Re: [Freesurfer] -qcache recon-all exciting with error

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

This usually happens when a subject was run all the way through recon-all once, 
then again but only part of the way (eg, after editing). Check those subjects 
to see what happened.

On 9/10/2019 5:34 PM, Swanson,Clayton wrote:

External Email - Use Caution

Hello FreeSurfer Developers,
I am attempting to run -qcache on a cohort (55) of participants and two of them 
excited with error.  It’s worth noting I am running recon-all -qcache after 
initial recon-all then correcting for errors and re-processing again.

The error I am receiving is
ERROR: number of vertices in 
/Users/claytonswanson/Desktop/Studies/Current_Studies/MS_Study/MRS_MRI/FreeSurfer/Subject_Dir_T1/Subj_010_T1/surf/lh.thickness
 does not match surface (154775,154624)
ERROR: reading curvature file
ERROR: number of vertices in 
/Users/claytonswanson/Desktop/Studies/Current_Studies/MS_Study/MRS_MRI/FreeSurfer/Subject_Dir_T1/Subj_008_T1/surf/lh.thickness
 does not match surface (141413,141431)
ERROR: reading curvature file

I have not been able to find anything in the mail archive to answer this 
particular question.  I have attached the recon-all.log file if its of use.

Thanks for your help,
Clayton

Clayton Swanson MS
Graduate Research Assistant & PhD Student
Sensorimotor Neuroimaging Laboratory
Colorado State University
Office: (970) 491-6160
clayton.swan...@colostate.edu




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Re: [Freesurfer] freeview crash -- petsc error when opening volume

[TRISTAN J PAUTSCH]

External Email - Use Caution

In fact, I think I have narrowed the issue completely down to PETSC, 
irrespective of FreeSurfer/FreeView.

In a Hail Mary attempt, I downloaded the PETSC source code and compiled it from 
scratch; I was going to try and replace the very out of date FreeSurfer version 
(2.3.x) with the latest (3.11.x). It includes a builtin post-compile check 
mechanism for testing the libraries, and wouldn't you know it, I get the exact 
same "signal number 11 SEGV: Segmentation Violation" error when running that 
check as I do with FreeView.

As such, I will take this error to the PETSC mailing list (or whatever else 
might be available), as I'm no longer convinced the issue is directly connected 
to FreeSurfer (which explains why literally everything else in FS still works).

Thank you everyone who replied in an attempt to help out, it is greatly 
appreciated.

Tristan


From: TRISTAN J PAUTSCH 
Sent: Tuesday, September 10, 2019 3:56 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] freeview crash -- petsc error when opening volume

I'd be willing to try pretty much anything at this point...what would be the 
best way to go about doing this?

Also, what exactly is PETSC? The error seems obviously related to it, and 
Googling the issue brings up many results that aren't even related to 
FreeSurfer, rather PETSC. Does FreeSurfer perhaps contain an old version of 
PETSC?


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Ruopeng Wang 

Sent: Tuesday, September 10, 2019 3:46 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] freeview crash -- petsc error when opening volume


Hi Tristan,

Would it be possible for you to try building against VTK 8.2 and Qt 5.12.x?

Best,
Ruopeng

On 9/10/19 2:51 PM, TRISTAN J PAUTSCH wrote:

External Email - Use Caution

Thank you for the reply.

Just to clarify, everything builds successfully and there are no errors (that 
I've been able to find) for running 99% of FS commands; I installed all the 
deps listed in the makefile and followed the instructions. As with my first 
message to the list, the only issue I appear to have is when trying to open 
surface files on top of volumes in freeview.

I've attached the requested logs.

Thank you!
Tristan


From: fsbuild 
Sent: Tuesday, September 10, 2019 1:19 PM
To: freesurfer@nmr.mgh.harvard.edu 

Cc: TRISTAN J PAUTSCH 
Subject: Re: [Freesurfer] freeview crash -- petsc error when opening volume

Hello Tristan,

Please check to see that what is listed in the makefile.wiki under the section 
for Ubuntu is installed on your machine.   I would also try building with the 
instructions in the makefile if you have not already done so; that works on my 
Ubuntu 18.04 system, although I am not running the server distribution, e.g., 
type “make -f makefile.wiki help”.   The makefile based build will also save 
logs for the cmake command, build and install pass, so you could send me those 
directly - look for ./freesurfer/{cmake.log, make.log, install.log}

- R.

On Sep 10, 2019, at 13:52, TRISTAN J PAUTSCH 
 wrote:

External Email - Use Caution
Thank you so much again for the detailed reply.

I attempted your suggestion, following the instructions from the wiki to a T 
and compiled everything from scratch, and I still get the same PETSC error from 
my first post. To be thorough, I again tested on multiple machines, 
experiencing the same error on each.

I also realized I've never posted the specs of the system on which I've been 
attempting all of this, so in case it's relevant to anyone else, here they are:

OS: Ubuntu 18.04 Server
CPU: 4x Xeon Platinum 8164
RAM: 512GB DDR4 ECC (16x32GB DIMMs)


From: TRISTAN J PAUTSCH mailto:tpaut...@wisc.edu>>
Sent: Thursday, August 29, 2019 10:27 AM
To: fsbuild mailto:fsbu...@contbay.com>>
Cc: freesurfer@nmr.mgh.harvard.edu 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] freeview crash -- petsc error when opening volume

Thank you for the reply, I will try this when time permits!

Tristan


From: fsbuild 
Sent: Tuesday, August 27, 2019 4:25 PM
To: TRISTAN J PAUTSCH 
Cc: freesurfer@nmr.mgh.harvard.edu 

Subject: Re: [Freesurfer] freeview crash -- petsc error when opening volume

Hello Tristan,

Please try rebuilding the dev branch on your Ubuntu 18 machine using the 
makefile listed from the wiki, (wiki page, 
https://surfer.nmr.mgh.harvard.edu/fswiki/CMake) where the download link to 
makefile is 

Re: [Freesurfer] freeview crash -- petsc error when opening volume

[TRISTAN J PAUTSCH]

External Email - Use Caution

I'd be willing to try pretty much anything at this point...what would be the 
best way to go about doing this?

Also, what exactly is PETSC? The error seems obviously related to it, and 
Googling the issue brings up many results that aren't even related to 
FreeSurfer, rather PETSC. Does FreeSurfer perhaps contain an old version of 
PETSC?


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Ruopeng Wang 

Sent: Tuesday, September 10, 2019 3:46 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] freeview crash -- petsc error when opening volume


Hi Tristan,

Would it be possible for you to try building against VTK 8.2 and Qt 5.12.x?

Best,
Ruopeng

On 9/10/19 2:51 PM, TRISTAN J PAUTSCH wrote:

External Email - Use Caution

Thank you for the reply.

Just to clarify, everything builds successfully and there are no errors (that 
I've been able to find) for running 99% of FS commands; I installed all the 
deps listed in the makefile and followed the instructions. As with my first 
message to the list, the only issue I appear to have is when trying to open 
surface files on top of volumes in freeview.

I've attached the requested logs.

Thank you!
Tristan


From: fsbuild 
Sent: Tuesday, September 10, 2019 1:19 PM
To: freesurfer@nmr.mgh.harvard.edu 

Cc: TRISTAN J PAUTSCH 
Subject: Re: [Freesurfer] freeview crash -- petsc error when opening volume

Hello Tristan,

Please check to see that what is listed in the makefile.wiki under the section 
for Ubuntu is installed on your machine.   I would also try building with the 
instructions in the makefile if you have not already done so; that works on my 
Ubuntu 18.04 system, although I am not running the server distribution, e.g., 
type “make -f makefile.wiki help”.   The makefile based build will also save 
logs for the cmake command, build and install pass, so you could send me those 
directly - look for ./freesurfer/{cmake.log, make.log, install.log}

- R.

