date:20210426

Re: [Freesurfer] mris_anatomical_stats() for ODI maps inflated to surface

2021-04-26 Thread Fischl, Bruce

Oh, then you don't need -l at all I don't think. Have you sampled your ODI file 
onto the surface?

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Jensen, Alexandria
Sent: Monday, April 26, 2021 5:01 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mris_anatomical_stats() for ODI maps inflated to 
surface

External Email - Use Caution
Hi Bruce,

Thank you for the help! If the -a option is the aparc.DKTatlas.annot file and 
the -l option should be a label file, where does the ODI surface file come into 
play? My ultimate goal is to get average ODI values for each ROI in the DKT 
atlas.

Alexandria

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 26, 2021 2:45 PM
To: freesurfer@nmr.mgh.harvard.edu 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] mris_anatomical_stats() for ODI maps inflated to 
surface

Hi Alexandria

The file given in the -l option should be an ascii label file, not a volume.

Cheers

Bruce

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

mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Jensen, Alexandria
Sent: Monday, April 26, 2021 4:26 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mris_anatomical_stats() for ODI maps inflated to 
surface

External Email - Use Caution

This is the command I use for mris_anatomical_stats and the terminal output. I 
have taken out some of the directory information for privacy reasons.

mris_anatomical_stats \

-a /.../freesurfer/label/lh.aparc.DLTatlas.annot \

-l odi_in_cortexL.nativespace.mgh \

-b subject_xxx \

lh

computing statistics for each annotation in 
/.../freesurfer/label/lh.aparc.DKTatlas.annot.

limiting computations to label ODI_in_cortexL.nativespace.mgh.

reading volume /.../freesurfer/mri/wm.mgz...

reading input surface /... /freesurfer/surf/lh.white...

Using TH3 vertex volume calc

Total face volume 227931

Total vertex volume 224122 (mask=0)

reading input pial surface /... /freesurfer/surf/lh.pial...

reading input white surface /.../freesurfer/surf/lh.white...

reading colortable from annotation file...

colortable with 36 entries read (originally 
/autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt)

mailto:freesurfer-boun...@nmr.mgh.harvard.edu>

mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Douglas N. Greve 
mailto:dgr...@mgh.harvard.edu>>
Sent: Sunday, April 25, 2021 8:35 PM
To: freesurfer@nmr.mgh.harvard.edu 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] mris_anatomical_stats() for ODI maps inflated to 
surface

what is your mris_anatomical_stats command and terminal output?

On 4/22/2021 4:48 PM, Jensen, Alexandria wrote:

External Email - Use Caution

Hello fellow Freesurfer users,

I am attempting to reproduce the analysis conducted by Parker et al. in their 
2018 paper, "Cortical microstructure in young onset Alzheimer's disease using 
neurite orientation dispersion and density imaging" (MailScanner has detected a 
possible fraud attempt from "secure-web.cisco.com" claiming to be 
https://onlinelibrary.wiley.com/doi/full/10.1002/hbm.24056).
 Cortical reconstruction of the T1 structural image was done in Freesurfer and 
NODDI processing using the NODDI toolbox in Matlab. The final steps I am 
attempting to complete include (1) projecting the ODI/NDI maps to an inflated 
surface to create surface maps (2. Materials and Methods, 2.5 
Diffusion-weighted MRI processing); and (2) calculating mean ODI/NDI values 
across both hemispheres for a selected number of ROIs from the Desikan 
parcellation (2. Materials and Methods, 2.6 Cortical ROIs). The Parker et al. 
paper has provided the Freesurfer functions used in each of these final steps, 
but I am getting stuck on step (2) and am now worried that I have made an error 
in step (1). Below is the code I have written so far to project an ODI map onto 
an inflated surface:

bbregister \

--s freesurfer \

--mov odi.nii \

--init-fsl \

--reg register.dat \

--dti

tkregister2 \

--s freesurfer \

--mov odi.nii \

--reg register.dat \

--surf

mri_vol2surf \

--src odi.nii \

--out odi_in_cortex.nativespace.mgh \

--srcreg register.dat \

--hemi lh \

[Freesurfer] mask error in glm_fit

2021-04-26 Thread Haley Park

External Email - Use Caution

Hello,

I am trying to run a correlational analysis with glm_fit on a masked area
with the code:

foreach hemi (lh)

  foreach smoothness (10)

foreach meas (volume thickness)

mri_glmfit \

--y {$hemi}.{$meas}.{$study}.{$smoothness}.mgh \

--fsgd FSGD/{$study}.fsgd \

--C Contrasts/Scores_Slope.mtx  \

--surf fsaverage {$hemi}  \

--mask lhYeo2011_7NetworksConfidence_N1000.mgz  \

--glmdir {$hemi}.{$meas}.{$study}.{$smoothness}.glmdir

end

  end

end

I get the error message:

ERROR: dimension mismatch 1 between y and mask



I've also tried to run it with the .nii file found at
https://secure-web.cisco.com/1sTopz8rXlJoh4VSQL7P0DYm1ff7H5Crs0Qg3iAG1M6HD6Vuyjn8ViA2fDeX0A7VIH_9-GSxTfaL35eIjCKAnbUd90wxlxBlgtdz3DVFpnalWP2oV1jHapx5B4tlAXHpUA9N18syK8T_8U3eUIX2YC8P7r4l3verT5XzzxpTkHDB7Nmuh-RYY63YVpXWmTl_xCbs105PDuuWwbrTX5RfdknvxXBksPePKuZnNwqmGz-GLy8z8xYTDCYxHegxv5wG_XMQjD1PxSwhpaqG0N-mGvQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FCorticalParcellation_Yeo2011


Any help would be appreciated!


Haley
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Re: [Freesurfer] mris_anatomical_stats() for ODI maps inflated to surface

2021-04-26 Thread Jensen, Alexandria

External Email - Use Caution

Hi Bruce,

Thank you for the help! If the -a option is the aparc.DKTatlas.annot file and 
the -l option should be a label file, where does the ODI surface file come into 
play? My ultimate goal is to get average ODI values for each ROI in the DKT 
atlas.

Alexandria

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

Sent: Monday, April 26, 2021 2:45 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] mris_anatomical_stats() for ODI maps inflated to 
surface


Hi Alexandria



The file given in the -l option should be an ascii label file, not a volume.



