[Freesurfer] dimension mismatch longitudinal

[KennethSPrice]

External Email - Use Caution

Hello Freesurfers!

In regards to the link below:
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg36839.html

Is there a way to fix a dimension mismatch?

Thanks,
Ken

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Re: [Freesurfer] Problems with freesurfer 7.1.0

[Angela Favaro]

External Email - Use Caution

Thank you!


> Il giorno 28 mag 2020, alle ore 20:27, Hoopes, Andrew 
>  ha scritto:
> 
> Hi Angela,
>  
> This is a bug on osx, which does not have the --preserve=timestamps flag 
> available to cp. This will be fixed in the next 7.1 patch, but in the 
> meantime, you can fix this manually via:
>  
> cd $FREESURFER_HOME/bin
> sudo rm rca-long-tp-init
> sudo curl 
> https://raw.githubusercontent.com/freesurfer/freesurfer/dev/scripts/rca-long-tp-init
>  
> 
>  -o rca-long-tp-init
> sudo chmod +x rca-long-tp-init
>  
> Best
> Andrew
>  
>  
> From:  on behalf of Angela Favaro 
> 
> Reply-To: FS Help 
> Date: Wednesday, May 27, 2020 at 4:27 PM
> To: FS Help 
> Subject: [Freesurfer] Problems with freesurfer 7.1.0
>  
> External Email - Use Caution
> Dear Freesurfer experts, 
> I am re-analyzing my longitudinal dataset using Freesurfer 7.1.0 with a McOS 
> Catalina. I found 2 main problems
> 1. About a 10% of cases failed at the segmentation stage during the recon-all 
> processing (I uploaded one of these cases in one of my previous mails)
> 2. After the building of the template during the longitudinal processing, at 
> the recon-all -long I found the following error:
>  
>  
>> longmc Done
>> /Users/angelafavaro/Desktop/Aachen/subj201.long.template4/mri
>> \n cp -f --preserve=timestamps 
>> /Users/angelafavaro/Desktop/Aachen/template4/mri/brainmask.mgz 
>> ./brainmask_template4.mgz \n
>> cp: illegal option -- -
>> usage: cp [-R [-H | -L | -P]] [-fi | -n] [-apvXc] source_file target_file
>>cp [-R [-H | -L | -P]] [-fi | -n] [-apvXc] source_file ... 
>> target_directory
>> ERROR:
>> Darwin iMac-di-Angela.local 19.0.0 Darwin Kernel Version 19.0.0: Thu Oct 17 
>> 16:17:15 PDT 2019; root:xnu-6153.41.3~29/RELEASE_X86_64 x86_64
> 
> 
>> recon-all -s subj201.long.template4 exited with ERRORS at Sat May 23 
>> 03:47:31 CEST 2020
>> 
>> 
> 
>  
> Can you please help me with this two issues?
> Thank you so much!
>  
> Angela
>  
>  
>  
> 
> 
>> Inizio messaggio inoltrato:
>>  
>> Da: Angela Favaro mailto:angela.fav...@unipd.it>>
>> Oggetto: [Freesurfer] Longitudinal processing with freesurfer 7.1.0
>> Data: 23 maggio 2020 10:41:02 CEST
>> A: Freesurfer support list > >
>> Rispondi a: Freesurfer support list > >
>>  
>> External Email - Use Caution
>>  
>> Dear Freesurfer experts, 
>> I am trying to process a dataset with a longitudinal design.
>> However, after building the template, at the “recon-all -long” command I got 
>> this error:
>>  
>> longmc Done
>> /Users/angelafavaro/Desktop/Aachen/subj201.long.template4/mri
>> \n cp -f --preserve=timestamps 
>> /Users/angelafavaro/Desktop/Aachen/template4/mri/brainmask.mgz 
>> ./brainmask_template4.mgz \n
>> cp: illegal option -- -
>> usage: cp [-R [-H | -L | -P]] [-fi | -n] [-apvXc] source_file target_file
>>cp [-R [-H | -L | -P]] [-fi | -n] [-apvXc] source_file ... 
>> target_directory
>> ERROR:
>> Darwin iMac-di-Angela.local 19.0.0 Darwin Kernel Version 19.0.0: Thu Oct 17 
>> 16:17:15 PDT 2019; root:xnu-6153.41.3~29/RELEASE_X86_64 x86_64
>>  
>> recon-all -s subj201.long.template4 exited with ERRORS at Sat May 23 
>> 03:47:31 CEST 2020
>>  
>> For more details, see the log file 
>> /Users/angelafavaro/Desktop/Aachen/subj201.long.template4/scripts/recon-all.log
>> 
>> 
>> 
>> 
>> Thank you for any help!
>> 
>> 
>> Angela
>> ___
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>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> 
> 
> 
> ___
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Re: [Freesurfer] ERROR: mri_fill: could not find any points where lh and rh wm are nbrs

[Bruce Fischl]

Hi Marina

can you upload this subject? I'm not sure what is going on. Or send us the 
recon-all.log?


The vertex error means that the surfaces don't match. This usually means 
that you recreated some but not all of the surfaces for one of the hemis


cheers
Bruce




On Thu, 28 May 2020, Marina Fernández wrote:



External Email - Use Caution

Hi Bruce,

The talairach transform is reasonable and the aseg segment the cc correctly.

I run with freesurfer dev version the same command (recon all -autorecon-2wm
-subjid post_006) and now I have more information about what could be the
problem. The output of the terminal (that you can see below) says that there
is a vertex in the curv file of each hemisphere that has one vertex number
that it  is not expected. When I open the curv file in tksurfer there is a 0
in these positions.

Maybe this output can be useful to help me solve the problem. 
What do you think I should do? Thanks in advance! 


mris_curvature -seed 1234 -thresh .999 -n -a 5 -w -distances 10 10
rh.inflated

setting seed for random number generator to 1234
normalizing curvature values.
averaging curvature patterns 5 times.
sampling 10 neighbors out to a distance of 10 mm
128 vertices thresholded to be in k1 ~ [-0.27 0.70], k2 ~ [-0.10 0.11]
total integrated curvature = 0.637*4pi (8.002) --> 0 handles
ICI = 1.5, FI = 8.0, variation=142.940
106 vertices thresholded to be in [-0.03 0.02]
writing Gaussian curvature to ./rh.inflated.K...thresholding curvature at
99.90% level
curvature mean = 0.000, std = 0.001
125 vertices thresholded to be in [-0.16 0.23]
done.
writing mean curvature to ./rh.inflated.H...curvature mean = -0.017, std =
0.023
done.
@#@FSTIME  2020:05:28:10:21:34 mris_curvature N 12 e 52.03 S 0.20 U 51.78 P
99% M 334852 F 0 R 89611 W 0 c 174 w 1 I 0 O 1888 L 2.00 2.00 1.76
@#@FSLOADPOST 2020:05:28:10:22:26 mris_curvature N 12 2.00 2.00 1.77

#-
#@# Curvature Stats lh Thu May 28 10:22:26 CEST 2020
/usr/local/freesurfer/subjects/post_006/surf

 mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats
-F smoothwm post_006 lh curv sulc

             Toggling save flag on curvature files                       [
ok ]
                 Outputting results using filestem   [
../stats/lh.curv.stats ]
             Toggling save flag on curvature files                       [
ok ]
                                   Setting surface     [
post_006/lh.smoothwm ]
                                Reading surface...                       [
ok ]
                                   Setting texture                     [
curv ]
                                Reading texture...error: No such file or
directory
error: MRISreadNewCurvature: incompatible vertex number in file
/usr/local/freesurfer/subjects/post_006/surf/lh.curv

***WARNING!***
Some error has occurred while reading 'lh.curv'.
This might be due a vertex incompatibility
between the surface 'lh.smoothwm' and curv 'lh.curv'.

You might be able to correct this by re-running
'mris_make_surfaces' on this dataset.

Skipping this (and any remaining) curvature files.
Any measurements / calcuations that depend on the
curvature file will be skipped.
*

      Calculating Discrete Principal Curvatures...
      Determining geometric order for vno faces... [] [
ok ]
                      Determining KH curvatures... [] [
ok ]
                    Determining k1k2 curvatures... [] [
ok ]
                                   deltaViolations                      [
208 ]

WARN:    S lookup   min:                          -0.238596
WARN:    S explicit min:                          0.00 vertex = 1525
@#@FSTIME  2020:05:28:10:22:26 mris_curvature_stats N 11 e 2.95 S 0.14 U
2.79 P 99% M 170736 F 6 R 48708 W 0 c 56 w 7 I 1104 O 7584 L 2.00 2.00 1.77
@#@FSLOADPOST 2020:05:28:10:22:29 mris_curvature_stats N 11 2.00 2.00 1.77

#-
#@# Curvature Stats rh Thu May 28 10:22:29 CEST 2020
/usr/local/freesurfer/subjects/post_006/surf

 mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats
-F smoothwm post_006 rh curv sulc

             Toggling save flag on curvature files                       [
ok ]
                 Outputting results using filestem   [
../stats/rh.curv.stats ]
             Toggling save flag on curvature files                       [
ok ]
                                   Setting surface     [
post_006/rh.smoothwm ]
                                Reading surface...                       [
ok ]
                                   Setting texture                     [
curv ]
                                Reading texture...error: No such file or
directory
error: MRISreadNewCurvature: incompatible vertex number in file
/usr/local/freesurfer/subjects/post_006/surf/rh.curv

***WARNING!***
Some error has occurred while reading 'rh.curv'.
This might be due a vertex

Re: [Freesurfer] fs_install_mcr error

[Hoopes, Andrew]

Hi Amir,

Is there any other terminal output? My guess is that the installer did not 
download correctly in the temporary directory.

Best
Andrew

From:  on behalf of AmirHussein 
Abdolalizadeh 
Reply-To: FS Help 
Date: Wednesday, May 27, 2020 at 12:02 PM
To: FS Help 
Subject: [Freesurfer] fs_install_mcr error


External Email - Use Caution
Hi all,

I have installed FS7 (centOS8 version) on ubuntu 18.04. I try to install MATLAB 
runtime but it gives an error when I type "fs_install_mcr R2014b":


Archive:  installer.zip

End-of-central-directory signature not found.  Either this file is not

a zipfile, or it constitutes one disk of a multi-part archive.  In the

latter case the central directory and zipfile comment will be found on

the last disk(s) of this archive.

unzip:  cannot find zipfile directory in one of installer.zip or

installer.zip.zip, and cannot find installer.zip.ZIP, period.



Since I suspected it might be an access issue, I have used chmod -R 777 on my 
FreeSurfer installation category. Also, using "sudo" before "fs_install_mcr" 
causes the bash not to recognise fs_install_mcr command. Any suggestions?