On Sep 10, 2019, at 13:52, TRISTAN J PAUTSCH 
 wrote:

External Email - Use Caution
Thank you so much again for the detailed reply.

I attempted your suggestion, following the instructions from the wiki to a T 
and compiled everything from scratch, and I still get the same PETSC error from 
my first post. To be thorough, I again tested on multiple machines, 
experiencing the same error on each.

I also realized I've never posted the specs of the system on which I've been 
attempting all of this, so in case it's relevant to anyone else, here they are:

OS: Ubuntu 18.04 Server
CPU: 4x Xeon Platinum 8164
RAM: 512GB DDR4 ECC (16x32GB DIMMs)


From: TRISTAN J PAUTSCH mailto:tpaut...@wisc.edu>>
Sent: Thursday, August 29, 2019 10:27 AM
To: fsbuild mailto:fsbu...@contbay.com>>
Cc: freesurfer@nmr.mgh.harvard.edu 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] freeview crash -- petsc error when opening volume

Thank you for the reply, I will try this when time permits!

Tristan


From: fsbuild 
Sent: Tuesday, August 27, 2019 4:25 PM
To: TRISTAN J PAUTSCH 
Cc: freesurfer@nmr.mgh.harvard.edu 

Subject: Re: [Freesurfer] freeview crash -- petsc error when opening volume

Hello Tristan,

Please try rebuilding the dev branch on your Ubuntu 18 machine using the 
makefile listed from the wiki, (wiki page, 
https://surfer.nmr.mgh.harvard.edu/fswiki/CMake) where the download link to 
makefile is 
https://drive.google.com/file/d/1IMEWQty_7zjsglbErQOlu_KpXb8Lmgmv/view?usp=sharing
It should go in the same subdirectory that contains the ./freesurfer tree

There are some comments in there which recommend the following be installed for 
Ubuntu, so please check these are installed before building,

  # sudo apt-get install build-essential
  # sudo apt-get install libgl1-mesa-dev freeglut3-dev mesa-common-dev
  # sudo apt-get install libblas-dev liblapack-dev
  # sudo apt-get install ocl-icd-opencl-dev
  # sudo apt-get install libxmu-dev libxi-dev
  # sudo apt-get install libopencv-dev
  # Ubuntu 16: sudo apt-get install gcc-4.9 g++-4.9 gfortran-4.9
  # Ubuntu 18: sudo apt-get install gcc-4.8 g++-4.8 gfortran-4.8 <
  # sudo apt-get install xorg xorg-dev libx11-dev
  # sudo apt-get install tcl tcl-dev tk tk-dev
  # sudo apt-get install qt5-default qtcreator
  # sudo apt-get install libqt5x11extras5-dev
  # sudo apt-get install git-annex
  # sudo apt-get install python3-dev

I’ve attached an archive containing that makefile along 

Re: [Freesurfer] freeview crash -- petsc error when opening volume

[Ruopeng Wang]

Hi Tristan,

Would it be possible for you to try building against VTK 8.2 and Qt 5.12.x?

Best,
Ruopeng

On 9/10/19 2:51 PM, TRISTAN J PAUTSCH wrote:


External Email - Use Caution

Thank you for the reply.

Just to clarify, everything builds successfully and there are no 
errors (that I've been able to find) for running 99% of FS commands; I 
installed all the deps listed in the makefile and followed the 
instructions. As with my first message to the list, the only issue I 
appear to have is when trying to open surface files on top of volumes 
in freeview.


I've attached the requested logs.

Thank you!
Tristan


*From:* fsbuild 
*Sent:* Tuesday, September 10, 2019 1:19 PM
*To:* freesurfer@nmr.mgh.harvard.edu 
*Cc:* TRISTAN J PAUTSCH 
*Subject:* Re: [Freesurfer] freeview crash -- petsc error when opening 
volume

Hello Tristan,

Please check to see that what is listed in the makefile.wiki under the 
section for Ubuntu is installed on your machine. I would also try 
building with the instructions in the makefile if you have not already 
done so; that works on my Ubuntu 18.04 system, although I am not 
running the server distribution, e.g., type “make -f makefile.wiki 
help”.   The makefile based build will also save logs for the cmake 
command, build and install pass, so you could send me those directly - 
look for ./freesurfer/{cmake.log, make.log, install.log}


- R.


On Sep 10, 2019, at 13:52, TRISTAN J PAUTSCH  wrote:

External Email - Use Caution
Thank you so much again for the detailed reply.

I attempted your suggestion, following the instructions from the wiki 
to a T and compiled everything from scratch, and I still get the same 
PETSC error from my first post. To be thorough, I again tested on 
multiple machines, experiencing the same error on each.


I also realized I've never posted the specs of the system on which 
I've been attempting all of this, so in case it's relevant to anyone 
else, here they are:


OS: Ubuntu 18.04 Server
CPU: 4x Xeon Platinum 8164
RAM: 512GB DDR4 ECC (16x32GB DIMMs)


*From:*TRISTAN J PAUTSCH mailto:tpaut...@wisc.edu>>
*Sent:*Thursday, August 29, 2019 10:27 AM
*To:*fsbuild mailto:fsbu...@contbay.com>>
*Cc:*freesurfer@nmr.mgh.harvard.edu 
>
*Subject:*Re: [Freesurfer] freeview crash -- petsc error when opening 
volume

Thank you for the reply, I will try this when time permits!

Tristan


*From:*fsbuild 
*Sent:*Tuesday, August 27, 2019 4:25 PM
*To:*TRISTAN J PAUTSCH 
*Cc:*freesurfer@nmr.mgh.harvard.edu 
*Subject:*Re: [Freesurfer] freeview crash -- petsc error when opening 
volume

Hello Tristan,

Please try rebuilding the dev branch on your Ubuntu 18 machine using 
the makefile listed from the wiki, (wiki page, 
https://surfer.nmr.mgh.harvard.edu/fswiki/CMake) where the download 
link to makefile is 
https://drive.google.com/file/d/1IMEWQty_7zjsglbErQOlu_KpXb8Lmgmv/view?usp=sharing

It should go in the same subdirectory that contains the ./freesurfer tree

There are some comments in there which recommend the following be 
installed for Ubuntu, so please check these are installed before 
building,


  # sudo apt-get install build-essential
      # sudo apt-get install libgl1-mesa-dev freeglut3-dev 
mesa-common-dev

      # sudo apt-get install libblas-dev liblapack-dev
      # sudo apt-get install ocl-icd-opencl-dev
      # sudo apt-get install libxmu-dev libxi-dev
      # sudo apt-get install libopencv-dev
      # Ubuntu 16: sudo apt-get install gcc-4.9 g++-4.9 gfortran-4.9
*      # Ubuntu 18: sudo apt-get install gcc-4.8 g++-4.8 gfortran-4.8 
<

*      # sudo apt-get install xorg xorg-dev libx11-dev
      # sudo apt-get install tcl tcl-dev tk tk-dev
      # sudo apt-get install qt5-default qtcreator
      # sudo apt-get install libqt5x11extras5-dev
      # sudo apt-get install git-annex
      # sudo apt-get install python3-dev

I’ve attached an archive containing that makefile along with the 
cmake output/build logs from my Ubuntu 18.04 machine so you can see 
what it looks like for me, see cmake_make_install_ubuntu18.tgz


I’ve run all the freeview tutorial commands using the 6.0.0 release 
on my Ubuntu 18.04 machine, but have not been able to reproduce a 
petsc error so far.