Cheers

Bruce



From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Jensen, Alexandria
Sent: Monday, April 26, 2021 4:26 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mris_anatomical_stats() for ODI maps inflated to 
surface



External Email - Use Caution

This is the command I use for mris_anatomical_stats and the terminal output. I 
have taken out some of the directory information for privacy reasons.



mris_anatomical_stats \

-a /.../freesurfer/label/lh.aparc.DLTatlas.annot \

-l odi_in_cortexL.nativespace.mgh \

-b subject_xxx \

lh



computing statistics for each annotation in 
/…/freesurfer/label/lh.aparc.DKTatlas.annot.

limiting computations to label ODI_in_cortexL.nativespace.mgh.

reading volume /…/freesurfer/mri/wm.mgz...

reading input surface /… /freesurfer/surf/lh.white...

Using TH3 vertex volume calc

Total face volume 227931

Total vertex volume 224122 (mask=0)

reading input pial surface /… /freesurfer/surf/lh.pial...

reading input white surface /…/freesurfer/surf/lh.white...

reading colortable from annotation file...

colortable with 36 entries read (originally 
/autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt)



mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Douglas N. Greve 
mailto:dgr...@mgh.harvard.edu>>
Sent: Sunday, April 25, 2021 8:35 PM
To: freesurfer@nmr.mgh.harvard.edu 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] mris_anatomical_stats() for ODI maps inflated to 
surface



what is your mris_anatomical_stats command and terminal output?

On 4/22/2021 4:48 PM, Jensen, Alexandria wrote:

External Email - Use Caution

Hello fellow Freesurfer users,



I am attempting to reproduce the analysis conducted by Parker et al. in their 
2018 paper, “Cortical microstructure in young onset Alzheimer's disease using 
neurite orientation dispersion and density imaging” (MailScanner has detected a 
possible fraud attempt from "secure-web.cisco.com" claiming to be 
https://secure-web.cisco.com/1qWAX2B5mEhr0gv-GWXk-eEvR5LEKky9C84EiA77Ru4of9porh_EdOvWFFIDtYy8HpLRuvNYw9UPO9b1fDMPpr3mJVcrUX8B27WCsXRCBbpUAxehPVetjwcHf6Z-ubeB5A3Cey9vulP53kZEM8MYFq1LCnyM7-Olv_Y270GqLnz98ye3k8F0AXH2TcU8J7PYjSUGuN3QuGlm9AiCXWlVJpw1kfPvDoRtNHKXowyK_I6YC9ivbNtXJvmHkwKPVuEwjmK1VZbacANIBr00yDvbFTA/https%3A%2F%2Fonlinelibrary.wiley.com%2Fdoi%2Ffull%2F10.1002%2Fhbm.24056).
 Cortical reconstruction of the T1 structural image was done in Freesurfer and 
NODDI processing using the NODDI toolbox in Matlab. The final steps I am 
attempting to complete include (1) projecting the ODI/NDI maps to an inflated 
surface to create surface maps (2. Materials and Methods, 2.5 
Diffusion-weighted MRI processing); and (2) calculating mean ODI/NDI values 
across both hemispheres for a selected number of ROIs from the Desikan 
parcellation (2. Materials and Methods, 2.6 Cortical ROIs). The Parker et al. 
paper has provided the Freesurfer functions used in each of these final steps, 
but I am getting stuck on step (2) and am now worried that I have made an error 
in step (1). Below is the code I have written so far to project an ODI map onto 
an inflated surface:

bbregister \

--s freesurfer \

--mov odi.nii \

--init-fsl \

--reg register.dat \

--dti



tkregister2 \

--s freesurfer \

--mov odi.nii \

--reg register.dat \

--surf



mri_vol2surf \

--src odi.nii \

--out odi_in_cortex.nativespace.mgh \

--srcreg register.dat \

--hemi lh \

--projfrac 0.5

When I load lh.inflated, the lh.aparc.DKTatlas.annot annotation file, and the 
odi_in_cortex.nativespace.mgh overlay in Freeview, things seem to be correct. 
The issue I have is when I try to use mris_anatomical_stats(). I have tried 
different combinations of label and annotation files but am either getting 
errors or no errors but also n

Re: [Freesurfer] mris_anatomical_stats() for ODI maps inflated to surface

2021-04-26 Thread Fischl, Bruce

Hi Alexandria

The file given in the -l option should be an ascii label file, not a volume.

Cheers
Bruce

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Jensen, Alexandria
Sent: Monday, April 26, 2021 4:26 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mris_anatomical_stats() for ODI maps inflated to 
surface


External Email - Use Caution
This is the command I use for mris_anatomical_stats and the terminal output. I 
have taken out some of the directory information for privacy reasons.

mris_anatomical_stats \
-a /.../freesurfer/label/lh.aparc.DLTatlas.annot \
-l odi_in_cortexL.nativespace.mgh \
-b subject_xxx \
lh

computing statistics for each annotation in 
/.../freesurfer/label/lh.aparc.DKTatlas.annot.
limiting computations to label ODI_in_cortexL.nativespace.mgh.
reading volume /.../freesurfer/mri/wm.mgz...
reading input surface /... /freesurfer/surf/lh.white...
Using TH3 vertex volume calc
Total face volume 227931
Total vertex volume 224122 (mask=0)
reading input pial surface /... /freesurfer/surf/lh.pial...
reading input white surface /.../freesurfer/surf/lh.white...
reading colortable from annotation file...
colortable with 36 entries read (originally 
/autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt)

mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Douglas N. Greve 
mailto:dgr...@mgh.harvard.edu>>
Sent: Sunday, April 25, 2021 8:35 PM
To: freesurfer@nmr.mgh.harvard.edu 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] mris_anatomical_stats() for ODI maps inflated to 
surface

what is your mris_anatomical_stats command and terminal output?
On 4/22/2021 4:48 PM, Jensen, Alexandria wrote:

External Email - Use Caution

Hello fellow Freesurfer users,



I am attempting to reproduce the analysis conducted by Parker et al. in their 
2018 paper, "Cortical microstructure in young onset Alzheimer's disease using 
neurite orientation dispersion and density imaging" (MailScanner has detected a 
possible fraud attempt from "secure-web.cisco.com" claiming to be 
https://onlinelibrary.wiley.com/doi/full/10.1002/hbm.24056).
 Cortical reconstruction of the T1 structural image was done in Freesurfer and 
NODDI processing using the NODDI toolbox in Matlab. The final steps I am 
attempting to complete include (1) projecting the ODI/NDI maps to an inflated 
surface to create surface maps (2. Materials and Methods, 2.5 
Diffusion-weighted MRI processing); and (2) calculating mean ODI/NDI values 
across both hemispheres for a selected number of ROIs from the Desikan 
parcellation (2. Materials and Methods, 2.6 Cortical ROIs). The Parker et al. 
paper has provided the Freesurfer functions used in each of these final steps, 
but I am getting stuck on step (2) and am now worried that I have made an error 
in step (1). Below is the code I have written so far to project an ODI map onto 
an inflated surface:

bbregister \

--s freesurfer \

--mov odi.nii \

--init-fsl \

--reg register.dat \

--dti



tkregister2 \

--s freesurfer \

--mov odi.nii \

--reg register.dat \

--surf



mri_vol2surf \

--src odi.nii \

--out odi_in_cortex.nativespace.mgh \

--srcreg register.dat \

--hemi lh \

--projfrac 0.5

When I load lh.inflated, the lh.aparc.DKTatlas.annot annotation file, and the 
odi_in_cortex.nativespace.mgh overlay in Freeview, things seem to be correct. 
The issue I have is when I try to use mris_anatomical_stats(). I have tried 
different combinations of label and annotation files but am either getting 
errors or no errors but also no output.
Any guidance would be much appreciated! I am new to Freesurfer and have been 
learning it as part of my graduate research assistantship. I am using 
Freesurfer version 7.1.1 on a macOS Catalina, version 10.15.7 operating system 
for reference.
Cheers,
Alexandria Jensen





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MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" 
claiming to be 
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Re: [Freesurfer] mris_anatomical_stats() for ODI maps inflated to surface

2021-04-26 Thread Jensen, Alexandria

External Email - Use Caution

This is the command I use for mris_anatomical_stats and the terminal output. I 
have taken out some of the directory information for privacy reasons.

mris_anatomical_stats \
-a /.../freesurfer/label/lh.aparc.DLTatlas.annot \
-l odi_in_cortexL.nativespace.mgh \
-b subject_xxx \
lh

computing statistics for each annotation in 
/…/freesurfer/label/lh.aparc.DKTatlas.annot.
limiting computations to label ODI_in_cortexL.nativespace.mgh.
reading volume /…/freesurfer/mri/wm.mgz...
reading input surface /… /freesurfer/surf/lh.white...
Using TH3 vertex volume calc
Total face volume 227931
Total vertex volume 224122 (mask=0)
reading input pial surface /… /freesurfer/surf/lh.pial...
reading input white surface /…/freesurfer/surf/lh.white...
reading colortable from annotation file...
colortable with 36 entries read (originally 
/autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt)

 on behalf of Douglas N. Greve 

Sent: Sunday, April 25, 2021 8:35 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] mris_anatomical_stats() for ODI maps inflated to 
surface

what is your mris_anatomical_stats command and terminal output?

On 4/22/2021 4:48 PM, Jensen, Alexandria wrote:

External Email - Use Caution

Hello fellow Freesurfer users,



I am attempting to reproduce the analysis conducted by Parker et al. in their 
2018 paper, “Cortical microstructure in young onset Alzheimer's disease using 
neurite orientation dispersion and density imaging” (MailScanner has detected a 
possible fraud attempt from "secure-web.cisco.com" claiming to be 
https://secure-web.cisco.com/16pE2vuqD539e7yrOp6VW_MoK0N1gOHieb7Nh9jiSQR2MMmvuoOVKiPgzRc-uBlwK1F4oO6izP1S3D5UMxYt2snfihG_LgApkQIGibEOrYnXrNNnyQRZvkGBxdD0I0Jwg-pYeW6vWtvrE_SvzzbgK5ENYures9AA5S7bf-rUYmoGp55wBuit-vsafysLUnnp-WY_u_H8sXdNp8EpEAfm9RKPeFf-Bpiyc8wct4KHS-UnUC56XSnRWySxASj5bm9bTgObBbCe2f_7uqPUOgR3lgA/https%3A%2F%2Fonlinelibrary.wiley.com%2Fdoi%2Ffull%2F10.1002%2Fhbm.24056).
 Cortical reconstruction of the T1 structural image was done in Freesurfer and 
NODDI processing using the NODDI toolbox in Matlab. The final steps I am 
attempting to complete include (1) projecting the ODI/NDI maps to an inflated 
surface to create surface maps (2. Materials and Methods, 2.5 
Diffusion-weighted MRI processing); and (2) calculating mean ODI/NDI values 
across both hemispheres for a selected number of ROIs from the Desikan 
parcellation (2. Materials and Methods, 2.6 Cortical ROIs). The Parker et al. 
paper has provided the Freesurfer functions used in each of these final steps, 
but I am getting stuck on step (2) and am now worried that I have made an error 
in step (1). Below is the code I have written so far to project an ODI map onto 
an inflated surface:

bbregister \

--s freesurfer \

--mov odi.nii \

--init-fsl \

--reg register.dat \

--dti


tkregister2 \

--s freesurfer \

--mov odi.nii \

--reg register.dat \

--surf



mri_vol2surf \

--src odi.nii \

--out odi_in_cortex.nativespace.mgh \

--srcreg register.dat \

--hemi lh \

--projfrac 0.5

When I load lh.inflated, the lh.aparc.DKTatlas.annot annotation file, and the 
odi_in_cortex.nativespace.mgh overlay in Freeview, things seem to be correct. 
The issue I have is when I try to use mris_anatomical_stats(). I have tried 
different combinations of label and annotation files but am either getting 
errors or no errors but also no output.
Any guidance would be much appreciated! I am new to Freesurfer and have been 
learning it as part of my graduate research assistantship. I am using 
Freesurfer version 7.1.1 on a macOS Catalina, version 10.15.7 operating system 
for reference.
Cheers,
Alexandria Jensen





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Re: [Freesurfer] Freeview issues with surfaces

2021-04-26 Thread Pål Gunnar Larsson

External Email - Use Caution

☺
Up and running.
Thank you!

Best
Pål


Denne meldingen innholder ikke sensitiv informasjon som bryter med Ous sine 
regler for taushetsplikt

Fra: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] På vegne av Wang, Ruopeng
Sendt: 26. april 2021 16:05
Til: Freesurfer support list
Emne: Re: [Freesurfer] Freeview issues with surfaces

There is a ‘Overlay’ drop down box on the left pane, where you can load overlay 
after loading a surface.

Ruopeng


On Apr 26, 2021, at 9:49 AM, Pål Gunnar Larsson 
mailto:p...@ous-hf.no>> wrote:

External Email - Use Caution

Thank you.
In version 5 I could load an overlay with e.g. thickness. I don’t see that 
alternative in Freeview?