Bests,

Amir
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Re: [Freesurfer] Recon-all error in CA Normalize (FreeSurfer V 7.1)

[Douglas N. Greve]

You can use ANTS N3 by adding -ants-n3 to the command line. In theory, 
you can use a mask, but I vaguely remember that there was a bug when 
someone tried it in our code



On 5/28/2020 12:37 PM, Schranzer René wrote:


External Email - Use Caution

Hi Douglas,

Thanks for your help!

Two more questions:

Is it possible to use the individual brain mask of my skull stripped 
data as a "mask image" for the step of the NU Intensity correction in 
recon-all with an additional flag to carry out a better bias correction?


And is it possible to use ANTsN3 instead of ANTsN4, if someone wants it?

Best,

René

*Von:*freesurfer-boun...@nmr.mgh.harvard.edu 
 *Im Auftrag von *Douglas N. Greve

*Gesendet:* Donnerstag, 28. Mai 2020 17:47
*An:* freesurfer@nmr.mgh.harvard.edu
*Betreff:* Re: [Freesurfer] Recon-all error in CA Normalize 
(FreeSurfer V 7.1)


You can use it with all subjects then

On 5/28/2020 3:28 AM, Schranzer René wrote:

*External Email - Use Caution *

All subjects.

Best,

René

*Von:*freesurfer-boun...@nmr.mgh.harvard.edu


 *Im Auftrag von
*Douglas N. Greve
*Gesendet:* Mittwoch, 27. Mai 2020 18:37
*An:* freesurfer@nmr.mgh.harvard.edu

*Betreff:* Re: [Freesurfer] Recon-all error in CA Normalize
(FreeSurfer V 7.1)


Are all your subjects skull stripped or just this one?

On 5/24/2020 9:08 AM, Schranzer René wrote:

*External Email - Use Caution *

Hi Douglas,

First of all, thank you for your help.

I forgot to mention that I am already using skull-stripped
data for the recon-all processing stream. Therefore, I stopped
after -autorecon1 and copied the T1.mgz to brainmask.mgz and
brainmask.auto.mgz and continued processing with -autorecon2
and -autorecon3. In some subjects (at some timepoints), the
recon-all -autorecon2 -autorecon3 excited with errors, as
mentioned below. Now I have used the following command
"recon-all -hires -skullstrip -no-wsgcaatlas -s ${sbjID} -i
${sbj} -all" with the skull-stripped data and it worked fine
without errors. I also compared the T1.mgz from both
approaches and they looked identical.

My question, can I use this approach with the "-no-wsgcaatlas"
for all subjects or is there something to consider here?

Best, René




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Re: [Freesurfer] ERROR: mri_fill: could not find any points where lh and rh wm are nbrs

[Marina Fernández]

External Email - Use Caution

Hi Bruce,

The talairach transform is reasonable and the aseg segment the cc correctly.

I run with freesurfer dev version the same command (recon all
-autorecon-2wm -subjid post_006) and now I have more information about what
could be the problem. The output of the terminal (that you can see below)
says that there is a vertex in the curv file of each hemisphere that has
one vertex number that it  is not expected. When I open the curv file in
tksurfer there is a 0 in these positions.

Maybe this output can be useful to help me solve the problem.
What do you think I should do? Thanks in advance!


mris_curvature -seed 1234 -thresh .999 -n -a 5 -w -distances 10 10
rh.inflated

setting seed for random number generator to 1234
normalizing curvature values.
averaging curvature patterns 5 times.
sampling 10 neighbors out to a distance of 10 mm
128 vertices thresholded to be in k1 ~ [-0.27 0.70], k2 ~ [-0.10 0.11]
total integrated curvature = 0.637*4pi (8.002) --> 0 handles
ICI = 1.5, FI = 8.0, variation=142.940
106 vertices thresholded to be in [-0.03 0.02]
writing Gaussian curvature to ./rh.inflated.K...thresholding curvature at
99.90% level
curvature mean = 0.000, std = 0.001
125 vertices thresholded to be in [-0.16 0.23]
done.
writing mean curvature to ./rh.inflated.H...curvature mean = -0.017, std =
0.023
done.
@#@FSTIME  2020:05:28:10:21:34 mris_curvature N 12 e 52.03 S 0.20 U 51.78 P
99% M 334852 F 0 R 89611 W 0 c 174 w 1 I 0 O 1888 L 2.00 2.00 1.76
@#@FSLOADPOST 2020:05:28:10:22:26 mris_curvature N 12 2.00 2.00 1.77

#-
#@# Curvature Stats lh Thu May 28 10:22:26 CEST 2020
/usr/local/freesurfer/subjects/post_006/surf

 mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats
-F smoothwm post_006 lh curv sulc

 Toggling save flag on curvature files   [
ok ]
 Outputting results using filestem   [
../stats/lh.curv.stats ]
 Toggling save flag on curvature files   [
ok ]
   Setting surface [
post_006/lh.smoothwm ]
Reading surface...   [
ok ]
   Setting texture [
curv ]
Reading texture...error: No such file or
directory
error: MRISreadNewCurvature: incompatible vertex number in file
/usr/local/freesurfer/subjects/post_006/surf/lh.curv

***WARNING!***
Some error has occurred while reading 'lh.curv'.
This might be due a vertex incompatibility
between the surface 'lh.smoothwm' and curv 'lh.curv'.

You might be able to correct this by re-running
'mris_make_surfaces' on this dataset.

Skipping this (and any remaining) curvature files.
Any measurements / calcuations that depend on the
curvature file will be skipped.
*

  Calculating Discrete Principal Curvatures...
  Determining geometric order for vno faces... [] [
ok ]
  Determining KH curvatures... [] [
ok ]
Determining k1k2 curvatures... [] [
ok ]
   deltaViolations  [
208 ]

WARN:S lookup   min:  -0.238596
WARN:S explicit min:  0.00 vertex = 1525
@#@FSTIME  2020:05:28:10:22:26 mris_curvature_stats N 11 e 2.95 S 0.14 U
2.79 P 99% M 170736 F 6 R 48708 W 0 c 56 w 7 I 1104 O 7584 L 2.00 2.00 1.77
@#@FSLOADPOST 2020:05:28:10:22:29 mris_curvature_stats N 11 2.00 2.00 1.77

#-
#@# Curvature Stats rh Thu May 28 10:22:29 CEST 2020
/usr/local/freesurfer/subjects/post_006/surf

 mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats
-F smoothwm post_006 rh curv sulc

 Toggling save flag on curvature files   [
ok ]
 Outputting results using filestem   [
../stats/rh.curv.stats ]
 Toggling save flag on curvature files   [
ok ]
   Setting surface [
post_006/rh.smoothwm ]
Reading surface...   [
ok ]
   Setting texture [
curv ]
Reading texture...error: No such file or
directory
error: MRISreadNewCurvature: incompatible vertex number in file
/usr/local/freesurfer/subjects/post_006/surf/rh.curv

***WARNING!***
Some error has occurred while reading 'rh.curv'.
This might be due a vertex incompatibility
between the surface 'rh.smoothwm' and curv 'rh.curv'.

You might be able to correct this by re-running
'mris_make_surfaces' on this dataset.

Skipping this (and any remaining) curvature files.
Any measurements / calcuations that depend on the
curvature file will be skipped.
*

  Calculat

Re: [Freesurfer] Problems with freesurfer 7.1.0

[Hoopes, Andrew]

Hi Angela,

This is a bug on osx, which does not have the --preserve=timestamps flag 
available to cp. This will be fixed in the next 7.1 patch, but in the meantime, 
you can fix this manually via:

cd $FREESURFER_HOME/bin
sudo rm rca-long-tp-init
sudo curl 
https://raw.githubusercontent.com/freesurfer/freesurfer/dev/scripts/rca-long-tp-init
 -o rca-long-tp-init
sudo chmod +x rca-long-tp-init

Best
Andrew


From:  on behalf of Angela Favaro 

Reply-To: FS Help 
Date: Wednesday, May 27, 2020 at 4:27 PM
To: FS Help 
Subject: [Freesurfer] Problems with freesurfer 7.1.0


External Email - Use Caution
Dear Freesurfer experts,
I am re-analyzing my longitudinal dataset using Freesurfer 7.1.0 with a McOS 
Catalina. I found 2 main problems
1. About a 10% of cases failed at the segmentation stage during the recon-all 
processing (I uploaded one of these cases in one of my previous mails)
2. After the building of the template during the longitudinal processing, at 
the recon-all -long I found the following error:


longmc Done
/Users/angelafavaro/Desktop/Aachen/subj201.long.template4/mri
\n cp -f --preserve=timestamps 
/Users/angelafavaro/Desktop/Aachen/template4/mri/brainmask.mgz 
./brainmask_template4.mgz \n
cp: illegal option -- -
usage: cp [-R [-H | -L | -P]] [-fi | -n] [-apvXc] source_file target_file
   cp [-R [-H | -L | -P]] [-fi | -n] [-apvXc] source_file ... 
target_directory
ERROR:
Darwin iMac-di-Angela.local 19.0.0 Darwin Kernel Version 19.0.0: Thu Oct 17 
16:17:15 PDT 2019; root:xnu-6153.41.3~29/RELEASE_X86_64 x86_64


recon-all -s subj201.long.template4 exited with ERRORS at Sat May 23 03:47:31 
CEST 2020



Can you please help me with this two issues?
Thank you so much!

Angela





Inizio messaggio inoltrato:

Da: Angela Favaro mailto:angela.fav...@unipd.it>>
Oggetto: [Freesurfer] Longitudinal processing with freesurfer 7.1.0
Data: 23 maggio 2020 10:41:02 CEST
A: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Rispondi a: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>

External Email - Use Caution

Dear Freesurfer experts,
I am trying to process a dataset with a longitudinal design.
However, after building the template, at the “recon-all -long” command I got 
this error:

longmc Done
/Users/angelafavaro/Desktop/Aachen/subj201.long.template4/mri
\n cp -f --preserve=timestamps 
/Users/angelafavaro/Desktop/Aachen/template4/mri/brainmask.mgz 
./brainmask_template4.mgz \n
cp: illegal option -- -
usage: cp [-R [-H | -L | -P]] [-fi | -n] [-apvXc] source_file target_file
   cp [-R [-H | -L | -P]] [-fi | -n] [-apvXc] source_file ... 
target_directory
ERROR:
Darwin iMac-di-Angela.local 19.0.0 Darwin Kernel Version 19.0.0: Thu Oct 17 
16:17:15 PDT 2019; root:xnu-6153.41.3~29/RELEASE_X86_64 x86_64

recon-all -s subj201.long.template4 exited with ERRORS at Sat May 23 03:47:31 
CEST 2020

For more details, see the log file 
/Users/angelafavaro/Desktop/Aachen/subj201.long.template4/scripts/recon-all.log




Thank you for any help!