- R.


On Aug 27, 2019, at 11:27, TRISTAN J PAUTSCH  wrote:

External Email - Use Caution
Some final bits of troubleshooting information for future readers, 
since I'm assuming this issue will now get lost in the sauce...I'll 
probably try compiling everything from scratch at some point, but my 
hopes aren't particularly high


I manually compiled the missing libs to get the CentOS7 version of 
FS-dev freeview running on Ubuntu 18, and ultimately the same errors 
occur. As 

Re: [Freesurfer] error in longitudinal stream command

[Alexandru Hanganu]

External Email - Use Caution

Hello Martin,

thanks a lot for your reply.

It works now, and it was probably an error in my script, though the
commands that were used are correct (as per log files), so I still don't
know what went wrong. Maybe, for the future, the 'unmatched' error message
ought to be adjusted to outline more possible errors.

Thanks !

Best,
Alex


Le mar. 10 sept. 2019, à 03 h 02, Martin Reuter 
a écrit :

> Hi Alexandru,
>
> not sure what you mean with "unmatched" error.
>
> If this is still a problem, can you send details?
>
> Best, Martin
>
> On Wed, 2019-08-07 at 08:31 -0400, Alexandru Hanganu wrote:
> > External Email - Use Caution
> > Hello Martin,
> >
> > I was wondering - how solved the "Unmatched" error ?
> >
> > In our case, this error appears for both 5.3, 6.0 and dev, on 2
> > different clusters.
> >
> > All folders exist, are filled with data and reecon-all finished
> > without error, plus hippocampus and brainstem
> > all folders and readable: drwxrwsrwx (chmod 777 -R)
> > In the base-tps - all time points are listed correctly.
> > Re-running -base - did not solve the issue.
> > Name has no underscores '_'
> >
> > I didn't have this error on the local installation, so, I suspect it
> > might be linked to sourcing some libraries/folders, since we had to
> > source the mni folder to make it work.
> >
> > Best,
> > Alexandru.
> >
> >
> > ___
> > 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
>
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Re: [Freesurfer] freeview crash -- petsc error when opening volume

[fsbuild]

External Email - Use Caution

Hello Tristan,
Please check to see that what is listed in the makefile.wiki under the section 
for Ubuntu is installed on your machine.  I would also try building with 
the instructions in the makefile if you have not already done so; that works on 
my Ubuntu 18.04 system, although I am not running the server distribution, 
e.g., type “make -f makefile.wiki help”.  The makefile based build will 
also save logs for the cmake command, build and install pass, so you could send 
me those directly - look for ./freesurfer/{cmake.log, make.log, install.log}

- R.

On Sep 10, 2019, at 13:52, TRISTAN J PAUTSCH tpaut...@wisc.edu 
wrote:External Email - Use 
CautionThank you so much again 
for the detailed reply.I attempted your suggestion, following the 
instructions from the wiki to a T and compiled everything from scratch, and I 
still get the same PETSC error from my first post. To be thorough, I again 
tested on multiple machines, experiencing the same error on each.I also 
realized I've never posted the specs of the system on which I've been 
attempting all of this, so in case it's relevant to anyone else, here they 
are:OS: Ubuntu 18.04 ServerCPU: 4x Xeon Platinum 8164RAM: 512GB DDR4 ECC 
(16x32GB DIMMs)From:TRISTAN J PAUTSCH 
tpaut...@wisc.eduSent:Thursday, August 29, 2019 10:27 
AMTo:fsbuild 
fsbu...@contbay.comCc:freesurfer@nmr.mgh.harvard.edufreesurfer@nmr.mgh.harvard.eduSubject:Re:
 [Freesurfer] freeview crash -- petsc error when opening volumeThank you 
for the reply, I will try this when time permits!TristanFrom:fsbuild 
fsbu...@contbay.comSent:Tuesday, August 27, 2019 4:25 
PMTo:TRISTAN J PAUTSCH 
tpaut...@wisc.eduCc:freesurfer@nmr.mgh.harvard.edu 
freesurfer@nmr.mgh.harvard.eduSubject:Re: [Freesurfer] freeview 
crash -- petsc error when opening volumeHello Tristan,Please try 
rebuilding the dev branch on your Ubuntu 18 machine using the makefile listed 
from the wiki, (wiki 
page,https://surfer.nmr.mgh.harvard.edu/fswiki/CMake)where the 
download link to makefile 
ishttps://drive.google.com/file/d/1IMEWQty_7zjsglbErQOlu_KpXb8Lmgmv/view?usp=sharingIt
 should go in the same subdirectory that contains the ./freesurfer treeThere 
are some comments in there which recommend the following be installed for 
Ubuntu, so please check these are installed before building,  
# sudo apt-get install build-essential  # 
sudo apt-get install libgl1-mesa-dev freeglut3-dev mesa-common-dev  
# sudo apt-get install libblas-dev liblapack-dev  
# sudo apt-get install ocl-icd-opencl-dev  
# sudo apt-get install libxmu-dev libxi-dev  
# sudo apt-get install libopencv-dev  
# Ubuntu 16: sudo apt-get install gcc-4.9 g++-4.9 
gfortran-4.9  # Ubuntu 18: sudo apt-get install gcc-4.8 
g++-4.8 gfortran-4.8   # sudo apt-get install 
xorg xorg-dev libx11-dev  # sudo apt-get install tcl 
tcl-dev tk tk-dev  # sudo apt-get install qt5-default 
qtcreator  # sudo apt-get install 
libqt5x11extras5-dev  # sudo apt-get install 
git-annex  # sudo apt-get install python3-devI’ve 
attached an archive containing that makefile along with the cmake output/build 
logs from my Ubuntu 18.04 machine so you can see what it looks like for me, 
seecmake_make_install_ubuntu18.tgzI’ve run all the freeview tutorial 
commands using the 6.0.0 release on my Ubuntu 18.04 machine, but have not been 
able to reproduce a petsc error so far.- R.On Aug 27, 2019, at 11:27, TRISTAN J 
PAUTSCH tpaut...@wisc.edu 
wrote:External Email - Use 
CautionSome final bits of 
troubleshooting information for future readers, since I'm assuming this issue 
will now get lost in the sauce...I'll probably try compiling everything from 
scratch at some point, but my hopes aren't particularly highI manually compiled 
the missing libs to get the CentOS7 version of FS-dev freeview running on 
Ubuntu 18, and ultimately the same errors occur. As well, I replicated this 
behavior on a separate Ubuntu 18 machine in the environment, this time using a 
different lab's T1/brainmask/surface files. It would definitely seem like there 
is some sort of hard incompatibility with newer versions of freeview and 
loading surface files on top of volumes in Ubuntu 18.For what it's worth, 
it's not evident that any other part of FS has an issue; all CLI tools seem to 
work just fine.TristanFrom:TRISTAN J PAUTSCH 
tpaut...@wisc.eduSent:Friday, August 23, 2019 11:38 
AMTo:Freesurfer support list 
freesurfer@nmr.mgh.harvard.eduSubject:Re: [Freesurfer] freeview 
crash -- petsc error when opening volumeGood morning Ruopeng, thank you 
for your continued assistance!Unfortunately, I get the same error using the 
CentOS6 dev version.. I tried the CentOS7 dev version, however this led to a 
series of library errors, the majority of which are unsolvable on Ubuntu 18 
without individually compiling each necessary library (sym-linking newer 
libraries does not work).I wanted to ensure I provide the most details 
possible, so I also installed FS 5.3.0 and tested the 

Re: [Freesurfer] freeview crash -- petsc error when opening volume

[TRISTAN J PAUTSCH]

External Email - Use Caution

Thank you so much again for the detailed reply.