Pål
not sensitive

Fra: 
freesurfer-boun...@nmr.mgh.harvard.edu
 [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] På vegne av Wang, Ruopeng
Sendt: 26. april 2021 15:42
Til: Freesurfer support list
Emne: Re: [Freesurfer] Freeview issues with surfaces

Hi Pål,

lh.area and lh.thickness are not surface files. They can be loaded as a surface 
overlay like this:

freeview -f lh.pial:overlay=lh.thickness

Best,
Ruopeng



On Apr 26, 2021, at 9:36 AM, Pål Gunnar Larsson 
mailto:p...@ous-hf.no>> wrote:

External Email - Use Caution

I have made a new install of everything, now running Ubuntu 20.04 with 
Virtualbox 6.0 and Freesurfer 7.1. Freesurfer  crashes with :
“nquads=10158084,  nvertices=529
terminate called after throwing an instance of 'int'
Aborted (core dumped)”
If I try to open surface lh.area or lh.thickness.
Others like lh.pial and lh.inflated works nicely.

I have tried this with one of “my” patients and bert with same result.
Suggestions?

Pål


Pål G. Larsson M.D., PhD.
not sensitive

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Re: [Freesurfer] Freeview issues with surfaces

2021-04-26 Thread Pål Gunnar Larsson

External Email - Use Caution

Thank you.
In version 5 I could load an overlay with e.g. thickness. I don’t see that
alternative in Freeview?

Pål
not sensitive

Fra: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] På vegne av Wang, Ruopeng
Sendt: 26. april 2021 15:42
Til: Freesurfer support list
Emne: Re: [Freesurfer] Freeview issues with surfaces

Hi Pål,

lh.area and lh.thickness are not surface files. They can be loaded as a surface
overlay like this:

freeview -f lh.pial:overlay=lh.thickness

Best,
Ruopeng

On Apr 26, 2021, at 9:36 AM, Pål Gunnar Larsson
mailto:p...@ous-hf.no>> wrote:

External Email - Use Caution

I have made a new install of everything, now running Ubuntu 20.04 with
Virtualbox 6.0 and Freesurfer 7.1. Freesurfer crashes with :
“nquads=10158084, nvertices=529
terminate called after throwing an instance of 'int'
Aborted (core dumped)”
If I try to open surface lh.area or lh.thickness.
Others like lh.pial and lh.inflated works nicely.

I have tried this with one of “my” patients and bert with same result.
Suggestions?

Pål

Pål G. Larsson M.D., PhD.
not sensitive

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[Freesurfer] Freeview issues with surfaces

2021-04-26 Thread Pål Gunnar Larsson

External Email - Use Caution

I have made a new install of everything, now running Ubuntu 20.04 with 
Virtualbox 6.0 and Freesurfer 7.1. Freesurfer  crashes with :
"nquads=10158084,  nvertices=529
terminate called after throwing an instance of 'int'
Aborted (core dumped)"
If I try to open surface lh.area or lh.thickness.
Others like lh.pial and lh.inflated works nicely.

I have tried this with one of "my" patients and bert with same result.
Suggestions?

Pål


Pål G. Larsson M.D., PhD.
not sensitive

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Re: [Freesurfer] Parcellation Error Pre-Post Central Gyrus R but not L Hemisphere

2021-04-26 Thread Fraser Smith

External Email - Use Caution

Thanks Bruce - getting back to this after quite some time now. I've managed
to make a central sulcus label file following these instructions (turns out
the CS was connected to the Post CS) and run it through mris-register.

I had a couple of follow up questions:
How can I use the results of the above to create a corrected parcellation?
I presume I need to recreate surfaces / labels afterwards - which command
should I use for this?

best
Fraser


On Fri, Mar 13, 2020 at 2:34 PM Bruce Fischl 
wrote:

> Hi Fraser
>
> if you look at the mris_register help there is an option to specify a
> manual label that corresponds to an atlas parcel:
>
> -L 
>  Specify a manual label to align with atlas label  name>
>
> in the past I have used this to draw a central sulcus and force it to
> align
> using the Destrieux atlas (since Desikan/Killiany is gyral). There are
> some
> very nice tools in freeview that make this pretty trivial. Overlay sulc on
> the inflated surface, make sure that the dark gray of the central sulcus
> (or red) isn't connected to anything else. If it is make a line using the
> custom fill tool, then fill and save. Once you are familiar with the tools
> it will take you about 60 seconds
>
> cheers
> Bruce
>
>
> On Fri, 13 Mar 2020,
> Fraser Smith wrote:
>
> >
> > External Email - Use Caution
> >
> > Hi there
> >
> > I have a clear parcellation error with one participant who does look to
> have
> > an atypical structure around the right post-central gyrus (looks split in
> > two).
> >
> > Both the pre and post central gyri are shifted significantly backwards –
> but
> > only for the right not the left hemisphere.
> >
> > I see this has been mentioned before in the archives – but I have been
> > unable to find a fix for this.
> >
> > Could you provide any tips on what to try? I am using v6.0.0.
> >
> > Best wishes
> >
> > Fraser Smith
> >
> >
> >___
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Re: [Freesurfer] Freeview slow on CentOS 8 Stream

2021-04-26 Thread Wang, Ruopeng

Hi Torkil,

Can you tell what part of the program slows down the most? Data loading? GUI 
responsiveness? Image/3D rendering? Or just in general? If it is the rendering, 
maybe try updating the graphics card driver to the latest?

Best,
Ruopeng

> On Apr 26, 2021, at 6:06 AM, Torkil Svensgaard  wrote:
> 
>External Email - Use Caution
> 
> Hi
> 
> We have an older Ubuntu 16.04 HPC installation on which Freeview runs 
> just fine. We also have a brand new CentOS 8 Stream HPC installation 
> with much better hardware on which Freeview slows to a crawl after a bit 
> of use.
> 
> There's no error as such, it just slows to the point of being unusable.
> 
> Any suggestions on how to fix it, or pinpoint the cause?
> 
> Thanks,
> 
> Torkil
> 
> 
> ___
> Freesurfer mailing list
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[Freesurfer] FW: make_average_subject without Talairach transform

2021-04-26 Thread Trisanna Sprung-Much

External Email - Use Caution

Hi there

Still hoping for some help on this.

