[Freesurfer] Rerunning freesurfer with manual edits and T2 or FLAIR pial refinement

[VINCENT KOPPELMANS]

External Email - Use Caution

I have made manual edits to a subject that was initially run with the -FLAIR 
 and -FLAIRpial input flags. When I want to rerun freesurfer to 
implement these edits should I add these flags again, or is it sufficient to 
run recon-all -all?
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Re: [Freesurfer] Freeview CLI feature request

[VINCENT KOPPELMANS]

External Email - Use Caution

Thank you for your quick and positive reply.

Best,
Vincent

From:  on behalf of Ruopeng Wang 

Reply-To: Freesurfer support list 
Date: Wednesday, 25 March 2020 at 16:41
To: Freesurfer support list 
Subject: Re: [Freesurfer] Freeview CLI feature request

Sure. We’ll add those in.

Best,
Ruopeng


On Mar 25, 2020, at 6:28 PM, VINCENT KOPPELMANS 
mailto:vincent.koppelm...@utah.edu>> wrote:

External Email - Use Caution

Dear FreeSurfer team,

I am currently using FreeView v3.0, Darwin Build Mar 25 2020 00:009:39

Would it be possible to add the following features as command line flags to 
FreeView?

1) Set opacity for a surface
It is currently only possible via CLI to set opacity for volumes, surface 
overlays, and labels, but not for the surface itself.

2) Set smoothing iterations for isosurfaces
This can only be done in the GUI, not yet via the CLI.

Thank you for your consideration.

- Vincent
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[Freesurfer] Freeview CLI feature request

[VINCENT KOPPELMANS]

External Email - Use Caution

Dear FreeSurfer team,

I am currently using FreeView v3.0, Darwin Build Mar 25 2020 00:009:39

Would it be possible to add the following features as command line flags to 
FreeView?

1) Set opacity for a surface
It is currently only possible via CLI to set opacity for volumes, surface 
overlays, and labels, but not for the surface itself.

2) Set smoothing iterations for isosurfaces
This can only be done in the GUI, not yet via the CLI.

Thank you for your consideration.

- Vincent
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Re: [Freesurfer] Surface edits: Cortex that extends into the putamen + Missing gray matter

[Vincent Koppelmans]

Hi Bruce,

Thank you for your reply. 

The aseg seems to be okay:
https://www.dropbox.com/s/j1ac0ftxw8iiv34/Putamen.png?dl=0 
<https://www.dropbox.com/s/j1ac0ftxw8iiv34/Putamen.png?dl=0> 
Do you have any other suggestions?

Here is an extra image of the cortical ribbon. Maybe this helps:
https://www.dropbox.com/s/ycav96v91e4ncbg/Cortex.png?dl=0 
<https://www.dropbox.com/s/ycav96v91e4ncbg/Cortex.png?dl=0> 

Thanks!

- Vincent



On Mon, 03 Jul 2017, Bruce Fischl wrote:

Hi Vincent

the putamen error probably means that the aseg is wrong, and if so, you can 
correct the aseg and rerun autorecon2-wm and autorecon3 I believe.
For the medial ttemporal lobe issue is that really cortex? I can't really tell 
from the single coronal slice. I'll cc Jean Augustinack to see if she has an 
opinion.
cheers
Bruce


On Fri, 30 Jun 2017, Vincent Koppelmans wrote:
Hi all,

I was wondering how to fix the following issues:
1) The cortical ribbon extends into the gray matter of the putamen (see the top 
row of the attached image).

2) Cortical gray matter is missing in the medial temporal lobes (see the bottom 
row of the attached image).

I can’t find solutions for these particular issues under 
https://surfer.nmr.mgh.harvard.edu/fswiki/Edits 
<https://surfer.nmr.mgh.harvard.edu/fswiki/Edits> 
<https://surfer.nmr.mgh.harvard.edu/fswiki/Edits 
<https://surfer.nmr.mgh.harvard.edu/fswiki/Edits>>

How should I approach this? Suggestions are very much welcome.

Thank you!