I attempted your suggestion, following the instructions from the wiki to a T 
and compiled everything from scratch, and I still get the same PETSC error from 
my first post. To be thorough, I again tested on multiple machines, 
experiencing the same error on each.

I also realized I've never posted the specs of the system on which I've been 
attempting all of this, so in case it's relevant to anyone else, here they are:

OS: Ubuntu 18.04 Server
CPU: 4x Xeon Platinum 8164
RAM: 512GB DDR4 ECC (16x32GB DIMMs)


From: TRISTAN J PAUTSCH 
Sent: Thursday, August 29, 2019 10:27 AM
To: fsbuild 
Cc: freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] freeview crash -- petsc error when opening volume

Thank you for the reply, I will try this when time permits!

Tristan


From: fsbuild 
Sent: Tuesday, August 27, 2019 4:25 PM
To: TRISTAN J PAUTSCH 
Cc: freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] freeview crash -- petsc error when opening volume

Hello Tristan,

Please try rebuilding the dev branch on your Ubuntu 18 machine using the 
makefile listed from the wiki, (wiki page, 
https://surfer.nmr.mgh.harvard.edu/fswiki/CMake) where the download link to 
makefile is 
https://drive.google.com/file/d/1IMEWQty_7zjsglbErQOlu_KpXb8Lmgmv/view?usp=sharing
It should go in the same subdirectory that contains the ./freesurfer tree

There are some comments in there which recommend the following be installed for 
Ubuntu, so please check these are installed before building,

  # sudo apt-get install build-essential
  # sudo apt-get install libgl1-mesa-dev freeglut3-dev mesa-common-dev
  # sudo apt-get install libblas-dev liblapack-dev
  # sudo apt-get install ocl-icd-opencl-dev
  # sudo apt-get install libxmu-dev libxi-dev
  # sudo apt-get install libopencv-dev
  # Ubuntu 16: sudo apt-get install gcc-4.9 g++-4.9 gfortran-4.9
  # Ubuntu 18: sudo apt-get install gcc-4.8 g++-4.8 gfortran-4.8 <
  # sudo apt-get install xorg xorg-dev libx11-dev
  # sudo apt-get install tcl tcl-dev tk tk-dev
  # sudo apt-get install qt5-default qtcreator
  # sudo apt-get install libqt5x11extras5-dev
  # sudo apt-get install git-annex
  # sudo apt-get install python3-dev

I’ve attached an archive containing that makefile along with the cmake 
output/build logs from my Ubuntu 18.04 machine so you can see what it looks 
like for me, see cmake_make_install_ubuntu18.tgz

I’ve run all the freeview tutorial commands using the 6.0.0 release on my 
Ubuntu 18.04 machine, but have not been able to reproduce a petsc error so far.

- R.

On Aug 27, 2019, at 11:27, TRISTAN J PAUTSCH  wrote:

External Email - Use Caution
Some final bits of troubleshooting information for future readers, since I'm 
assuming this issue will now get lost in the sauce...I'll probably try 
compiling everything from scratch at some point, but my hopes aren't 
particularly high

I manually compiled the missing libs to get the CentOS7 version of FS-dev 
freeview running on Ubuntu 18, and ultimately the same errors occur. As well, I 
replicated this behavior on a separate Ubuntu 18 machine in the environment, 
this time using a different lab's T1/brainmask/surface files. It would 
definitely seem like there is some sort of hard incompatibility with newer 
versions of freeview and loading surface files on top of volumes in Ubuntu 18.

For what it's worth, it's not evident that any other part of FS has an issue; 
all CLI tools seem to work just fine.

Tristan


From: TRISTAN J PAUTSCH mailto:tpaut...@wisc.edu>>
Sent: Friday, August 23, 2019 11:38 AM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] freeview crash -- petsc error when opening volume

Good morning Ruopeng, thank you for your continued assistance!

Unfortunately, I get the same error using the CentOS6 dev version.. I tried the 
CentOS7 dev version, however this led to a series of library errors, the 
majority of which are unsolvable on Ubuntu 18 without individually compiling 
each necessary library (sym-linking newer libraries does not work).

I wanted to ensure I provide the most details possible, so I also installed FS 
5.3.0 and tested the files...interestingly, they opened just fine, no errors at 
all.

This leads me to believe there is some strange incompatibility between Ubuntu 
18 and the 6.x/dev version of FS (at least when it comes to surface files), 
specifically related to PETSC. Is there anything else I can do to help 
troubleshoot?

Tristan


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Ruopeng Wang 

Sent: Thursday, August 22, 2019 5:00 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] freeview crash -- petsc error when opening volume

Hi Tristan,

Re: [Freesurfer] Opseq2 question

[Nasiriavanaki, Zahra]

Thank you so much.


Zahra (Mona) Nasiriavanaki

Postdoctoral Research Fellow

Martinos Center for Biomedical Imaging

Massachusetts General Hospital

149 13th Street, 149-2615

Charlestown, MA, USA, 02129




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

Sent: Tuesday, September 10, 2019 11:46 AM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] Opseq2 question

The FIR assumes that your stimuli will be presented on a "clock", eg, on
a TR (not necessarily ever TR, but every time a stimulus is presented,
it starts on a TR). The "tick" of the clock can be the TR or it can be
an integer divisor of the TR (eg, TR/2 TR/3). The finer you make it, the
more flexibility you have as to when a stimulus can occur. But you loose
power based on the divisor, eg, TR/3 means that you'll have 1/3 the power.

On 9/10/19 11:35 AM, Nasiriavanaki, Zahra wrote:
> Hi Doug
>
> Thank you very much for your reply. How does it make a difference if I
> use FIR? Could you please explain a little bit more?
>
> Thanks
> Mona
>
> *Zahra (Mona) Nasiriavanaki*
>
> Postdoctoral Research Fellow
>
> Martinos Center for Biomedical Imaging
>
> Massachusetts General Hospital
>
> 149 13th Street, 149-2615
>
> Charlestown, MA, USA, 02129
>
>
>
> 
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu
>  on behalf of Greve, Douglas
> N.,Ph.D. 
> *Sent:* Tuesday, September 10, 2019 11:24 AM
> *To:* freesurfer@nmr.mgh.harvard.edu 
> *Subject:* Re: [Freesurfer] Opseq2 question
> If you are going to assume a shape to the hemodynamic response, then I
> don't think it makes much difference. It will make a difference if you
> are going to use an FIR.
>
> On 9/9/19 10:49 AM, Nasiriavanaki, Zahra wrote:
> > Hi Freesurfer experts
> >
> > I have a question about designing an event related task. We are
> > designing a task for fear conditioning. Each stimuli presentation
> > lasts 4 seconds. My question is if we set the TR to 2 (which is a
> > multiply of 4), will it make the paradigm to have more power in signal
> > detection? Or does it not matter if the TR and stimuli presentation be
> > a multiply of each other or not?
> > I appreciate if you give me your comments on that.
> >
> > Thanks a lot
> > Mona
> >
> > *Zahra (Mona) Nasiriavanaki*
> >
> > Postdoctoral Research Fellow
> >
> > Martinos Center for Biomedical Imaging
> >
> > Massachusetts General Hospital
> >
> > 149 13th Street, 149-2615
> >
> > Charlestown, MA, USA, 02129
> >
> >
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> ___
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> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> ___
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> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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Re: [Freesurfer] Custom Segmentation of the Cortex usable with mri_compute_volume_fractions

[Pfannmoeller, Joerg Peter]

Hello Doug,

I have two different separations that I would like to achieve. Both are about a 
finer subdivision of the cortex:

1) I would like to separate the volume fractions between two directly 
neighboring cortical regions (close in 2-D surface space).
2) I would like to separate the volume fractions between two neighboring gyri 
(close together in 3-D space but far away from each other in 2-D space).