Trisanna
--


From:  on behalf of Trisanna 
Sprung-Much 
Reply-To: Freesurfer support list 
Date: Tuesday, April 20, 2021 at 10:50 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] make_average_subject without Talairach transform


External Email - Use Caution
Hi there,

Still wondering if we can get some help with this. Our update is the following:


  1.  When we run make_average_subject with some chimp scans, with default 
settings, it runs but the average surfaces are inflated compared to the 
individual subjects, presumably because the Talairach.xfm is being used.
  2.  When we replace the ?h.sphere.reg of each subject with one that was 
generated by registering each subject’s surfaces to those of the average chimp 
template, it runs as well, but the average surfaces are still inflated, again I 
presume because it is using Talairach.xfm.
  3.  When we insert an .xfm of each subject to the average chimp template into 
each subject/mri/transforms and use make_average_subject with –-xform flag, it 
crashes at the same spot every time. (See below for where it crashes)
  4.  If I try to start from mris_make_average_surface with –x transform.xfm, I 
get the output “don’t know what to do with transform.xfm” and it crashes.


#@# Making average lh.white surface -
Tue Apr 20 10:31:38 EDT 2021
/data-01/trisanna/freesurfer/freesurfer_7.1.1/from_sebas_cluster/average_test_April20/avgtest
mris_make_average_surface -X 2GabrielApril15.xfm -i 7 -o white -sdir-out 
/data-01/trisanna/freesurfer/freesurfer_7.1.1/from_sebas_cluster/average_test_April20/
 lh white sphere.reg avgtest Abby Agatha
using xform 2GabrielApril15.xfm...
reading vertex positions from white...
---
hemi= lh
avg_surf_name   = white
canon_surf_name = sphere.reg
out_sname   = avgtest
xform   = 2GabrielApril15.xfm
---


mris_average_surface failed



Trisanna Sprung-Much
Research Associate
McGill University
MD Anderson Cancer Centre
--


From:  on behalf of Trisanna 
Sprung-Much 
Reply-To: Freesurfer support list 
Date: Wednesday, April 14, 2021 at 7:32 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] make_average_subject without Talairach transform


External Email - Use Caution
Hi there

As a follow-up, we realized that we had to also replace the lh.sphere.reg and 
rh.sphere.reg in the subject folders with new ones that were created by 
registering each subject lh and rh.sphere to those of the average chimp 
template. Once we did this, the script ran. However, as you can see, some 
serious scaling took place, I presume because it is still incorporating 
somewhere MNI space. I can see in the log that MNI305 seems to be called.

Any thoughts?

Trisanna
--


From:  on behalf of Trisanna 
Sprung-Much 
Reply-To: Freesurfer support list 
Date: Tuesday, April 13, 2021 at 3:47 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] make_average_subject without Talairach transform


External Email - Use Caution
Hi Doug

I did try as you suggested and no matter what I do, I get the following error 
after about 10 seconds of make_average_subject. The transforms to the average 
chimp template are in .xfm format and are in the subject/mri/transforms folder. 
These subjects were created with --hires, could that be creating a problem?


trisanna@kaplan:/data-01/trisanna/freesurfer/freesurfer_7.1.1$ 
make_average_subject --out avgApril13 --subjects Abby Agatha Amanda Artemus 
Arthur --xform 2GabrielApril13

setenv SUBJECTS_DIR 
/data-01/trisanna/freesurfer/freesurfer_7.1.1/from_sebas_cluster
/usr/local/freesurfer-7.1.1//bin/make_average_subject --out avgApril13 
--subjects Abby Agatha Amanda Artemus Arthur --xform 2GabrielApril13

make_average_subject 7.1.1
Tue Apr 13 15:30:50 EDT 2021
/data-01/trisanna/freesurfer/freesurfer_7.1.1
output ddir is /data-01/trisanna/freesurfer/freesurfer_7.1.1/from_sebas_cluster
uid=1001(trisanna) gid=1001(trisanna) groups=1001(trisanna),27(sudo)
make_average_surface --out avgApril13 --subjects Abby Agatha Amanda Artemus 
Arthur --xform 2GabrielApril13

setenv SUBJECTS_DIR 
/data-01/trisanna/freesurfer/freesurfer_7.1.1/from_sebas_cluster
/usr/local/freesurfer-7.1.1//bin/make_average_surface --out avgApril13 
--subjects Abby Agatha Amanda Artemus Arthur --xform 2GabrielApril13

make_average_surface 7.1.1
Tue Apr 13 15:30:50 EDT 2021
/data-01/trisanna/freesurfer/freesurfer_7.1.1/from_sebas_cluster/avgApril13
output ddir is /data-01/trisanna/freesurfer/freesurfer_7.1.1/from_sebas_cluster
uid=1001(trisanna) gid=1001(trisanna) groups=1001(trisanna),27(sudo)

make_average_surface

Tue Apr 13 15:30:50 EDT 2021
/data-01/trisanna/freesurfer/freesurfer_7.1.1/from_sebas_cluster/avgApril13
/usr/local/freesurfer-7.1.1//bin/make_average_sur

Re: [Freesurfer] Native volume to fs_average surface

2021-04-26 Thread Mason Wells

External Email - Use Caution

Hi Doug,

Sorry for the slow reply to this. I am not sure I follow your suggestion. Are 
you suggesting I register the filtered_func to the T1 with bbregister which 
results in a reg.lta/dat file? How does one then use this transformation matrix 
to move from native space to fs_average space?

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



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

Sent: Tuesday, April 20, 2021 3:06 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] Native volume to fs_average surface

use the filtered func data. reg.lta  the output of bbregister (might also be a 
.dat file). If the output is on fsaverage, then you can use nifit as output. FV 
will read mgh, mgz, nii, nii.gz, as well as dicom

On 4/19/2021 10:26 AM, Mason Wells wrote:

External Email - Use Caution

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

Re: [Freesurfer] Freeview issues with surfaces

2021-04-26 Thread Fischl, Bruce

Hi Pål


Thickness and curvature are overlays, not surfaces. Load a surface then load 
them as either overlays or curvature files.

Cheers
Bruce

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Pål Gunnar Larsson
Sent: Monday, April 26, 2021 9:50 AM
To: 'Freesurfer support list' 
Subject: Re: [Freesurfer] Freeview issues with surfaces


External Email - Use Caution
Thank you.
In version 5 I could load an overlay with e.g. thickness. I don’t see that 
alternative in Freeview?