- Vincent



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[Freesurfer] Surface edits: Cortex that extends into the putamen + Missing gray matter

[Vincent Koppelmans]

Hi all,

I was wondering how to fix the following issues:
1) The cortical ribbon extends into the gray matter of the putamen (see 
the top row of this image: 
https://www.dropbox.com/s/x1euf9otl2nv6ff/Fix.png?dl=0).

2) Cortical gray matter is missing in the medial temporal lobes (see the 
bottom row of this image: 
https://www.dropbox.com/s/x1euf9otl2nv6ff/Fix.png?dl=0).

I can’t find solutions for these particular issues under 
https://surfer.nmr.mgh.harvard.edu/fswiki/Edits

How should I approach this? Suggestions are very much welcome.

Thank you!

- Vincent


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Re: [Freesurfer] Longitudinal TRACULA: mri_convert

[Vincent Koppelmans]

Dear Anastasia,

I emailed with Dr. Knut Jørgen Bjuland because he had a similar issue 
(https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg39745.html). 
He mentioned that obtaining a new license could solve the issue. It did, 
so my problem is resolved.

Best,

Vincent




Dear Anastasia,

I have checked the image and it looks good. I don't think the image is
the problem, especially considering that my issue is also popping up
with standard data. See for example the following code:


$ echo $FREESURFER_HOME
/home/mriuser/privatemodules/freesurfer

$ cksum $(which mri_convert)
1305133180 29171478 /home/mriuser/privatemodules/freesurfer/bin/mri_convert

$ echo $FSLDIR
/home/mriuser/privatemodules/fsl

$ mri_convert ${FSLDIR}/data/standard/MNI152_T1_1mm.nii.gz test.mgh
mri_convert
/home/mriuser/privatemodules/fsl/data/standard/MNI152_T1_1mm.nii.gz
test.mgh
$Id: mri_convert.c,v 1.213 2014/07/29 19:22:31 fischl Exp $
reading from
/home/mriuser/privatemodules/fsl/data/standard/MNI152_T1_1mm.nii.gz...
crypt_gkey = (null)
Segmentation fault (core dumped)




The reason I am posting this with 'Longitudinal TRACULA' in the title is
because I only have this issue with the mri_convert that is bundled with
the TRACULA update (see my first post). The original mri_convert bundled
with the centOS6 64bit version of FS 5.3.0 (stable) does let me convert
files. However, this version does not allow multiple frame numbers:

Original frame options of mri_convert (FS v5.3.0 stable centos6 64)
  -f,  --frame frameno
  keep only 0-based frame number

Frame options of the updated mri_convert
(tracula.update.centos6_x86_64.5.3.2014_05_26.tar.gz)
  -f,  --frame frameno [...]
  keep only 0-based frame number(s)

Longitudinal TRACULA pushes multiple files as arguments to 'mri_convert
--frame', which is why I need the updated version.

Do you have any suggestions for me?

Thank you!

best,

Vincent




Hi Vincent - Looks like an mri_convert error, so not specific to TRACULA
but
probably something about the format of your input nifti volume. How did you
create that volume? Can you open it in freeview and view it normally?


a.y


From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Vincent Koppelmans
[vkop...@umich.edu]
Sent: Wednesday, November 30, 2016 1:33 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Longitudinal TRACULA: mri_convert

Hello Freesurfer experts,

I am trying to run longitudinal TRACULA but I am getting an error early
on in the process that seems to originate from mri_convert:



#-
/home/mriuser/privatemodules/freesurfer/bin/trac-preproc
#-
#@# Image corrections Wed Nov 30 09:10:55 EST 2016
mri_convert /datapath/2171/01_Raw_Data/DWI/2171_02_DWI.nii.gz
/datapath/2171/04_TRACULA/2171_02.long.2171_T/dmri/dwi_orig.nii.gz
mri_convert /datapath/2171/01_Raw_Data/DWI/2171_02_DWI.nii.gz
/datapath/2171/04_TRACULA/2171_02.long.2171_T/dmri/dwi_orig.nii.gz
Segmentation fault (core dumped)
Linux 3.10.0-327.4.4.el7.x86_64 #1 SMP Tue Jan 5 16:07:00 UTC 2016
x86_64 x86_64 x86_64 GNU/Linux