My naive idea is to generate new sub-segmentations of the cortex. Since they 
are for highly specialized applications I will most probably need to generate 
them by myself. Is that possible or is there another way to achieve this in 
FreeSurfer that I am not aware of?

Best Joerg

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

Sent: Tuesday, September 10, 2019 11:48 AM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] Custom Segmentation of the Cortex usable with 
mri_compute_volume_fractions

Do you mean you want to separate the volume fractions between two
adjacent segmentations rather than just all of cortex?

On 9/10/19 10:04 AM, Pfannmoeller, Joerg Peter wrote:
> Hello,
>
> I would like to generate a custom segmentation of the cortex. That
> segmentation should be restricted to a certain labeled region (e.g. a
> Brodmann Area). If possible I would also like to restrict the region
> to the lower half or upper half of the cortex. Let's call these new
> segmentations sub-segmentations. I would like to use
> mri_compute_volume_fractions with this segmentation to compute the
> volume fractions of the voxels in a scan that overlap with these new
> sub-segmentations of the cortex. Are there tools for this purpose in
> FreeSurfer?
>
> Best Joerg
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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Re: [Freesurfer] Custom Segmentation of the Cortex usable with mri_compute_volume_fractions

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

Do you mean you want to separate the volume fractions between two 
adjacent segmentations rather than just all of cortex?

On 9/10/19 10:04 AM, Pfannmoeller, Joerg Peter wrote:
> Hello,
>
> I would like to generate a custom segmentation of the cortex. That 
> segmentation should be restricted to a certain labeled region (e.g. a 
> Brodmann Area). If possible I would also like to restrict the region 
> to the lower half or upper half of the cortex. Let's call these new 
> segmentations sub-segmentations. I would like to use 
> mri_compute_volume_fractions with this segmentation to compute the 
> volume fractions of the voxels in a scan that overlap with these new 
> sub-segmentations of the cortex. Are there tools for this purpose in 
> FreeSurfer?
>
> Best Joerg
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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Re: [Freesurfer] Opseq2 question

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

The FIR assumes that your stimuli will be presented on a "clock", eg, on 
a TR (not necessarily ever TR, but every time a stimulus is presented, 
it starts on a TR). The "tick" of the clock can be the TR or it can be 
an integer divisor of the TR (eg, TR/2 TR/3). The finer you make it, the 
more flexibility you have as to when a stimulus can occur. But you loose 
power based on the divisor, eg, TR/3 means that you'll have 1/3 the power.

On 9/10/19 11:35 AM, Nasiriavanaki, Zahra wrote:
> Hi Doug
>
> Thank you very much for your reply. How does it make a difference if I 
> use FIR? Could you please explain a little bit more?
>
> Thanks
> Mona
>
> *Zahra (Mona) Nasiriavanaki*
>
> Postdoctoral Research Fellow
>
> Martinos Center for Biomedical Imaging
>
> Massachusetts General Hospital
>
> 149 13th Street, 149-2615
>
> Charlestown, MA, USA, 02129
>
>
>
> 
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu 
>  on behalf of Greve, Douglas 
> N.,Ph.D. 
> *Sent:* Tuesday, September 10, 2019 11:24 AM
> *To:* freesurfer@nmr.mgh.harvard.edu 
> *Subject:* Re: [Freesurfer] Opseq2 question
> If you are going to assume a shape to the hemodynamic response, then I
> don't think it makes much difference. It will make a difference if you
> are going to use an FIR.
>
> On 9/9/19 10:49 AM, Nasiriavanaki, Zahra wrote:
> > Hi Freesurfer experts
> >
> > I have a question about designing an event related task. We are
> > designing a task for fear conditioning. Each stimuli presentation
> > lasts 4 seconds. My question is if we set the TR to 2 (which is a
> > multiply of 4), will it make the paradigm to have more power in signal
> > detection? Or does it not matter if the TR and stimuli presentation be
> > a multiply of each other or not?
> > I appreciate if you give me your comments on that.
> >
> > Thanks a lot
> > Mona
> >
> > *Zahra (Mona) Nasiriavanaki*
> >
> > Postdoctoral Research Fellow
> >
> > Martinos Center for Biomedical Imaging
> >
> > Massachusetts General Hospital
> >
> > 149 13th Street, 149-2615
> >
> > Charlestown, MA, USA, 02129
> >
> >
> >
> >
> > ___
> > 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
>
> ___
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> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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Re: [Freesurfer] Opseq2 question

[Nasiriavanaki, Zahra]

Hi Doug

Thank you very much for your reply. How does it make a difference if I use FIR? 
Could you please explain a little bit more?

Thanks
Mona


Zahra (Mona) Nasiriavanaki

Postdoctoral Research Fellow

Martinos Center for Biomedical Imaging

Massachusetts General Hospital

149 13th Street, 149-2615

Charlestown, MA, USA, 02129




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

Sent: Tuesday, September 10, 2019 11:24 AM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] Opseq2 question

If you are going to assume a shape to the hemodynamic response, then I
don't think it makes much difference. It will make a difference if you
are going to use an FIR.

On 9/9/19 10:49 AM, Nasiriavanaki, Zahra wrote:
> Hi Freesurfer experts
>
> I have a question about designing an event related task. We are
> designing a task for fear conditioning. Each stimuli presentation
> lasts 4 seconds. My question is if we set the TR to 2 (which is a
> multiply of 4), will it make the paradigm to have more power in signal
> detection? Or does it not matter if the TR and stimuli presentation be
> a multiply of each other or not?
> I appreciate if you give me your comments on that.
>
> Thanks a lot
> Mona
>
> *Zahra (Mona) Nasiriavanaki*
>
> Postdoctoral Research Fellow
>
> Martinos Center for Biomedical Imaging
>
> Massachusetts General Hospital
>
> 149 13th Street, 149-2615
>
> Charlestown, MA, USA, 02129
>
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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Re: [Freesurfer] Fw: question on GLM

