfer
recon-all command. In the surface reconstruction section,
it starts by running the following command:

recon-all -autorecon1

-i /path-to /sub-03_ses-20140624_T1w.nii

-T2 /path-to/sub-03_ses-20140624_T2w.nii

-noskullstrip

-hires

-openmp 1

-subjid sub-03

-sd
/Users/abdollahis2/Desktop/fcd_nipype/derivatives/freesurfer

-expert

/Users/abdollahis2/Desktop/fcd_nipype/single_subject_03/anat_preproc_wf/surface_recon_wf/_subject_id_03/autorecon1/expert.opts

And surely soon, it gives me an error that it can not read
mgh file (brainmask.mgz). looking into
freesurfer/sub-03/mri directory I can see that
brainmask.mgz is not created and I am not sure if this is
because the option -noskullstrip was used? I have attached
the recon-all.log file. I would appreciate any suggestion
on how to debug this problem.

 1. Freesurfer version: 7.1.1
(freesurfer-darwin-macOS-7.1.1-20200811-8b40551)
 2. Platform: macOS Catalina, Version 10.15.7
 3. uname -a: Darwin 

Re: [Freesurfer] recon_all subcortical volume adjuested eTIV

[Douglas N. Greve]

It is not done. If you are running asegstats2table, you can have it 
perform the correction by adding --etiv to the command line


On 4/19/2021 7:41 AM, Jaime Gomez wrote:


External Email - Use Caution


Hi,

Does the asegs.stats produced by recon_all have the volume estimates 
of subcortical structures adjusted by the eTIV?
I want to understand the effect of sex in the segmented structures. 
Should normalize the volumes of aseg.stats (Vol/eTIV) or is already 
done in recon_all?

Thank you!




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Re: [Freesurfer] Native volume to fs_average surface

[Douglas N. Greve]

If you have the data in the native functional space, then just
mri_vol2surf --mov func.nii --hemi rh --reg reg.lta --trgsubject 
fsaverage --projfrac 0.5 --o rh.func.fsa.mgz



On 4/19/2021 5:23 AM, Mason Wells wrote:


External Email - Use Caution

External Email - Use Caution

Hi experts,

I have some fMRI data that I have pre-processed in Feat. I want to 
resample a single subject's data to the fs_average surface but unsure 
of the most optimal way of doing this. At present I am warping the 
functional data to the MNI brain in the volume (using FSL's applywarp) 
and then resampling to fs_average using the following command.


  * mri_vol2surf --src filtered_func_MNI.nii --out
filtered_func_surf.mgh --hemi rh --mni152reg


My question is whether you think this is the most appropriate 
approach, and/or if there is way to move directly from native volume 
to fs_average surface without needing to go via MNI volume?


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



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Re: [Freesurfer] Abormally high foldind index

[Ellen Ji]

External Email - Use Caution

Hi Bruce,

I looked at the pial surfaces and WM by running this for the outlier 
subjects:

freeview -v subject1/mri/T1.mgz \
subject1/mri/brainmask.mgz \
-f subject1/surf/lh.white:edgecolor=yellow \
subject1/surf/lh.pial:edgecolor=red \
subject1/surf/rh.white:edgecolor=yellow \
subject1/surf/rh.pial:edgecolor=red

Nothing stood out to me. Is there anything else you suggest I 
investigate? What could explain a negative folding index?

Best,
Ellen



On 3/31/2021 12:18 AM, Fischl, Bruce wrote:
> Hi Ellen
>
> It is certainly possible. Have you looked at the surfaces for those subjects?
>
> Cheers
> Bruce
>
> -Original Message-
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>  On Behalf Of Ellen Ji
> Sent: Tuesday, March 30, 2021 5:44 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: [Freesurfer] Abormally high foldind index
>
>  External Email - Use Caution
>
> Dear Experts,
>
> While the majority of our subjects have a folding index between 5-30, there 
> are a couple of *extreme* outliers in the thousands or even negative.
>
> Could this hint that a particular part of recon-all failed and should be 
> rerun?
>
> Thank you for your interpretation and advice!
>
> -Ellen
>
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[Freesurfer] Longitudinal processing: QA

[Malo Gaubert]