Some information about my setup:

*Freesurfer version:
freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0

*Freesurfer TRACULA update installed:
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0-tracula-addons/tracula.update.centos6_x86_64.5.3.2014_05_26.tar.gz

*Linux version:
CentOS Linux release 7.2.1511 (Core)
centos-release-7-2.1511.el7.centos.2.10.x86_64



Is there a fix for this problem?

Thanks!

- Vincent

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Re: [Freesurfer] Longitudinal TRACULA: mri_convert

[Vincent Koppelmans]

Dear Anastasia,

I have checked the image and it looks good. I don't think the image is 
the problem, especially considering that my issue is also popping up 
with standard data. See for example the following code:


$ echo $FREESURFER_HOME
/home/mriuser/privatemodules/freesurfer

$ cksum $(which mri_convert)
1305133180 29171478 /home/mriuser/privatemodules/freesurfer/bin/mri_convert

$ echo $FSLDIR
/home/mriuser/privatemodules/fsl

$ mri_convert ${FSLDIR}/data/standard/MNI152_T1_1mm.nii.gz test.mgh
mri_convert 
/home/mriuser/privatemodules/fsl/data/standard/MNI152_T1_1mm.nii.gz 
test.mgh
$Id: mri_convert.c,v 1.213 2014/07/29 19:22:31 fischl Exp $
reading from 
/home/mriuser/privatemodules/fsl/data/standard/MNI152_T1_1mm.nii.gz...
crypt_gkey = (null)
Segmentation fault (core dumped)




The reason I am posting this with 'Longitudinal TRACULA' in the title is 
because I only have this issue with the mri_convert that is bundled with 
the TRACULA update (see my first post). The original mri_convert bundled 
with the centOS6 64bit version of FS 5.3.0 (stable) does let me convert 
files. However, this version does not allow multiple frame numbers:

Original frame options of mri_convert (FS v5.3.0 stable centos6 64)
 -f,  --frame frameno
 keep only 0-based frame number

Frame options of the updated mri_convert 
(tracula.update.centos6_x86_64.5.3.2014_05_26.tar.gz)
 -f,  --frame frameno [...]
 keep only 0-based frame number(s)

Longitudinal TRACULA pushes multiple files as arguments to 'mri_convert 
--frame', which is why I need the updated version.

Do you have any suggestions for me?

Thank you!

best,

Vincent




Hi Vincent - Looks like an mri_convert error, so not specific to TRACULA 
but
probably something about the format of your input nifti volume. How did you
create that volume? Can you open it in freeview and view it normally?


a.y


From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Vincent Koppelmans
[vkop...@umich.edu]
Sent: Wednesday, November 30, 2016 1:33 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Longitudinal TRACULA: mri_convert

Hello Freesurfer experts,

I am trying to run longitudinal TRACULA but I am getting an error early
on in the process that seems to originate from mri_convert:



#-
/home/mriuser/privatemodules/freesurfer/bin/trac-preproc
#-
#@# Image corrections Wed Nov 30 09:10:55 EST 2016
mri_convert /datapath/2171/01_Raw_Data/DWI/2171_02_DWI.nii.gz
/datapath/2171/04_TRACULA/2171_02.long.2171_T/dmri/dwi_orig.nii.gz
mri_convert /datapath/2171/01_Raw_Data/DWI/2171_02_DWI.nii.gz
/datapath/2171/04_TRACULA/2171_02.long.2171_T/dmri/dwi_orig.nii.gz
Segmentation fault (core dumped)
Linux 3.10.0-327.4.4.el7.x86_64 #1 SMP Tue Jan 5 16:07:00 UTC 2016
x86_64 x86_64 x86_64 GNU/Linux



Some information about my setup:

*Freesurfer version:
freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0

*Freesurfer TRACULA update installed:
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0-tracula-addons/tracula.update.centos6_x86_64.5.3.2014_05_26.tar.gz

*Linux version:
CentOS Linux release 7.2.1511 (Core)
centos-release-7-2.1511.el7.centos.2.10.x86_64



Is there a fix for this problem?

