Re: [Freesurfer] recommendation for T1 and T2-based sequences use with FreeSurfer

[Matt Glasser]

I think the HCP CCF protocol is a good start:

http://protocols.humanconnectome.org/

Peace,

Matt.

From:   on behalf of Colm Connolly

Reply-To:  Freesurfer support list 
Date:  Tuesday, February 6, 2018 at 10:41 AM
To:  "freesurfer@nmr.mgh.harvard.edu" 
Subject:  [Freesurfer] recommendation for T1 and T2-based sequences use with
FreeSurfer

Hi everybody, 

I¹m endeavoring to help a researcher come up with a protocol which might be
³optimal² (in some sense) for use with FreeSurfer. I¹ve not really used
FreeSurfer much hence my lack of familiarity with what the recommended
sequences are for use with FreeSurfer.

Having searched around, I¹ve found [1]. Do the recommendations in [1] still
apply?

I¹d like the researcher to get good pial surface estimate so would like to
be able to recommend that he perform a T2 scan as well. Having read through
[2], it makes mention of T2 and FLAIR images for improving pial surface
estimation. Is the FLASH image recommended in [1] appropriate for use with
the -T2 or -FLAIR args to recon-all?

We¹ll be running these scans on a 3T Siemens Prisma running V11c software.
Are there particular scans that you recommend for this particular scanner or
again does [1] apply?

[1] 
https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferWiki?action=AttachFile
o=get=FreeSurfer_Suggested_Morphometry_Protocols.pdf
[2] 
https://surfer.nmr.mgh.harvard.edu/fswiki/recon-all#UsingT2orFLAIRdatatoimpr
ovepialsurfaces

Thanks in advance for you time,

Regards,
--
Colm G. Connolly, PhD
Dept of Biomedical Sciences
Florida State University
Tallahassee, FL 32306
Tel: +1-850-644-2105
https://www.researchgate.net/profile/Colm_Connolly2

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Re: [Freesurfer] bbregister error -- Human Connectome Project Data

[Matt Glasser]

There is a structural extended package that has the FreeSurfer folders.

Peace,

Matt.

From:  <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Lana Ruck
<lr...@umail.iu.edu>
Reply-To:  Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date:  Thursday, December 28, 2017 at 12:56 PM
To:  Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject:  Re: [Freesurfer] bbregister error -- Human Connectome Project Data

Okay so if I am going to try and run this option, recon-all must also be
done on the structural scans. I have the pre-processed structurals, and I
understand from y'all's 2013 paper
<http://linkinghub.elsevier.com/retrieve/pii/S1053811913005053>  that they
have already been through all of the steps in recon-all. First--is it
correct that all steps (1-31) have been done on the data? Second, as with my
original question, it seems that the HCP directories are quite different
than the defaults that would be created by a standard Freesurfer recon-all
run. Assuming that Freesurfer scripts will look for recon-all files in
directories not present in the HCP data as downloaded, (for example,
subjid/mri/... and subj/surf/... are not valid paths in the pre-processed
data), would it just be better to get the un-processed structurals and
re-run all of the recon-all steps myself?

I guess I'm just wondering what the value of the pre-processed data is if it
is re-organized as to be un-readable by Freesurfer defaults.

Lana

   
Lana Ruck, M.A.
Associate Instructor, Department of Anthropology
Graduate Scholars Fellow, Cognitive Science Program
Indiana University, Bloomington
Student Building 166
lr...@umail.iu.edu


On Wed, Dec 27, 2017 at 7:02 PM, Matt Glasser <m...@ma-tea.com> wrote:
> I wouldn¹t trust resting state data that have not been properly denoised.  You
> should only need the structural and FIX cleaned packages for what you are
> doing.  The link that I put below explains how to get HCP data onto the
> fsaverage4 surface.  You will need FreeSurfer and Connectome Workbench for
> this.  
> 
> Peace,
> 
> Matt.
> 
> From:  <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Lana Ruck
> <lr...@umail.iu.edu>
> Reply-To:  Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
> Date:  Wednesday, December 27, 2017 at 5:55 PM
> To:  Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
> 
> Subject:  Re: [Freesurfer] bbregister error -- Human Connectome Project Data
> 
> Matt,
> 
> Thanks for the quick reply! I'll check out that Wiki document and the 2016
> Nature paper first.
> 
> The reason I have the pre-processed (but not ICA-FIX'ed) rfMRI data is because
> I would like to use the iterative parcellation algorithm from the Liu Lab
> @Harvard (as described in Wang, D. et al. 2015: Parcellating Cortical
> Functional Networks in Individuals. Nat. Neurosci;
> http://nmr.mgh.harvard.edu/bid/DownLoad.html), but I am unsure if the ICA-FIX
> data are appropriate for this. I know that the minimally pre-processed rfMRI
> data just need to be smoothed and projected to fsaverage4 for the MATLAB
> algorithm to work, but I didn't see a clear way to get the ICA-FIX data in the
> right format, as per the specifications provided by the Lui Lab. I am also not
> using a local machine to do the processing (I am using my Uni's supercomputing
> infrastructure), so I don't know if I can get connectome workbench installed
> in order to pre-process CIFTI data. That's why I am working with standard
> formats (the supercomputer has freesurfer, fsl, etc.).
> 
> Assuming I can get cnm-wb installed by admins on the supercomputer, and that I
> can use it to get the ICA-FIX data appropriately formatted for parcellation
> with MATLAB, do you suggest I download the extended packages, or will the
> compact ones have everything I need?
> 
> Lana
> 
>  
> Lana Ruck, M.A.
> Associate Instructor, Department of Anthropology
> Graduate Scholars Fellow, Cognitive Science Program
> Indiana University, Bloomington
> Student Building 166
> lr...@umail.iu.edu
> 
> 
> On Wed, Dec 27, 2017 at 6:26 PM, Matt Glasser <m...@ma-tea.com> wrote:
>> You would be better off resampling the existing CIFTI data to the fsaverage4
>> surface rather than redoing the projection and smoothing in the volume.
>> Instructions for getting to fsaverage are available here:
>> 
>> https://wiki.humanconnectome.org/display/PublicData/HCP+Users+FAQ#HCPUsersFAQ
>> -9.HowdoImapdatabetweenFreeSurferandHCP?
>> 
>> Also I would recommend starting from the ICA+FIX cleaned data, not the
>> minimally preprocessed data.  If you must smooth the data, you can do that
>> with wb_command -cifti-smoothing before following the above steps.
>> 
>

Re: [Freesurfer] bbregister error -- Human Connectome Project Data

[Matt Glasser]

I wouldn¹t trust resting state data that have not been properly denoised.
You should only need the structural and FIX cleaned packages for what you
are doing.  The link that I put below explains how to get HCP data onto the
fsaverage4 surface.  You will need FreeSurfer and Connectome Workbench for
this.  

Peace,

Matt.

From:  <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Lana Ruck
<lr...@umail.iu.edu>
Reply-To:  Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date:  Wednesday, December 27, 2017 at 5:55 PM
To:  Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject:  Re: [Freesurfer] bbregister error -- Human Connectome Project Data

Matt,

Thanks for the quick reply! I'll check out that Wiki document and the 2016
Nature paper first.

The reason I have the pre-processed (but not ICA-FIX'ed) rfMRI data is
because I would like to use the iterative parcellation algorithm from the
Liu Lab @Harvard (as described in Wang, D. et al. 2015: Parcellating
Cortical Functional Networks in Individuals. Nat. Neurosci;
http://nmr.mgh.harvard.edu/bid/DownLoad.html), but I am unsure if the
ICA-FIX data are appropriate for this. I know that the minimally
pre-processed rfMRI data just need to be smoothed and projected to
fsaverage4 for the MATLAB algorithm to work, but I didn't see a clear way to
get the ICA-FIX data in the right format, as per the specifications provided
by the Lui Lab. I am also not using a local machine to do the processing (I
am using my Uni's supercomputing infrastructure), so I don't know if I can
get connectome workbench installed in order to pre-process CIFTI data.
That's why I am working with standard formats (the supercomputer has
freesurfer, fsl, etc.).

Assuming I can get cnm-wb installed by admins on the supercomputer, and that
I can use it to get the ICA-FIX data appropriately formatted for
parcellation with MATLAB, do you suggest I download the extended packages,
or will the compact ones have everything I need?

Lana

   
Lana Ruck, M.A.
Associate Instructor, Department of Anthropology
Graduate Scholars Fellow, Cognitive Science Program
Indiana University, Bloomington
Student Building 166
lr...@umail.iu.edu


On Wed, Dec 27, 2017 at 6:26 PM, Matt Glasser <m...@ma-tea.com> wrote:
> You would be better off resampling the existing CIFTI data to the fsaverage4
> surface rather than redoing the projection and smoothing in the volume.
> Instructions for getting to fsaverage are available here:
> 
> https://wiki.humanconnectome.org/display/PublicData/HCP+Users+FAQ#HCPUsersFAQ-
> 9.HowdoImapdatabetweenFreeSurferandHCP?
> 
> Also I would recommend starting from the ICA+FIX cleaned data, not the
> minimally preprocessed data.  If you must smooth the data, you can do that
> with wb_command -cifti-smoothing before following the above steps.
> 
> Peace,
> 
> Matt.
> 
> From:  <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Lana Ruck
> <lr...@umail.iu.edu>
> Reply-To:  Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
> Date:  Wednesday, December 27, 2017 at 4:41 PM
> To:  <freesurfer@nmr.mgh.harvard.edu>
> Subject:  Re: [Freesurfer] bbregister error -- Human Connectome Project Data
> 
> As a work-around to the above issue, I did the registrations directly in FSL
> using FLIRT, and then converted the resultant fsl reg.mat files to freesurfer
> reg.dat files (using tkregister2; they all look fine). Now, all I need is to
> project these rfMRI data to fsaverage4, and I thought mri_vol2surf was the
> right way to do this.
> 
> Unfortunately, I am now having the same directory issue with mri_vol2surf (new
> error log below), where it can't find /surf/lh.white for my subject. The HCP
> pre-processed data has already been through recon-all, so there are several
> *white*surf* files to choose from for each subject, but they are not in the
> directory specified by default in MRISread (subjid/surf/).
> 
> I thought I could fix this by specifying the right target subject
> (--trgsubject fsaverage4, which I have manually copied, along with the other
> $FREESURFER_HOME/subjects, to my own $SUBJECTS_DIR as per the message boards),
> or specifying the right directory (I've tried the --surf command with both the
> fsaverage4 path, and to multiple [subject]?h.white paths, but it just appends
> them to the non-existent default path--see below). Thus, regardless of what I
> specify, I keep getting the same error related to a default search in
> subjid/surf/.
> 
> Is there a way to point MRISread to the correct surf files, without re-doing
> recon-all or moving the pre-processed surfaces to a "surf" folder for all 40
> subjects?
> 
> Lana
> 
>> [lruck@c5 LH_all]$ mri_vol2surf --mov
>> /N/dc2/scratch/lruck/LH_all/101915/MNINonLinear/Results/rfMRI_REST1_

Re: [Freesurfer] bbregister error -- Human Connectome Project Data

[Matt Glasser]

You would be better off resampling the existing CIFTI data to the fsaverage4
surface rather than redoing the projection and smoothing in the volume.
Instructions for getting to fsaverage are available here:

https://wiki.humanconnectome.org/display/PublicData/HCP+Users+FAQ#HCPUsersFA
Q-9.HowdoImapdatabetweenFreeSurferandHCP?

Also I would recommend starting from the ICA+FIX cleaned data, not the
minimally preprocessed data.  If you must smooth the data, you can do that
with wb_command -cifti-smoothing before following the above steps.

Peace,

Matt.

From:   on behalf of Lana Ruck

Reply-To:  Freesurfer support list 
Date:  Wednesday, December 27, 2017 at 4:41 PM
To:  
Subject:  Re: [Freesurfer] bbregister error -- Human Connectome Project Data

As a work-around to the above issue, I did the registrations directly in FSL
using FLIRT, and then converted the resultant fsl reg.mat files to
freesurfer reg.dat files (using tkregister2; they all look fine). Now, all I
need is to project these rfMRI data to fsaverage4, and I thought
mri_vol2surf was the right way to do this.

Unfortunately, I am now having the same directory issue with mri_vol2surf
(new error log below), where it can't find /surf/lh.white for my subject.
The HCP pre-processed data has already been through recon-all, so there are
several *white*surf* files to choose from for each subject, but they are not
in the directory specified by default in MRISread (subjid/surf/).

I thought I could fix this by specifying the right target subject
(--trgsubject fsaverage4, which I have manually copied, along with the other
$FREESURFER_HOME/subjects, to my own $SUBJECTS_DIR as per the message
boards), or specifying the right directory (I've tried the --surf command
with both the fsaverage4 path, and to multiple [subject]?h.white paths, but
it just appends them to the non-existent default path--see below). Thus,
regardless of what I specify, I keep getting the same error related to a
default search in subjid/surf/.

Is there a way to point MRISread to the correct surf files, without re-doing
recon-all or moving the pre-processed surfaces to a "surf" folder for all 40
subjects?

Lana

> [lruck@c5 LH_all]$ mri_vol2surf --mov
> /N/dc2/scratch/lruck/LH_all/101915/MNINonLinear/Results/rfMRI_REST1_LR/REST1LR
> .img --src_type analyze --reg
> /N/dc2/scratch/lruck/LH_all/101915/MNINonLinear/Results/rfMRI_REST1_LR/REST1LR
> _register.dat --hemi lh --fwhm 6 --trgsubject fsaverage4 --surf
> /N/dc2/scratch/lruck/LH_all/fsaverage4/surf/lh.white --out
> /N/dc2/scratch/lruck/LH_all/101915/MNINonLinear/Results/rfMRI_REST1_LR/
> srcvol = 
> /N/dc2/scratch/lruck/LH_all/101915/MNINonLinear/Results/rfMRI_REST1_LR/REST1LR
> .img
> srctype = analyze
> srcreg = 
> /N/dc2/scratch/lruck/LH_all/101915/MNINonLinear/Results/rfMRI_REST1_LR/REST1LR
> _register.dat
> srcregold = 0
> srcwarp unspecified
> surf = /N/dc2/scratch/lruck/LEH_all/fsaverage4/surf/lh.white
> hemi = lh
> trgsubject = fsaverage4
> surfreg = sphere.reg
> reshape = 0
> interp = nearest
> float2int = round
> GetProjMax = 0
> INFO: float2int code = 0
>   analyzeRead() roi_scale   0.0
> Done loading volume
> INFO: This REGISTER_DAT transform is valid only for volumes between  COR types
> with c_(r,a,s) = 0.
> Input reg is register.dat
>  original matrix ---
>  0.96607   0.00120   0.00047  -0.78994;
>  0.01685   0.96915  -0.00899   2.16005;
> -0.00580  -0.00642   0.98726  -0.56166;
>  0.0   0.0   0.0   1.0;
>  original matrix ---
> INFO: smoothing volume at fwhm = 6 mm (std = 2.54797)
> Reading surface 
> /N/dc2/scratch/lruck/LH_all//101915/surf/lh./N/dc2/scratch/lruck/LH_all/fsaver
> age4/surf/lh.white
> MRISread(/N/dc2/scratch/lruck/LH_all//101915/surf/lh./N/dc2/scratch/lruck/LH_a
> ll/fsaverage4/surf/lh.white): could not open file
> No such file or directory
> mri_vol2surf: could not read surface
> /N/dc2/scratch/lruck/LH_all//101915/surf/lh./N/dc2/scratch/lruck/LH_all/fsaver
> age4/surf/lh.white
> No such file or directory


   
Lana Ruck, M.A.
Associate Instructor, Department of Anthropology
Graduate Scholars Fellow, Cognitive Science Program
Indiana University, Bloomington
Student Building 166
lr...@umail.iu.edu


On Wed, Dec 27, 2017 at 1:43 PM, Lana Ruck  wrote:
> Hello, 
> 
> I am currently starting a project with the minimally pre-processed rfMRI from
> the Human Connectome Project, but I need to do some additional processing
> first. This includes smoothing at 6mm FWHM and projection onto the fsaverage4
> surface. I have smoothed the pre-processed rfMRI data using mri_convert (and
> have also converted the provided brain-extracted anatomical), but I am having
> issues registering the smoothed rfMRI volumes, and I understand that I need
> these register.dat files for mri_vol2surf.
> 
> I have tried 

Re: [Freesurfer] asking for literature

[Matt Glasser]

Also we used T2w scans in the HCP Pipelines Paper and have Figure 14
showing the effects of using T2w scan vs not using one.