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

Yes, I think so

On 9/6/19 12:56 PM, Barletta, Valeria wrote:
> I did a correction for multiple comparison for every analysis... The 
> interaction survived.
> The interaction voxels do not overlap, apparently. So can I use doss 
> and consider my results ok?
> 
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu 
>  on behalf of Greve, Douglas 
> N.,Ph.D. 
> *Sent:* Friday, September 6, 2019 12:46 PM
> *To:* freesurfer@nmr.mgh.harvard.edu 
> *Subject:* Re: [Freesurfer] Fw: question on GLM
> See whether the interaction survives correction for multiple 
> comparisons. If it does not, then proceed with doss. If it does not, 
> see whether the interaction voxels overlap with your contrast of 
> interest; if not, then proceed with doss.
>
> On 9/6/2019 11:28 AM, Barletta, Valeria wrote:
>> So when I use doss   (and the contrast  -1 +1 0), I have very similar 
>> results to those that I got when I completely remove age:
>>
>>
>> 
>> *From:* freesurfer-boun...@nmr.mgh.harvard.edu 
>>  
>>  
>>  on behalf of Greve, 
>> Douglas N.,Ph.D.  
>> *Sent:* Friday, September 6, 2019 10:38 AM
>> *To:* freesurfer@nmr.mgh.harvard.edu 
>>  
>>  
>> *Subject:* Re: [Freesurfer] Fw: question on GLM
>> Did you try using DOSS?
>>
>> On 9/6/2019 9:51 AM, Barletta, Valeria wrote:
>>> Dear Doug,
>>> As you suggested yesterday, I launched the GLM to check for 
>>> interactions group-age with the contrast:
>>> 0 0 +1 -1
>>> And I obtained this image:
>>>
>>> Then I re-launched my model including age as a covariate and I 
>>> obtained very similar results:
>>>
>>>
>>> Finally, I re-launched the model excluding age and I obtained a very 
>>> different thing, which is actually more consistent with my data:
>>>
>>>
>>> How shall I interpret this? Shall I exclude age from my analysis? (I 
>>> do not really expect it to have an influence on my variable y)
>>>
>>> Thank you,
>>> Vale
>>> 
>>> *From:* freesurfer-boun...@nmr.mgh.harvard.edu 
>>>  
>>>  
>>>  on behalf of Greve, 
>>> Douglas N.,Ph.D.  
>>> 
>>> *Sent:* Wednesday, August 28, 2019 6:03 PM
>>> *To:* freesurfer@nmr.mgh.harvard.edu 
>>>  
>>>  
>>> *Subject:* Re: [Freesurfer] Fw: question on GLM
>>> It is showing
>>> b = g2 - g1
>>> so negative means that g1 > g2
>>>
>>>
>>> On 8/28/19 1:59 PM, Barletta, Valeria wrote:
>>> >
>>> > Forgot to report my contrast matrix:
>>> >
>>> > -1 1 0 0
>>> >
>>> >
>>> > Thanks,
>>> > Valeria
>>> > 
>>> 
>>> > *From:* Barletta, Valeria
>>> > *Sent:* Wednesday, August 28, 2019 1:02 PM
>>> > *To:* Freesurfer support list  
>>> 
>>> > *Subject:* question on GLM
>>> > Good afternoon!
>>> > I have a question on the Freesurfer GLM.
>>> > The command:
>>> >
>>> > mri_glmfit-sim --glmdir
>>> > ${glm_dir}/${hemi}_contrast-${contrast}_${surfname_cme} --cache 
>>> 1.3 neg
>>> >
>>> > is giving me blue clusters (see attached picture). Do blue clusters
>>> > mean that my variable y is LOWER in the FIRST or the SECOND group
>>> > listed in the FSGD file?
>>> >
>>> > Thanks,
>>> > Valeria
>>> >
>>> > ___
>>> > Freesurfer mailing list
>>> > Freesurfer@nmr.mgh.harvard.edu 
>>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>
>>>
>>> ___
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>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>
>>> ___
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>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
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>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
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Re: [Freesurfer] Opseq2 question

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

If you are going to assume a shape to the hemodynamic response, then I 
don't think it makes much difference. It will make a difference if you 
are going to use an FIR.

On 9/9/19 10:49 AM, Nasiriavanaki, Zahra wrote:
> Hi Freesurfer experts
>
> I have a question about designing an event related task. We are 
> designing a task for fear conditioning. Each stimuli presentation 
> lasts 4 seconds. My question is if we set the TR to 2 (which is a 
> multiply of 4), will it make the paradigm to have more power in signal 
> detection? Or does it not matter if the TR and stimuli presentation be 
> a multiply of each other or not?
> I appreciate if you give me your comments on that.
>
> Thanks a lot
> Mona
>
> *Zahra (Mona) Nasiriavanaki*
>
> Postdoctoral Research Fellow
>
> Martinos Center for Biomedical Imaging
>
> Massachusetts General Hospital
>
> 149 13th Street, 149-2615
>
> Charlestown, MA, USA, 02129
>
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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Re: [Freesurfer] Command line tksurfer: use of the color scale "Color Wheel" {Disarmed}

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

When you run rtview, it will run tksurfer. To get to the color wheel, 
open View->Configure->Overlay, then select "Color Wheel" under the 
"Color Scale" tab.

On 9/10/19 4:03 AM, Caspar M. Schwiedrzik wrote:
>
> External Email - Use Caution
>
> Hi Doug and Roupeng,
> did you already have the chance to look into the question how to 
> display the color wheel with rtview and/or freeview?
> Thank you! Caspar
>
> Am Sa., 7. Sept. 2019 um 13:13 Uhr schrieb Caspar M. Schwiedrzik 
>  >:
>
> External Email - Use Caution
>
> Hi Doug and Ruopeng,
> it would be amazing if you could dig out the information on how to
> display the color wheel.
> Looking forward to what you find!
> Caspar
>
>
> Am Fr., 6. Sept. 2019 um 17:14 Uhr schrieb Greve, Douglas N.,Ph.D.
> mailto:dgr...@mgh.harvard.edu>>:
>
> Hi Caspar, sorry for the delay. I have not used the retinotoy
> stream in a long, long time so I don't know off the top of my
> head. I'll have to look into it. tksurfer (from rtview) does
> have a way to display using the color wheel, but I don't
> remember how to do it.
>
> Ruopeng, can freeview display using a color wheel?
>
> On 9/6/2019 6:16 AM, Caspar M. Schwiedrzik wrote:
>>
>> External Email - Use Caution
>>
>> Hi!
>> I wanted to ask again whether there is a way to display the
>> color wheel in rtview and/or freeview. We are debugging our
>> analyses and it would be immensely helpful to have a legend
>> that specifies the color assignments.
>> Thank you,
>> Caspar
>>
>> On Wed, Sep 4, 2019 at 14:30 Caspar M. Schwiedrzik
>> > > wrote:
>>
>> Hi!
>> I am following up on this thread trying to understand how
>> to make the color wheel visible in rtview, or, if
>> necessary, in freeview.
>> Thank you! Caspar
>>
>>
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>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer  
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>
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Re: [Freesurfer] Command failed in QDEC

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

It might be that the design matrix is ill-conditioned. Did it print 
anything to the terminal? Also, we are not really supporting qdec 
anymore, so you can try using the command-line stream (ie, mris_preproc, 
mri_surf2surf, mri_glmfit, mri_glmfit-sim)

On 9/10/19 2:36 AM, James Karantonis wrote:
>
> External Email - Use Caution
>
> Hi there,
>
> In QDEC, I have successfully imported my data tables, generated stats, 
> and when I go to analyse, I get the following error: “Error in 
> Analyze: command failed mri_glmfit –y…”. It seems this error only 
> occurs when I use the two variables of age and ICV. Whenever I remove 
> one of those variables, or add any additional variables, it appears to 
> work. Specifically, this is for two comparisons, between bipolar 
> patients and healthy controls, bipolar and schizophrenia patients, but 
> it works for schizophrenia and healthy control comparisons. I’m 
> working on an iMac running High Sierra and Freesurfer v.6.
>
> Any information on how to resolve this error would be greatly 
> appreciated! I’ve attached a screenshot for reference.
>
> Kind regards,
>
> James
>
>
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Re: [Freesurfer] Convert nifti atlas into .annot file

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

Run recon-all on the anatomical templates, then use mri_vol2surf (wiht 
--projfrac 0.5) to sample the segmentations onto the surface, then use 
mris_seg2annot to convert to annotation

On 9/9/19 6:10 PM, Dev vasu wrote:
>
> External Email - Use Caution
>
>
> Dear all,
>
> How can i create .annot files for both left and right hemisphere from 
> nifti atlases http://www.gin.cnrs.fr/en/tools/aal/
>
> are there any specific guidelines or  commands for surface based 
> parcellation ?
>
> Thanks
> Vasudev
>
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Re: [Freesurfer] Command line tksurfer: use of the color scale "Color Wheel" {Disarmed}

[Ruopeng Wang]

Hi Caspar,

In freeview, once you load a overlay onto a surface, you can click on 
"Configure" button under "overlay" settings on the panel to adjust 
overlay display. There is a colorwheel option in it. From command-line, 
it can be activated like this:


freeview -f lh.orig:overlay=lh.thickness:overlay_color=colorwheel

Best,
Ruopeng

On 9/10/19 4:03 AM, Caspar M. Schwiedrzik wrote:


External Email - Use Caution

Hi Doug and Roupeng,
did you already have the chance to look into the question how to 
display the color wheel with rtview and/or freeview?