Thanks!

- Vincent
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[Freesurfer] Longitudinal TRACULA: mri_convert

[Vincent Koppelmans]

Hello Freesurfer experts,

I am trying to run longitudinal TRACULA but I am getting an error early 
on in the process that seems to originate from mri_convert:



#-
/home/mriuser/privatemodules/freesurfer/bin/trac-preproc
#-
#@# Image corrections Wed Nov 30 09:10:55 EST 2016
mri_convert /datapath/2171/01_Raw_Data/DWI/2171_02_DWI.nii.gz 
/datapath/2171/04_TRACULA/2171_02.long.2171_T/dmri/dwi_orig.nii.gz
mri_convert /datapath/2171/01_Raw_Data/DWI/2171_02_DWI.nii.gz 
/datapath/2171/04_TRACULA/2171_02.long.2171_T/dmri/dwi_orig.nii.gz
Segmentation fault (core dumped)
Linux 3.10.0-327.4.4.el7.x86_64 #1 SMP Tue Jan 5 16:07:00 UTC 2016 
x86_64 x86_64 x86_64 GNU/Linux



Some information about my setup:

*Freesurfer version:
freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0

*Freesurfer TRACULA update installed:
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0-tracula-addons/tracula.update.centos6_x86_64.5.3.2014_05_26.tar.gz

*Linux version:
CentOS Linux release 7.2.1511 (Core)
centos-release-7-2.1511.el7.centos.2.10.x86_64



Is there a fix for this problem?

Thanks!

- Vincent

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[Freesurfer] Freeview nightly / dev / beta

[Vincent Koppelmans]

Hello Freesurfer developers,

I am looking for a version of Freeview that recognizes the -noquit flag. 

V 1.0 Build Aug 24 2015 14:50:08 allows this, but is no longer available from 
"ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev 
”. 

I am particularly interested in a Linux version.

Would it be possible to open up access to the beta versions of Freeview to us 
endusers again?

Thanks!

- Vincent


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[Freesurfer] [Vacancy] Postdoc Position to Study Brain and Behavioral Plasticity Occurring with Spaceflight and Analog Environments.

[Vincent Koppelmans]

A funded postdoctoral position is available immediately (with start date in 
summer 2016) to work in Dr. Rachael Seidler’s laboratory at the University of 
Michigan studying brain and behavioral plasticity occurring with spaceflight 
and analog environments.  As one of the world’s leading research institutions, 
the University of Michigan provides an exceptionally supportive environment for 
research. University support includes integrated and state of the art computer 
technology, exceptional students and staff, and a network of world-renowned 
scientists. The Neuromotor Behavior Laboratory (directed by Dr. Seidler) is an 
interdisciplinary, productive, and dynamic group of students and staff 
researching the neurocognitive control of movement.


The post-doctoral researcher will study cognitive, sensory, and motor 
behavioral plasticity and their neural correlates using functional MRI and 
resting state connectivity.  The candidate will be expected to work 
collaboratively with a research team to collect and analyze data, prepare 
manuscripts for publication, and participate at national and international 
level meetings.  The candidate must be willing and able to travel 
internationally for data collection. Interested applicants should submit a 
cover letter, curriculum vita, and the names and contact information for two 
referees to Rachael D. Seidler, Ph.D. via e-mail (rseid...@umich.edu 
). Review of applications will begin immediately. 


Necessary Qualifications: Ph.D. in psychology, neuroscience, kinesiology or 
related field and experience with MRI techniques including structural MRI, DTI, 
and / or functional MRI.  The candidate must possess excellent verbal and 
written communication skills, be strongly motivated, and work well in a team 
setting. Experience with computer programming a plus (MATLAB, LabView, and / or 
E-Prime).