Peace,

Matt.

On 10/20/17, 10:00 AM, "Bruce Fischl"
 wrote:

>Hi Jiook
>
>this paper:
>
>https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2408694/
>
>discusses the basic algorithm (it is based on T2* but is pretty much the
>same for T2)
>
>cheers
>Bruce
>On Fri, 20 Oct 2017,
>Jiook Cha wrote:
>
>> Hello,
>> 
>> Could anybody please point me to a paper/asbtract showing meaningful
>>improvement of pial surface
>> segmentation using additional T2 or Flair images in the recon-all
>>procedure?
>> 
>> 
>> Thanks,
>> 
>> Jiook
>> 
>>[t?sender=aY2hhLmppb29rQGdtYWlsLmNvbQ%3D%3D=zerocontent=4aae682
>>8-1e3e-430a-9278-8ede4ceeb
>> f60] ᐧ
>> 
>>___
>Freesurfer mailing list
>Freesurfer@nmr.mgh.harvard.edu
>https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>The information in this e-mail is intended only for the person to whom it
>is
>addressed. If you believe this e-mail was sent to you in error and the
>e-mail
>contains patient information, please contact the Partners Compliance
>HelpLine at
>http://www.partners.org/complianceline . If the e-mail was sent to you in
>error
>but does not contain patient information, please contact the sender and
>properly
>dispose of the e-mail.



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Re: [Freesurfer] volume vs surface-based and surface smoothing

[Matt Glasser]

My understanding of the FreeSurfer surface-based functional processing is
that it adheres to the below guidelines; however, I have not personally used
it so we¹ll have to see what the FreeSurfer experts say.

Peace,

Matt.

From:  <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Alissa Stafford
<alissa.staff...@jhu.edu>
Reply-To:  Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date:  Thursday, October 12, 2017 at 12:42 PM
To:  Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject:  Re: [Freesurfer] volume vs surface-based and surface smoothing

Thanks Matt! Does rawfunc2surf-sess create the surface and smooth?

From: <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Matt Glasser
<m...@ma-tea.com>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Thursday, October 12, 2017 at 1:39 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] volume vs surface-based and surface smoothing

Volume-based registration is fine with subject as you have the same brain
that you are registering (ideally such registrations are 6 DOF rigid
registrations and any image distortions are corrected for).  Surface-based
registration is better when comparing across subjects due to the variability
in cortical folding patterns and locations of areas relative to folds across
subjects.  Smoothing is best done on the surface if it is done at all.
Smoothing in the volume harms one¹s spatial localization precision much more
than smoothing on the surface for an equivalent FWMH in mm.  It is worth
keeping in mind that smoothing on the surface does still blur across
cortical areal boundaries, however, so for many analyses it may be better to
average within cortical areas rather than to smooth a lot.

Peace,

Matt.

From: <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Alissa Stafford
<alissa.staff...@jhu.edu>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Thursday, October 12, 2017 at 12:29 PM
To: "Freesurfer@nmr.mgh.harvard.edu" <Freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] volume vs surface-based and surface smoothing

Hello,

I am trying to understand the preprocessing functions to successfully
complete surface-based analysis. I am confused about what is happening on
the volume level and when exactly the surface is being created. My questions
revolve around register-sess and rawfunc2surf-sess.

Registration has 2 parts:
1: the native anatomical space is registered with the fsaverage space. This
is happening during recon-all.
2: native functional data is registered with the native anatomical data.
This is happening during register-sess in preprocess-sess.
Aren¹t these both volume-based registrations? If not when are the surfaces
created? My concern is that it is volume-based and I was under the
impression from this article:
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2862732/ , that all
registrations should be done on the surface.

I am also confused about rawfunc2surf-sess. I believe up until this function
in preprocess-sess, everything has been done in the volume so this is the
first step that is done in the surface, is that correct? And then does this
do smoothing? I realized it has a fwhm input option so it must smooth. So is
this where the functional data is now expressed in the surface and it also
smooths? Or does surfsmooth-sess need to be run in addition to
rawfunc2surf-sess?

I basically just want to be making sure I understand when registration is
volume-based or surface-based and when it¹s appropriate to use volume-based.
And I was using the rawfunc2surf function assuming it was for smoothing, but
I am not so sure if this only creates the surface or also smooths.

Thanks,
Alissa
___ Freesurfer mailing list
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you believe this e-mail was sent to you in error and the e-mail contains
patient information, please contact the Partners Compliance HelpLine at
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in this e-mail is intended only for the person to whom it is addressed. If
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patient information, please contact the Partners Compliance HelpLine at
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error but does not contain patient information, please contact the sender
and properly dispose of th

Re: [Freesurfer] volume vs surface-based and surface smoothing

[Matt Glasser]

Volume-based registration is fine with subject as you have the same brain
that you are registering (ideally such registrations are 6 DOF rigid
registrations and any image distortions are corrected for).  Surface-based
registration is better when comparing across subjects due to the variability
in cortical folding patterns and locations of areas relative to folds across
subjects.  Smoothing is best done on the surface if it is done at all.
Smoothing in the volume harms one¹s spatial localization precision much more
than smoothing on the surface for an equivalent FWMH in mm.  It is worth
keeping in mind that smoothing on the surface does still blur across
cortical areal boundaries, however, so for many analyses it may be better to
average within cortical areas rather than to smooth a lot.

Peace,

Matt.

From:   on behalf of Alissa Stafford

Reply-To:  Freesurfer support list 
Date:  Thursday, October 12, 2017 at 12:29 PM
To:  "Freesurfer@nmr.mgh.harvard.edu" 
Subject:  [Freesurfer] volume vs surface-based and surface smoothing

Hello,

I am trying to understand the preprocessing functions to successfully
complete surface-based analysis. I am confused about what is happening on
the volume level and when exactly the surface is being created. My questions
revolve around register-sess and rawfunc2surf-sess.

Registration has 2 parts:
1: the native anatomical space is registered with the fsaverage space. This
is happening during recon-all.
2: native functional data is registered with the native anatomical data.
This is happening during register-sess in preprocess-sess.
Aren¹t these both volume-based registrations? If not when are the surfaces
created? My concern is that it is volume-based and I was under the
impression from this article:
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2862732/ , that all
registrations should be done on the surface.

I am also confused about rawfunc2surf-sess. I believe up until this function
in preprocess-sess, everything has been done in the volume so this is the
first step that is done in the surface, is that correct? And then does this
do smoothing? I realized it has a fwhm input option so it must smooth. So is
this where the functional data is now expressed in the surface and it also
smooths? Or does surfsmooth-sess need to be run in addition to
rawfunc2surf-sess?

I basically just want to be making sure I understand when registration is
volume-based or surface-based and when it¹s appropriate to use volume-based.
And I was using the rawfunc2surf function assuming it was for smoothing, but
I am not so sure if this only creates the surface or also smooths.

Thanks,
Alissa
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Re: [Freesurfer] Transformation between spaces

[Matt Glasser]

You would be running melodic from the command line.  If you have further
questions on CIFTI, the better place to ask would be the HCP-Users mailing
list:

https://www.humanconnectome.org/contact-us

Peace,

Matt.

From:  <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Florence
Campana <campana.flore...@gmail.com>
Reply-To:  Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date:  Tuesday, October 10, 2017 at 12:12 PM
To:  Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject:  Re: [Freesurfer] Transformation between spaces

Hi Matt,

I follow-up on your suggestion of running MELODIC in surface. I am unsure
about the registration files that I should use (I guess that they should be
surface files?), notably for the Main Structural Images and the Standard
Space.
I am sorry if this sounds like a naive question.

Thank you very much,

Florence

2017-10-09 22:28 GMT-04:00 Matt Glasser <m...@ma-tea.com>:
> The latest version of melodic is compatible with CIFTI data (e.g. From the
> HCP).
> 
> Peace,
> 
> Matt.
> 
> From:  <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Florence  Campana
> <campana.flore...@gmail.com>
> Reply-To:  Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
> Date:  Monday, October 9, 2017 at 9:25 PM
> To:  Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
> Subject:  [Freesurfer] Transformation between spaces
> 
> Hi Matt,
> 
> Thank you for your quick input ; I did not try yet to use melodic, it seems
> indeed to be the most straightforward solution, I will try it, thank you
> again!
> 
> Florence
> 
> Le lundi 9 octobre 2017, Matt Glasser <m...@ma-tea.com> a écrit :
>> I¹d note that you can run the group ICA on surface data in surface space
>> pretty easily using melodic, which would avoid the issue that Doug mentions.
>> 
>> Peace,
>> 
>> Matt.
>> 
>> From:  <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas Greve
>> <gr...@nmr.mgh.harvard.edu>
>> Reply-To:  Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
>> Date:  Monday, October 9, 2017 at 7:20 PM
>> To:  <freesurfer@nmr.mgh.harvard.edu>
>> Subject:  Re: [Freesurfer] Transformation between spaces
>> 
>> 
>>  
>> 
>> 
>>  
>>  
>> 
>> How did you get your ICA analysis into MNI305 (or MNI152) space?  You're ICA
>> intergroup comparisons will only be as good as that space -- how you get it
>> onto the surface from there is not so important. You can run recon-all on the
>> MNI152, sample the ICA maps onto the surface, then use the surface-based
>> registration to map it to fsaverage.
>>  
>>  
>>  
>> On 10/9/17 7:20 PM, Florence Campana wrote:
>>  
>>  
>>>  
>>> Dear freesurfer experts,
>>> 
>>>  
>>>  
>>> I ran a spatial ICA in volume and would like to visualize the components in
>>> surface in order to assess the overlap between the  independent components
>>> and my ROI (defined on surface). However after reading this paper,
>>> https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2862732/, I am  concerned with
>>> transformations between the MNI 305 space and the surface space without
>>> totally understanding the nature of the distortions unfortunately. Would you
>>> mind explaining it briefly to me and let me know whether you think that the
>>> transformation of the components from the MNI305 space to the surface will
>>> lead to distorted results in the case of our spatial overlap estimates? (in
>>> which case I can define the ROI in volume and conduct all the analyses in
>>> volume).
>>>  
>>> 
>>>  
>>>  
>>> Thank you very much,
>>>  
>>> Florence Campana
>>>  
>>>  
>>>   
>>>  
>>> ___
>>> Freesurfer mailing list
>>> freesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listi
>>> nfo/freesurfer
>>>  
>>  
>>  
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>> fo/freesurfer The information in this e-mail is intended only for the person
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>> and the e-mail contains patient information, please contact the Partners
>> Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail
>> was sent to you in error but does not conta

Re: [Freesurfer] Transformation between spaces

[Matt Glasser]

The latest version of melodic is compatible with CIFTI data (e.g. From the
HCP).

Peace,

Matt.

From:  <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Florence
Campana <campana.flore...@gmail.com>
Reply-To:  Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date:  Monday, October 9, 2017 at 9:25 PM
To:  Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject:  [Freesurfer] Transformation between spaces

Hi Matt,

Thank you for your quick input ; I did not try yet to use melodic, it seems
indeed to be the most straightforward solution, I will try it, thank you
again!

Florence

Le lundi 9 octobre 2017, Matt Glasser <m...@ma-tea.com
<javascript:_e(%7B%7D,'cvml','m...@ma-tea.com');> > a écrit :
> I¹d note that you can run the group ICA on surface data in surface space
> pretty easily using melodic, which would avoid the issue that Doug mentions.
> 
> Peace,
> 
> Matt.
> 
> From:  <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas Greve
> <gr...@nmr.mgh.harvard.edu>
> Reply-To:  Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
> Date:  Monday, October 9, 2017 at 7:20 PM
> To:  <freesurfer@nmr.mgh.harvard.edu>
> Subject:  Re: [Freesurfer] Transformation between spaces
> 
> 
>  
> 
> 
>  
>  
> 
> How did you get your ICA analysis into MNI305 (or MNI152) space?  You're ICA
> intergroup comparisons will only be as good as that space -- how you get it
> onto the surface from there is not so important. You can run recon-all on the
> MNI152, sample the ICA maps onto the surface, then use the surface-based
> registration to map it to fsaverage.
>  
>  
>  
> On 10/9/17 7:20 PM, Florence Campana wrote:
>  
>  
>>  
>> Dear freesurfer experts,
>> 
>>  
>>  
>> I ran a spatial ICA in volume and would like to visualize the components in
>> surface in order to assess the overlap between the  independent components
>> and my ROI (defined on surface). However after reading this paper,
>> https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2862732/, I am  concerned with
>> transformations between the MNI 305 space and the surface space without
>> totally understanding the nature of the distortions unfortunately. Would you
>> mind explaining it briefly to me and let me know whether you think that the
>> transformation of the components from the MNI305 space to the surface will
>> lead to distorted results in the case of our spatial overlap estimates? (in
>> which case I can define the ROI in volume and conduct all the analyses in
>> volume).
>>  
>> 
>>  
>>  
>> Thank you very much,
>>  
>> Florence Campana
>>  
>>  
>>   
>>  
>> ___
>> Freesurfer mailing list
>> freesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listin
>> fo/freesurfer
>>  
>  
>  
> ___ Freesurfer mailing list
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> o/freesurfer The information in this e-mail is intended only for the person to
> whom it is addressed. If you believe this e-mail was sent to you in error and
> the e-mail contains patient information, please contact the Partners
> Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail
> was sent to you in error but does not contain patient information, please
> contact the sender and properly dispose of the e-mail.
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Re: [Freesurfer] Transformation between spaces

[Matt Glasser]

I¹d note that you can run the group ICA on surface data in surface space
pretty easily using melodic, which would avoid the issue that Doug mentions.

Peace,

Matt.

From:   on behalf of Douglas Greve

Reply-To:  Freesurfer support list 
Date:  Monday, October 9, 2017 at 7:20 PM
To:  
Subject:  Re: [Freesurfer] Transformation between spaces


 


 
 

How did you get your ICA analysis into MNI305 (or MNI152) space?  You're ICA
intergroup comparisons will only be as good as that space -- how you get it
onto the surface from there is not so important. You can run recon-all on
the MNI152, sample the ICA maps onto the surface, then use the surface-based
registration to map it to fsaverage.
 
 
 
On 10/9/17 7:20 PM, Florence Campana wrote:
 
 
>  
> Dear freesurfer experts,
> 
>  
>  
> I ran a spatial ICA in volume and would like to visualize the components in
> surface in order to assess the overlap between the  independent components and
> my ROI (defined on surface). However after reading this paper,
> https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2862732/, I am  concerned with
> transformations between the MNI 305 space and the surface space without
> totally understanding the nature of the distortions unfortunately. Would you
> mind explaining it briefly to me and let me know whether you think that the
> transformation of the components from the MNI305 space to the surface will
> lead to distorted results in the case of our spatial overlap estimates? (in
> which case I can define the ROI in volume and conduct all the analyses in
> volume).
>  
> 
>  
>  
> Thank you very much,
>  
> Florence Campana
>  
>  
>   
>  
> ___
> Freesurfer mailing list
> freesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinf
> o/freesurfer
>  
 
 
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Re: [Freesurfer] Brodmann areas - exvivo labels

[Matt Glasser]

I would use the versions where the group size approximately matched the
individual size.  

Peace,

Matt.