Angela
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Re: [Freesurfer] [EXT]Re: mri_cnr label flag

[Pradyumna Bharadwaj]

External Email - Use Caution

Is it the pctsurfcon tool? (
https://surfer.nmr.mgh.harvard.edu/fswiki/pctsurfcon)

On Thu, May 28, 2020 at 10:12 AM Bruce Fischl 
wrote:

> External Email
>
> David and Doug: can you point Prad in the right direction for looking at
> gray and white signal changes and ratios?
> On Thu, 28 May 2020, Pradyumna
> Bharadwaj wrote:
>
> >
> > External Email - Use Caution
> >
> > Hi Dr. Fischl,
> > Thank you for suggesting that.
> > Would it be possible to share a link to a page with information about
> this
> > stream or to a patch?
> >
> > Thanks,
> > Prad
> >
> > On Thu, May 28, 2020 at 9:46 AM Bruce Fischl  >
> > wrote:
> >   External Email
> >
> >   I see. I think Doug has a more modern stream for this that David
> >   Salat
> >   has also used a lot
> >   On Thu, 28 May 2020, Pradyumna Bharadwaj wrote:
> >
> >   >
> >   > External Email - Use Caution
> >   >
> >   > Hi Dr. Fischl,
> >   > Thanks for confirming that!
> >   > We were broadly interested in testing whether age-related
> >   differences in
> >   > cortical measures were impacted by the CNR in each ROI.
> >   >
> >   > Best,
> >   > Prad
> >   >
> >   > On Thu, May 28, 2020 at 9:33 AM Bruce Fischl
> >   
> >   > wrote:
> >   >   External Email
> >   >
> >   >   Hi Prad
> >   >
> >   >   what is your goal? What you describe below should work
> >   >
> >   >   cheers
> >   >   Bruce
> >   >   On Thu, 28 May 2020,
> >   >   Pradyumna Bharadwaj wrote:
> >   >
> >   >   >
> >   >   > External Email - Use Caution
> >   >   >
> >   >   > Hi Dr. Fischl,
> >   >   > Thank you for clarifying that!
> >   >   >
> >   >   > As a follow up question, I just wanted to double check
> >   that
> >   >   the method
> >   >   > outlined in this post is still a valid approach to
> >   obtaining
> >   >   the CNR values
> >   >   > for each of the ROIs in theDesikan-Killianyatlas(
> https://www.mail-archive.com/freesurfer@nmr.mgh.harva
> >   rd.edu/msg62066.
> >   >   html)
> >   >   > .
> >   >   >
> >   >   > Briefly, you recommended converting the aparc
> >   annotation to
> >   >   labels in the
> >   >   > atlas, and applying mri_cnr to each label.
> >   >   >
> >   >   > Best,
> >   >   > Prad
> >   >   >
> >   >   > On Thu, May 28, 2020 at 9:14 AM Bruce Fischl
> >   >   
> >   >   > wrote:
> >   >   >   External Email
> >   >   >
> >   >   >   Hi Prad
> >   >   >
> >   >   >   if you use the cortex.label is will avoid using
> >   the
> >   >   non-cortical
> >   >   >   regions in
> >   >   >   the surface, like the midline, so should be a
> >   more
> >   >   accurate
> >   >   >   measure
> >   >   >
> >   >   >   cheers
> >   >   >   Bruce
> >   >   >
> >   >   >
> >   >   >   On Thu, 28 May 2020, Pradyumna Bharadwaj wrote:
> >   >   >
> >   >   >   >
> >   >   >   > External Email - Use Caution
> >   >   >   >
> >   >   >   > Hi,
> >   >   >   >
> >   >   >   > I had a question about the -label flag in
> >   mri_cnr.
> >   >   >   >
> >   >   >   > 1) When you do not use the -label option and
> >   just use
> >   >   the
> >   >   >   following command:
> >   >   >   >  mri_cnr $FREESURFER_HOME/subjects/bert/surf
> >
> >   >   >   $FREESURFER_HOME/subjects/be
> >   >   >   > rt/mri/norm.mgz
> >   >   >   >
> >   >   >   > The output is as follows
> >   >   >   >
> >   >   >   >   white = 96.6+-6.0, gray = 75.7+-13.5, csf =
> >   >   55.3+-16.6
> >   >   >   gray/white CNR = 1.
> >   >   >   > 983, gray/csf CNR = 0.907
> >   >   >   >
> >   >   >   >  lh CNR = 1.445
> >   >   >   >
> >   >   >   > white = 96.4+-6.0, gray = 76.0+-13.3, csf =
> >   55.6+-16.2
> >   >   >   gray/white CNR = 1.95
> >   >   >   > 2, gray/csf CNR = 0.943
> >   >   >   >
> >   >   >   > rh CNR = 1.448
> >   >   >   >
> >   >   >   >  total CNR = 1.446
> >   >   >   >
> >   >   >   >
> >   >   >   > 2) When you add  -label
> >   >   >
> >$FREESURFER_HOME/subjects/bert/label/lh.cortex.label
> >   >   >   >
> >   $FREESURFER_HOME/subjects/bert/label/rh.co

Re: [Freesurfer] [EXT]Re: mri_cnr label flag

[Pradyumna Bharadwaj]

External Email - Use Caution

Hi Dr. Fischl,

Thank you for suggesting that.
Would it be possible to share a link to a page with information about this
stream or to a patch?

Thanks,
Prad

On Thu, May 28, 2020 at 9:46 AM Bruce Fischl 
wrote:

> External Email
>
> I see. I think Doug has a more modern stream for this that David Salat
> has also used a lot
> On Thu, 28 May 2020, Pradyumna Bharadwaj wrote:
>
> >
> > External Email - Use Caution
> >
> > Hi Dr. Fischl,
> > Thanks for confirming that!
> > We were broadly interested in testing whether age-related differences in
> > cortical measures were impacted by the CNR in each ROI.
> >
> > Best,
> > Prad
> >
> > On Thu, May 28, 2020 at 9:33 AM Bruce Fischl  >
> > wrote:
> >   External Email
> >
> >   Hi Prad
> >
> >   what is your goal? What you describe below should work
> >
> >   cheers
> >   Bruce
> >   On Thu, 28 May 2020,
> >   Pradyumna Bharadwaj wrote:
> >
> >   >
> >   > External Email - Use Caution
> >   >
> >   > Hi Dr. Fischl,
> >   > Thank you for clarifying that!
> >   >
> >   > As a follow up question, I just wanted to double check that
> >   the method
> >   > outlined in this post is still a valid approach to obtaining
> >   the CNR values
> >   > for each of the ROIs in the Desikan-Killianyatlas(
> https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg62066.
> >   html)
> >   > .
> >   >
> >   > Briefly, you recommended converting the aparc annotation to
> >   labels in the
> >   > atlas, and applying mri_cnr to each label.
> >   >
> >   > Best,
> >   > Prad
> >   >
> >   > On Thu, May 28, 2020 at 9:14 AM Bruce Fischl
> >   
> >   > wrote:
> >   >   External Email
> >   >
> >   >   Hi Prad
> >   >
> >   >   if you use the cortex.label is will avoid using the
> >   non-cortical
> >   >   regions in
> >   >   the surface, like the midline, so should be a more
> >   accurate
> >   >   measure
> >   >
> >   >   cheers
> >   >   Bruce
> >   >
> >   >
> >   >   On Thu, 28 May 2020, Pradyumna Bharadwaj wrote:
> >   >
> >   >   >
> >   >   > External Email - Use Caution
> >   >   >
> >   >   > Hi,
> >   >   >
> >   >   > I had a question about the -label flag in mri_cnr.
> >   >   >
> >   >   > 1) When you do not use the -label option and just use
> >   the
> >   >   following command:
> >   >   >  mri_cnr $FREESURFER_HOME/subjects/bert/surf
> >   >   $FREESURFER_HOME/subjects/be
> >   >   > rt/mri/norm.mgz
> >   >   >
> >   >   > The output is as follows
> >   >   >
> >   >   >   white = 96.6+-6.0, gray = 75.7+-13.5, csf =
> >   55.3+-16.6
> >   >   gray/white CNR = 1.
> >   >   > 983, gray/csf CNR = 0.907
> >   >   >
> >   >   >  lh CNR = 1.445
> >   >   >
> >   >   > white = 96.4+-6.0, gray = 76.0+-13.3, csf = 55.6+-16.2
> >   >   gray/white CNR = 1.95
> >   >   > 2, gray/csf CNR = 0.943
> >   >   >
> >   >   > rh CNR = 1.448
> >   >   >
> >   >   >  total CNR = 1.446
> >   >   >
> >   >   >
> >   >   > 2) When you add  -label
> >   >   $FREESURFER_HOME/subjects/bert/label/lh.cortex.label
> >   >   >  $FREESURFER_HOME/subjects/bert/label/rh.cortex.label
> >   to the
> >   >   first command,
> >   >   > you get different (lower) cnr values.
> >   >   >
> >   >   > white = 96.6+-6.0, gray = 73.1+-18.9, csf = 50.8+-20.5
> >   >   gray/white CNR = 1.38
> >   >   > 9, gray/csf CNR = 0.644
> >   >   >
> >   >   > lh CNR = 1.016
> >   >   >
> >   >   > white = 96.4+-6.0, gray = 73.4+-18.8, csf = 51.0+-20.3
> >   >   gray/white CNR = 1.35
> >   >   > 3, gray/csf CNR = 0.652
> >   >   >
> >   >   > rh CNR = 1.002
> >   >   >
> >   >   > total CNR = 1.009
> >   >   >
> >   >   > How is the lh.cortex and rh.cortex label changing the
> >   CNR
> >   >   computation?
> >   >   >
> >   >   > Any inputs or thoughts on this matter are greatly
> >   appreciated!
> >   >   >
> >   >   > Thanks,
> >   >   > Prad
> >   >   >
> >   >   >___
> >   >   Freesurfer mailing list
> >   >   Freesurfer@nmr.mgh.harvard.edu
> >   >
> >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >   >
> >   >
> >   >___
> >   Freesurfer mailing list
> >   Freesurfer@nmr.mgh.harvard.edu
> 

Re: [Freesurfer] [EXT]Re: mri_cnr label flag

[Bruce Fischl]

David and Doug: can you point Prad in the right direction for looking at 
gray and white signal changes and ratios?
On Thu, 28 May 2020, Pradyumna 
Bharadwaj wrote:




External Email - Use Caution

Hi Dr. Fischl,
Thank you for suggesting that. 
Would it be possible to share a link to a page with information about this
stream or to a patch?