External Email - Use Caution

Hello FreeSurfer developers,

I am trying to apply longitudinal processing on T1w MRI data for two
timepoints (~8 months between the two TP) in adolescents in order to
perform vertex-based analyses.
I am following the online tutorial here for the preprocessing:
https://secure-web.cisco.com/1AR-A4eBY63Zb7ogV-L0wed0Mf63cN1cf9Evvcu56pwG2mEf9LvTFus4zaos9QqygGOWZ8BgmmC4RMvMfE5zNf2Je5rgm9IW1XaeE_6_sNjrQE6WaXOp8FjjSRWAeVoQb0zZO71FPNvgk4c5WKgfyUzFo8iDaY_zJQY2mNwych8RK3rXx9rO7ngQd7gFN8Y6Hhnis_4AWfiEYpqcMmZQjJRenE6tG2KBjizNvXV8dATp-qKPtLhP2L3LzWCYbC3IMtyoRl1PEHVEuOaXOXoVFxQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FLongitudinalTutorial
Thus I launched the creation of BASE followed by the LONGITUDINAL.
Everything went well for recon-all for these 3 steps.
Now, I want to do the QA on the data and I have two questions regarding
this QA:

1/ For one subject, for the two timepoints, the white and pial surface are
entering in the left lateral ventricle as displayed in figure 1 below
(session 1 of the subject; cross-sectional), while the aseg is fine (this
area is considered as Lateral ventricle, see figure 2, see below).
What correction could I apply for this case ?

2/ For some subjects, there is a small shift between the pial of the two
sessions (or the white; see figure 3 (see below)=display of the norm of my
norm and pial/white for the two timepoints (long)) and/or some weird/non
straight/zigzag lines for pial or white (see figure 3, especially between
temporal pole and the rest of the brain). What could be the problem in this
case? Could it be related to some bad quality of T1w images?

1) FreeSurfer version: freesurfer-linux-centos7_x86_64-7.1.0.tar.gz
2) Platform: Ubuntu 18 (Virtual Machine on remote server)
3) uname -a: Linux ubuntu18-cbrain-042020 4.15.0-135-generic #139-Ubuntu
SMP Mon Jan 18 17:38:24 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux

Any help would be appreciated.

Best regards,
Malo

Link to figure 1:
https://secure-web.cisco.com/1Z0OIVNfAyd0P4dX5TvUfticgFxyac5XLFP9qZ15LY2KoHskWdAzJX_gGdfCw5X82CUm4tqdSGHzSj0WbrGTnkeLY5G_mVLf68DjbgDSC-xRbRT5QaeW2mMYp5QJdiYpfNHDdMmcGg4cgk_aC-nwYOrT-o-uRfUSbMQceX06rRep2G7uq339vdTeZEmEvgfcbF-avVOyM9yDOP7BnkmQoy-sGjhnzLbmeBhubK66u2wNAzlNPc8enWUMiPnNjqLMdxOR0sTnbRsRtU2mD05NxnA/https%3A%2F%2Fsyncandshare.lrz.de%2Fgetlink%2FfirX4m94zEkMQG17AR9vpEm%2Ffigure_1_cross_pial-white.PNG
Link to figure2:
https://secure-web.cisco.com/1dkQLGxh5x41ISY3MzCyMUowvQmrn9m-TXAqgZfq29hFI5LjInJXCxyxE2LyE7-XrsfmD8UMI_DG-4fR9lptGcPfVMft9c5rW6Xa2Q3WMPtXLHSwZpksyQu57ualrN7htcbizk4gKW7XM_S46uEdUzF7SFByOwLN8kI6if9nQi6ybWaAmOLZmJUIHXO2WUSyPrCqFYwHPxD0M8arXXhSg7lgznju4KnIrOghRYoNv2mrVMZzjlqaMdAs6Vf4-tdpvioEx8j41Kxbvok2uaLiecg/https%3A%2F%2Fsyncandshare.lrz.de%2Fgetlink%2FfiFdfAfGsWA3Mtk7eHPiLiPE%2Ffigure_2_cross_aseg.PNG