From:   on behalf of Trisanna
Sprung-Much 
Reply-To:  Freesurfer support list 
Date:  Tuesday, October 3, 2017 at 7:36 PM
To:  Freesurfer support list 
Subject:  [Freesurfer] Brodmann areas - exvivo labels

Hi there

If I wanted to compare some spatial probability maps of some sulci of
interest with the Juelich Data provided by FreeSurfer, would it make more
sense to use the unthresholded Brodmann areas or the .thresh ones? Based on
my understanding of how the .thresh was created (by creating a surface area
of the average BA label that best resembled the average surface area of the
label from each individual hemisphere) in order to avoid including vertices
that had a probability of 10%, for instance, I think using .thresh would be
fine. However, I thought I would verify. In input would be greatly
appreciated.


Best
Trisanna
--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology


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Re: [Freesurfer] Need Urgent Help!! Regarding FreeSurfer Installation

[Matt Glasser]

No.

From:   on behalf of "Tabassum,
Ruchira" 
Reply-To:  Freesurfer support list 
Date:  Saturday, August 5, 2017 at 12:22 PM
To:  "freesurfer@nmr.mgh.harvard.edu" 
Subject:  [Freesurfer] Need Urgent Help!! Regarding FreeSurfer Installation

Hi,
 
I need Freesurfer for my windows OS. Is there any windows version of
FreeSurfer? Please let me know ASAP.
 
Kind Regards
Ruchira Tabassum
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Re: [Freesurfer] smoothing data

[Matt Glasser]

Smoothing in the volume is the single worst thing that is traditionally
done to brain imaging data as far as precision of spatial localization
goes.  

Peace,

Matt.

On 7/12/17, 5:46 PM, "Douglas N Greve"
 wrote:

>you should definitely not smooth the volume data. Smoothing should be
>limited to the surface.
>
>
>On 07/10/2017 11:33 AM, Tamara Tavares wrote:
>> Hi All,
>>
>> I was hoping someone can help me with two naive questions I have:
>>
>> I have read on the Freesufer wiki that you should smooth surface data
>> before analyzing. Should I smooth the data only after I have ran
>> recon-all and have made edits? Also, should volumetric data be
>> smoothed or is this limited to surface data?
>>
>> Thank you in advance for your help.
>>
>> Best,
>> Tamara
>>
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>-- 
>Douglas N. Greve, Ph.D.
>MGH-NMR Center
>gr...@nmr.mgh.harvard.edu
>Phone Number: 617-724-2358
>Fax: 617-726-7422
>
>Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
>www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
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>
>
>The information in this e-mail is intended only for the person to whom it
>is
>addressed. If you believe this e-mail was sent to you in error and the
>e-mail
>contains patient information, please contact the Partners Compliance
>HelpLine at
>http://www.partners.org/complianceline . If the e-mail was sent to you in
>error
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>properly
>dispose of the e-mail.
>


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Re: [Freesurfer] difference in T1 and T2 resolution

[Matt Glasser]

What was the error message?

Peace,

Matt.

From:   on behalf of John Anderson

Reply-To:  Freesurfer support list 
Date:  Sunday, June 11, 2017 at 9:06 AM
To:  
Subject:  [Freesurfer] difference in T1 and T2 resolution

Dear Freesurfer experts,
I have T1 and T2 images were unfortunately acquired with different
resolution (i.e the voxel sizes is not the same)
T1 is 280X280X208
T2 is 270X270X200

I tried to run "recon-all"  but it failed to process the data. The command
that I used is :
pbsubmit -c " recon-all -subjid subj1 -T2  PATH_TO_/T2.nii.gz -qcache
-T2pial -all" 
 
How can I analyze these images? Is it a correct procedure to conform the
voxels using "mri_convert". Is this procedure correct? does it hurt the
anatomy of the images?
 
I highly appreciate your help
John
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Re: [Freesurfer] Can we use fressurfer 6 with the Human connectome project's pipeline ?

[Matt Glasser]

With FreeSurfer V6.1.

Peace,

Matt.

From:  <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of CAGNA Bastien
<bastien.ca...@univ-amu.fr>
Reply-To:  Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date:  Tuesday, March 14, 2017 at 11:32 AM
To:  "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Subject:  Re: [Freesurfer] Can we use fressurfer 6 with the Human connectome
project's pipeline ?

Hi everyone,
Thanks for all your answers Bruce, Matt and Antonin.


Matt, may I ask you when do you think that a freesurfer6-compliant version
of the pipeline will be available ?



Best regards,

Bastien 

On 3/13/17, 9:40 PM, "Bruce Fischl"
<freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
fis...@nmr.mgh.harvard.edu> wrote:
>Hi Matt
>
>To state without qualification that "6.0 has some regressions as far as
>surface placement" is incorrect. We quantified its test-retest
>reliability, 
>accuracy and power to detect disease effects and all were improved
>relative 
>to 5.3. We tested V6 on hundreds of datasets across an array of
>pathologies 
>and different MR sequences, field strengths and scanners. We visually
>inspected dozens of brains multiple times in the process of improving
>accuracy and robustness. I can believe that on Wash U HCP data there
>could 
>be some specific issues, but to imply that V6 is generally less accurate
>is 
>simply incorrect.
>
>cheers
>Bruce
>
>
>On Mon, 13 Mar 2017, Matt Glasser wrote:
>
>> Not yet. We are hoping FreeSurfer 6.1 will work nicely with the HCP
>> Pipelines. For now version 6.0 has some regressions as far as surface
>> placement goes and there are also some adaptations we need to make to
>>the
>> pipelines. 
>> 
>> Peace,
>> 
>> Matt.
>> 
>> From: <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of CAGNA
>>Bastien
>> <bastien.ca...@univ-amu.fr>
>> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
>> Date: Monday, March 13, 2017 at 7:21 AM
>> To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
>> Subject: [Freesurfer] Can we use fressurfer 6 with the Human connectome
>> project's pipeline ?
>> 
>> Dear freesurfer experts,
>> 
>> 
>> I'm wondering if it's possible to run the human connetome project's
>>minimal
>> processing pipeline using freesurfer 6 ?
>> 
>> 
>> Does it require some update of the pipeline or is there anybody that
>>have
>> already enjoyed the new freesurfer version with this pipeline ?
>> 
>> 
>> Thank you for your attention and your help,
>> 
>> Bastien Cagna
>> 
>> 
>> 
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>> in this e-mail is intended only for the person to whom it is addressed.
>>If
>> you believe this e-mail was sent to you in error and the e-mail contains
>> patient information, please contact the Partners Compliance HelpLine at
>> http://www.partners.org/complianceline . If the e-mail was sent to you
>>in
>> error but does not contain patient information, please contact the
>>sender
>> and properly dispose of the e-mail.
>>___
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>
>
>The information in this e-mail is intended only for the person to whom it
>is
>addressed. If you believe this e-mail was sent to you in error and the
>e-mail
>contains patient information, please contact the Partners Compliance
>HelpLine at
>http://www.partners.org/complianceline . If the e-mail was sent to you in
>error
>but does not contain patient information, please contact the sender and
>properly
>dispose of the e-mail.
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] Can we use fressurfer 6 with the Human connectome project's pipeline ?

[Matt Glasser]

Hi Bruce,

I don¹t think the hires T1w and T2w stuff are as accurate as 5.3 in the
HCP 0.7mm data that I have looked at (and as I recall at least one other
user had some similar issues, as did one of my collaborators), but that
was all I meant to refer to.  Sorry if my reply came across more general
than that, as of course we want to move to using FreeSurfer V6+ in the
future.  It is the highres T1w and T2w stuff that my pipelines are
designed to exploit, however.  Also there are some changes I have to make
to the HCP Pipelines for FreeSurfer V6+ because of differing file names,
etc.

Best,

Matt.

On 3/13/17, 9:40 PM, "Bruce Fischl"
<freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
fis...@nmr.mgh.harvard.edu> wrote:

>Hi Matt
>
>To state without qualification that "6.0 has some regressions as far as
>surface placement" is incorrect. We quantified its test-retest
>reliability, 
>accuracy and power to detect disease effects and all were improved
>relative 
>to 5.3. We tested V6 on hundreds of datasets across an array of
>pathologies 
>and different MR sequences, field strengths and scanners. We visually
>inspected dozens of brains multiple times in the process of improving
>accuracy and robustness. I can believe that on Wash U HCP data there
>could 
>be some specific issues, but to imply that V6 is generally less accurate
>is 
>simply incorrect.
>
>cheers
>Bruce
>
>
>On Mon, 13 Mar 2017, Matt Glasser wrote:
>
>> Not yet.  We are hoping FreeSurfer 6.1 will work nicely with the HCP
>> Pipelines.  For now version 6.0 has some regressions as far as surface
>> placement goes and there are also some adaptations we need to make to
>>the
>> pipelines.  
>> 
>> Peace,
>> 
>> Matt.
>> 
>> From: <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of CAGNA
>>Bastien
>> <bastien.ca...@univ-amu.fr>
>> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
>> Date: Monday, March 13, 2017 at 7:21 AM
>> To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
>> Subject: [Freesurfer] Can we use fressurfer 6 with the Human connectome
>> project's pipeline ?
>> 
>> Dear freesurfer experts,
>> 
>> 
>> I'm wondering if it's possible to run the human connetome project's
>>minimal
>> processing pipeline using freesurfer 6 ?
>> 
>> 
>> Does it require some update of the pipeline or is there anybody that
>>have
>> already enjoyed the new freesurfer version with this pipeline ?
>> 
>> 
>> Thank you for your attention and your help,
>> 
>> Bastien Cagna
>> 
>> 
>> 
>> ___ Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The
>>information
>> in this e-mail is intended only for the person to whom it is addressed.
>>If
>> you believe this e-mail was sent to you in error and the e-mail contains
>> patient information, please contact the Partners Compliance HelpLine at
>> http://www.partners.org/complianceline . If the e-mail was sent to you
>>in
>> error but does not contain patient information, please contact the
>>sender
>> and properly dispose of the e-mail.
>>___
>Freesurfer mailing list
>Freesurfer@nmr.mgh.harvard.edu
>https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>The information in this e-mail is intended only for the person to whom it
>is
>addressed. If you believe this e-mail was sent to you in error and the
>e-mail
>contains patient information, please contact the Partners Compliance
>HelpLine at
>http://www.partners.org/complianceline . If the e-mail was sent to you in
>error
>but does not contain patient information, please contact the sender and
>properly
>dispose of the e-mail.



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Re: [Freesurfer] Can we use fressurfer 6 with the Human connectome project's pipeline ?

[Matt Glasser]

Not yet.  We are hoping FreeSurfer 6.1 will work nicely with the HCP
Pipelines.  For now version 6.0 has some regressions as far as surface
placement goes and there are also some adaptations we need to make to the
pipelines.  

Peace,

Matt.

From:   on behalf of CAGNA Bastien

Reply-To:  Freesurfer support list 
Date:  Monday, March 13, 2017 at 7:21 AM
To:  "freesurfer@nmr.mgh.harvard.edu" 
Subject:  [Freesurfer] Can we use fressurfer 6 with the Human connectome
project's pipeline ?

Dear freesurfer experts,



I'm wondering if it's possible to run the human connetome project's minimal
processing pipeline using freesurfer 6 ?



Does it require some update of the pipeline or is there anybody that have
already enjoyed the new freesurfer version with this pipeline ?



Thank you for your attention and your help,

Bastien Cagna




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Re: [Freesurfer] issues with -T2pial option in v.5.3

[Matt Glasser]

You could try with the HCP Pipelines and see if that helps:

https://github.com/Washington-University/Pipelines

Peace,

Matt.

From:   on behalf of Petr Bednarik

Reply-To:  Freesurfer support list 
Date:  Monday, February 20, 2017 at 12:26 PM
To:  
Subject:  [Freesurfer] issues with -T2pial option in v.5.3

Hi everyone, 

I am using Freesurfer version 5.3. I tried to refine the pial surfaces by
using  -T2pial option:

recon-all -subjid $SUBJ -T2/SUBJECT_DIR/$SUBJ/mri/orig/T2raw.mgz -T2pial
-autorecon3 

This step was helpful - e.g. it removed nicely residuals of venous sinuses,
but in some subjects it also removed part of the parietal or frontal cortex,
while the white matter is appropriately segmented.

https://www.dropbox.com/s/4gzsvrg85xsfdkn/surfaces_over_brainmask.mgz.png?dl
=0

The T2-space images had the same resolution as T1-MPRAGE (1x1x1mm) and were
acquired in the same session (3T Siemens Trio, standard 32 channel coil).
The problem does not seem to be caused by T2 misregistration :

https://www.dropbox.com/s/a7gdpxom0cqgj1u/surfaces_over_T2.mgz.png?dl=0

Question : What could cause this error and how could I extend pial surfaces
and get correct final segmentation ?

Thanks a lot !

PB
   
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Re: [Freesurfer] -FLAIRpial in v6.0 positions pial surfaces much more externally in comparison to v5.3

[Matt Glasser]

Since I believe you said you are using my code, I would recommend to stick
with 5.3 at this time.

Peace,

Matt.

From:   on behalf of Antonin Skoch

Reply-To:  Freesurfer support list 
Date:  Tuesday, February 7, 2017 at 2:59 PM
To:  
Subject:  Re: [Freesurfer] -FLAIRpial in v6.0 positions pial surfaces much
more externally in comparison to v5.3

Dear Bruce,

thank you for the feedback. I would definitely be interested in 6.1 beta.
What is the approximate timeline of release?
We are working on quite large project (involving -FLAIRpial) and I have to
decide whether to go to v6.0 or to stick with v5.3.
Do you think that so far the 5.3 version is better for T2/FLAIR? Why this is
the case?

Antonin

Hi Antonin

yes, V6 was not meant for T2/FLAIR and we didn't test it extensively. We
have been optimizing things in the past week for T2/FLAIR and I expect 6.1
will be better for them. We can give you a beta soon if you like.
cheers
Bruce
  On Tue, 7 
Feb 2017, Antonin Skoch wrote:

> Dear experts,
> 
> I have reprocessed my groups of subjects (originally processed by v5.3) by
> v6.0. I am using -FLAIRpial for pial surface refinement.
> 
> I have noticed that the pial surfaces in v6.0 after -FLAIRpial are positioned
> much more externally in comparison to -FLAIRpial in v5.3. The v6.0 version
> includes to pial sheet much more partial volume voxels in
> comparison to v5.3.
> 
> In contrast to v5.3, where the surfaces after -FLAIRpial were mostly
> internally with respect to pial surfaces determined by T1, in v6.0 there are
> many regions where the pial surfaces after -FLAIRpial are placed
> much externally with respect to pial surfaces determined by T1.
> 
> See the screenshot (red surfaces are pial surfaces after -FLAIRpial with
> v6.0, yellow are surfaces after -FLAIRpial with v.5.3).
> 
> I have used -nsigma_above 8 in mris_make_surfaces to prevent excluding some
> cortical regions with high signal intensity but this I used consistently in
> both versions so it should not be the reason of difference.
> 
> I have uploaded the subject processed both by 5.3 and 6.0 version to your
> server, files FLAIRpial_v5.3.tar.gz and FLAIRpial_v6.0.tar.gz.
> 
> Could you please look at my data and check whether the pial surfaces after
> -FLAIRpial in v6.0 look OK from your perspective?
> 
> Regards,
> 
> Antonin Skoch
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Re: [Freesurfer] license file not working

[Matt Glasser]

No worries Bruce!

Matt.