The position is initially available for one year and may be renewable.  
Questions regarding the position can be emailed to rseid...@umich.edu 
. 


The University of Michigan is an Equal Opportunity, Affirmative Action Employer.

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[Freesurfer] mri_vol2surf: convert stats volume to surface

[Vincent Koppelmans]

Hello Freesurfer experts,

I would like to display stats images that are in MNI space on an MNI surface 
volume. 

I found this thread on the mailing list that explains how to use mri_vol2surf 
to convert volumetric images to a surface:
https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2014-April/037809.html 
https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2014-April/037809.html

From this thread, I distilled the following command:
mri_vol2surf --mov ./my_results.nii --mni152reg --hemi lh --surf white --o 
./output.mgh

The code produces the following output:
 srcvol = out.nii
 srcreg = /Applications/freesurfer/average/mni152.register.dat
 srcregold = 0
 srcwarp unspecified
 surf = white
 hemi = lh
 trgsubject = fsaverage
 surfreg = sphere.reg
 reshape = 0
 interp = nearest
 float2int = round
 GetProjMax = 0
 INFO: float2int code = 0
 Done loading volume
 Reading surface /Applications/freesurfer/subjects/fsaverage/surf/lh.white
 Done reading source surface
 Mapping Source Volume onto Source Subject Surface
  1 0 0 0
 using old
 Done mapping volume to surface
 Number of source voxels hit = 73964
 Writing to output2.mgh
 Dim: 163842 1 1

However, I am not able to load the file in Freeview. The error that I receive 
is:
 ERROR: MRISread: file '/Volumes/Data/tmp/output.mgh' has 0 vertices!
 Probably trying to use a scalar data file as a surface!

FYI: my stats file (my_results.nii) is already in MNI space and is definitely 
not empty. 

What can I do to get obtain surface maps from my stats images?

Thanks!

- Vincent___
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[Freesurfer] Gray Matter probabilistic Segmentation

[Vincent Koppelmans]

Dear FreeSurfer experts,

I have some experience with FSL and SPM, but not a lot with FreeSurfer, so 
please bear with me. 

When I observe FreeSurfer segmentations, I see that images are binary (either a 
voxel belongs to a tissue class, or it does not) and not probabilistic. I want 
to obtain total gray matter volume from the FreeSurfer segmentation, so I 
searched the forum and came across the following post: 

http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg11790.html

I followed directions which resulted in three whole-brain gray-matter 
probabilistic map:

https://dl.dropbox.com/u/6747155/FS_GM_prob.png

The three maps end in 000.mgz, 001.mgz, and 002.mgz. 

 Could Somebody explain to me the differences between these images?

Furthermore, the intensity range in the maps goes from 0 to 40 (as can be 
observed from the histogram). How do I convert this image to probabilities 0-1? 
I don't believe dividing by 40 is correct, because that would mean that the 
very few voxels will have a probability of being grey matter higher than 50% 
(see the histogram). 

Thanks in advance,

Vincent
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[Freesurfer] mri_label2vol: Brodmann Areas

[Vincent Koppelmans]

Hi all,

I am trying to convert Brodmann area 4a and 4p to .nii file format in native 
space. I have used to following syntax:



tkregister2 --mov ${SUBJECTS_DIR}/mri/rawavg.mgz --noedit --s [SUBJECT_ID] 
--regheader --reg ./register.dat
mri_label2vol --label [PATH-TO-LABEL-FILE] --temp 
${SUBJECTS_DIR}/mri/rawavg.mgz --subject [SUBJECT_ID] --hemi lh --o 
[OUTPUT-FILE-NAME] --proj frac 0 1 .1 --fillthresh .0 --reg 
[PATH-TO-register.dat-FILE]



This is the result: https://dl.dropbox.com/u/6747155/BA4a.png

As you can see, there are 'missing' voxels in the volume: it is not one smooth 
shape. However, when I convert aseg or aparc structures to volumes, I don't 
have this problem. Is it possible to get a a smooth, fully filled shape from a 
Brodmann label?

Thanks in advance,

Vincent

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