Thank you! Caspar

Am Sa., 7. Sept. 2019 um 13:13 Uhr schrieb Caspar M. Schwiedrzik 
>:


External Email - Use Caution

Hi Doug and Ruopeng,
it would be amazing if you could dig out the information on how to
display the color wheel.
Looking forward to what you find!
Caspar


Am Fr., 6. Sept. 2019 um 17:14 Uhr schrieb Greve, Douglas N.,Ph.D.
mailto:dgr...@mgh.harvard.edu>>:

Hi Caspar, sorry for the delay. I have not used the retinotoy
stream in a long, long time so I don't know off the top of my
head. I'll have to look into it. tksurfer (from rtview) does
have a way to display using the color wheel, but I don't
remember how to do it.

Ruopeng, can freeview display using a color wheel?

On 9/6/2019 6:16 AM, Caspar M. Schwiedrzik wrote:


External Email - Use Caution

Hi!
I wanted to ask again whether there is a way to display the
color wheel in rtview and/or freeview. We are debugging our
analyses and it would be immensely helpful to have a legend
that specifies the color assignments.
Thank you,
Caspar

On Wed, Sep 4, 2019 at 14:30 Caspar M. Schwiedrzik
mailto:cschwie...@rockefeller.edu>> wrote:

Hi!
I am following up on this thread trying to understand how
to make the color wheel visible in rtview, or, if
necessary, in freeview.
Thank you! Caspar


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[Freesurfer] Custom Segmentation of the Cortex usable with mri_compute_volume_fractions

[Pfannmoeller, Joerg Peter]

Hello,

I would like to generate a custom segmentation of the cortex. That segmentation 
should be restricted to a certain labeled region (e.g. a Brodmann Area). If 
possible I would also like to restrict the region to the lower half or upper 
half of the cortex. Let's call these new segmentations sub-segmentations. I 
would like to use mri_compute_volume_fractions with this segmentation to 
compute the volume fractions of the voxels in a scan that overlap with these 
new sub-segmentations of the cortex. Are there tools for this purpose in 
FreeSurfer?

Best Joerg
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Re: [Freesurfer] Fwd: eTIV and brainmask mismatch on Philips data

[Agnieszka Sabisz]

External Email - Use Caution

Dear Doug,
Thanks a lot!!!
3t flag helps very much. The data looks fine now.
All the best
Agnieszka

pon., 19 sie 2019 o 15:59 Greve, Douglas N.,Ph.D. 
napisał(a):

> Hi Agnieska, sorry for the delay. It looks like the contrast is slightly
> different than FS expects. I ran it with the -3T flag (which changes the
> talairach atlas), and it seemed to run fine on that subject. Try it out.
> best
> doug
>
> On 8/19/2019 1:23 AM, Agnieszka Sabisz wrote:
>
> External Email - Use Caution
> Dear Doug,
> I uploaded the data by ftp in Windows 10 on 1st Aug. I hope You can see a
> tar file. The file's name is HTN_Con_096 and it contains the subject's
> folder after recon_all. Do You need any other data?
> All the best
>
> czw., 1 sie 2019 o 11:44 Agnieszka Sabisz 
> napisał(a):
>
>> Dear Doug,
>> I uploaded the data by ftp in Windows 10. I hope You can see a tar file.
>> The file's name is HTN_Con_096 and it contains the subject's folder after
>> recon_all. Do You need any other data?
>> All the best
>> Agnieszka
>>
>> pon., 29 lip 2019 o 22:44 Greve, Douglas N.,Ph.D. 
>> napisał(a):
>>
>>> That is a little strange. Can you tar up the data and upload it to
>>> ftp://surfer.nmr.mgh.harvard.edu/transfer/incoming
>>> Let me know when it is there and what the file name is
>>>
>>> On 7/24/19 4:53 AM, Agnieszka Sabisz wrote:
>>> >
>>> > External Email - Use Caution
>>> >
>>> > Dear Freesurfer Team,
>>> > I checked skull stripping and I think it's all right. (see in
>>> attachment)
>>> > The registration looks all right in translational directions but not
>>> > in scaling. In the attachment you can see the comparison between
>>> > tkregister view and freeview of the same patient.
>>> > What may be the reason and how to cope with that? We cannot normalize
>>> > the volume data to eTIV (as it is not proper), what value should we
>>> > use instead?
>>> > Best regards,
>>> > Agnieszka
>>> >
>>> > sob., 22 cze 2019 o 02:15 Greve, Douglas N.,Ph.D.
>>> > mailto:dgr...@mgh.harvard.edu>> napisał(a):
>>> >
>>> > If the registration looks ok then it probably means that the skull
>>> > stripping was too aggressive. Have you looked at the skull
>>> stripping?
>>> >
>>> > On 6/14/2019 1:40 PM, Agnieszka Sabisz wrote:
>>> >>
>>> >> External Email - Use Caution
>>> >>
>>> >> Hi all!
>>> >>
>>> >> We are running FS v.6.0. on a supercomputer operating on Linux.
>>> >> We have two sets of data - one from 1.5T Aera Siemens, second
>>> >> from 3.0T Achieva TX Philips. The T1 images on both scanners have
>>> >> comparable CNR, with an isotropic resolution of 1mm3 each. The
>>> >> recon-all finished with no errors, but in approximately half of
>>> >> the Philips data there is a significant (up to 40%) difference
>>> >> between the brain mask volume and eTIV (no such problem on
>>> >> Siemens). We inspected the Talairach registration (as is pointed
>>> >> that eTIV is calculated upon it) in the mismatched data with:
>>> >> tkregister2 --mgz --s  --fstal --surf orig
>>> >> and in the corrupted data the brain mask and the WM-GM borders
>>> >> align in terms of placement but are of a wrong scale
>>> >> (proportionate to the "brainmask-to-eTIV" difference).
>>> >>
>>> >> What may be the reason and how to cope with that? We cannot
>>> >> normalize the volume data to eTIV (as it is not proper), what
>>> >> value should we use instead?
>>> >>
>>> >> Attached you will find example tkregister2 output screenshots.
>>> >>
>>> >> Best regards,
>>> >> Agnieszka Sabisz
>>> >>
>>> >>
>>> >>
>>> >>
>>> >> ___
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>>> >
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>>> >
>>> >
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>>
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Re: [Freesurfer] Command line tksurfer: use of the color scale "Color Wheel" {Disarmed}

[Caspar M. Schwiedrzik]

External Email - Use Caution

Hi Doug and Roupeng,
did you already have the chance to look into the question how to display
the color wheel with rtview and/or freeview?
Thank you! Caspar