On 2/3/17, 12:52 PM, "Bruce Fischl"
<freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
fis...@nmr.mgh.harvard.edu> wrote:

>Hi Matt
>
>just to clarify - our old license format stopped working with newer
>versions of libcrypt and so we were forced to change to the new format.
>It 
>was not done gratuitously on our part or as a way to get people to
>request 
>new licenses - we had no choice.
>
>cheers
>Bruce
>
>
>On Thu, 2 Feb 2017, Matt Glasser wrote:
>
>> Like I said, they changed the format at some point and stopped
>>accepting the old format with FS 6.0.  I
>> have used FreeSurfer for a long time too and found that I had to get a
>>new license file with this
>> version.
>> 
>> Peace,
>> 
>> Matt.
>> 
>> From: <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Anthony
>>Dick <ad...@fiu.edu>
>> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
>> Date: Thursday, February 2, 2017 at 5:18 PM
>> To: <freesurfer@nmr.mgh.harvard.edu>
>> Subject: Re: [Freesurfer] license file not working
>> 
>> Hello,
>> 
>> I have used my old file, registered under two different emails (and
>>received the code and made new files
>> each time, named both .license and license.txt). Restarted the computer
>>etc. I am wondering if it is a
>> permissions issue. It seems to be finding the file where I put it. Have
>>never encountered this issue and
>> have been using Freesurfer for 11 years. If history is any guide, it
>>will probably turn out to be
>> something stupid that I did :)
>> 
>> Anthony
>> 
>> 
>> On 2/2/17 3:40 PM, Trisanna Sprung-Much wrote:
>>   The .license that it comes with is not the same as the
>>license.txt that you have to acquire.
>>   I was able to use an old license.txt from my Freesurfer 5.3 for
>>6.0.
>> Best
>> 
>> Trisanna
>> 
>> --
>> Ph.D. Candidate McGill University
>> Integrated Program in Neuroscience
>> Psychology
>> 
>> 
>> On Thu, Feb 2, 2017 at 3:21 PM, X K <bnu...@gmail.com> wrote:
>>   try to rename the file to license.txt?
>> 
>> On Thu, Feb 2, 2017 at 9:13 PM, Anthony Dick <ad...@fiu.edu> wrote:
>>   Hello,
>>
>>   I have been using Freesurfer for a number of years, and just
>>installed
>>   v6.0. I run into this problem:
>>
>>   
>>-
>>-
>>   ERROR: Invalid FreeSurfer license key found in license file
>>   /Applications/freesurfer/.license
>>  If you are outside the NMR-Martinos Center,
>>  go to http://surfer.nmr.mgh.harvard.edu/registration.html to
>>  get a valid license file (it's free).
>>  If you are inside the NMR-Martinos Center,
>>  make sure to source the standard environment.
>>   
>>-
>>-
>>
>>   I have a valid .license file, in the Freesurfer home directory
>>
>>   Last login: Thu Feb  2 15:04:01 on ttys005
>>    freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c 
>>   Setting up environment for FreeSurfer/FS-FAST (and FSL)
>>   FREESURFER_HOME   /Applications/freesurfer
>>   FSFAST_HOME   /Applications/freesurfer/fsfast
>>   FSF_OUTPUT_FORMAT nii.gz
>>   SUBJECTS_DIR  /Applications/freesurfer/subjects
>>   MNI_DIR   /Applications/freesurfer/mni
>>   [38c9862eb0b0:~] adick% cd /Applications/freesurfer
>>   [38c9862eb0b0:/Applications/freesurfer] adick% ls -al .license
>>   -rw-r--r--  1 root  wheel  140 Feb  2 15:06 .license
>>   [38c9862eb0b0:/Applications/freesurfer] adick%
>>
>>   Any ideas?
>>
>>   Thanks!
>>
>>   Anthony
>> 
>>
>>   --
>>   Anthony Steven Dick, Ph.D.
>>   Associate Professor
>>   Director, Cognitive Neuroscience Program and Graduate Certificate
>>in Cognitive
>>   Neuroscience
>>   Department of Psychology
>>   Florida International University Modesto A. Maidique Campus AHC4
>>454
>>   11200 S.W. 8th Street
>>   Miami, FL 33199
>>   Ph: 305-348-4202; Lab Ph: 305-348-9055; Fx: 305-348-3879
>>   Email: ad...@fiu.edu
>>   Webpage: http://myweb.fiu.edu/adick
>>   Join the Society for the Stu

Re: [Freesurfer] license file not working

[Matt Glasser]

Strange, that fixed things right up for me.  You might make sure you know
where you are calling FreeSurfer from and that there are no old license
files lying around.

Peace,

Matt.

From:  <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Anthony Dick
<ad...@fiu.edu>
Reply-To:  Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date:  Thursday, February 2, 2017 at 5:46 PM
To:  <freesurfer@nmr.mgh.harvard.edu>
Subject:  Re: [Freesurfer] license file not working


 

Thanks Matt. I already tried it with a new registration, but it doesn't hurt
to try it again. That may be where the issue is. I'll post if that turns out
to be the problem. Thanks!
 

Anthony
 
 
 
On 2/2/17 6:28 PM, Matt Glasser wrote:
 
 
>   
> Like I said, they changed the format at some point and stopped accepting the
> old format with FS 6.0.  I have used FreeSurfer for a long time too and found
> that I had to get a new license file with this version.
>  
> 
>  
>  
> Peace,
>  
> 
>  
>  
> Matt.
>  
> 
>  
>   
> From:  <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Anthony Dick
> <ad...@fiu.edu>
>  Reply-To:  Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
>  Date:  Thursday, February 2, 2017 at 5:18 PM
>  To:  <freesurfer@nmr.mgh.harvard.edu>
>  Subject:  Re: [Freesurfer] license file not working
>  
>  
> 
>  
>  
>  
>  
> 
> Hello,
>  
> 
> I have used my old file, registered under two different emails (and received
> the code and made new files each time, named both .license and license.txt).
> Restarted the computer etc. I am wondering if it is a permissions issue. It
> seems to be finding the file where I put it. Have never encountered this issue
> and have been using Freesurfer for 11 years. If history is any guide, it will
> probably turn out to be something stupid that I did :)
>  
> 
> Anthony
>  
>  
>  
> On 2/2/17 3:40 PM, Trisanna Sprung-Much wrote:
>  
>  
>>  
>> The .license that it comes with is not the same as the license.txt that you
>> have to acquire. I was able to use an old license.txt from my Freesurfer 5.3
>> for 6.0. 
>> 
>>  
>>  
>> Best
>>  
>> 
>>  
>>  
>> Trisanna
>>  
>>  
>> 
>>  
>>  
>>  
>>  
>>  
>> --
>>  
>> Ph.D. Candidate 
>> McGill University
>>   
>> Integrated Program in Neuroscience
>>  
>> Psychology
>>  
>> 
>>  
>>  
>>  
>>  
>>  
>>  
>>  
>>  
>>  
>> On Thu, Feb 2, 2017 at 3:21 PM, X K <bnu...@gmail.com> wrote:
>>  
>>>  
>>> try to rename the file to license.txt?
>>>  
>>>  
>>>  
>>> 
>>>  
>>> On Thu, Feb 2, 2017 at 9:13 PM, Anthony Dick <ad...@fiu.edu> wrote:
>>>  
>>>> Hello,
>>>>  
>>>>  I have been using Freesurfer for a number of years, and just installed
>>>>  v6.0. I run into this problem:
>>>>  
>>>>  --
>>>>  ERROR: Invalid FreeSurfer license key found in license file
>>>>  /Applications/freesurfer/.license
>>>> If you are outside the NMR-Martinos Center,
>>>> go to http://surfer.nmr.mgh.harvard.edu/registration.html to
>>>> get a valid license file (it's free).
>>>> If you are inside the NMR-Martinos Center,
>>>> make sure to source the standard environment.
>>>>  --
>>>>  
>>>>  I have a valid .license file, in the Freesurfer home directory
>>>>  
>>>>  Last login: Thu Feb  2 15:04:01 on ttys005
>>>>   freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c 
>>>>  Setting up environment for FreeSurfer/FS-FAST (and FSL)
>>>>  FREESURFER_HOME   /Applications/freesurfer
>>>>  FSFAST_HOME   /Applications/freesurfer/fsfast
>>>>  FSF_OUTPUT_FORMAT nii.gz
>>>>  SUBJECTS_DIR  /Applications/freesurfer/subjects
>>>>  MNI_DIR   /Applications/freesurfer/mni
>>>>  [38c9862eb0b0:~] adick% cd /Applications/freesurfer
>>>>  [38c9862eb0b0:/Applications/freesurfer] adick% ls -al .license
>>>>  -rw-r--r--  1 root  wheel  140 Feb  2 15:06 .license
>>>>  [38c9862eb0b0:/Applications/freesurfer] adick%
>>>>  
>>>>  Any ideas?
>>>>  
>>>>  Tha

Re: [Freesurfer] license file not working

[Matt Glasser]

Like I said, they changed the format at some point and stopped accepting the
old format with FS 6.0.  I have used FreeSurfer for a long time too and
found that I had to get a new license file with this version.

Peace,

Matt.

From:   on behalf of Anthony Dick

Reply-To:  Freesurfer support list 
Date:  Thursday, February 2, 2017 at 5:18 PM
To:  
Subject:  Re: [Freesurfer] license file not working


 

Hello,
 

I have used my old file, registered under two different emails (and received
the code and made new files each time, named both .license and license.txt).
Restarted the computer etc. I am wondering if it is a permissions issue. It
seems to be finding the file where I put it. Have never encountered this
issue and have been using Freesurfer for 11 years. If history is any guide,
it will probably turn out to be something stupid that I did :)
 

Anthony
 
 
 
On 2/2/17 3:40 PM, Trisanna Sprung-Much wrote:
 
 
>   
> The .license that it comes with is not the same as the license.txt that you
> have to acquire. I was able to use an old license.txt from my Freesurfer 5.3
> for 6.0. 
> 
>  
>  
> Best
>  
> 
>  
>  
> Trisanna
>  
>  
> 
>  
>  
>  
>  
>  
> --
>  
> Ph.D. Candidate 
> McGill University
>   
> Integrated Program in Neuroscience
>  
> Psychology
>  
> 
>  
>  
>  
>  
>  
>  
>  
>  
>  
> On Thu, Feb 2, 2017 at 3:21 PM, X K  wrote:
>  
>>  
>> try to rename the file to license.txt?
>>  
>>  
>>  
>> 
>>  
>> On Thu, Feb 2, 2017 at 9:13 PM, Anthony Dick  wrote:
>>  
>>> Hello,
>>>  
>>>  I have been using Freesurfer for a number of years, and just installed
>>>  v6.0. I run into this problem:
>>>  
>>>  --
>>>  ERROR: Invalid FreeSurfer license key found in license file
>>>  /Applications/freesurfer/.license
>>> If you are outside the NMR-Martinos Center,
>>> go to http://surfer.nmr.mgh.harvard.edu/registration.html to
>>> get a valid license file (it's free).
>>> If you are inside the NMR-Martinos Center,
>>> make sure to source the standard environment.
>>>  --
>>>  
>>>  I have a valid .license file, in the Freesurfer home directory
>>>  
>>>  Last login: Thu Feb  2 15:04:01 on ttys005
>>>   freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c 
>>>  Setting up environment for FreeSurfer/FS-FAST (and FSL)
>>>  FREESURFER_HOME   /Applications/freesurfer
>>>  FSFAST_HOME   /Applications/freesurfer/fsfast
>>>  FSF_OUTPUT_FORMAT nii.gz
>>>  SUBJECTS_DIR  /Applications/freesurfer/subjects
>>>  MNI_DIR   /Applications/freesurfer/mni
>>>  [38c9862eb0b0:~] adick% cd /Applications/freesurfer
>>>  [38c9862eb0b0:/Applications/freesurfer] adick% ls -al .license
>>>  -rw-r--r--  1 root  wheel  140 Feb  2 15:06 .license
>>>  [38c9862eb0b0:/Applications/freesurfer] adick%
>>>  
>>>  Any ideas?
>>>  
>>>  Thanks!
>>>  
>>>  Anthony
>>>  
>>>  
>>>  --
>>>  Anthony Steven Dick, Ph.D.
>>>  Associate Professor
>>>  Director, Cognitive Neuroscience Program and Graduate Certificate in
>>> Cognitive Neuroscience
>>>  Department of Psychology
>>>  Florida International University Modesto A. Maidique Campus AHC4 454
>>>  11200 S.W. 8th Street
>>>  Miami, FL 33199
>>>  Ph: 305-348-4202  ; Lab Ph: 305-348-9055
>>>  ; Fx: 305-348-3879 
>>>  Email: ad...@fiu.edu
>>>  Webpage: http://myweb.fiu.edu/adick
>>>  Join the Society for the Study of Human Development:
>>> http://www.sshdonline.org
>>>  
>>>  ___
>>>  Freesurfer mailing list
>>>  Freesurfer@nmr.mgh.harvard.edu
>>>  https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>  
>>>  
>>>  The information in this e-mail is intended only for the person to whom it
>>> is
>>>  addressed. If you believe this e-mail was sent to you in error and the
>>> e-mail
>>>  contains patient information, please contact the Partners Compliance
>>> HelpLine at
>>>  http://www.partners.org/complianceline . If the e-mail was sent to you in
>>> error
>>>  but does not contain patient information, please contact the sender and
>>> properly
>>>  dispose of the e-mail.
>>>  
>>>  
>>  
>>  
>>  
>>  
>> 
>>  
>>  
>>  
>>  -- 
>>  
>>  
>> -
>> 
>>  
>> Kong Xiangzhen
>>  State Key Laboratory of Cognitive Neuroscience and Learning,
>>  Beijing Normal University,
>>  Beijing, China, 100875.
>>  
>>  
>>  ___
>>  Freesurfer mailing list
>>  Freesurfer@nmr.mgh.harvard.edu
>>  https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>  
>>  
>>  The information in this e-mail is intended 

Re: [Freesurfer] license file not working

[Matt Glasser]

They updated the format so you have to get another.

Peace,

Matt.

On 2/2/17, 2:13 PM, "Anthony Dick"  wrote:

>Hello,
>
>I have been using Freesurfer for a number of years, and just installed
>v6.0. I run into this problem:
>
>--
>ERROR: Invalid FreeSurfer license key found in license file
>/Applications/freesurfer/.license
>   If you are outside the NMR-Martinos Center,
>   go to http://surfer.nmr.mgh.harvard.edu/registration.html to
>   get a valid license file (it's free).
>   If you are inside the NMR-Martinos Center,
>   make sure to source the standard environment.
>--
>
>I have a valid .license file, in the Freesurfer home directory
>
>Last login: Thu Feb  2 15:04:01 on ttys005
> freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c 
>Setting up environment for FreeSurfer/FS-FAST (and FSL)
>FREESURFER_HOME   /Applications/freesurfer
>FSFAST_HOME   /Applications/freesurfer/fsfast
>FSF_OUTPUT_FORMAT nii.gz
>SUBJECTS_DIR  /Applications/freesurfer/subjects
>MNI_DIR   /Applications/freesurfer/mni
>[38c9862eb0b0:~] adick% cd /Applications/freesurfer
>[38c9862eb0b0:/Applications/freesurfer] adick% ls -al .license
>-rw-r--r--  1 root  wheel  140 Feb  2 15:06 .license
>[38c9862eb0b0:/Applications/freesurfer] adick%
>
>Any ideas?
>
>Thanks!
>
>Anthony
>
>
>-- 
>Anthony Steven Dick, Ph.D.
>Associate Professor
>Director, Cognitive Neuroscience Program and Graduate Certificate in
>Cognitive Neuroscience
>Department of Psychology
>Florida International University Modesto A. Maidique Campus AHC4 454
>11200 S.W. 8th Street
>Miami, FL 33199
>Ph: 305-348-4202; Lab Ph: 305-348-9055; Fx: 305-348-3879
>Email: ad...@fiu.edu
>Webpage: http://myweb.fiu.edu/adick
>Join the Society for the Study of Human Development:
>http://www.sshdonline.org
>
>___
>Freesurfer mailing list
>Freesurfer@nmr.mgh.harvard.edu
>https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>The information in this e-mail is intended only for the person to whom it
>is
>addressed. If you believe this e-mail was sent to you in error and the
>e-mail
>contains patient information, please contact the Partners Compliance
>HelpLine at
>http://www.partners.org/complianceline . If the e-mail was sent to you in
>error
>but does not contain patient information, please contact the sender and
>properly
>dispose of the e-mail.
>


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Re: [Freesurfer] freesufer v6 beta - T2 pial refinement performance and nsigma_below setting

[Matt Glasser]

Hi Antonin,

In our experience with FreeSurfer 5.3 we were getting very consistent
results.  We are going to try some of this locally and work with the
FreeSurfer folks to get the T2w stream working robustly in FreeSurfer v6.0+.