Pål
not sensitive

Fra: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] På vegne av Wang, Ruopeng
Sendt: 26. april 2021 15:42
Til: Freesurfer support list
Emne: Re: [Freesurfer] Freeview issues with surfaces

Hi Pål,

lh.area and lh.thickness are not surface files. They can be loaded as a surface 
overlay like this:

freeview -f lh.pial:overlay=lh.thickness

Best,
Ruopeng

On Apr 26, 2021, at 9:36 AM, Pål Gunnar Larsson 
mailto:p...@ous-hf.no>> wrote:

External Email - Use Caution

I have made a new install of everything, now running Ubuntu 20.04 with 
Virtualbox 6.0 and Freesurfer 7.1. Freesurfer  crashes with :
“nquads=10158084,  nvertices=529
terminate called after throwing an instance of 'int'
Aborted (core dumped)”
If I try to open surface lh.area or lh.thickness.
Others like lh.pial and lh.inflated works nicely.

I have tried this with one of “my” patients and bert with same result.
Suggestions?

Pål


Pål G. Larsson M.D., PhD.
not sensitive

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The information in this e-mail is intended only for the person to whom it is 
addressed. If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at http://www.massgeneralbrigham.org/complianceline . If 
the e-mail was sent to you in error but does not contain patient information, 
please contact the sender and properly dispose of the e-mail.
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail.

Re: [Freesurfer] Parcellation Error Pre-Post Central Gyrus R but not L Hemisphere

2021-04-26 Thread Fischl, Bruce

You just need to rerun mris_register using the options I included in my 
previous email. This will recreate the ?h.sphere.reg, after which you can 
recreate the parcellation
Cheers
Bruce

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Fraser Smith
Sent: Monday, April 26, 2021 9:33 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Parcellation Error Pre-Post Central Gyrus R but not L 
Hemisphere

External Email - Use Caution
Thanks Bruce - getting back to this after quite some time now. I've managed to 
make a central sulcus label file following these instructions (turns out the CS 
was connected to the Post CS) and run it through mris-register.

I had a couple of follow up questions:
How can I use the results of the above to create a corrected parcellation? I 
presume I need to recreate surfaces / labels afterwards - which command should 
I use for this?

best
Fraser

On Fri, Mar 13, 2020 at 2:34 PM Bruce Fischl 
mailto:fis...@nmr.mgh.harvard.edu>> wrote:
Hi Fraser

if you look at the mris_register help there is an option to specify a
manual label that corresponds to an atlas parcel:

-L 
 Specify a manual label to align with atlas label 

in the past I have used this to draw a central sulcus and force it to align
using the Destrieux atlas (since Desikan/Killiany is gyral). There are some
very nice tools in freeview that make this pretty trivial. Overlay sulc on
the inflated surface, make sure that the dark gray of the central sulcus
(or red) isn't connected to anything else. If it is make a line using the
custom fill tool, then fill and save. Once you are familiar with the tools
it will take you about 60 seconds

cheers
Bruce

On Fri, 13 Mar 2020,
Fraser Smith wrote:

>
> External Email - Use Caution
>
> Hi there
>
> I have a clear parcellation error with one participant who does look to have
> an atypical structure around the right post-central gyrus (looks split in
> two).
>
> Both the pre and post central gyri are shifted significantly backwards – but
> only for the right not the left hemisphere.
>
> I see this has been mentioned before in the archives – but I have been
> unable to find a fix for this.
>
> Could you provide any tips on what to try? I am using v6.0.0.
>
> Best wishes
>
> Fraser Smith
>
>
>___
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contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at http://www.massgeneralbrigham.org/complianceline . If 
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Please note that this e-mail is not secure (encrypted).  If you do not wish to 
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receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail.

Re: [Freesurfer] Freeview issues with surfaces

2021-04-26 Thread Wang, Ruopeng

There is a ‘Overlay’ drop down box on the left pane, where you can load overlay 
after loading a surface.

Ruopeng

On Apr 26, 2021, at 9:49 AM, Pål Gunnar Larsson 
mailto:p...@ous-hf.no>> wrote:


External Email - Use Caution

Thank you.
In version 5 I could load an overlay with e.g. thickness. I don’t see that 
alternative in Freeview?

Pål
not sensitive

Fra: 
freesurfer-boun...@nmr.mgh.harvard.edu
 [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] På vegne av Wang, Ruopeng
Sendt: 26. april 2021 15:42
Til: Freesurfer support list
Emne: Re: [Freesurfer] Freeview issues with surfaces

Hi Pål,

lh.area and lh.thickness are not surface files. They can be loaded as a surface 
overlay like this:

freeview -f lh.pial:overlay=lh.thickness

Best,
Ruopeng


On Apr 26, 2021, at 9:36 AM, Pål Gunnar Larsson 
mailto:p...@ous-hf.no>> wrote:

External Email - Use Caution

I have made a new install of everything, now running Ubuntu 20.04 with 
Virtualbox 6.0 and Freesurfer 7.1. Freesurfer  crashes with :
“nquads=10158084,  nvertices=529
terminate called after throwing an instance of 'int'
Aborted (core dumped)”
If I try to open surface lh.area or lh.thickness.
Others like lh.pial and lh.inflated works nicely.

I have tried this with one of “my” patients and bert with same result.
Suggestions?

Pål


Pål G. Larsson M.D., PhD.
not sensitive

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Re: [Freesurfer] Freeview issues with surfaces

2021-04-26 Thread Wang, Ruopeng

Hi Pål,

lh.area and lh.thickness are not surface files. They can be loaded as a surface 
overlay like this:

freeview -f lh.pial:overlay=lh.thickness

Best,
Ruopeng

On Apr 26, 2021, at 9:36 AM, Pål Gunnar Larsson 
mailto:p...@ous-hf.no>> wrote:


External Email - Use Caution

I have made a new install of everything, now running Ubuntu 20.04 with 
Virtualbox 6.0 and Freesurfer 7.1. Freesurfer  crashes with :
“nquads=10158084,  nvertices=529
terminate called after throwing an instance of 'int'
Aborted (core dumped)”
If I try to open surface lh.area or lh.thickness.
Others like lh.pial and lh.inflated works nicely.

I have tried this with one of “my” patients and bert with same result.
Suggestions?

Pål


Pål G. Larsson M.D., PhD.
not sensitive

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[Freesurfer] aseg+ striatum parcellation_choi'2012

2021-04-26 Thread Laila Khedher-Brahim

External Email - Use Caution

Hi,

after the transformation of the Choi's striatal 2012 to the individual subject, 
I would like to do the segmentation + the striatum parcellation_Choi2012. How I 
can do that in order to have in the end the aseg + aparc.mgz file in order to 
have the volume of this ROI.