Am Sa., 7. Sept. 2019 um 13:13 Uhr schrieb Caspar M. Schwiedrzik <
cschwie...@mail.rockefeller.edu>:

> External Email - Use Caution
>
> Hi Doug and Ruopeng,
> it would be amazing if you could dig out the information on how to display
> the color wheel.
> Looking forward to what you find!
> Caspar
>
>
> Am Fr., 6. Sept. 2019 um 17:14 Uhr schrieb Greve, Douglas N.,Ph.D. <
> dgr...@mgh.harvard.edu>:
>
>> Hi Caspar, sorry for the delay. I have not used the retinotoy stream in a
>> long, long time so I don't know off the top of my head. I'll have to look
>> into it. tksurfer (from rtview) does have a way to display using the color
>> wheel, but I don't remember how to do it.
>>
>> Ruopeng, can freeview display using a color wheel?
>>
>> On 9/6/2019 6:16 AM, Caspar M. Schwiedrzik wrote:
>>
>> External Email - Use Caution
>> Hi!
>> I wanted to ask again whether there is a way to display the color wheel
>> in rtview and/or freeview. We are debugging our analyses and it would be
>> immensely helpful to have a legend that specifies the color assignments.
>> Thank you,
>> Caspar
>>
>> On Wed, Sep 4, 2019 at 14:30 Caspar M. Schwiedrzik <
>> cschwie...@rockefeller.edu> wrote:
>>
>>> Hi!
>>> I am following up on this thread trying to understand how to make the
>>> color wheel visible in rtview, or, if necessary, in freeview.
>>> Thank you! Caspar
>>>
>>>
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Re: [Freesurfer] error in longitudinal stream command

[Martin Reuter]

Hi Alexandru, 

not sure what you mean with "unmatched" error. 

If this is still a problem, can you send details?

Best, Martin

On Wed, 2019-08-07 at 08:31 -0400, Alexandru Hanganu wrote:
> External Email - Use Caution
> Hello Martin,
> 
> I was wondering - how solved the "Unmatched" error ?
> 
> In our case, this error appears for both 5.3, 6.0 and dev, on 2
> different clusters.
> 
> All folders exist, are filled with data and reecon-all finished
> without error, plus hippocampus and brainstem
> all folders and readable: drwxrwsrwx (chmod 777 -R)
> In the base-tps - all time points are listed correctly.
> Re-running -base - did not solve the issue.
> Name has no underscores '_'
> 
> I didn't have this error on the local installation, so, I suspect it
> might be linked to sourcing some libraries/folders, since we had to
> source the mni folder to make it work.
> 
> Best,
> Alexandru.
> 
> 
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Re: [Freesurfer] [FREESURFER] longitudinal processing base_tmps does not exist error

[Martin Reuter]

Hi Seonjoo, 

your base command is missing the "-all" so no processing is done in the
base, which is why the file is missing later..

Best, Martin



On Wed, 2019-08-07 at 17:27 +, Lee, Seonjoo wrote:
> External Email - Use Caution
> Dear Freesurfer,
> Could you help me to resolve this error? I looked up the previous
> postings, but the recommendation (copying files in the same folder
> etc.) did not help.
> Thank you.
>  
>  
> $ recon-all -base template -tp 002_S_0295_S32678 -tp
> 002_S_0295_S567612 -sd $SUBJECTS_DIR
> Subject Stamp: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c
> Current Stamp: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c
> INFO: SUBJECTS_DIR is /Users/seonjoolee/ADNI_long/tmp
> Actual FREESURFER_HOME /Applications/freesurfer
> Darwin Seonjoos-iMac.nyspi.local 18.5.0 Darwin Kernel Version 18.5.0:
> Mon Mar 11 20:40:32 PDT 2019; root:xnu-4903.251.3~3/RELEASE_X86_64
> x86_64
>  
> Started at Wed Aug 7 10:24:55 EDT 2019 
> Ended   at Wed Aug 7 10:24:56 EDT 2019
> #@#%# recon-all-run-time-hours 0.000
> recon-all -s template finished without error at Wed Aug  7 10:24:56
> EDT 2019
> done
>  
>  
> $ recon-all -long 002_S_0295_S32678 template -all
> ERROR: file /Users/ll/ADNI_long/tmp/template/base-tps does not exist!
>  
>  
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Re: [Freesurfer] Correcting defect problem after checking skull stripped and editing wm.mgz

[Jiun Wei Chen]

External Email - Use Caution

Hi Bruce

Thanks so much for your quick reply.
I had overlaid the ?h.defect_labels on the inflated.nofix and orig.nofix. I
adjusted the threshold to focus on the largest defect. Although I could
look at the defect, I couldn't figure how to fix it manually because the
defect is too large.
In addition, I separately overlaid the ?h.defect_labels on the
inflated.nofix and orig.nofix but I actually don't know how to use
inflated.nofix to look for the defect. I don't know the difference between
defect_labels overlaid on the inflated.nofix and orig.nofix.

Excuse me, I also want to ask another question. Because I also check the
aseg.auto and aseg.presurf and find there is bad segmentation, can I
only modify segmentation results manually or is there another approach to
solve the bad segmentation problem? In some cases, the contrast of the
image is not obvious and thus modifying segmentation results manually is
hard.

I have put these two subject directories named Stroke_subject001.tar.gz and
Stroke_subject001.tar.gz on your ftp.

Thank you so much for your help.

Best regards,

Jiun-Wei

On Mon, 9 Sep 2019 at 20:39, Bruce Fischl 
wrote:

> Hi Jiun-Wei
>
> have you looked at the ?h.defect_labels overlaid on the inflated.nofix
> and orig.nofix surfaces? That will tell you where the defect is that is
> causing you trouble. If you have lesions they may be the source of the
> issue. If you can't sort it out you can tar and gzip the entire subject
> directory and put it on our ftp site for us to have a look
> cheers
> Bruce
> On Mon, 9 Sep
> 2019, Jiun Wei Chen wrote:
>
> >
> > External Email - Use Caution
> >
> > Dear freesurfer experts,
> > When executing recon-all in two subjects with brain lesions, the
> recon-all
> > process stopped at CORRECTING DEFECT 13 (vertices=49319, convex
> hull=12973,
> > v0=65403) and
> > CORRECTING DEFECT 6 (vertices=23529, convex hull=6740, v0=16029),
> > respectively.
> >
> > After reading the relevant problem from freesufer mailing list, I had
> > checked the skull and cerebellum not attached to the surface, two
> > hemispheres are separated using freeview. In addition, I also load
> > the brain.mgz, wm.mgz, ?h.orig.nofix and ?h.inflated.nofix and separately
> > overlap the ?h.defect_label onto ?h.orig.nofix  , ?h.inflated.nofix to
> edit
> > wm.mgz to solve this problem.
> >
> > However, after editing wm.mgz in two subjects, the recon-all process
> still
> > stopped at CORRECTING DEFECT 0 (vertices=32853, convex hull=7926) and
> > CORRECTING DEFECT 6 (vertices=16533, convex hull= 4510) , respectively.
> >
> > Although I try to erase the non-white matter and label voxels as white
> > matter as much as possible, there are too many voxels I think I need to
> > label, which may cause the failure.
> >
> > I can't figure out how to continue to solve this problem. I use
> freesurfer
> > version 6.0.0.
> >
> > I really appreciate your help. Thanks a lot.
> >
> > Best regards,
> >
> > Jiun-Wei
> >
> >
> >
> >
> >
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