Thanks for testing this,

Matt.

From:   on behalf of Antonin Skoch

Reply-To:  Freesurfer support list 
Date:  Wednesday, November 30, 2016 at 3:31 PM
To:  
Subject:  Re: [Freesurfer] freesufer v6 beta - T2 pial refinement
performance and nsigma_below setting

Dear experts,

given sub-optimal results of my surfaces I referred to in my previous post,
I have tested several different settings and input data preparation to
obtain optimal pial surfaces in my modified HCP pipeline. I tested all
variants in 5 representative subjects.

My modified HCP pipeline uses FreeSurfer V6beta and full hires recon (-cm
option) with 0.7mm3 data (including FreeSurferHiResWhite.sh and
FreeSurferHiResPial.sh where effectively no up and downsampling is done
since all steps are done in original 0.7 mm3 resolution).

I have played with input data and parameters of 2nd pass mris_make_surfaces
-T2pial in FreeSurferHiResPial.sh
Since FreeSurferHiResPial.sh does not use aseg-informed and white
surface-informed normalization and brain masking of T2 (which is default in
recon-all), I also tested performance of this option (using commands
borrowed from recon-all -T2pial). Since -nsigma_below 3 (default in
FreeSurferHiResPial.sh) with combination of freeSurfer V6beta version of
mris_make_surfaces cuts out some portions of gray matter in my data (in
contrast to FreeSurfer 5.3 version where it seems that nsigma_below 3
suffices!), I increased -nsigma_below to 5 (which is default value used in
recon-all -T2pial).

My tested versions were following:
For modified full hires HCP pipeline with FreeSurfer V6beta:
1. -nsigma_below 3 (original FreeSurferHiResPial.sh)
2. -nsigma_below 5 
3. -nsigma_below 5 with additional masking of T2 by brainmask.mgz
4. -nsigma_below 5 with aseg-informed normalization of T2 (using
mri_normalize)
5. -nsigma_below 5 with aseg-informed normalization of T2 (using
mri_normalize) and masking of T2 by brainmask.mgz

And, as Matt suggested, I also tried:
6. standard FreeSurfer V6 beta recon-all -pial and -T2pial (apart from
standard recon-all I used as ?h.white input the output of
FreeSurferHiResWhite.sh , but I think it should not matter in this context).

My observations are following:

It is definitely needed to increase -nsigma_below from 3 due to significant
cut out of portions of gray matter in some regions, in some subjects these
regions are very large.

Increase nsigma_below to 5 prevents cutting out of gray matter, however it
leads to leak of surfaces to cerebellum (as I showed in my previous post)
for all my versions (to varying extent). I am not sure how much significant
the extend of error is, looking subjective it seems significant, but
accounting the fact that the data is of high resolution, the maximal error
would be approx. 2 mm.

-nsigma_below 5 with aseg-informed normalization does not work well in some
areas and results in cutting out gray matter in some regions (but not to
such great extend as in nsigma_below 3)

FreeSurfer V6beta tends in some (not very large) areas to cut out gray
matter. On the other hand, in some areas and in some subjects it produces
largest leak of surfaces to dura and cerebellum from all my tested versions.

mri_normalize of T2 has in some regions  sub-optimal performance on pial
surface estimation and actually performs worse than global (no aseg-informed
and no white surface-informed) normalization ( especially at temporal poles,
but also in some areas at convexity).

I have indecisive results with masking. In some subjects it had almost no
effect, in one subject it definitely improved the leak to dura, but in some
subjects the results were quite opposite. I am not sure why the masking
should matter since the mask is larger than the regions where the surfaces
are extending, but I am not very familiar with internals of
mris_make_surfaces (the masked T2 maybe after internal smoothing in
mris_make_surfaces can propagate the voxel values even to regions relevant
for surface estimation). Therefore I would tend to use the masking.

Overall best results (better than with V6beta recon-all) I obtained with
-nsigma_below 5 with global (no aseg-informed and white surface-informed)
normalization of T2 as it is done in FreeSurferHiResPial.sh.

My overall impresion: I was quite frustrated to observe, how much the
results are dependent on particular setting of the parameters and input
data. But maybe my expectations of accuracy of surfaces were unrealistically
high

Regards,

Antonin
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Re: [Freesurfer] freesufer v6 beta - T2 pial refinement performance and nsigma_below setting

[Matt Glasser]

How does it work if you just use vanilla recon-all v6 beta with the T2
refinement flag and the hires option?  We haven¹t yet updated the HCP
scripts for FreeSurfer v6, but this is on our to do list.

Peace,

Matt.

From:   on behalf of Antonin Skoch

Reply-To:  Freesurfer support list 
Date:  Sunday, November 27, 2016 at 7:03 PM
To:  
Subject:  [Freesurfer] freesufer v6 beta - T2 pial refinement performance
and nsigma_below setting

Dear FreeSurfer experts,

I have processed a group of subjects by the freesurfer v6 beta version
(with recent upgrade of mris_make_surfaces from 2016/11/21).

It seems to me that in contrast to v5.3 version (with the same nsigma_above
2, nsigma_below 3) the T2 pial refinement cuts out too much gray matter in
regions where the gray matter has rather low intensity in T2 images. I have
observed this behavior quite often in my subjects.

I have uploaded the example subject cut_gm_T2pial.tar.gz to the server. The
problematic area has RAS location 3.9, -70, 0. Also see the screenshot.

My command line was:

mris_make_surfaces -nsigma_above 2 -nsigma_below 3 -aseg aseg.hires -filled
filled.hires -wm wm.hires -mgz -sdir $my_subject_dir -orig white.deformed
-nowhite -orig_white white.deformed -orig_pial pial.preT2.pass2 -T2
my_subject/mri/T2w_hires.norm -T1 T1w_hires.norm -output .postT2.pass2
my_subject rh

and for FS 5.3

mris_make_surfaces -nsigma_above 2 -nsigma_below 3 -aseg aseg.hires -filled
filled.hires -wm wm.hires -mgz -sdir $my_subject_dir -orig white.deformed
-nowhite -orig_white white.deformed -orig_pial pial.preT2.pass2 -T2
my_subject/mri/T2w_hires.norm -T1 T1w_hires.norm -output
.postT2.pass2.FS_5.3 my_subject rh

Could you please comment on how to proceed?

It seems that in contrast to v5.3 it is necessary to increase nsigma_below
value since the nsigma values seem to be more "sensitive" in v6beta version.
I tried to increase nsigma_below (nsigma_below for T2 in recon-all is 5) but
it seemed to me that it leads to "leak" of the pial surface out of the gray
matter in other areas, mainly in regions adjacent to cerebellum. See the
example leaking the pial surface to the cerebellum in left hemisphere with
nsigma_below 5 in the second screenshot in attachment ( I have uploaded this
subject as file cut_gm_T2pial2.tar.gz, his cut-out gray matter RAS location
is -33.7, -18, 45, command line is similar as above, but for left
hemisphere). Yellow surface is with nsigma_below 5, blue is nsigma_below 3.
Btw, the -aseg option in mris_make_surfaces does not prevent to leak
surfaces into the cerebellum?

Could also be the reason of these problems, that I used HCP scripts which do
not do the T2 normalization with anatomy-informed mri_normalize (using aseg
and white surface), but only global normalization and bias field correction?

Regards,

Antonin Skoch
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but does not contain patient information, please contact the sender and properly
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Re: [Freesurfer] Optimal combination of MRI-sequences

[Matt Glasser]

What do you mean by ³combining² sequences?

Peace,

Matt.

From:   on behalf of Erik Lindberg

Reply-To:  Freesurfer support list 
Date:  Tuesday, October 18, 2016 at 2:52 PM
To:  
Subject:  [Freesurfer] Optimal combination of MRI-sequences

Dear Freesufer experts,
 
We are in the process of starting a large MRI project on normal aging and
dementia.
 
There has been a lot of discussions about what sequences to use.
 
We are now thinking about combining several sequences. Is there an optimal
combination of MRI sequences for Freesufer?
 
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Re: [Freesurfer] inclusion of both T1 and T2 in a recon-all run

[Matt Glasser]

Sure there¹s a publication.  See Figure 14:

http://www.sciencedirect.com/science/article/pii/S1053811913005053

Peace,

Matt.

On 8/30/16, 10:21 AM, "Bruce Fischl"
 wrote:

>Hi Don
>
>the T2 or FLAIR helps us avoid dura. It is still a beta version though as
>we don't have a ton of experience with it, and no, there is no reference
>for it yet (or maybe ever) :)
>Bruce
>
>
>On Tue, 30 Aug 2016, Krieger, Donald N. wrote:
>
>> 
>> Dear list:
>> 
>>  
>> 
>> What are the advantages of including a T2 scan when running recon-all
>>­all
>>  ?
>> 
>> Which results can it effect and to what extent?
>> 
>> And how sensitive is freesurfer to artifacts in the T2 scan?
>> 
>> Is there a good reference for this/
>> 
>>  
>> 
>> Thanks and best - Don
>> 
>>  
>> 
>> 
>>___
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>
>
>The information in this e-mail is intended only for the person to whom it
>is
>addressed. If you believe this e-mail was sent to you in error and the
>e-mail
>contains patient information, please contact the Partners Compliance
>HelpLine at
>http://www.partners.org/complianceline . If the e-mail was sent to you in
>error
>but does not contain patient information, please contact the sender and
>properly
>dispose of the e-mail.



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Re: [Freesurfer] mri_glmfit-sim permutation testing running after 3 days!

[Matt Glasser]

PALM handles GIFTI and CIFTI data.

Peace,

Matt.

On 8/29/16, 6:21 PM, "Douglas N Greve"
 wrote:

>Does PALM do surface-based? Also, there is no way to appropriately
>handle this. For permutation, non-orthogonal designs are wrong. There
>are ways to try to compensate for it, which is what PALM is doing. Sorry
>to be nit-picky!
>
>
>On 08/29/2016 06:12 PM, Harms, Michael wrote:
>> Hi Maaike,
>> Why not just use PALM?  Then you don¹t have to worry about this (since
>> PALM appropriately handles the situation of correlated covariates).
>>
>> cheers,
>> -MH
>>
>> --
>> Michael Harms, Ph.D.
>>
>> ---
>> Conte Center for the Neuroscience of Mental Disorders
>> Washington University School of Medicine
>> Department of Psychiatry, Box 8134
>> 660 South Euclid Ave.Tel: 314-747-6173
>> St. Louis, MO  63110Email: mha...@wustl.edu
>>
>>
>>
>>
>> On 8/29/16, 4:45 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf
>>of
>> Douglas N Greve" > gr...@nmr.mgh.harvard.edu> wrote:
>>
>> It is hard to say. Since the subjects are not exchangeable, the
>> permutation is technically not appropriate. Check the winkler paper,  I
>> think he talks about what happens if you just don't do anything.
>>
>>
>> On 08/29/2016 11:07 AM, maaike rive wrote:
>>> Hi all,
>>>
>>>
>>> Is using forced permutation for non-orthogonal design matrices wrong
>>> or is it allowed to do this instead of using tools like palm (what
>>> happens eg with the covariates when using forced permutation)? I
>>> used forced permutation  and it seemed to work, results were (partly)
>>> comparable to what I found with monte carlo simulations.
>>>
>>>
>>> Thanks, Maaike
>>>
>>> 
>>>
>>> *Van:* freesurfer-boun...@nmr.mgh.harvard.edu
>>>  namens Harms, Michael
>>> 
>>> *Verzonden:* vrijdag 26 augustus 2016 01:00:13
>>> *Aan:* Freesurfer support list
>>> *Onderwerp:* Re: [Freesurfer] mri_glmfit-sim permutation testing
>>> running after 3 days!
>>>
>>> Hi,
>>> You might want to check out FSL¹s PALM tool, which has a bit more
>>> sophisticated permutation framework, and allows for permutation in the
>>> context of non-orthogonal covariates.
>>>
>>> cheers,
>>> -MH
>>>
>>> --
>>> Michael Harms, Ph.D.
>>> ---
>>> Conte Center for the Neuroscience of Mental Disorders
>>> Washington University School of Medicine
>>> Department of Psychiatry, Box 8134
>>> 660 South Euclid Ave.Tel: 314-747-6173
>>> St. Louis, MO  63110Email: mha...@wustl.edu
>>>
>>> From: >> > on behalf of Ajay
>>> Kurani >
>>> Reply-To: Freesurfer support list >> >
>>> Date: Thursday, August 25, 2016 at 4:13 PM
>>> To: Freesurfer support list >> >
>>> Subject: Re: [Freesurfer] mri_glmfit-sim permutation testing running
>>> after 3 days!
>>>
>>> Hi Doug,
>>> Thanks for the help!  I think I figured out the issue based on your
>>> response.
>>> 1) I created a template to use for this group and named it fsaverage
>>> (including creating monte carlo simulations) for simplicity of
>>> integrating with freesurfer as I am newer to it.  This is why the
>>> sizes didn't match up as you expected
>>>  but the mri_glmfit still ran.
>>>
>>> 2) I deleted the folder and restarted without background processes.
>>> The error became apparent.  Of my covariates (2 fix factors and 3
>>> quantitative), not all were orthogonal.  In looking at the error more,
>>> it seems that i need to add the
>>> --perm-force if I wanted the simulation to run, however the background
>>> processes were not aware of this error and kept polling as you
>>>mentioned.
>>>
>>> This brings me to a new but related issue.  From what I have read in
>>> other freesurfer posts, it is statistically incorrect to use
>>> --perm-force for non-orthogonal covariates (or continuous covariates).
>>> I am unsure how to proceed.
>>> a) If I ran permutation testing (to overcome the issue of incorrect
>>> smoothness estimations from the gaussian distribution assumption),
>>> then I run into the issue of non-orthogonal covariates.  Is there a
>>> way to orthogonalize the data in
>>>  freesurfer, or a solution to this issue?
>>>
>>> b) If orthogonalizing is difficult to implement, another option is
>>> running Qdec with the montecarlo simulation at a more conservative p
>>> value (p< 0.001).  From your previous posts, the testing at this p
>>> value for 10mm seems to meet the 5% FPR.  One question is if the

Re: [Freesurfer] Support for surface data on NeuroVault.org

[Matt Glasser]

GIFTI has two identical formats for scalar (e.g. Statistical) data.
.func.gii and .shape.gii are basically identical.  It is also a good idea to
provide some surfaces upon which to display the GIFTI data.

I¹m a bit puzzled as to how to display arbitrary scalar overlays at all in
FreeView (though I figured out how to display label/annot files which worked
fine as GIFTI).  I don¹t know anything about pysurfer.

Peace,

Matt.

From:  <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Chris Filo
Gorgolewski <chris.gorgolew...@gmail.com>
Reply-To:  Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date:  Saturday, August 20, 2016 at 1:51 PM
To:  Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject:  Re: [Freesurfer] Support for surface data on NeuroVault.org

On Sat, Aug 20, 2016 at 10:39 AM, Matt Glasser <m...@ma-tea.com> wrote:
> Why not focus on distributing GIFTI files that are viewable both by FreeSurfer
> and many other applications instead of FreeSurfer¹s native format?  For the
> same reason that it is helpful to provide NIFTI files because of their strong,
> cross-platform adoption, it would be more helpful to provide GIFTI files in
> your database so that a wider range of users could use them without converting
> them.  You could probably automatically convert FreeSurfer¹s native formats to
> GIFTI with FreeSurfer¹s utility mris_convert on upload if you didn¹t want your
> uploading users to have to do the conversions.
I was merely discussing the format required for the upload - which I want to
keep as straightforward as possible for the users. As you mentioned we can
do a conversion server side and provide other file formats. Having an
optional download the data as gifti might be very useful. Would that be a
"Functional" gifti file? So .func.gii? This does not seem right since many
statistical maps will come from anatomical data. I cannot find the right
intent in the GIFTI spec (section 13): it's not a set of coordinates,
neither a label map... How are statistical maps usually stored in gifti?