Thanks,
Prad

On Thu, May 28, 2020 at 9:46 AM Bruce Fischl 
wrote:
  External Email

  I see. I think Doug has a more modern stream for this that David
  Salat
  has also used a lot
  On Thu, 28 May 2020, Pradyumna Bharadwaj wrote:

  >
  > External Email - Use Caution
  >
  > Hi Dr. Fischl,
  > Thanks for confirming that!
  > We were broadly interested in testing whether age-related
  differences in
  > cortical measures were impacted by the CNR in each ROI.
  >
  > Best,
  > Prad
  >
  > On Thu, May 28, 2020 at 9:33 AM Bruce Fischl
  
  > wrote:
  >       External Email
  >
  >       Hi Prad
  >
  >       what is your goal? What you describe below should work
  >
  >       cheers
  >       Bruce
  >       On Thu, 28 May 2020,
  >       Pradyumna Bharadwaj wrote:
  >
  >       >
  >       > External Email - Use Caution
  >       >
  >       > Hi Dr. Fischl,
  >       > Thank you for clarifying that!
  >       >
  >       > As a follow up question, I just wanted to double check
  that
  >       the method
  >       > outlined in this post is still a valid approach to
  obtaining
  >       the CNR values
  >       > for each of the ROIs in 
theDesikan-Killianyatlas(https://www.mail-archive.com/freesurfer@nmr.mgh.harva
  rd.edu/msg62066.
  >       html)
  >       > .
  >       >
  >       > Briefly, you recommended converting the aparc
  annotation to
  >       labels in the
  >       > atlas, and applying mri_cnr to each label.
  >       >
  >       > Best,
  >       > Prad
  >       >
  >       > On Thu, May 28, 2020 at 9:14 AM Bruce Fischl
  >       
  >       > wrote:
  >       >       External Email
  >       >
  >       >       Hi Prad
  >       >
  >       >       if you use the cortex.label is will avoid using
  the
  >       non-cortical
  >       >       regions in
  >       >       the surface, like the midline, so should be a
  more
  >       accurate
  >       >       measure
  >       >
  >       >       cheers
  >       >       Bruce
  >       >
  >       >
  >       >       On Thu, 28 May 2020, Pradyumna Bharadwaj wrote:
  >       >
  >       >       >
  >       >       > External Email - Use Caution
  >       >       >
  >       >       > Hi,
  >       >       >
  >       >       > I had a question about the -label flag in
  mri_cnr.
  >       >       >
  >       >       > 1) When you do not use the -label option and
  just use
  >       the
  >       >       following command:
  >       >       >  mri_cnr $FREESURFER_HOME/subjects/bert/surf 
   
  >       >       $FREESURFER_HOME/subjects/be
  >       >       > rt/mri/norm.mgz
  >       >       >
  >       >       > The output is as follows
  >       >       >
  >       >       >   white = 96.6+-6.0, gray = 75.7+-13.5, csf =
  >       55.3+-16.6
  >       >       gray/white CNR = 1.
  >       >       > 983, gray/csf CNR = 0.907
  >       >       >
  >       >       >  lh CNR = 1.445
  >       >       >
  >       >       > white = 96.4+-6.0, gray = 76.0+-13.3, csf =
  55.6+-16.2
  >       >       gray/white CNR = 1.95
  >       >       > 2, gray/csf CNR = 0.943
  >       >       >
  >       >       > rh CNR = 1.448
  >       >       >
  >       >       >  total CNR = 1.446
  >       >       >
  >       >       >
  >       >       > 2) When you add  -label
  >       >     
   $FREESURFER_HOME/subjects/bert/label/lh.cortex.label
  >       >       > 
  $FREESURFER_HOME/subjects/bert/label/rh.cortex.label
  >       to the
  >       >       first command,
  >       >       > you get different (lower) cnr values.
  >       >       >
  >       >       > white = 96.6+-6.0, gray = 73.1+-18.9, csf =
  50.8+-20.5
  >       >       gray/white CNR = 1.38
  >       >       > 9, gray/csf CNR = 0.644
  >       >       >
  >       >       > lh CNR = 1.016
  >       >       >
  >       >       > white = 96.4+-6.0, gray = 73.4+-18.8, csf =
  51.0+-20.3
  >       >       gray/white CNR = 1.35
  >       >       > 3, gray/csf CNR = 0.652
  >       >       >
  >       >       > rh CNR = 1.002
  >       >       >
  >       

Re: [Freesurfer] [EXT]Re: mri_cnr label flag

[Bruce Fischl]

I see. I think Doug has a more modern stream for this that David Salat 
has also used a lot

On Thu, 28 May 2020, Pradyumna Bharadwaj wrote:



External Email - Use Caution

Hi Dr. Fischl,
Thanks for confirming that!
We were broadly interested in testing whether age-related differences in
cortical measures were impacted by the CNR in each ROI.

Best,
Prad

On Thu, May 28, 2020 at 9:33 AM Bruce Fischl 
wrote:
  External Email

  Hi Prad

  what is your goal? What you describe below should work

  cheers
  Bruce
  On Thu, 28 May 2020,
  Pradyumna Bharadwaj wrote:

  >
  > External Email - Use Caution
  >
  > Hi Dr. Fischl,
  > Thank you for clarifying that!
  >
  > As a follow up question, I just wanted to double check that
  the method
  > outlined in this post is still a valid approach to obtaining
  the CNR values
  > for each of the ROIs in the 
Desikan-Killianyatlas(https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg62066.
  html)
  > .
  >
  > Briefly, you recommended converting the aparc annotation to
  labels in the
  > atlas, and applying mri_cnr to each label.
  >
  > Best,
  > Prad
  >
  > On Thu, May 28, 2020 at 9:14 AM Bruce Fischl
  
  > wrote:
  >       External Email
  >
  >       Hi Prad
  >
  >       if you use the cortex.label is will avoid using the
  non-cortical
  >       regions in
  >       the surface, like the midline, so should be a more
  accurate
  >       measure
  >
  >       cheers
  >       Bruce
  >
  >
  >       On Thu, 28 May 2020, Pradyumna Bharadwaj wrote:
  >
  >       >
  >       > External Email - Use Caution
  >       >
  >       > Hi,
  >       >
  >       > I had a question about the -label flag in mri_cnr.
  >       >
  >       > 1) When you do not use the -label option and just use
  the
  >       following command:
  >       >  mri_cnr $FREESURFER_HOME/subjects/bert/surf   
  >       $FREESURFER_HOME/subjects/be
  >       > rt/mri/norm.mgz
  >       >
  >       > The output is as follows
  >       >
  >       >   white = 96.6+-6.0, gray = 75.7+-13.5, csf =
  55.3+-16.6
  >       gray/white CNR = 1.
  >       > 983, gray/csf CNR = 0.907
  >       >
  >       >  lh CNR = 1.445
  >       >
  >       > white = 96.4+-6.0, gray = 76.0+-13.3, csf = 55.6+-16.2
  >       gray/white CNR = 1.95
  >       > 2, gray/csf CNR = 0.943
  >       >
  >       > rh CNR = 1.448
  >       >
  >       >  total CNR = 1.446
  >       >
  >       >
  >       > 2) When you add  -label
  >       $FREESURFER_HOME/subjects/bert/label/lh.cortex.label
  >       >  $FREESURFER_HOME/subjects/bert/label/rh.cortex.label
  to the
  >       first command,
  >       > you get different (lower) cnr values.
  >       >
  >       > white = 96.6+-6.0, gray = 73.1+-18.9, csf = 50.8+-20.5
  >       gray/white CNR = 1.38
  >       > 9, gray/csf CNR = 0.644
  >       >
  >       > lh CNR = 1.016
  >       >
  >       > white = 96.4+-6.0, gray = 73.4+-18.8, csf = 51.0+-20.3
  >       gray/white CNR = 1.35
  >       > 3, gray/csf CNR = 0.652
  >       >
  >       > rh CNR = 1.002
  >       >
  >       > total CNR = 1.009
  >       >
  >       > How is the lh.cortex and rh.cortex label changing the
  CNR
  >       computation?
  >       >
  >       > Any inputs or thoughts on this matter are greatly
  appreciated!
  >       >
  >       > Thanks,
  >       > Prad
  >       >
  >       >___
  >       Freesurfer mailing list
  >       Freesurfer@nmr.mgh.harvard.edu
  >     
   https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
  >
  >
  >___
  Freesurfer mailing list
  Freesurfer@nmr.mgh.harvard.edu
  https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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

Re: [Freesurfer] [EXT]Re: mri_cnr label flag

[Pradyumna Bharadwaj]

External Email - Use Caution

Hi Dr. Fischl,

Thanks for confirming that!
We were broadly interested in testing whether age-related differences in
cortical measures were impacted by the CNR in each ROI.

Best,
Prad

On Thu, May 28, 2020 at 9:33 AM Bruce Fischl 
wrote:

> External Email
>
> Hi Prad
>
> what is your goal? What you describe below should work
>
> cheers
> Bruce
> On Thu, 28 May 2020,
> Pradyumna Bharadwaj wrote:
>
> >
> > External Email - Use Caution
> >
> > Hi Dr. Fischl,
> > Thank you for clarifying that!
> >
> > As a follow up question, I just wanted to double check that the method
> > outlined in this post is still a valid approach to obtaining the CNR
> values
> > for each of the ROIs in the Desikan-Killiany atlas(
> https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg62066.html)
> > .
> >
> > Briefly, you recommended converting the aparc annotation to labels in the
> > atlas, and applying mri_cnr to each label.
> >
> > Best,
> > Prad
> >
> > On Thu, May 28, 2020 at 9:14 AM Bruce Fischl  >
> > wrote:
> >   External Email
> >
> >   Hi Prad
> >
> >   if you use the cortex.label is will avoid using the non-cortical
> >   regions in
> >   the surface, like the midline, so should be a more accurate
> >   measure
> >
> >   cheers
> >   Bruce
> >
> >
> >   On Thu, 28 May 2020, Pradyumna Bharadwaj wrote:
> >
> >   >
> >   > External Email - Use Caution
> >   >
> >   > Hi,
> >   >
> >   > I had a question about the -label flag in mri_cnr.
> >   >
> >   > 1) When you do not use the -label option and just use the
> >   following command:
> >   >  mri_cnr $FREESURFER_HOME/subjects/bert/surf
> >   $FREESURFER_HOME/subjects/be
> >   > rt/mri/norm.mgz
> >   >
> >   > The output is as follows
> >   >
> >   >   white = 96.6+-6.0, gray = 75.7+-13.5, csf = 55.3+-16.6
> >   gray/white CNR = 1.
> >   > 983, gray/csf CNR = 0.907
> >   >
> >   >  lh CNR = 1.445
> >   >
> >   > white = 96.4+-6.0, gray = 76.0+-13.3, csf = 55.6+-16.2
> >   gray/white CNR = 1.95
> >   > 2, gray/csf CNR = 0.943
> >   >
> >   > rh CNR = 1.448
> >   >
> >   >  total CNR = 1.446
> >   >
> >   >
> >   > 2) When you add  -label
> >   $FREESURFER_HOME/subjects/bert/label/lh.cortex.label
> >   >  $FREESURFER_HOME/subjects/bert/label/rh.cortex.label to the
> >   first command,
> >   > you get different (lower) cnr values.
> >   >
> >   > white = 96.6+-6.0, gray = 73.1+-18.9, csf = 50.8+-20.5
> >   gray/white CNR = 1.38
> >   > 9, gray/csf CNR = 0.644
> >   >
> >   > lh CNR = 1.016
> >   >
> >   > white = 96.4+-6.0, gray = 73.4+-18.8, csf = 51.0+-20.3
> >   gray/white CNR = 1.35
> >   > 3, gray/csf CNR = 0.652
> >   >
> >   > rh CNR = 1.002
> >   >
> >   > total CNR = 1.009
> >   >
> >   > How is the lh.cortex and rh.cortex label changing the CNR
> >   computation?
> >   >
> >   > Any inputs or thoughts on this matter are greatly appreciated!
> >   >
> >   > Thanks,
> >   > Prad
> >   >
> >   >___
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> >
> >
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Re: [Freesurfer] Recon-all error in CA Normalize (FreeSurfer V 7.1)