Link to figure3:
https://secure-web.cisco.com/1Nqbq7hapdkZjMI0hXAMBIcoKgeG0dkh3UzuuOGbjE_sUP9tB41ThsdkSchjSXtOqfP7Cu0da1aZz6o5TR1L-WZb87eB6G7U7Hm4FwYFXbtAYqN28-OCfZH_TgHyTlO0ByyCmtAzwkCrH_BR6ZRtqfVhtUtDNvDMkoM86oG4L0OKKjyrqEHE43a0PfJc3CBPVIPpxw1M-fadT5YDPPH-Xa7jEmutbAEvGLI8ZfGCna__4JiRXXh27NFoNj9iyIYk2Fp6p_Ef-tYkjf5vixj9Z9Q/https%3A%2F%2Fsyncandshare.lrz.de%2Fgetlink%2FfiQ3nGkLbtSdBEZLLsvmmgqg%2Ffigure_3_longitudinal.PNG
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[Freesurfer] Freeview - manjaro

[Vishnu S]

External Email - Use Caution

I'm getting a repeated error with libjpeg.so.62. is there any known fix?
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[Freesurfer] recon_all subcortical volume adjuested eTIV

[Jaime Gomez]

External Email - Use Caution

Hi,

Does the asegs.stats produced by recon_all have the volume estimates of
subcortical structures adjusted by the eTIV?
I want to understand the effect of sex in the segmented structures. Should
normalize the volumes of aseg.stats (Vol/eTIV) or is already done in
recon_all?
Thank you!
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Re: [Freesurfer] Native volume to fs_average surface

[Glasser, Matthew]

External Email - Use Caution

What is most important is that you map to your individual’s surface (whether 
that is in subject’s physical space or MNI space doesn’t matter so much).  If 
you are using FreeSurfer formatted data, others can suggest how to do this.  
With NIFTI/GIFTI/CIFTI, it can be accomplished with wb_command 
-volume-to-surface-mapping and wb_command -metric-resampling among other things 
(e.g. see 
https://secure-web.cisco.com/1_Cq1etkFEJqfTFb_02eCv_lWyZdh6vGfkdd5A81SPw-162gbs9u3HNA1PnuI7IsLrhkGjH3RxADhe1uk6zpOS4uCtg9YOdXFh8Z0VVcD8z-PgaZzq3v-LlDwgk5DfFfrJE-OMomZ4ZIA9-Q8Ihk3gRZ0O4LWEOd6nvAZ3AdlWe0nxXANY2zKCNEgv_fUrnQq3PJEce8MeX5SdLB-FImrnAJX6gVvKh18gh6sVI9yzAfTF0TcJQ5eLy-JcnQzrOFcFPp4ssonrJT6Tcfqvk0m3w/https%3A%2F%2Fgithub.com%2FWashington-University%2FHCPpipelines%2Fblob%2Fmaster%2FfMRISurface%2Fscripts%2FRibbonVolumeToSurfaceMapping.sh).

Matt.

From:  on behalf of Mason Wells 

Reply-To: Freesurfer support list 
Date: Monday, April 19, 2021 at 4:45 AM
To: Freesurfer support list , 
"freesurfer-boun...@nmr.mgh.harvard.edu" 

Subject: Re: [Freesurfer] Native volume to fs_average surface





External Email - Use Caution
HI Matt,

Thanks for the reply. Are you suggesting I go native volume > native surface > 
fs_average? If so, can you recommend the best can I go from native to group 
average surface?


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


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

Sent: Monday, April 19, 2021 10:27 AM
To: Freesurfer support list ; 
freesurfer-boun...@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] Native volume to fs_average surface

External email to Cardiff University - Take care when replying/opening 
attachments or links.
Nid ebost mewnol o Brifysgol Caerdydd yw hwn - Cymerwch ofal wrth ateb/agor 
atodiadau neu ddolenni.


External Email - Use Caution

You would do that through the subject’s own surface.  It does not work very 
well to map data directly from the volume onto group average surfaces (see e.g. 
Coalson et al., 2018 PNAS).



Matt.



From:  on behalf of Mason Wells 

Reply-To: Freesurfer support list 
Date: Monday, April 19, 2021 at 4:23 AM
To: Freesurfer support list , 
"freesurfer-boun...@nmr.mgh.harvard.edu" 

Subject: [Freesurfer] Native volume to fs_average surface





External Email - Use Caution

Hi experts,



I have some fMRI data that I have pre-processed in Feat. I want to resample a 
single subject's data to the fs_average surface but unsure of the most optimal 
way of doing this. At present I am warping the functional data to the MNI brain 
in the volume (using FSL's applywarp) and then resampling to fs_average using 
the following command.