Would we also need to provide each map in .mgh or is .gii sufficient for
FreeSurfer users? Is displaying statistical map overlay coming in a form of
a .gii file easy in FreeView? What about pysurfer?

> Generally inflated surfaces are easiest for viewing patterns, but it is often
> helpful to include anatomical surfaces as well.
Thanks!

Best,
Chris 
> 
> Peace,
> 
> Matt.
> 
> From:  <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Chris Filo
> Gorgolewski <chris.gorgolew...@gmail.com>
> Reply-To:  Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
> Date:  Saturday, August 20, 2016 at 12:21 PM
> To:  freesurfer <freesurfer@nmr.mgh.harvard.edu>
> Subject:  [Freesurfer] Support for surface data on NeuroVault.org
> 
> Dear FreeSurfer community,
> I am one of the developers of NeuroVault.org <http://NeuroVault.org>  - an
> open repository for vizualizing, analyzing, and sharing of statistical and
> parcellation maps of the human brain. So far NeuroVault was limited only to
> volumetric data in the MNI space since this is the most common way of
> reporting MRI results. Now I would like to start working on adding support for
> surface data beginning with outputs of FreeSurfer. Since I'm not a FreeSurfer
> expert I would like to ask the community a few questions:
> 
> 1. In NeuroVault users are asked to upload their statistical maps in form of
> files. I'm planning to target outputs of mri_glmfit: preferably Z.mgh but also
> sig.mgh. Is this the most sensible thing to do?
> 
> 2. I want to be able to tell if a given map is in fsaverage space. Is there
> any place in the .mgh header that specifies which space the map is in?
> 
> 3. fsaverage has different subsampling flavours - how often are they used? Is
> support for them an important feature?
> 
> 4. Results come in two files - one per each hemisphere. Is there any way (from
> the headers) to check if two files provided by a user match?
> 
> 5. As with the volumetric data I want to provide a 3D interactive viewer. I
> had some initial success with Brain Browser. Are you aware of any other
> javascript based viewers that work well with FreeSurfer data?
> 
> 6. Which surface should be the default view: inflated, pial, or white?
> 
> 7. Finally NeuroVault gives users ability to compare maps and even search
> through the whole repository to find statistical maps with similar patterns.
> This is currently implemented for volumetric data, but could be extended to
> surface data. The problem arises when one wants to compare MNI volumetric data
> with fsaverage surface data. So far I have been using mri_vol2surf with target
> subject being fsaverage (with a supplied affine correction matrix), b

Re: [Freesurfer] Support for surface data on NeuroVault.org

[Matt Glasser]

Hi Chris,

Why not focus on distributing GIFTI files that are viewable both by
FreeSurfer and many other applications instead of FreeSurfer¹s native
format?  For the same reason that it is helpful to provide NIFTI files
because of their strong, cross-platform adoption, it would be more helpful
to provide GIFTI files in your database so that a wider range of users could
use them without converting them.  You could probably automatically convert
FreeSurfer¹s native formats to GIFTI with FreeSurfer¹s utility mris_convert
on upload if you didn¹t want your uploading users to have to do the
conversions.  

Generally inflated surfaces are easiest for viewing patterns, but it is
often helpful to include anatomical surfaces as well.

Peace,

Matt.

From:   on behalf of Chris Filo
Gorgolewski 
Reply-To:  Freesurfer support list 
Date:  Saturday, August 20, 2016 at 12:21 PM
To:  freesurfer 
Subject:  [Freesurfer] Support for surface data on NeuroVault.org

Dear FreeSurfer community,
I am one of the developers of NeuroVault.org   - an
open repository for vizualizing, analyzing, and sharing of statistical and
parcellation maps of the human brain. So far NeuroVault was limited only to
volumetric data in the MNI space since this is the most common way of
reporting MRI results. Now I would like to start working on adding support
for surface data beginning with outputs of FreeSurfer. Since I'm not a
FreeSurfer expert I would like to ask the community a few questions:

1. In NeuroVault users are asked to upload their statistical maps in form of
files. I'm planning to target outputs of mri_glmfit: preferably Z.mgh but
also sig.mgh. Is this the most sensible thing to do?

2. I want to be able to tell if a given map is in fsaverage space. Is there
any place in the .mgh header that specifies which space the map is in?

3. fsaverage has different subsampling flavours - how often are they used?
Is support for them an important feature?

4. Results come in two files - one per each hemisphere. Is there any way
(from the headers) to check if two files provided by a user match?

5. As with the volumetric data I want to provide a 3D interactive viewer. I
had some initial success with Brain Browser. Are you aware of any other
javascript based viewers that work well with FreeSurfer data?

6. Which surface should be the default view: inflated, pial, or white?

7. Finally NeuroVault gives users ability to compare maps and even search
through the whole repository to find statistical maps with similar patterns.
This is currently implemented for volumetric data, but could be extended to
surface data. The problem arises when one wants to compare MNI volumetric
data with fsaverage surface data. So far I have been using mri_vol2surf with
target subject being fsaverage (with a supplied affine correction matrix),
but this solution is far from optimal since fsaverage folding patterns are
quite different from MNI. I was thinking that maybe a more accurate way of
dealing with this would be to reconstruct MNI152 cortical surface model, do
surface registration of it to fsaverage, and use that to sample statistical
maps in MNI space. What do you think?

Thank you for any help feedback you can provide!

Best,
Chris Gorgolewski
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Re: [Freesurfer] T2 vs. T2-FLAIR update

[Matt Glasser]

And I would say if you want to do T1w/T2w myelin mapping the T2w scan will
give you more contrast for that, as the fluid inversion does seem to
reduce your contrast for myelin some (though it may increase your contrast
for CSF).  FLAIR can be useful for other things (like seeing some kinds of
brain lesions more easily) so your choice might depend on what else you
want to do with the images.

Peace,

Matt.

On 7/18/16, 6:59 PM, "Bruce Fischl"
 wrote:

>Hi Michelle
>
>that's a tough question. We don't have a ton of experience with it one
>way or the other, but if I had to pick one I would pick FLAIR as long as
>you are getting a 3D FLAIR with around 1mm voxels
>
>cheers
>Bruce
>On Mon, 18 Jul 2016,
>Michelle T Kassel wrote:
>
>> 
>> Hello, 
>> 
>> 
>> I am beginning a new study and would like to determine the
>> optimal T2 acquisition parameters for improved pial surface
>> results from FreeSurfer. I am wondering if there is a difference in
>>using a
>> T2 or T2-FLAIR. I have found a discussion post from 2014 which provided
>> useful 
>>information(https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2014-J
>>uly/039580.ht
>> ml), however, it seems from reading the post that newer developments
>>were
>> underway, and I was wondering if I could get an updated answer to the
>> question:
>> 
>> 
>> is there any difference from freesurfer's perspective of using T2-space
>>or
>> T2-space-flair?
>> 
>> 
>> Thank you for your help!
>> 
>> 
>> Michelle
>> 
>> 
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Re: [Freesurfer] FreesurferNHP

[Matt Glasser]

We haven¹t yet released our NHP pipeline yet, mainly because the software
support requirements are a bit higher and so it has made more sense to
work with people as a part of collaborations.  This is more of a question
for the HCP Users list or an off-list inquiry because the FreeSurfer group
doesn¹t have anything to do with the FreeSurferNHP pipeline.

Peace,

Matt.

On 7/12/16, 9:17 AM, "Moeller, Sebastian"
 wrote:

>Hi Peter,
>
>> On Jul 12, 2016, at 14:42 , Lauro, Peter  wrote:
>> 
>> Hello,
>> 
>> I'm trying to reconstruct cortical surfaces from non-human primate
>>MRIs. I tried following the instructions/scripts listed here
>>(https://surfer.nmr.mgh.harvard.edu/fswiki/MonkeyData), but I was unable
>>to make it work (I¹m also running FS 5.3).
>
>   What went wrong?
>
>Best Regards
>   Sebastian
>
>> I noticed on the Washington-Pipelines github FAQ page listed a
>>FreesurferNHP pipeline
>>(https://github.com/Washington-University/Pipelines/wiki/FAQ#9-what-if-i-
>>want-to-process-non-human-primate-nhp-data-with-the-hcp-pipelines), but
>>it hasn't been released yet.
>> 
>> Do you know when this pipeline will be available? Alternatively, is
>>there another way I can obtain the pipeline scripts and template volumes?
>> 
>> Thank you,
>> Pete Lauro
>> 
>> ___
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>> 
>> 
>> The information in this e-mail is intended only for the person to whom
>>it is
>> addressed. If you believe this e-mail was sent to you in error and the
>>e-mail
>> contains patient information, please contact the Partners Compliance
>>HelpLine at
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>>in error
>> but does not contain patient information, please contact the sender and
>>properly
>> dispose of the e-mail.
>
>
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Re: [Freesurfer] modifying files on older versions of FS

[Matt Glasser]

Why would  you want to do that?

Peace,

Matt.

From:   on behalf of "Alexopoulos,
Dimitrios" 
Reply-To:  Freesurfer support list 
Date:  Thursday, June 16, 2016 at 4:06 PM
To:  Freesurfer support list 
Subject:  [Freesurfer] modifying files on older versions of FS

I have successfully processed data with FS v5.3 (linux/CentOS) using
recon-all -all.
 
Is it possible to make modifications to the 5.3-generated brainmask.mgz
(primarily dura removal) and wm.mgz files using a much older 4.4 version of
FS and then re-run recon-all on 5.3 with these modified files. I¹d also be
generating control points (control.dat file) on 4.4 as well.
 
In other works are there file formatting differences between these FS
versions for just these 3 files that could pose a problem when re-running
the dataset.
 
Jim


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Re: [Freesurfer] Fwd: concerting surface format

[Matt Glasser]

Look at mris_convert.  If that doesn¹t help would also see if BrainVisa
allows conversion to a third format that mris_convert works with.  Finally,
does BrainVisa not support GIFTI (the standard, cross-neuroimaging software
surface format)?

Peace,

Matt.

From:   on behalf of Trisanna
Sprung-Much 
Reply-To:  Freesurfer support list 
Date:  Wednesday, June 15, 2016 at 9:33 AM
To:  Freesurfer support list 
Subject:  [Freesurfer] Fwd: concerting surface format



Hi there

is there a way to convert .mesh (BrainVisa) to the Freesurfer surface
format? mri_convert doesn't seem to do it.

best wishes

Trisanna

--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology



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Re: [Freesurfer] using both T1/T2 and resolutions

[Matt Glasser]

Hi Eugenio,

I think he is just after cortical surfaces.

Matt.

From:  <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of "Iglesias,
Eugenio" <e.igles...@ucl.ac.uk>
Reply-To:  Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date:  Friday, June 10, 2016 at 12:30 PM
To:  Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject:  Re: [Freesurfer] using both T1/T2 and resolutions

Hi! 
I actually sent out an email yesterday regarding this. The way that the
subfield module is set up, you cannot take advantage of your full res T1 and
your T1. We are working on a solution.
Cheers,
Eugenio

Juan Eugenio Iglesias
Translational Imaging Group
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/


> On 10 Jun 2016, at 17:04, Matt Glasser <m...@ma-tea.com> wrote:
> 
> Hi Jim,
> 
> I would just use the HCP Pipelines for that:
> https://github.com/Washington-University/Pipelines, as they take care of all
> of those things re FreeSurfer.  I would set to using the 0.8mm templates so
> that nothing is down sampled.
> 
> Peace,
> 
> Matt.
> 
> From: <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of "Alexopoulos,
> Dimitrios" <alexopoulo...@kids.wustl.edu>
> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
> Date: Friday, June 10, 2016 at 10:56 AM
> To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
> Subject: [Freesurfer] using both T1/T2 and resolutions
> 
> Hi,
>  
> We¹d like to process pediatric data through the complete FS 5.3 pipeline. The
> T1/T2 data are acquired with a 3T Siemens as follows:
> T1 mpr sag - 0.82x0.82x0.85
> T2 Space - 1x1x1
>  
> We¹d like to process using both the T1 and T2 (for better dura removal and
> possible myelin analysis).
> Is it possible to use the hires T1 and have data not downsampled to 1x1x1?
> Ifpossible, can this be done in tandem with the lower resolution T2-space?
>  
> What recon-all command would be best for this process?
>  
> Jim
> 
> 
> The materials in this email are private and may contain Protected Health
> Information. If you are not the intended recipient, be advised that any
> unauthorized use, disclosure, copying, distribution or the taking of any
> action in reliance on the contents of this information is strictly prohibited.
> If you have received this email in error, please immediately notify the sender
> via telephone or return email.
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> 
> 
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> at
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> but does not contain patient information, please contact the sender and
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Re: [Freesurfer] using both T1/T2 and resolutions

[Matt Glasser]

Hi Jim,

I would just use the HCP Pipelines for that:
https://github.com/Washington-University/Pipelines, as they take care of all
of those things re FreeSurfer.  I would set to using the 0.8mm templates so
that nothing is down sampled.

Peace,

Matt.

From:   on behalf of "Alexopoulos,
Dimitrios" 
Reply-To:  Freesurfer support list 
Date:  Friday, June 10, 2016 at 10:56 AM
To:  "freesurfer@nmr.mgh.harvard.edu" 
Subject:  [Freesurfer] using both T1/T2 and resolutions

Hi,
 
We¹d like to process pediatric data through the complete FS 5.3 pipeline.
The T1/T2 data are acquired with a 3T Siemens as follows:
T1 mpr sag - 0.82x0.82x0.85
T2 Space - 1x1x1
 
We¹d like to process using both the T1 and T2 (for better dura removal and
possible myelin analysis).
Is it possible to use the hires T1 and have data not downsampled to 1x1x1?
Ifpossible, can this be done in tandem with the lower resolution T2-space?
 
What recon-all command would be best for this process?
 
Jim


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Re: [Freesurfer] Hippocampal subfields segmentation - what is the voxel size of the input?

[Matt Glasser]

Hi Eugenio,

Did you already do this?  If so, a published reference would be more useful
to me than instructions for how to do it, as I¹m more interested in making
an argument for an acquisition protocol modification.

Matt.

From:  <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of "Iglesias,
Eugenio" <e.igles...@ucl.ac.uk>
Reply-To:  Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date:  Thursday, June 9, 2016 at 1:37 PM
To:  Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject:  Re: [Freesurfer] Hippocampal subfields segmentation - what is the
voxel size of the input?

Hi Matt, 
you can use strategy 3 of my previous email ;-)
Cheers,
Eugenio

Juan Eugenio Iglesias
Translational Imaging Group
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/


> On 9 Jun 2016, at 19:31, Matt Glasser <m...@ma-tea.com> wrote:
> 
> I would be interested to know how well 0.7mm isotropic resolution data
> performs at hippocampal segmentation.  It would be better if folks could do
> this then needing to acquire specialized anisotropic scans for hippocampal
> segmentation.
> 
> Peace,
> 
> Matt.
> 
> From: <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Fernando Pasquini
> Santos <fernandop...@gmail.com>
> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
> Date: Thursday, June 9, 2016 at 1:23 PM
> To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
> Subject: [Freesurfer] Hippocampal subfields segmentation - what is the voxel
> size of the input?
> 
> Dear,
> 
> I have a doubt regarding the input T1 image used for the Hippocampal Subfield
> segmentation in Freesurfer 6.0 -
> https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfields
> 
> In this documentation it says that I can use a standard 1mm T1 image or the
> same standard 1mm T1 image with an additional scan. However, I want to use a
> 0.7mm T1 image as input, with an additional T2 scan. When I run the program
> with it, the output images (nu.mgz and orig.mgz) are downsampled to 1mm voxel
> size. So, I don't know if this happens just because of the recon-all program
> or if the segmentation is being done in the downsampled T1 image or in the
> original 0.7mm.
> 
> By reading the article "A computational atlas of the hippocampal formation
> using ex vivo, ultra-high resolution MRI: Application to adaptive segmentation
> of in vivo MRI" I saw that, in the methods section, the algorithm is used to
> segment 0.6mm T1 images. But is this possible to do in the Freesurfer package?
> Obviously, doing the segmentation directly on 0.7mm data would be better than
> a downsampled version to 1mm...
> 
> Thanks,
> 
> Fernando Pasquini Santos
> PhD student in Dynamic Systems
> fernandosan...@pitt.edu
> fernando.pasquini.san...@usp.br
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> contains patient information, please contact the Partners Compliance HelpLine
> at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.