[Schranzer René]

External Email - Use Caution

Hi Douglas,

Thanks for your help!
Two more questions:
Is it possible to use the individual brain mask of my skull stripped data as a 
"mask image" for the step of the NU Intensity correction in recon-all with an 
additional flag to carry out a better bias correction?
And is it possible to use ANTsN3 instead of ANTsN4, if someone wants it?

Best,
René
Von: freesurfer-boun...@nmr.mgh.harvard.edu 
 Im Auftrag von Douglas N. Greve
Gesendet: Donnerstag, 28. Mai 2020 17:47
An: freesurfer@nmr.mgh.harvard.edu
Betreff: Re: [Freesurfer] Recon-all error in CA Normalize (FreeSurfer V 7.1)

You can use it with all subjects then
On 5/28/2020 3:28 AM, Schranzer René wrote:

External Email - Use Caution
All subjects.

Best,
René

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

 Im Auftrag von Douglas N. Greve
Gesendet: Mittwoch, 27. Mai 2020 18:37
An: freesurfer@nmr.mgh.harvard.edu
Betreff: Re: [Freesurfer] Recon-all error in CA Normalize (FreeSurfer V 7.1)


Are all your subjects skull stripped or just this one?
On 5/24/2020 9:08 AM, Schranzer René wrote:

External Email - Use Caution
Hi Douglas,

First of all, thank you for your help.
I forgot to mention that I am already using skull-stripped data for the 
recon-all processing stream. Therefore, I stopped after -autorecon1 and copied 
the T1.mgz to brainmask.mgz and brainmask.auto.mgz and continued processing 
with -autorecon2 and -autorecon3. In some subjects (at some timepoints), the 
recon-all -autorecon2 -autorecon3 excited with errors, as mentioned below. Now 
I have used the following command "recon-all -hires -skullstrip -no-wsgcaatlas 
-s ${sbjID} -i ${sbj} -all" with the skull-stripped data and it worked fine 
without errors. I also compared the T1.mgz from both approaches and they looked 
identical.
My question, can I use this approach with the "-no-wsgcaatlas" for all subjects 
or is there something to consider here?

Best, René




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Re: [Freesurfer] [EXT]Re: mri_cnr label flag

[Bruce Fischl]

Hi Prad

what is your goal? What you describe below should work

cheers
Bruce
On Thu, 28 May 2020, 
Pradyumna Bharadwaj wrote:




External Email - Use Caution

Hi Dr. Fischl,
Thank you for clarifying that!

As a follow up question, I just wanted to double check that the method
outlined in this post is still a valid approach to obtaining the CNR values
for each of the ROIs in the Desikan-Killiany 
atlas(https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg62066.html)
.

Briefly, you recommended converting the aparc annotation to labels in the
atlas, and applying mri_cnr to each label.

Best,
Prad

On Thu, May 28, 2020 at 9:14 AM Bruce Fischl 
wrote:
  External Email

  Hi Prad

  if you use the cortex.label is will avoid using the non-cortical
  regions in
  the surface, like the midline, so should be a more accurate
  measure

  cheers
  Bruce


  On Thu, 28 May 2020, Pradyumna Bharadwaj wrote:

  >
  > External Email - Use Caution
  >
  > Hi,
  >
  > I had a question about the -label flag in mri_cnr.
  >
  > 1) When you do not use the -label option and just use the
  following command:
  >  mri_cnr $FREESURFER_HOME/subjects/bert/surf   
  $FREESURFER_HOME/subjects/be
  > rt/mri/norm.mgz
  >
  > The output is as follows
  >
  >   white = 96.6+-6.0, gray = 75.7+-13.5, csf = 55.3+-16.6
  gray/white CNR = 1.
  > 983, gray/csf CNR = 0.907
  >
  >  lh CNR = 1.445
  >
  > white = 96.4+-6.0, gray = 76.0+-13.3, csf = 55.6+-16.2
  gray/white CNR = 1.95
  > 2, gray/csf CNR = 0.943
  >
  > rh CNR = 1.448
  >
  >  total CNR = 1.446
  >
  >
  > 2) When you add  -label
  $FREESURFER_HOME/subjects/bert/label/lh.cortex.label
  >  $FREESURFER_HOME/subjects/bert/label/rh.cortex.label to the
  first command,
  > you get different (lower) cnr values.
  >
  > white = 96.6+-6.0, gray = 73.1+-18.9, csf = 50.8+-20.5
  gray/white CNR = 1.38
  > 9, gray/csf CNR = 0.644
  >
  > lh CNR = 1.016
  >
  > white = 96.4+-6.0, gray = 73.4+-18.8, csf = 51.0+-20.3
  gray/white CNR = 1.35
  > 3, gray/csf CNR = 0.652
  >
  > rh CNR = 1.002
  >
  > total CNR = 1.009
  >
  > How is the lh.cortex and rh.cortex label changing the CNR
  computation?
  >
  > Any inputs or thoughts on this matter are greatly appreciated!
  >
  > Thanks,
  > Prad
  >
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Re: [Freesurfer] [EXT]Re: mri_cnr label flag

[Pradyumna Bharadwaj]

External Email - Use Caution

Hi Dr. Fischl,

Thank you for clarifying that!

As a follow up question, I just wanted to double check that the method
outlined in this post is still a valid approach to obtaining the CNR values
for each of the ROIs in the Desikan-Killiany atlas (
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg62066.html).

Briefly, you recommended converting the aparc annotation to labels in the
atlas, and applying mri_cnr to each label.

Best,
Prad

On Thu, May 28, 2020 at 9:14 AM Bruce Fischl 
wrote:

> External Email
>
> Hi Prad
>
> if you use the cortex.label is will avoid using the non-cortical regions
> in
> the surface, like the midline, so should be a more accurate measure
>
> cheers
> Bruce
>
>
> On Thu, 28 May 2020, Pradyumna Bharadwaj wrote:
>
> >
> > External Email - Use Caution
> >
> > Hi,
> >
> > I had a question about the -label flag in mri_cnr.
> >
> > 1) When you do not use the -label option and just use the following
> command:
> >  mri_cnr $FREESURFER_HOME/subjects/bert/surf
> $FREESURFER_HOME/subjects/be
> > rt/mri/norm.mgz
> >
> > The output is as follows
> >
> >   white = 96.6+-6.0, gray = 75.7+-13.5, csf = 55.3+-16.6 gray/white CNR
> = 1.
> > 983, gray/csf CNR = 0.907
> >
> >  lh CNR = 1.445
> >
> > white = 96.4+-6.0, gray = 76.0+-13.3, csf = 55.6+-16.2 gray/white CNR =
> 1.95
> > 2, gray/csf CNR = 0.943
> >
> > rh CNR = 1.448
> >
> >  total CNR = 1.446
> >
> >
> > 2) When you add  -label
> $FREESURFER_HOME/subjects/bert/label/lh.cortex.label
> >  $FREESURFER_HOME/subjects/bert/label/rh.cortex.label to the first
> command,
> > you get different (lower) cnr values.
> >
> > white = 96.6+-6.0, gray = 73.1+-18.9, csf = 50.8+-20.5 gray/white CNR =
> 1.38
> > 9, gray/csf CNR = 0.644
> >
> > lh CNR = 1.016
> >
> > white = 96.4+-6.0, gray = 73.4+-18.8, csf = 51.0+-20.3 gray/white CNR =
> 1.35
> > 3, gray/csf CNR = 0.652
> >
> > rh CNR = 1.002
> >
> > total CNR = 1.009
> >
> > How is the lh.cortex and rh.cortex label changing the CNR computation?
> >
> > Any inputs or thoughts on this matter are greatly appreciated!
> >
> > Thanks,
> > Prad
> >
> >___
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Re: [Freesurfer] mri_cnr label flag

[Bruce Fischl]

Hi Prad

if you use the cortex.label is will avoid using the non-cortical regions in 
the surface, like the midline, so should be a more accurate measure


cheers
Bruce


On Thu, 28 May 2020, Pradyumna Bharadwaj wrote:



External Email - Use Caution

Hi,

I had a question about the -label flag in mri_cnr.

1) When you do not use the -label option and just use the following command:
 mri_cnr $FREESURFER_HOME/subjects/bert/surf    $FREESURFER_HOME/subjects/be
rt/mri/norm.mgz

The output is as follows

  white = 96.6+-6.0, gray = 75.7+-13.5, csf = 55.3+-16.6 gray/white CNR = 1.
983, gray/csf CNR = 0.907 


 lh CNR = 1.445

white = 96.4+-6.0, gray = 76.0+-13.3, csf = 55.6+-16.2 gray/white CNR = 1.95
2, gray/csf CNR = 0.943 


rh CNR = 1.448

 total CNR = 1.446


2) When you add  -label $FREESURFER_HOME/subjects/bert/label/lh.cortex.label
 $FREESURFER_HOME/subjects/bert/label/rh.cortex.label to the first command, 
you get different (lower) cnr values.


white = 96.6+-6.0, gray = 73.1+-18.9, csf = 50.8+-20.5 gray/white CNR = 1.38
9, gray/csf CNR = 0.644 


lh CNR = 1.016

white = 96.4+-6.0, gray = 73.4+-18.8, csf = 51.0+-20.3 gray/white CNR = 1.35
3, gray/csf CNR = 0.652 


rh CNR = 1.002

total CNR = 1.009

How is the lh.cortex and rh.cortex label changing the CNR computation?