Cordially,

Laila



Laila Khedher Brahim

Docteur en technologies d'information et de communication- Traitement des 
données

 laila.khedher-bra...@inra.fr

Laboratoire Neuro-psychopharmacologie des systèmes dopaminergiques 
sous-corticaux (Facultés de Médecine et de Pharmacie) &&  Plateforme 
AgroResonance 
(https://secure-web.cisco.com/11FFmmQRyEScyxQhBuoUqIhMH3n21rZigLqcx-nZj13jlG6nCFER-K4amMNSIm0EvUPO_jbwMVmi7lJ0S1Z-F4o8ybtjYgmBbKCk4aasngqF8J_UGGGjWACI_WH678f6JHYkCC6peJDw2omAexk9fk7I4w9bXsZ-XZUIDkWMVC-vJaAzz1lp54nKMKtuoE-CFMNwM_gacZCJKafotwbr0jA1lNl0EgFjlVVBm9p8Ds7LgPbPVASlDR-VVmwpMSvzlfNtxpKAYUsy6G3vWZTt86Q/https%3A%2F%2Fwww6.inra.fr%2Fagroresonance)

Tel: +33 (0)4 73 62 4177
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Re: [Freesurfer] T2 lesion editing

2021-04-26 Thread AJ

External Email - Use Caution

Many thanks.  This really helps.
My best
AJ

On Mon, Apr 26, 2021, 02:21 Stefano Cerri  wrote:

> Hi AJ,
>
>
> Did you already use the *--lesion-mask-pattern *flag for the T2 contrast
> (Cf. 
> https://secure-web.cisco.com/1Nr9ikQiL70M1xJaljJ-ChTPoG2jOGZUYBEWZ8Wn-vfbZR3wVTBOWsjJ3Dpkhl8uYSJ4t-uvJ76fmq7gIt7rNQtluL7gk_Z08Jk5Gl_mGN6p4XNtpZNFOvpgJbyohBtm-9AC9mq-g8P5QFuKFI0ZONvb_VIapxucwVpfV0hqe8b-0GNi3Rc9rxXQPc40rDqwfd_kmdtPsK5CUw_fdQV19Vz_B1_15P6J7co11JfjNURHBO-sBdLgAr1UwxtxFHa_YZOlO9xunFdk8WRyRSdtpWQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FSamseg)?
>  The default
> behavior will mask lesion voxels with respect to the cortical gray matter,
> but you can also try to relax the constraint by masking them with respect
> to the white matter (you need to include the flag *--lesion-mask-structure
> 'White'). *
>
> Also, instead of trying different --threshold flags, you can save
> segmentation maps with the flag *--save-posteriors *and check the lesions
> map at /yourOutput/posteriors/Lesion.mgz*. *This volume will give you a
> rough idea of which threshold is the most suitable.
>
> If lesions are still not segmented well, as last resort you can always
> manually edit them from the seg.mgz.
>
> Hope it helps.
>
> Best,
> Stefano
>
> --
> *From:* AJ 
> *Sent:* 26 April 2021 04:52
> *To:* Freesurfer support list
> *Cc:* Stefano Cerri
> *Subject:* Re: [Freesurfer] T2 lesion editing
>
> Many thanks.
> Best.
> AJ
>
> On Sun, Apr 25, 2021, 21:45 Douglas N. Greve 
> wrote:
>
>>
>>
>> On 4/24/2021 5:56 PM, AJ wrote:
>>
>> External Email - Use Caution
>> Hi,
>> Once SAMSEG has finished segmenting T2 lesions, other than trying
>> different --threshold flags, any way to manually modify them?
>>
>> I'll let Stefano (cc'ed) weigh in.
>>
>>
>> Can --eTIV be added to SAMSEG?
>>
>> Not sure what you mean here. There is an etiv value that is output in the
>> samseg folder
>>
>>
>> In Samseg, can brainstem be segmented into parts, such as medulla, pons,
>> mid brain like through recon all?
>>
>> No, not yet
>>
>>
>> Can corpus callosum be segmented separately in Samseg?
>>
>> I have not tried this, but you can try
>> mri_cc -aseg seg.mgz -o seg.cc.mgz
>>
>>
>> Sorry for all the questions.
>>
>> Many thanks.
>>
>>
>>
>> ___
>> Freesurfer mailing 
>> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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>>
>> ___
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>> The information in this e-mail is intended only for the person to whom it
>> is addressed. If you believe this e-mail was sent to you in error and the
>> e-mail contains patient information, please contact the Mass General
>> Brigham Compliance HelpLine at
>> http://secure-web.cisco.com/1lIYzjYqBo16WL-6ifINShVIeB7LXmhUw0DCmWcVTzMDW75qCpBeSCgybdX2qEC4f5Qn57xl4f2UuCiMBfmaaDGp9zF-JCvZrA0D_Gj2ekDbP2UCr8pqTJPkdCKN2p5PTBpkD_Y0mYDbttQKJW9T2Wr1MUH7PIBBNgTwBbG8FWIeI3FwSqdV_n5UKI1b6_9_6ctqepbsLfglVWRoBC3bfk-9ADjSqiwCWru4KsYt9xffbZSXoXgKeA5TbPQQJt5ldK83UDWmcG7ZEKgrAa5yUEA/http%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline
>>  . If the e-mail was
>> sent to you in error but does not contain patient information, please
>> contact the sender and properly dispose of the e-mail.
>> Please note that this e-mail is not secure (encrypted).  If you do not
>> wish to continue communication over unencrypted e-mail, please notify the
>> sender of this message immediately.  Continuing to send or respond to
>> e-mail after receiving this message means you understand and accept this
>> risk and wish to continue to communicate over unencrypted e-mail.
>>
>
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Re: [Freesurfer] FA map registration to T1

2021-04-26 Thread Russo, Andrew William

We don't have B0 fieldmap data, would I still be able to perform this 
correction? For preprocessing we ran eddy_openmp and dtifit.

The helpdesk has added klawms to your sudo groups for access to the data. 
Please let me know if you need any more information.

Thanks so much for your help,
Andrew

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

Sent: Sunday, April 25, 2021 10:39 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] FA map registration to T1

Everything looks ok in the log file. Did you do an B0 distortion correction? 
Can you give me access to that data?

On 4/20/2021 10:34 AM, Russo, Andrew William wrote:
Log file is attached.