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Re: [Freesurfer] Hippocampal subfields segmentation - what is the voxel size of the input?

[Matt Glasser]

I would be interested to know how well 0.7mm isotropic resolution data
performs at hippocampal segmentation.  It would be better if folks could do
this then needing to acquire specialized anisotropic scans for hippocampal
segmentation.

Peace,

Matt.

From:   on behalf of Fernando
Pasquini Santos 
Reply-To:  Freesurfer support list 
Date:  Thursday, June 9, 2016 at 1:23 PM
To:  "freesurfer@nmr.mgh.harvard.edu" 
Subject:  [Freesurfer] Hippocampal subfields segmentation - what is the
voxel size of the input?

Dear,

I have a doubt regarding the input T1 image used for the Hippocampal
Subfield segmentation in Freesurfer 6.0 -
https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfields

In this documentation it says that I can use a standard 1mm T1 image or the
same standard 1mm T1 image with an additional scan. However, I want to use a
0.7mm T1 image as input, with an additional T2 scan. When I run the program
with it, the output images (nu.mgz and orig.mgz) are downsampled to 1mm
voxel size. So, I don't know if this happens just because of the recon-all
program or if the segmentation is being done in the downsampled T1 image or
in the original 0.7mm.

By reading the article "A computational atlas of the hippocampal formation
using ex vivo, ultra-high resolution MRI: Application to adaptive
segmentation of in vivo MRI" I saw that, in the methods section, the
algorithm is used to segment 0.6mm T1 images. But is this possible to do in
the Freesurfer package? Obviously, doing the segmentation directly on 0.7mm
data would be better than a downsampled version to 1mm...

Thanks,

Fernando Pasquini Santos
PhD student in Dynamic Systems
fernandosan...@pitt.edu
fernando.pasquini.san...@usp.br
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contains patient information, please contact the Partners Compliance HelpLine at
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but does not contain patient information, please contact the sender and properly
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Re: [Freesurfer] axial or sagittal?

[Matt Glasser]

I¹d add that SNR may also change if you don¹t acquire as much data axially
as you did sagittally.  Really it¹s better to acquire your 3D
T1w/T2w/FLAIR scans sagittally as this is most efficient.

Peace,

Matt.

On 4/8/16, 10:23 AM, "Bruce Fischl"
 wrote:

>Hi Gamaliel
>
>many things will change when you change the slice direction - amount of
>wrap, possibly your FOV, slab-selection profile if your protocol is
>slab-selective, and some types of distortion. These will all change the
>image which will change our results. Of course even if you don't change
>anything you won't get identical results if you scan twice, but our
>longitudinal stream is pretty reliable. Andre van der Kouwe has
>acquitisiton recommendations here:
>
>http://www.nmr.mgh.harvard.edu/~andre/FreeSurfer_recommended_morphometry_p
>rotocols.pdf
>
>cheers
>Bruce
>
>On Fri, 8 Apr 2016, Gamaliel
>Huerta Urrea wrote:
>
>> 
>> 
>> 2016-04-08 12:09 GMT-03:00 Gamaliel Huerta Urrea
>>:
>>   Hello Freesurfers
>> I'm trying to do volumetric reconstruction, i already have done this
>> but. i wanted to see if for the same subject, with different
>> directions of slices i have the same result, and obviously i had
>> different results of volumetric measures. i have used the sequence
>> FSPGR T1 ponderation, with the same parameters for both data
>> acquisition; with voxel 1 mm3, but the direction is changed in both
>> studies axial and sagittal. Both studies are in *.dcm format, and i
>> used the next command for convert dicom to .mgz and after to apply
>> recon-all process:
>>
>>  1.
>>
>> mri_convert firstdicom.dcm 001.mgz
>> 
>> I would like to know why would i have this problem?
>> 
>> There is some specific slice direction for this kind of study which is
>> suitable ?
>> 
>> I'm interested in cerebellum volumetric information. I attached my
>> results for volumetry.
>> 
>> Cheers
>> 
>> --
>> Gamaliel Huerta
>> Ingeniero Civil Biomédico
>> HealthCare Analytics
>> Centro Interdisciplinario de Innovación en Salud
>> Universidad de Valparaíso
>> 
>> 
>> 
>> 
>> --
>> Gamaliel Huerta
>> Ingeniero Civil Biomédico
>> HealthCare Analytics
>> Centro Interdisciplinario de Innovación en Salud
>> Universidad de Valparaíso
>> 
>> 
>>___
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>
>
>The information in this e-mail is intended only for the person to whom it
>is
>addressed. If you believe this e-mail was sent to you in error and the
>e-mail
>contains patient information, please contact the Partners Compliance
>HelpLine at
>http://www.partners.org/complianceline . If the e-mail was sent to you in
>error
>but does not contain patient information, please contact the sender and
>properly
>dispose of the e-mail.



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Re: [Freesurfer] Surface based analysis using FA maps

[Matt Glasser]

The point is that more than tissue damage will cause changes to FA.

Matt.

On 3/23/16, 9:17 PM, "Alshikho, Mohamad J."
<freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
malshi...@mgh.harvard.edu> wrote:

>This is theoritically correct!
>If we do DTI to study the liver. How these measures can explain the
>tissue? It is not only white matter and gray matter!
>
>All DTI measures can explain how much space we have between the cells.
>More space means low FA and high RD. The opposit correct as well.
>Given that they share the same formula. If we accept RD as a marker for
>gray matter integrity. We should accept FA a marker for gray matter
>integrity.
>
>Yes I am looking for an optimal measure to evaluate tissue damage.
>
>Mohamad
>
>From: freesurfer-boun...@nmr.mgh.harvard.edu
>[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Matt Glasser
>[m...@ma-tea.com]
>Sent: Wednesday, March 23, 2016 9:29 PM
>To: Freesurfer support list
>Subject: Re: [Freesurfer] Surface based analysis using FA maps
>
>FA or fractional anisotropy explains the fraction of the diffusion that is
>along the long axis of the diffusion tensor.  In so far as the diffusion
>tensor is an accurate model of the underlying structural architecture,
>what you say might be true (e.g. in the small number of white matter
>regions with only one main fiber orientation).  Most of white matter has
>multiple fiber orientations and thus the diffusion tensor is not a great
>model.  In grey matter, the principle orientation of processes is radial
>to the surface (e.g. radial fibers, major dendrites), but there are are
>also tangential processes (e.g. Bands of Baillarger).  To get a decrease
>in FA, one could do a number of things:
>
>1) Decrease the strength of radial diffusion
>2) Increase the strength of tangential diffusion
>3) Decrease the strength of both radial and tangential diffusion
>
>Are you looking for a measure that shows tissue damage?
>
>Matt.
>
>On 3/23/16, 7:55 PM, "Alshikho, Mohamad J."
><freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
>malshi...@mgh.harvard.edu> wrote:
>
>>It can explain one thing "tissue integrity"
>>
>>It will tell us neurobiologically exactly what can tell us in tissues
>>other than the brain such as liver, lung, heart, joints,  etc
>>
>>Mohamad
>>
>>
>>-Original Message-
>>From: freesurfer-boun...@nmr.mgh.harvard.edu
>>[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Matt Glasser
>>Sent: Wednesday, March 23, 2016 8:49 PM
>>To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
>>Subject: Re: [Freesurfer] Surface based analysis using FA maps
>>
>>Right but what do you think FA, MD, AD, RD, etc are telling you
>>neurobiologically in the grey matter?
>>
>>Matt.
>>
>>On 3/23/16, 7:18 PM, "Alshikho, Mohamad J."
>><freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
>>malshi...@mgh.harvard.edu> wrote:
>>
>>>Hi Matt,
>>>I highly appreciate your input on this!!
>>>
>>>Actually my goal is to study the difference in FA values between groups
>>>within the cortex. I know that diffusivities ( MD, AD and RD) can be
>>>used to evaluate gray matter and many people claim that it is much
>>>better to use diffusivities to evaluate gray matter But my interest is
>>>specifically in FA within the gray matter.
>>>
>>>For that reason I want to do surface based analysis to study the
>>>differences in FA between my study groups. I checked for the optimal
>>>ways to do it:
>>>1. I found https://surfer.nmr.mgh.harvard.edu/fswiki/dt_recon
>>>2. And I found
>>>https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2013-February/028
>>>109
>>>.html
>>>
>>>I ran the analysis using both methods.
>>>
>>>For the second method I replaced PET maps by FA maps and this was the
>>>reason for my question! If we can do the analysis that way using PET
>>>maps, why we can't do it using FA maps?
>>>
>>>I will be more than happy if you can suggest me an alternative approach
>>>to study FA on a surface.
>>>
>>>
>>>Best,
>>>Mohamad
>>>
>>>-Original Message-
>>>From: freesurfer-boun...@nmr.mgh.harvard.edu
>>>[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Matt
>>>Glasser
>>>Sent: Wednesday, March 23, 2016 8:04 PM
>>>To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
>>>Subject: Re: [

Re: [Freesurfer] Surface based analysis using FA maps

[Matt Glasser]

FA or fractional anisotropy explains the fraction of the diffusion that is
along the long axis of the diffusion tensor.  In so far as the diffusion
tensor is an accurate model of the underlying structural architecture,
what you say might be true (e.g. in the small number of white matter
regions with only one main fiber orientation).  Most of white matter has
multiple fiber orientations and thus the diffusion tensor is not a great
model.  In grey matter, the principle orientation of processes is radial
to the surface (e.g. radial fibers, major dendrites), but there are are
also tangential processes (e.g. Bands of Baillarger).  To get a decrease
in FA, one could do a number of things:

1) Decrease the strength of radial diffusion
2) Increase the strength of tangential diffusion
3) Decrease the strength of both radial and tangential diffusion

Are you looking for a measure that shows tissue damage?

Matt.

On 3/23/16, 7:55 PM, "Alshikho, Mohamad J."
<freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
malshi...@mgh.harvard.edu> wrote:

>It can explain one thing "tissue integrity"
>
>It will tell us neurobiologically exactly what can tell us in tissues
>other than the brain such as liver, lung, heart, joints,  etc
>
>Mohamad
>
>
>-Original Message-
>From: freesurfer-boun...@nmr.mgh.harvard.edu
>[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Matt Glasser
>Sent: Wednesday, March 23, 2016 8:49 PM
>To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
>Subject: Re: [Freesurfer] Surface based analysis using FA maps
>
>Right but what do you think FA, MD, AD, RD, etc are telling you
>neurobiologically in the grey matter?
>
>Matt.
>
>On 3/23/16, 7:18 PM, "Alshikho, Mohamad J."
><freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
>malshi...@mgh.harvard.edu> wrote:
>
>>Hi Matt,
>>I highly appreciate your input on this!!
>>
>>Actually my goal is to study the difference in FA values between groups
>>within the cortex. I know that diffusivities ( MD, AD and RD) can be
>>used to evaluate gray matter and many people claim that it is much
>>better to use diffusivities to evaluate gray matter But my interest is
>>specifically in FA within the gray matter.
>>
>>For that reason I want to do surface based analysis to study the
>>differences in FA between my study groups. I checked for the optimal
>>ways to do it:
>>1. I found https://surfer.nmr.mgh.harvard.edu/fswiki/dt_recon
>>2. And I found
>>https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2013-February/028
>>109
>>.html
>>
>>I ran the analysis using both methods.
>>
>>For the second method I replaced PET maps by FA maps and this was the
>>reason for my question! If we can do the analysis that way using PET
>>maps, why we can't do it using FA maps?
>>
>>I will be more than happy if you can suggest me an alternative approach
>>to study FA on a surface.
>>
>>
>>Best,
>>Mohamad
>>
>>-Original Message-
>>From: freesurfer-boun...@nmr.mgh.harvard.edu
>>[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Matt
>>Glasser
>>Sent: Wednesday, March 23, 2016 8:04 PM
>>To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
>>Subject: Re: [Freesurfer] Surface based analysis using FA maps
>>
>>I too am puzzled as to why you would want to do this.  In terms of
>>getting improvement in the alignment across subjects TBSS is one way to
>>approach this.  Another would be to use the fiber orientations in the
>>registration like these folks have done:
>>http://dti-tk.sourceforge.net/pmwiki/pmwiki.php?n=Main.HomePage
>>
>>If you are interested in studying the properties of cortical grey
>>matter there might be better modalities than FA.  If you can provide
>>more details on what you are trying to do, perhaps that would clarify
>>how to go about it?
>>
>>Peace,
>>
>>Matt.
>>
>>On 3/22/16, 2:49 PM, "Douglas N Greve"
>><freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
>>gr...@nmr.mgh.harvard.edu> wrote:
>>
>>>I don't know of a reference where someone has done this (though I
>>>would be surprised if it is not out there), so just be aware of this
>>>if you try to publish. The commands look correct, however, you may or
>>>may not want to sample in the middle of the cortical ribbon (--projfrac
>>>0.5).
>>>Since this is a DTI analysis, wouldn't you want to sample in the WM?
>>>Doing that is a little tricky, but you can use something like
>>>--projabs
>>>-1 to sample 1mm *away

Re: [Freesurfer] Surface based analysis using FA maps

[Matt Glasser]

Right but what do you think FA, MD, AD, RD, etc are telling you
neurobiologically in the grey matter?

Matt.