Any inputs or thoughts on this matter are greatly appreciated!

Thanks,
Prad

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[Freesurfer] mri_cnr label flag

[Pradyumna Bharadwaj]

External Email - Use Caution

Hi,


I had a question about the -label flag in mri_cnr.

1) When you do not use the -label option and just use the following
command: mri_cnr $FREESURFER_HOME/subjects/bert/surf
$FREESURFER_HOME/subjects/bert/mri/norm.mgz

The output is as follows

  white = 96.6+-6.0, gray = 75.7+-13.5, csf = 55.3+-16.6 gray/white
CNR = 1.983, gray/csf CNR = 0.907

 lh CNR = 1.445

white = 96.4+-6.0, gray = 76.0+-13.3, csf = 55.6+-16.2 gray/white CNR
= 1.952, gray/csf CNR = 0.943

rh CNR = 1.448

 total CNR = 1.446


2) When you add  -label
$FREESURFER_HOME/subjects/bert/label/lh.cortex.label
$FREESURFER_HOME/subjects/bert/label/rh.cortex.label to the first
command, you get different (lower) cnr values.

white = 96.6+-6.0, gray = 73.1+-18.9, csf = 50.8+-20.5 gray/white CNR
= 1.389, gray/csf CNR = 0.644

lh CNR = 1.016

white = 96.4+-6.0, gray = 73.4+-18.8, csf = 51.0+-20.3 gray/white CNR
= 1.353, gray/csf CNR = 0.652

rh CNR = 1.002

total CNR = 1.009

How is the lh.cortex and rh.cortex label changing the CNR computation?

Any inputs or thoughts on this matter are greatly appreciated!

Thanks,
Prad
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Re: [Freesurfer] AAL parcellation for Freesurfer

[Douglas N. Greve]

Not that I know of. I played around a little with them. Below are my 
notes on getting it onto the colin27 brain. Good luck!


Downloaded AAL from http://www.gin.cnrs.fr/spip.php?article217,
specifically http://www.gin.cnrs.fr/AAL/aal_for_SPM8.tar.gz

The ROIs are in ROI_MNI_V4.nii, but they need to be left right
reversed

mri_convert ROI_MNI_V4.nii ROI_MNI_V4.lrrev.nii --left-right-reverse-pix

To map to the raw colin27 brain

 mri_label2vol --seg ROI_MNI_V4.lrrev.nii --temp colin27_t1_tal_lin.nii \
   --regheader colin27_t1_tal_lin.nii --o  ROI_MNI_V4.anat.lrrev.nii


On 5/28/2020 9:37 AM, Bastian Cheng wrote:


External Email - Use Caution

Dear all,

does anyone know if there is a surface parcellation file based on the 
AAL for freesurfer? I am aware that I could recon-all the MNI brain 
and project the atlas on the surface. (but maybe someone already did that)


I spend some time googeling this, but haven't found it, therefore my 
question.


all the best,
Bastian

 
	Virenfrei. www.avast.com 
 




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Re: [Freesurfer] lta_convert

[Douglas N. Greve]

lta_convert was not introduced until 6.0. You can just copy it from 6.0 
into 5.3


On 5/28/2020 11:24 AM, Alshelh, Zeynab wrote:

Hi everyone,

I am running this version of 
fs: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0


But I am having trouble running lta_convert, it returns with command 
not found.


Is there something I am missing?

Thanks



*Zeynab Alshelh, PhD*| Postdoctoral Research Fellow

Pain and Neuroinflammation Imaging Laboratory


Harvard Medical School | A. A. Martinos Center for Biomedical Imaging

Massachusetts General Hospital | 149 Thirteenth Street, Room 1101

Charlestown, MA 02129

+1 (617) 794 6838

zalsh...@mgh.harvard.edu | www.nmr.mgh.harvard.edu



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Re: [Freesurfer] Recon-all error in CA Normalize (FreeSurfer V 7.1)

[Douglas N. Greve]

You can use it with all subjects then

On 5/28/2020 3:28 AM, Schranzer René wrote:


External Email - Use Caution

All subjects.

Best,

René

*Von:*freesurfer-boun...@nmr.mgh.harvard.edu 
 *Im Auftrag von *Douglas N. Greve

*Gesendet:* Mittwoch, 27. Mai 2020 18:37
*An:* freesurfer@nmr.mgh.harvard.edu
*Betreff:* Re: [Freesurfer] Recon-all error in CA Normalize 
(FreeSurfer V 7.1)



Are all your subjects skull stripped or just this one?

On 5/24/2020 9:08 AM, Schranzer René wrote:

*External Email - Use Caution *

Hi Douglas,

First of all, thank you for your help.

I forgot to mention that I am already using skull-stripped data
for the recon-all processing stream. Therefore, I stopped after
-autorecon1 and copied the T1.mgz to brainmask.mgz and
brainmask.auto.mgz and continued processing with -autorecon2 and
-autorecon3. In some subjects (at some timepoints), the recon-all
-autorecon2 -autorecon3 excited with errors, as mentioned below.
Now I have used the following command "recon-all -hires
-skullstrip -no-wsgcaatlas -s ${sbjID} -i ${sbj} -all" with the
skull-stripped data and it worked fine without errors. I also
compared the T1.mgz from both approaches and they looked identical.

My question, can I use this approach with the "-no-wsgcaatlas" for
all subjects or is there something to consider here?

Best, René



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[Freesurfer] lta_convert

[Alshelh, Zeynab]

Hi everyone,

I am running this version of fs: 
freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0

But I am having trouble running lta_convert, it returns with command not found.

Is there something I am missing?

Thanks



Zeynab Alshelh, PhD | Postdoctoral Research Fellow

Pain and Neuroinflammation Imaging Laboratory


Harvard Medical School | A. A. Martinos Center for Biomedical Imaging

Massachusetts General Hospital | 149 Thirteenth Street, Room 1101

Charlestown, MA 02129

+1 (617) 794 6838

zalsh...@mgh.harvard.edu | www.nmr.mgh.harvard.edu

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Re: [Freesurfer] ERROR: mri_fill: could not find any points where lh and rh wm are nbrs

[Bruce Fischl]

have you also looked at the talairach transform to make sure it is 
reasonable? And does the aseg segment the cc properly? That is, does it 
label it as wm as it crosses from one hemi to the other?
On Thu, 28 May 
2020, Marina Fernández wrote:




External Email - Use Caution

Hi Bruce,
Yes, everything seems normal in the input files of mri_fill. We review it
slice by slice in freeview.

Do you know what could have happened?

Best regards,
Marina



---
---


  Hi Marina

 
  have you looked at the inputs to mri_fill? Does the
  aseg.auto_noCCseg.mgz and the wm.mgz look ok?
  Bruce

  On Wed, 27 May 2020, Marina Fernández wrote:
  External Email - Use Caution Dear Freesurfer
  experts, When I run "recon-all -autorecon2-wm -subjid post_006"
  I get the following
  error: ... #
  #@# Fill Tue May 26 16:13:33 CEST 2020
  /usr/local/freesurfer/subjects/post_006/mri  mri_fill -a
  ../scripts/ponscc.cut.log -xform transforms/talairach.lta
  -segmentation aseg.auto_noCCseg.mgz wm.mgz filled.mgz logging
  cutting plane coordinates to ../scripts/ponscc.cut.log...
  INFO: Using transforms/talairach.lta and its offset for
  Talairach volume ...
  using segmentation aseg.auto_noCCseg.mgz...
  reading input volume...done.
  searching for cutting planes...voxel to talairach voxel
  transform
   1.03994   0.01456   0.07738  -16.87541;
  -0.02607   1.18971   0.24142  -16.40842;
  -0.06544  -0.23822   1.03825   18.09422;
   0.0   0.0   0.0   1.0;
  reading colortable from MGH file...
  colortable with 14176 entries read (originally
  /usr/local/freesurfer/FreeSurferColorLUT.txt)
  voxel to talairach voxel transform
   1.03994   0.01456   0.07738  -16.87541;
  -0.02607   1.18971   0.24142  -16.40842;
  -0.06544  -0.23822   1.03825   18.09422;
   0.0   0.0   0.0   1.0;
  reading segmented volume aseg.auto_noCCseg.mgz...
  mri_fill: could not find any points where lh and rh wm  are nbrs
  No such file or directory
  Linux sleep2014 4.13.0-45-generic #50~16.04.1-Ubuntu SMP Wed May
  30 11:18:27
  UTC 2018 x86_64 x86_64 x86_64 GNU/Linux recon-all -s post_006
  exited with ERRORS at Tue May 26 16:13:41 CEST 2020 To report a
  problem, see
  http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting I have
  seen in other questions that this error may be due to the CC and
  the
  aseg files, and it is interesting because when I load
  aseg.auto.mgz or
  aseg.auto_noCCseg.mgz files in Freeview, the following message
  in Freeview
  terminal is shown in red:
  "colortable with 14176 entries read (originally
  /usr/local/freesurfer/FreesurferColorLUT.txt)", when I think
  they should be
  1475 entries. I'm using freesurfer v6.0. Could you help me to
  solve this problem?
  Thank you in advance! Marina.


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[Freesurfer] AAL parcellation for Freesurfer

[Bastian Cheng]

External Email - Use Caution

Dear all,

does anyone know if there is a surface parcellation file based on the AAL
for freesurfer? I am aware that I could recon-all the MNI brain and project
the atlas on the surface. (but maybe someone already did that)

I spend some time googeling this, but haven't found it, therefore my
question.

all the best,
Bastian


Virenfrei.
www.avast.com

<#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>
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Re: [Freesurfer] FS6: Mapping data to fsaverage6

[Tim Schäfer]

External Email - Use Caution

Nevermind, I solved it. One has to replace '--s subject1' with '--s fsaverage6' 
in the call to mri_surf2surf. Makes sense.

The lh.fsaverage6.sphere.reg file is not needed.