Thank you,
Andrew

Andrew Russo
Clinical Research Coordinator
Multiple Sclerosis Imaging Lab
Massachusetts General Hospital
149 13th Street | Boston, MA 02129
617-726-7531

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

 on behalf of Douglas N. Greve 

Sent: Tuesday, April 20, 2021 10:09 AM
To: freesurfer@nmr.mgh.harvard.edu 

Subject: Re: [Freesurfer] FA map registration to T1

can you send the bbr log file?

On 4/19/2021 2:29 PM, Russo, Andrew William wrote:
Hello FreeSurfer Developers,

I am registering FA maps to T1 for a group of subjects with MS and in many 
cases the registration is poor for the anterior corpus callosum (attached), 
cerebellum, pons, and temporal lobe. I am using the following commands 
(FreeSurfer version 6.0):

bbregister \
--dti \
--reg diff2T1_reg.dat \
--mov eddy_corrected_b0.nii.gz \
--s subject_temp

mri_vol2vol \
--mov dtifit_FA.nii.gz \
--targ orig.mgz \
--o FA2T1.nii.gz \
--reg diff2T1_reg.dat

Do you have any suggestions for improving this registration?

Thank you,
Andrew

Andrew Russo
Clinical Research Coordinator
Multiple Sclerosis Imaging Lab
Massachusetts General Hospital
149 13th Street | Boston, MA 02129
617-726-7531



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Re: [Freesurfer] T2 lesion editing

2021-04-26 Thread Stefano Cerri

External Email - Use Caution

Hi AJ,


Did you already use the --lesion-mask-pattern flag for the T2 contrast (Cf. 
https://secure-web.cisco.com/1_LCeYfRehXKnxqg96wNDurvB9Z24rRz-AYFwjNiTlLrgbpmm6ba7EZ0BgiqnhStFN-rFwH4oBu_s8BYrMkVJQAmhEgHrTvNHwV_2M2-IuAwLSLKNHdpkoyUel0ZbKG_kx3paAQ-bTS8RdQEOheBY3xuW56h3dfID9Mf6TtsLMmJ860YSwJCcLhAj88uRqyZxA8rbMPjEYKucvrfA-mfK_sV0wX96bZcaB3emO1JdVuoHtdSKG0q-nCZbPYFWFUgzAB0-ZizY_2_IBWzHaqKaUw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FSamseg)?
 The default behavior will mask lesion voxels with respect to the cortical gray 
matter, but you can also try to relax the constraint by masking them with 
respect to the white matter (you need to include the flag 
--lesion-mask-structure 'White').

Also, instead of trying different --threshold flags, you can save segmentation 
maps with the flag --save-posteriors and check the lesions map at 
/yourOutput/posteriors/Lesion.mgz. This volume will give you a rough idea of 
which threshold is the most suitable.

If lesions are still not segmented well, as last resort you can always manually 
edit them from the seg.mgz.

Hope it helps.

Best,
Stefano


From: AJ 
Sent: 26 April 2021 04:52
To: Freesurfer support list
Cc: Stefano Cerri
Subject: Re: [Freesurfer] T2 lesion editing

Many thanks.
Best.
AJ

On Sun, Apr 25, 2021, 21:45 Douglas N. Greve 
mailto:dgr...@mgh.harvard.edu>> wrote:


On 4/24/2021 5:56 PM, AJ wrote:

External Email - Use Caution

Hi,
Once SAMSEG has finished segmenting T2 lesions, other than trying different 
--threshold flags, any way to manually modify them?
I'll let Stefano (cc'ed) weigh in.

Can --eTIV be added to SAMSEG?
Not sure what you mean here. There is an etiv value that is output in the 
samseg folder

In Samseg, can brainstem be segmented into parts, such as medulla, pons, mid 
brain like through recon all?
No, not yet

Can corpus callosum be segmented separately in Samseg?
I have not tried this, but you can try
mri_cc -aseg seg.mgz -o seg.cc.mgz

Sorry for all the questions.

Many thanks.





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[Freesurfer] Freeview slow on CentOS 8 Stream

2021-04-26 Thread Torkil Svensgaard

External Email - Use Caution

Hi

We have an older Ubuntu 16.04 HPC installation on which Freeview runs 
just fine. We also have a brand new CentOS 8 Stream HPC installation 
with much better hardware on which Freeview slows to a crawl after a bit 
of use.

There's no error as such, it just slows to the point of being unusable.

Any suggestions on how to fix it, or pinpoint the cause?

Thanks,

Torkil


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[Freesurfer] average thickness lobe stats

2021-04-26 Thread Agurne Sampedro Calvete

External Email - Use Caution

Dear Freesurfer experts,

I am trying to obtain the average thickness of the brain lobes. I am
particularly interested in the temporal lobe.
I have run "mri_annotation2label" (--lobeStrict) and
"mris_anatomical_stats" commands and I have obtained the average thickness
of the different lobes in each hemisphere. However, I am interested in
obtaining data of both hemispheres together, that is, a single thickness
average for example for the temporal lobe. Is there a way to calculate it?
Could I just sum both averages from each hemisphere?

Thank you very much in advance.

Kind regards,

Agurne
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Re: [Freesurfer] mris_anatomical_stats() for ODI maps inflated to surface

[Freesurfer] mask error in glm_fit

Re: [Freesurfer] mris_anatomical_stats() for ODI maps inflated to surface

Re: [Freesurfer] mris_anatomical_stats() for ODI maps inflated to surface

Re: [Freesurfer] mris_anatomical_stats() for ODI maps inflated to surface

Re: [Freesurfer] Freeview issues with surfaces

Re: [Freesurfer] Freeview issues with surfaces

[Freesurfer] Freeview issues with surfaces

Re: [Freesurfer] Parcellation Error Pre-Post Central Gyrus R but not L Hemisphere

Re: [Freesurfer] Freeview slow on CentOS 8 Stream

[Freesurfer] FW: make_average_subject without Talairach transform

Re: [Freesurfer] Native volume to fs_average surface

Re: [Freesurfer] Freeview issues with surfaces

Re: [Freesurfer] Parcellation Error Pre-Post Central Gyrus R but not L Hemisphere

Re: [Freesurfer] Freeview issues with surfaces

Re: [Freesurfer] Freeview issues with surfaces

[Freesurfer] aseg+ striatum parcellation_choi'2012

Re: [Freesurfer] T2 lesion editing

Re: [Freesurfer] FA map registration to T1

Re: [Freesurfer] T2 lesion editing

[Freesurfer] Freeview slow on CentOS 8 Stream

[Freesurfer] average thickness lobe stats

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