  *   mri_vol2surf --src filtered_func_MNI.nii --out filtered_func_surf.mgh 
--hemi rh --mni152reg



My question is whether you think this is the most appropriate approach, and/or 
if there is way to move directly from native volume to fs_average surface 
without needing to go via MNI volume?



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 

Re: [Freesurfer] Native volume to fs_average surface

[Mason Wells]

External Email - Use Caution

HI Matt,

Thanks for the reply. Are you suggesting I go native volume > native surface > 
fs_average? If so, can you recommend the best can I go from native to group 
average surface?


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



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

Sent: Monday, April 19, 2021 10:27 AM
To: Freesurfer support list ; 
freesurfer-boun...@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] Native volume to fs_average surface

External email to Cardiff University - Take care when replying/opening 
attachments or links.
Nid ebost mewnol o Brifysgol Caerdydd yw hwn - Cymerwch ofal wrth ateb/agor 
atodiadau neu ddolenni.



External Email - Use Caution

You would do that through the subject’s own surface.  It does not work very 
well to map data directly from the volume onto group average surfaces (see e.g. 
Coalson et al., 2018 PNAS).



Matt.



From:  on behalf of Mason Wells 

Reply-To: Freesurfer support list 
Date: Monday, April 19, 2021 at 4:23 AM
To: Freesurfer support list , 
"freesurfer-boun...@nmr.mgh.harvard.edu" 

Subject: [Freesurfer] Native volume to fs_average surface





External Email - Use Caution

Hi experts,



I have some fMRI data that I have pre-processed in Feat. I want to resample a 
single subject's data to the fs_average surface but unsure of the most optimal 
way of doing this. At present I am warping the functional data to the MNI brain 
in the volume (using FSL's applywarp) and then resampling to fs_average using 
the following command.

  *   mri_vol2surf --src filtered_func_MNI.nii --out filtered_func_surf.mgh 
--hemi rh --mni152reg



My question is whether you think this is the most appropriate approach, and/or 
if there is way to move directly from native volume to fs_average surface 
without needing to go via MNI volume?



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

Re: [Freesurfer] Native volume to fs_average surface

[Glasser, Matthew]

External Email - Use Caution

You would do that through the subject’s own surface.  It does not work very 
well to map data directly from the volume onto group average surfaces (see e.g. 
Coalson et al., 2018 PNAS).

Matt.

From:  on behalf of Mason Wells 

Reply-To: Freesurfer support list 
Date: Monday, April 19, 2021 at 4:23 AM
To: Freesurfer support list , 
"freesurfer-boun...@nmr.mgh.harvard.edu" 

Subject: [Freesurfer] Native volume to fs_average surface





External Email - Use Caution
Hi experts,

I have some fMRI data that I have pre-processed in Feat. I want to resample a 
single subject's data to the fs_average surface but unsure of the most optimal 
way of doing this. At present I am warping the functional data to the MNI brain 
in the volume (using FSL's applywarp) and then resampling to fs_average using 
the following command.

  *   mri_vol2surf --src filtered_func_MNI.nii --out filtered_func_surf.mgh 
--hemi rh --mni152reg

My question is whether you think this is the most appropriate approach, and/or 
if there is way to move directly from native volume to fs_average surface 
without needing to go via MNI volume?

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



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[Freesurfer] Native volume to fs_average surface

[Mason Wells]

External Email - Use Caution

Hi experts,

I have some fMRI data that I have pre-processed in Feat. I want to resample a 
single subject's data to the fs_average surface but unsure of the most optimal 
way of doing this. At present I am warping the functional data to the MNI brain 
in the volume (using FSL's applywarp) and then resampling to fs_average using 
the following command.

  *   mri_vol2surf --src filtered_func_MNI.nii --out filtered_func_surf.mgh 
--hemi rh --mni152reg

My question is whether you think this is the most appropriate approach, and/or 
if there is way to move directly from native volume to fs_average surface 
without needing to go via MNI volume?

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

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