Tim

> On May 28, 2020 at 11:00 AM Tim Schäfer  wrote:
> 
> 
> External Email - Use Caution
> 
> Hi Doug,
> 
> thanks for your answer, that worked:
> 
> mris_apply_reg --src subject1/surf/rh.thickness --streg 
> subject1/surf/rh.sphere.reg fsaverage6/surf/rh.sphere.reg --trg 
> subject1/rh.thickness.fsaverage6.mgz
> 
> I do now want to smooth the data. For an FWHM of 5, I tried (adapted from the 
> recon-all script):
> 
> mri_surf2surf --prune --s subject1 --hemi lh --fwhm 5 --sval 
> subject1/surf/lh.thickness.fsaverage6.mgz --tval 
> subject1/surf/lh.thickness.fwhm5.fsaverage6.mgz
> 
> 
> This fails with (full output attached):
> ERROR: dimension inconsistency in source data
>Number of surface vertices = 149244
>Number of value vertices = 40962
> 
> The first value is the number of vertices in the original surface, the second 
> one is the fsaverage6 vertex count.
> 
> So I think it's once more because I do not have (and did not explicitly set 
> as '--surfreg' in the call to mri_surf2surf) the lh.fsaverage6.sphere.reg 
> file.
> 
> From reading the recon-all script, it seems I would need a file equivalent to 
> $FREESURFER_HOME/average/folding.atlas.acfb40.noaparc.i12.2016-08-02.tif to 
> obtain the reg file, but for fsaverage6. I have no idea how to get it.
> 
> So I'm stuck. Is there any way I can smooth the data?
> 
> 
> Tim
> 
> --
> Dr. Tim Schäfer
> Postdoc Computational Neuroimaging
> Department of Child and Adolescent Psychiatry, Psychosomatics and 
> Psychotherapy
> University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany
> 
> 
> > On May 27, 2020 at 6:48 PM "Douglas N. Greve"  
> > wrote:
> > 
> > 
> > It is probably easier if you don't use mris_preproc and run the 
> > resampling yourself, eg,
> > 
> > mris_apply_reg --src lh.thickness --streg lh.sphere.reg 
> > $SUBJECTS_DIR/fsaverage/surf/lh.sphere.reg --streg 
> > $SUBJECTS_DIR/fsaverage/surf/lh.sphere.reg 
> > $SUBJECTS_DIR/fsaverage6/surf/lh.sphere.reg --trg lh.thickness.fsa6.mgz
> > 
> > 
> > 
> > On 5/27/2020 7:06 AM, Tim Schäfer wrote:
> > >  External Email - Use Caution
> > >
> > > Dear FreeSurfer experts,
> > >
> > > I'm trying to resample cortical thickness data onto the fsaverage6 
> > > template subject in FreeSurfer v6. I have copied fsaverage6 into my 
> > > $SUBJECTS_DIR.
> > >
> > > I tried the following 2 commands:
> > > * mris_preproc --s subject1 --target fsaverage6 --hemi lh --meas 
> > > thickness --fwhm 5 --out lh.thickness.fwhm5.fsaverage6.mgh
> > >
> > > and alternatively:
> > >
> > > * recon-all -s subject1 -qcache -measure thickness -target fsaverage6
> > >
> > > Both fail because the file subject1/surf/lh.fsaverage6.sphere.reg is 
> > > missing (see attached recon-all.log file).
> > >
> > > How can I generate the ?h.fsaverage6.sphere.reg file?
> > >
> > > I tried:
> > > mris_register subject1/surf/lh.sphere fsaverage6/surf/lh.sphere 
> > > subject1/surf/lh.fsaverage6.sphere.reg
> > >
> > > However, that fails as well, see attached file mris_reg_output.txt for 
> > > the error message.
> > >
> > >
> > > All the best,
> > >
> > > Tim
> > >
> > > --
> > > Dr. Tim Schäfer
> > > Postdoc Computational Neuroimaging
> > > Department of Child and Adolescent Psychiatry, Psychosomatics and 
> > > Psychotherapy
> > > University Hospital Frankfurt, Goethe University Frankfurt am Main, 
> > > Germany
> > >
> > > ___
> > > Freesurfer mailing list
> > > Freesurfer@nmr.mgh.harvard.edu
> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> > 
> > ___
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> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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

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Re: [Freesurfer] Running amygdala segmentation on a warped brain (fsaverage-to-MNI152)

[Iglesias Gonzalez, Juan E.]

Hi Elizabeth,
segment_T1.sh uses a bunch of files in native space for initialization that 
you’d also have to deform, if you wanted to run it in MNI space.
I think the easiest would be to run it in native space, and then warp the 
segmentation to MNI, using e.g., the registration given by CVS.
Cheers,
/Eugenio


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



From:  on behalf of Elizabeth Haris 

Reply-To: Freesurfer support list 
Date: Wednesday, May 27, 2020 at 23:11
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: [Freesurfer] Running amygdala segmentation on a warped brain 
(fsaverage-to-MNI152)


External Email - Use Caution
Hi guys,

I’m wanting to run segmentHA_T1.sh on an MNI152 registered brain. On my 
subject, I have run recon-all, then run mri_cvs_register to obtain a brain 
image registered in MNI152 space. My questions are:


  1.  In recon-all, is there a way to specify registration to MNI152 space, or 
is it necessary to first run recon-all and then to run mri_cvs_register?
  2.  Is it possible to run the segmentHA script on the brain registered in 
MNI152 space? I’m unable to find where I would specify the use the cvs/norm.mgz 
(instead of the mri/norm.mgz file). And from what I can see in the script, the 
parameters set in lines 179/180/181 (below) point to fsaverage brain files, 
which don’t appear to be the correct targets for the new MNI152 brain; however, 
there are no corresponding output files in the cvs folder, so I am unsure how 
to define these parameters.
  3.  Is there anything I have missed and would also need to do to run the 
segmentHA script on an MNI152 brain? (I have previously run the script on the 
average brain and all went well.)

179 set ATLASMESH="$FREESURFER_HOME/average/HippoSF/atlas/AtlasMesh.gz";
180 set 
ATLASDUMP="$FREESURFER_HOME/average/HippoSF/atlas/AtlasDump.mgz";
181 set 
LUT="$FREESURFER_HOME/average/HippoSF/atlas/compressionLookupTable.txt";

Thanks in advance,

Elizabeth
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[Freesurfer] Postdoctoral position on real-time layer-fMRI at 7T available at MPI in Leipzig

[Romy Lorenz]

External Email - Use Caution

Postdoctoral position on real-time layer-fMRI at 7T

The Max Planck Institute for Human Cognitive and Brain Sciences (MPI CBS) in 
Leipzig (Germany) invites applications for a Postdoctoral Researcher Positionin 
the Department of Neurophysics with Dr. Romy Lorenz and Prof. Dr. Nikolaus 
Weiskopf.

We are looking for an ambitious postdoc interested in pushing the frontiers of 
high-resolution fMRI with the aim to resolve laminar activation in higher-level 
cognitive brain regions in real-time. In this novel and highly ambitious 
project, we want to combine real-time fMRI at 7T with machine learning (i.e., 
neuroadaptive Bayesian optimization) to advance our understanding about the 
specific functional role of different layers in higher-level brain regions. The 
postdoc will develop methods for and conduct offline (i.e., not real-time) and 
online (i.e., real-time) experiments with healthy human participants undergoing 
different cognitive tasks in the 7T scanner. The postdoc will compare different 
MR acquisition sequences (e.g., gradient-echo BOLD and VASO) and develop 
offline as well as real-time laminar analyses pipelines of 7T fMRI data. Dr. 
Romy Lorenz is also affiliated with the University of Cambridge and Stanford 
University; the postdoc will have the opportunity to benefit from our network 
of international collaborators. This project is funded by the Klaus Tschira 
Foundation (PI: RL) and the Max Planck Society. 

The ideal candidate should have a strong interest in research on high-level 
cognition and curiosity for real-time and closed-loop experimentation with 
machine learning. A strong background in fMRI data analysis is essential. The 
candidate needs to be proficient in MRI data acquisition (i.e., can operate the 
scanner and modify scanning protocols) as well as MRI data analyses packages 
(e.g., FSL/SPM and Freesurfer). Strong programming skills in Bash, Matlab 
and/or Python are required. Prior experience with 7T functional imaging is 
highly desirable but not necessary. Equally, experience with machine 
learning-methods and data/code sharing platforms (e.g. GitHub) are desirable. 
Candidates are expected to have a PhD in physics, computer science, 
mathematics, biomedical engineering, or cognitive (neuro)science and psychology.

The Max Planck Institute offers a world-leading research environment and the 
postdoc will have access to the latest cutting-edge MRI hardware (including a 
Siemens Terra 7T, Prisma 3T, Verio 3T and 3T Connectom equipped with 300mT/m 
gradients) and other excellent research facilities (306-channel MEG, EEG, 
virtual reality, eye-tracking, TMS/tES). Dedicated support staff will assist 
with the recruitment of study participants and a team of MR physicists will 
support the postdoc in the technical realisation of the project. The Institute 
offers a vibrant and engaging community of international researchers. The 
working language is English. Leipzig has been called “Germany’s new cultural 
hot spot” (The Guardian) and is located just a little over an hour train ride 
south of the center of Berlin.

The starting date for the position is 1st September 2020. The duration of the 
post is 2 years. Remuneration is based on the pay scale of the Max Planck 
Society. Female and international applicants are particularly encouraged to 
apply. The Max-Planck Society is committed to increasing the number of 
individuals with disabilities in its workforce and therefore encourages 
applications from such qualified individuals.

To apply, please submit a single PDF file containing a curriculum vitae 
(including publication list), personal statement (describing your personal 
qualifications, research interests and motivation for applying), contact 
information of three referees and academic certificates (PhD, Diploma/Master, 
Bachelor certificates). Please submit your application via our online system at 
http://www.cbs.mpg.de/vacancies (subject heading: “PD 05/20”). The deadline for 
application submission is 6th July 2020. Interviews of shortlisted candidates 
will take place likely via Zoom between 13th-17thJuly 2020.

In case of questions, please contact Romy Lorenz at lore...@cbs.mpg.de.

 

Dr. Romy Lorenz
Sir Henry Wellcome Postdoctoral Fellow

University of Cambridge & Max-Planck Institute for Human Cognitive and Brain 
Sciences 

romylorenz.com

 

 

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[Freesurfer] Postdoc position available - computational modeling and real-time fMRI neurofeedback of language

[Narly Golestani]

External Email - Use Caution


With the launch of a new ‘NCCR Evolving Language’ 
(http://www.snf.ch/SiteCollectionDocuments/nfs/Faktenblatt_NCCR_evolvinglanguage_en.pdf),
 which involves nearly 40 different research groups from a large variety of 
disciplines across Switzerland, we seek to fill a Postdoc position for a 
four-year project starting in September 2020, or at the selected candidate’s 
earliest convenience.


Our goal is to make progress in understanding the importance of prosody in 
language processing. To this end, we plan to carry out a set of studies 
involving both computational modeling of fMRI data and real-time fMRI 
neurofeedback to understand the mechanisms whereby prosody and rhythm support 
linguistic processing per se. The computational modeling work will be an 
extension of our recent work on the neural encoding of acoustic information in 
speech sounds (https://www.ncbi.nlm.nih.gov/pubmed/31285622).


The research will be done in the group of Narly Golestani 
(www.brainandlanguagelab.org) in Geneva, in 
collaboration with researchers in Switzerland and abroad (Elia Formisano in 
Maastricht, and Frank Scharnowski in Vienna).


Applicants should hold a degree in Biomedical Engineering, Computational 
Neuroscience, or a related field, and should have solid experience in human 
brain imaging, and ideally also in computational modelling (i.e. encoding / 
decoding) of fMRI data, real-time fMRI based neurofeedback, machine learning, 
statistics and programming.


The NCCR places great emphasis on gender diversity and we particularly 
encourage women to apply.


To apply, please send a cover letter, CV, names and contact information of 2-3 
references as well as any other relevant documents to 
narly.golest...@unige.ch. Feel free to contact 
me should you have any questions.

Deadline for application: June 20th 2020

-
Brain and Language Lab
Prof. Narly GOLESTANI
Department of Psychology
Campus Biotech
9 Chemin des Mines,
1202 Genève
+41 22 379 53 52
http://www.brainandlanguagelab.org
https://twitter.com/brain_lang_lab
-

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Re: [Freesurfer] FS6: Mapping data to fsaverage6

[Tim Schäfer]

External Email - Use Caution

Hi Doug,

thanks for your answer, that worked:

mris_apply_reg --src subject1/surf/rh.thickness --streg 
subject1/surf/rh.sphere.reg fsaverage6/surf/rh.sphere.reg --trg 
subject1/rh.thickness.fsaverage6.mgz

I do now want to smooth the data. For an FWHM of 5, I tried (adapted from the 
recon-all script):

mri_surf2surf --prune --s subject1 --hemi lh --fwhm 5 --sval 
subject1/surf/lh.thickness.fsaverage6.mgz --tval 
subject1/surf/lh.thickness.fwhm5.fsaverage6.mgz


This fails with (full output attached):
ERROR: dimension inconsistency in source data
   Number of surface vertices = 149244
   Number of value vertices = 40962

The first value is the number of vertices in the original surface, the second 
one is the fsaverage6 vertex count.

So I think it's once more because I do not have (and did not explicitly set as 
'--surfreg' in the call to mri_surf2surf) the lh.fsaverage6.sphere.reg file.

From reading the recon-all script, it seems I would need a file equivalent to 
$FREESURFER_HOME/average/folding.atlas.acfb40.noaparc.i12.2016-08-02.tif to 
obtain the reg file, but for fsaverage6. I have no idea how to get it.

So I'm stuck. Is there any way I can smooth the data?


Tim

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


> On May 27, 2020 at 6:48 PM "Douglas N. Greve"  wrote:
> 
> 
> It is probably easier if you don't use mris_preproc and run the 
> resampling yourself, eg,
> 
> mris_apply_reg --src lh.thickness --streg lh.sphere.reg 
> $SUBJECTS_DIR/fsaverage/surf/lh.sphere.reg --streg 
> $SUBJECTS_DIR/fsaverage/surf/lh.sphere.reg 
> $SUBJECTS_DIR/fsaverage6/surf/lh.sphere.reg --trg lh.thickness.fsa6.mgz
> 
> 
> 
> On 5/27/2020 7:06 AM, Tim Schäfer wrote:
> >  External Email - Use Caution
> >
> > Dear FreeSurfer experts,
> >
> > I'm trying to resample cortical thickness data onto the fsaverage6 template 
> > subject in FreeSurfer v6. I have copied fsaverage6 into my $SUBJECTS_DIR.
> >
> > I tried the following 2 commands:
> > * mris_preproc --s subject1 --target fsaverage6 --hemi lh --meas thickness 
> > --fwhm 5 --out lh.thickness.fwhm5.fsaverage6.mgh
> >
> > and alternatively:
> >
> > * recon-all -s subject1 -qcache -measure thickness -target fsaverage6
> >
> > Both fail because the file subject1/surf/lh.fsaverage6.sphere.reg is 
> > missing (see attached recon-all.log file).
> >
> > How can I generate the ?h.fsaverage6.sphere.reg file?
> >
> > I tried:
> > mris_register subject1/surf/lh.sphere fsaverage6/surf/lh.sphere 
> > subject1/surf/lh.fsaverage6.sphere.reg
> >
> > However, that fails as well, see attached file mris_reg_output.txt for the 
> > error message.
> >
> >
> > All the best,
> >
> > Tim
> >
> > --
> > Dr. Tim Schäfer
> > Postdoc Computational Neuroimaging
> > Department of Child and Adolescent Psychiatry, Psychosomatics and 
> > Psychotherapy
> > University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> 
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfermri_surf2surf --s $SUBJECT --hemi lh --fwhm 5 --sval 
$SUBJECT/surf/lh.thickness.fsaverage6.mgz --tval 
$SUBJECT/surf/lh.thickness.fwhm5.fsaverage6.mgz

$Id: mri_surf2surf.c,v 1.103 2015/11/05 22:07:33 greve Exp $

setenv SUBJECTS_DIR /Users/timschaefer/data/tim_only
cd /Users/timschaefer/data/tim_only
mri_surf2surf --s subject1 --hemi lh --fwhm 5 --sval 
subject1/surf/lh.thickness.fsaverage6.mgz --tval 
subject1/surf/lh.thickness.fwhm5.fsaverage6.mgz

sysname  Darwin
hostname BloodyiMac4.local
machine  x86_64
user timschaefer
srcsubject = subject1
srcval = subject1/surf/lh.thickness.fsaverage6.mgz
srctype=
trgsubject = subject1
trgval = subject1/surf/lh.thickness.fwhm5.fsaverage6.mgz
trgtype=
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
srchemi= lh
trghemi= lh
frame  = 0
fwhm-in= 0
fwhm-out   = 5
label-src  = (null)
label-trg  = (null)
OKToRevFaceOrder  = 1
UseDualHemi = 0
Reading source surface reg 
/Users/timschaefer/data/tim_only/subject1/surf/lh.sphere.reg
Loading source data
ERROR: dimension inconsistency in source data
   Number of surface vertices = 149244
   Number of value vertices = 40962
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Re: [Freesurfer] ERROR: mri_fill: could not find any points where lh and rh wm are nbrs

[Marina Fernández]

External Email - Use Caution

Hi Bruce,

Yes, everything seems normal in the input files of mri_fill. We review it
slice by slice in freeview.

Do you know what could have happened?

Best regards,
Marina



--


> Hi Marina



> have you looked at the inputs to mri_fill? Does the aseg.auto_noCCseg.mgz and
> the wm.mgz look ok?
> Bruce
>
> On Wed, 27 May 2020, Marina Fernández wrote:
> External Email - Use Caution Dear Freesurfer experts, When
> I run "recon-all -autorecon2-wm -subjid post_006" I get the following
> error: ... #
> #@# Fill Tue May 26 16:13:33 CEST 2020
> /usr/local/freesurfer/subjects/post_006/mri  mri_fill -a
> ../scripts/ponscc.cut.log -xform transforms/talairach.lta
> -segmentation aseg.auto_noCCseg.mgz wm.mgz filled.mgz logging cutting
> plane coordinates to ../scripts/ponscc.cut.log...
> INFO: Using transforms/talairach.lta and its offset for Talairach volume
> ...
> using segmentation aseg.auto_noCCseg.mgz...
> reading input volume...done.
> searching for cutting planes...voxel to talairach voxel transform
>  1.03994   0.01456   0.07738  -16.87541;
> -0.02607   1.18971   0.24142  -16.40842;
> -0.06544  -0.23822   1.03825   18.09422;
>  0.0   0.0   0.0   1.0;
> reading colortable from MGH file...
> colortable with 14176 entries read (originally
> /usr/local/freesurfer/FreeSurferColorLUT.txt)
> voxel to talairach voxel transform
>  1.03994   0.01456   0.07738  -16.87541;
> -0.02607   1.18971   0.24142  -16.40842;
> -0.06544  -0.23822   1.03825   18.09422;
>  0.0   0.0   0.0   1.0;
> reading segmented volume aseg.auto_noCCseg.mgz...
> mri_fill: could not find any points where lh and rh wm  are nbrs
> No such file or directory
> Linux sleep2014 4.13.0-45-generic #50~16.04.1-Ubuntu SMP Wed May 30
> 11:18:27
> UTC 2018 x86_64 x86_64 x86_64 GNU/Linux recon-all -s post_006 exited with
> ERRORS at Tue May 26 16:13:41 CEST 2020 To report a problem, see
> http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting I have seen in
> other questions that this error may be due to the CC and the
> aseg files, and it is interesting because when I load aseg.auto.mgz or
> aseg.auto_noCCseg.mgz files in Freeview, the following message in Freeview
> terminal is shown in red:
> "colortable with 14176 entries read (originally
> /usr/local/freesurfer/FreesurferColorLUT.txt)", when I think they should be
> 1475 entries. I'm using freesurfer v6.0. Could you help me to solve this
> problem?
> Thank you in advance! Marina.
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Re: [Freesurfer] Recon-all error in CA Normalize (FreeSurfer V 7.1)

[Schranzer René]

External Email - Use Caution

All subjects.

Best,
René

Von: freesurfer-boun...@nmr.mgh.harvard.edu 
 Im Auftrag von Douglas N. Greve
Gesendet: Mittwoch, 27. Mai 2020 18:37
An: freesurfer@nmr.mgh.harvard.edu
Betreff: Re: [Freesurfer] Recon-all error in CA Normalize (FreeSurfer V 7.1)


Are all your subjects skull stripped or just this one?
On 5/24/2020 9:08 AM, Schranzer René wrote:

External Email - Use Caution
Hi Douglas,

First of all, thank you for your help.
I forgot to mention that I am already using skull-stripped data for the 
recon-all processing stream. Therefore, I stopped after -autorecon1 and copied 
the T1.mgz to brainmask.mgz and brainmask.auto.mgz and continued processing 
with -autorecon2 and -autorecon3. In some subjects (at some timepoints), the 
recon-all -autorecon2 -autorecon3 excited with errors, as mentioned below. Now 
I have used the following command "recon-all -hires -skullstrip -no-wsgcaatlas 
-s ${sbjID} -i ${sbj} -all" with the skull-stripped data and it worked fine 
without errors. I also compared the T1.mgz from both approaches and they looked 
identical.
My question, can I use this approach with the "-no-wsgcaatlas" for all subjects 
or is there something to consider here?

Best, René



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