On 3/23/16, 7:18 PM, "Alshikho, Mohamad J."
<freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
malshi...@mgh.harvard.edu> wrote:

>Hi Matt,
>I highly appreciate your input on this!!
>
>Actually my goal is to study the difference in FA values between groups
>within the cortex. I know that diffusivities ( MD, AD and RD) can be used
>to evaluate gray matter and many people claim that it is much better to
>use diffusivities to evaluate gray matter But my interest is specifically
>in FA within the gray matter.
>
>For that reason I want to do surface based analysis to study the
>differences in FA between my study groups. I checked for the optimal ways
>to do it: 
>1. I found https://surfer.nmr.mgh.harvard.edu/fswiki/dt_recon
>2. And I found 
>https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2013-February/028109
>.html
>
>I ran the analysis using both methods.
>
>For the second method I replaced PET maps by FA maps and this was the
>reason for my question! If we can do the analysis that way using PET
>maps, why we can't do it using FA maps?
>
>I will be more than happy if you can suggest me an alternative approach
>to study FA on a surface.
>
>
>Best,
>Mohamad
>
>-Original Message-
>From: freesurfer-boun...@nmr.mgh.harvard.edu
>[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Matt Glasser
>Sent: Wednesday, March 23, 2016 8:04 PM
>To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
>Subject: Re: [Freesurfer] Surface based analysis using FA maps
>
>I too am puzzled as to why you would want to do this.  In terms of
>getting improvement in the alignment across subjects TBSS is one way to
>approach this.  Another would be to use the fiber orientations in the
>registration like these folks have done:
>http://dti-tk.sourceforge.net/pmwiki/pmwiki.php?n=Main.HomePage
>
>If you are interested in studying the properties of cortical grey matter
>there might be better modalities than FA.  If you can provide more
>details on what you are trying to do, perhaps that would clarify how to
>go about it?
>
>Peace,
>
>Matt.
>
>On 3/22/16, 2:49 PM, "Douglas N Greve"
><freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
>gr...@nmr.mgh.harvard.edu> wrote:
>
>>I don't know of a reference where someone has done this (though I would
>>be surprised if it is not out there), so just be aware of this if you
>>try to publish. The commands look correct, however, you may or may not
>>want to sample in the middle of the cortical ribbon (--projfrac 0.5).
>>Since this is a DTI analysis, wouldn't you want to sample in the WM?
>>Doing that is a little tricky, but you can use something like --projabs
>>-1 to sample 1mm *away* from the ribbon into the WM.
>>
>>On 03/22/2016 11:08 AM, Alshikho, Mohamad J. wrote:
>>>
>>> Dear FS experts,
>>>
>>> I would like to run surface based analysis using FA maps. I am not
>>> exactly sure that what I am doing is totally right specially step 2 .
>>> I used the following commands:
>>>
>>> 1.I registered the FA maps to T1 using the command:  bbregister --s
>>> bert --mov dtifit_FA.nii --bold --init-fsl --reg  reg.dat
>>>
>>> 2.I concatenated the subject¹s FA maps using the command :
>>>  mris_preproc ­target fsaverage ­hemi lh ­iv .bert1/dtifit_FA.nii
>>>reg.dat ­iv bert2/dtifit_FA.nii reg.dat Š. --projfrac 0.5 --out
>>>lh.FA.mgz
>>>
>>> 3.Then smoothing mri_surf2surf --hemi lh --s fsaverage --fwhm 5
>>> --cortex --sval  lh.FA.mgz --tval lh.FA_5mm.mgz
>>>
>>> 4.Then GLM analysis using mri_glmfit
>>>
>>> 5.Correction for multiple comparison mri_glmfit-sim
>>>
>>> Kindly, are these steps correct? I used the previous steps to do
>>> surface based analysis using PET images and it worked very well.
>>> While for the FA maps it seems that there is something wrong and I
>>> can¹t figure out what it is!
>>>
>>> I highly appreciate any input on this!
>>>
>>> Best,
>>>
>>> Mohamad
>>>
>>>
>>>
>>> ___
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>--
>>Douglas N. Greve, Ph.D.
>>MGH-NMR Center
>>gr...@nmr.mgh.harvard.edu
>>Phone Number: 617-724-2358
>>Fax: 617-726-7422
>>
>>Bugs: surfer.nmr.mgh.har

Re: [Freesurfer] Surface based analysis using FA maps

[Matt Glasser]

I too am puzzled as to why you would want to do this.  In terms of getting
improvement in the alignment across subjects TBSS is one way to approach
this.  Another would be to use the fiber orientations in the registration
like these folks have done:
http://dti-tk.sourceforge.net/pmwiki/pmwiki.php?n=Main.HomePage

If you are interested in studying the properties of cortical grey matter
there might be better modalities than FA.  If you can provide more details
on what you are trying to do, perhaps that would clarify how to go about
it?

Peace,

Matt.

On 3/22/16, 2:49 PM, "Douglas N Greve"
 wrote:

>I don't know of a reference where someone has done this (though I would
>be surprised if it is not out there), so just be aware of this if you
>try to publish. The commands look correct, however, you may or may not
>want to sample in the middle of the cortical ribbon (--projfrac 0.5).
>Since this is a DTI analysis, wouldn't you want to sample in the WM?
>Doing that is a little tricky, but you can use something like --projabs
>-1 to sample 1mm *away* from the ribbon into the WM.
>
>On 03/22/2016 11:08 AM, Alshikho, Mohamad J. wrote:
>>
>> Dear FS experts,
>>
>> I would like to run surface based analysis using FA maps. I am not
>> exactly sure that what I am doing is totally right specially step 2 .
>> I used the following commands:
>>
>> 1.I registered the FA maps to T1 using the command:  bbregister --s
>> bert --mov dtifit_FA.nii --bold --init-fsl --reg  reg.dat
>>
>> 2.I concatenated the subject¹s FA maps using the command :
>>  mris_preproc ­target fsaverage ­hemi lh ­iv .bert1/dtifit_FA.nii
>> reg.dat ­iv bert2/dtifit_FA.nii reg.dat Š. --projfrac 0.5 --out
>>lh.FA.mgz
>>
>> 3.Then smoothing mri_surf2surf --hemi lh --s fsaverage --fwhm 5
>> --cortex --sval  lh.FA.mgz --tval lh.FA_5mm.mgz
>>
>> 4.Then GLM analysis using mri_glmfit
>>
>> 5.Correction for multiple comparison mri_glmfit-sim
>>
>> Kindly, are these steps correct? I used the previous steps to do
>> surface based analysis using PET images and it worked very well. While
>> for the FA maps it seems that there is something wrong and I can¹t
>> figure out what it is!
>>
>> I highly appreciate any input on this!
>>
>> Best,
>>
>> Mohamad
>>
>>
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>-- 
>Douglas N. Greve, Ph.D.
>MGH-NMR Center
>gr...@nmr.mgh.harvard.edu
>Phone Number: 617-724-2358
>Fax: 617-726-7422
>
>Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
>www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
>___
>Freesurfer mailing list
>Freesurfer@nmr.mgh.harvard.edu
>https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>The information in this e-mail is intended only for the person to whom it
>is
>addressed. If you believe this e-mail was sent to you in error and the
>e-mail
>contains patient information, please contact the Partners Compliance
>HelpLine at
>http://www.partners.org/complianceline . If the e-mail was sent to you in
>error
>but does not contain patient information, please contact the sender and
>properly
>dispose of the e-mail.
>



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Re: [Freesurfer] T2pial shrinks pial surface

[Matt Glasser]

What FreeSurfer version are you using?  Very small changes to the input
images (e.g. a different random see for FreeSurfer) may be able to kick
mris_make_surfaces out of that bug, though perhaps Bruce has fixed it.

Peace,

Matt.

From:   on behalf of Chris Adamson

Reply-To:  Freesurfer support list 
Date:  Sunday, March 6, 2016 at 6:14 PM
To:  "freesurfer@nmr.mgh.harvard.edu" 
Subject:  [Freesurfer] T2pial shrinks pial surface

The T2pial option mostly works beautifully. I have a few cases where the
pial surface just shrinks globally and wraps over the white surface (see
attached). I have checked the T2.mgz and the registration with the T1 is
fine. This happens sometimes in one hemisphere only.
Any ideas?
 
Chris Adamson
Senior Research Officer
Developmental Imaging
Murdoch Childrens Research Institute
The Royal Children¹s Hospital
Flemington Rd Parkville, Victoria 3052 AUS
T: (03) 9936 6780
E: chris.adam...@mcri.edu.au
www.mcri.edu.au 
 
 




 
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Re: [Freesurfer] MPRAGE SNR

[Matt Glasser]

There is also the issue that grey and white matter are not truly a
homogeneous single intensity anatomically.

Peace,

Matt.

On 10/19/15, 9:23 AM, "Harms, Michael"

wrote:

>
>Hi,
>
>FWIW, I've looked at a number of these measures in 500+ subjects from HCP
>data -- wm-anat-snr, pctsurfcon, G/W cnr, G/CSF cnr -- to see how they
>relate to each other, and whether they correlate with mean cortical
>thickness, white matter surface area, or number of SurfaceHoles (prior to
>topology correction).
>
>I didn't find much of note.  e.g., the highest correlations were:
>
>r = -0.32 between mean cortical thickness and G/CSF cnr (from norm.mgz)
>r = -0.25 between white surface area and wmanatsnr
>r = -0.39 between SurfaceHoles and pctsurfcon (and same with G/W cnr from
>norm.mgz)
>
>Not surprisingly, pctsurfcon and G/W cnr are reasonably correlated (r =
>0.49).
>
>G/W cnr from norm.mgz and orig.mgz are correlated at r=0.80.
>G/CSF cnr from norm.mgz and orig.mgz are correlated at r=0.97
>
>In another context (but smaller number of subjects), I've looked to see if
>these various snr, cnr measures from FS were related to manual quality
>ratings, and the relationship was rather weak.
>
>All-in-all, I haven't seen much that would indicate that these measures
>can be used as a sort of "automated" QC measure.  Manual review of the
>structurals and FS results is still needed.
>
>That said, the structurals from the HCP 500 release were all of reasonably
>good quality to begin with.  So, it is possible that these snr/cnr
>measures might be more informative in identifying truly awful scans in a
>clinical population with a wider variability in MPRAGE scan quality.
>
>I'd certainly be interested in hearing from anyone if they have found that
>to be the case in their data.
>
>BTW: Average value for G/W cnr for the HCP 500 is 1.99 and 1.81 from
>orig.mgz and norm.mgz respectively.
>Average value for G/CSF cnr for the same is 0.78 and 0.79, respectively.
>
>cheers,
>-MH
>
>--
>Michael Harms, Ph.D.
>
>---
>Conte Center for the Neuroscience of Mental Disorders
>Washington University School of Medicine
>Department of Psychiatry, Box 8134
>660 South Euclid Ave.Tel: 314-747-6173
>St. Louis, MO  63110Email: mha...@wustl.edu
>
>
>
>
>On 10/19/15 8:09 AM, "Bruce Fischl"  wrote:
>
>probably similar, although maybe Doug can comment. You probably want to
>run
>it on the orig.mgz as the intensity normalization can artificially
>increase
>the SNR (which is kind of the point)
>Bruce
>
>
>On Mon, 19 Oct 2015, John
>Anderson wrote:
>
>> Hi Bruce,
>> Thanks a lot!! this is really great!
>> I ran the command as the following :
>>
>> mri_cnr subj_01/surf subj_01/mri/norm.mgz
>> processing MRI volume subj_01/mri/norm.mgz...
>> white = 97.2+-9.5, gray = 69.0+-16.1, csf = 47.8+-16.5
>> gray/white CNR = 2.291, gray/csf CNR = 0.848
>> lh CNR = 1.569
>> white = 97.2+-9.3, gray = 69.4+-15.9, csf = 48.6+-17.0
>> gray/white CNR = 2.278, gray/csf CNR = 0.798
>> rh CNR = 1.538
>> total CNR = 1.554
>>
>>
>> I noticed that the normal range for the SNR  (15-20) when using the
>>command
>> "wm-anat-snr"
>>
>> What is the normal range for cnr generated by the binary "mri_cnr"?
>>
>>
>> Bests,
>> John Anderson
>>
>> Senior Research Associate
>> Psychological and Brain Sciences Dept.
>> Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755
>> Phone: +1 (603) 646-9834
>> Fax: +1 (603) 646-1419
>> Sent: Monday, October 19, 2015 at 8:36 AM
>> From: "Bruce Fischl" 
>> To: "Freesurfer support list" 
>> Cc: j.haen...@psychologie.uzh.ch
>> Subject: Re: [Freesurfer] MPRAGE SNR
>> Hi John
>>
>> there is also a binary called mri_cnr that will compute the
>> contrast-to-noise ratio (CNR), which is really the more interesting
>> metric. It will also spit out the WM means+- std, and the ratio of these
>> two can be used as an SNR measure.
>>
>> cheers
>> Bruce
>>
>>
>> On Mon, 19 Oct 2015, John Anderson wrote:
>>
>> > Dear Jürgen
>> > This really helps!
>> > I highly appreciate your input on this.
>> >
>> > Bests,
>> > John Anderson
>> >
>> > Senior Research Associate
>> > Psychological and Brain Sciences Dept.
>> > Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755
>> > Phone: +1 (603) 646-9834
>> > Fax: +1 (603) 646-1419
>> > Sent: Monday, October 19, 2015 at 1:30 AM
>> > From: JuergenHaenggi 
>> > To: "Freesurfer support list" 
>> > Subject: Re: [Freesurfer] MPRAGE SNR
>> > Dear John
>> > FS's QA tools provide the SNR
>> > see https://surfer.nmr.mgh.harvard.edu/fswiki/QATools
>> >
>> > there is also a FS function called wm-anat-snr that can be used for
>>that.
>> >
>> > Hope this helps
>> > Cheers
>> > Jürgen
>> >
>>

Re: [Freesurfer] Basic error

[Matt Glasser]

You cannot have spaces in the file name unless you enclose it with quotes.

Peace,

Matt.

From:  freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Hugh Pemberton
hughpembert...@gmail.com
Reply-To:  Freesurfer support list freesurfer@nmr.mgh.harvard.edu
Date:  Sunday, August 16, 2015 at 1:34 PM
To:  Freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu
Subject:  [Freesurfer] Basic error

Hi freesurfer team,

I think this is a very basic error with the mri_convert command but I can't
seem to make it work, I'm getting this:

mri_convert $PWD 001.nii

mri_convert /Applications/freesurfer/subjects/DEM009/dicom/20140731/1835
001.nii 

$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $

reading from 
/Applications/freesurfer/subjects/DEM009/dicom/20140731/1835...

corRead(): can't open file
/Applications/freesurfer/subjects/DEM009/dicom/20140731/1835/COR-.info

Any ideas what I'm missing?
Thanks,
Hugh
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Re: [Freesurfer] Caret Human_Macaque.PALS_B12 to freesurfer

[Matt Glasser]

I agree this would be best asked on the Caret list to begin with (as far
as conversion from Caret formats to FreeSurfer formats), however I don’t
provide Caret support either having not used it in years (I can be more
helpful with Connectome Workbench stuff).  Donna on the Caret list can
perhaps provide further help.

Peace,

Matt.

On 8/13/15, 12:12 PM, Bruce Fischl
freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
fis...@nmr.mgh.harvard.edu wrote:

Hi Jan

have you asked the HCP/Wash U group? I bet that they would know. Maybe
Mike 
Harms or Matt Glasser can chime in?
Bruce


On Thu, 13 
Aug 2015, Jan Willem Koten wrote:

 
 Dear ladies and possibly gentlemen as well,
 
  
 
 I have got a rather nasty question. I would like to import the following
 caret file
 
 „Human_Macaque.PALS_B12.RIGHT-DEPTH_Expansion.73730.surface_shape“
 
 into free surfer and bring it into fs average space. In a next step I
would
 like to import the caret/fsaverage result into matlab and do some stuff
with
 it.
 
 There seems to be a mismatch between caret and freesurfer in the vertex
 numbers. Has somebody every tried this? Can it be done?
 
 I am not familiar with caret and would like to avoid using it.
Alternatively
 there is matlab toolbox for caret. But I have no clue how to get from
one
 ico vertex system into another.
 
  
 
 Greetings
 
  
 
 Jan
 
 Jan Willem Koten (van Grevenbicht) Neurological Clinic at the RWTH
Aachen
 Pauwelstraße 30, 52074 Aachen, Germany Telephone: (0049) (0)241 8089909
 
 
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Re: [Freesurfer] mris_convert gifti

[Matt Glasser]

Does SUMA support GIFTI and provide a utility to convert between its
formats and GIFTI?  I was also wondering what a .dset was and how to get
it into GIFTI so it could be easily used across software platforms.

Thanks,

Matt.

On 5/5/15, 5:30 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote:

sorry, I think this may be a question for the SUMA people - I don't know
what .dset format is. Are you going to do the masking within SUMA? I'll
cc 
Ziad so he can chime in.

cheers
Bruce

On Tue, 5 May 2015, Francesca Strappini wrote:

 I'm trying to mask a time series dataset that I mapped to the surface in
 SUMA (surface created with freesurfer and imported into SUMA). I think
the
 input should be in the .dset fomat (region mapped to the surface). The
 problem is that when I save my label the annotation file has only a
list of
 vertexes related to the region and not all the surface vertexes.
 Thanks for the help!
 Francesca
 
 2015-05-05 23:04 GMT+02:00 Bruce Fischl fis...@nmr.mgh.harvard.edu:
   you can just create a label file I guess. What input does SUMA
   take?
   On Tue, 5 May 2015, Francesca Strappini wrote:

 Sorry, just to be clear, I meant how can I create a
 mask on the surface in
 which at each vertex is assigned a value, 0 or 1.
 I need to create this mask for exporting the
 freesurfer labels into SUMA and
 ultimately to extract the time series from each
 vertex.

 Thanks
 Francesca

 2015-05-05 16:06 GMT+03:00 Francesca Strappini
 francescastrapp...@gmail.com:
   Thank you! Do you know which function should I
 use?

 Best
 Francesca

 2015-05-05 15:30 GMT+03:00 Bruce Fischl
 fis...@nmr.mgh.harvard.edu:
   yes, you can use a label for this (we use the
   ?h.cortex.label for this purpose routinely to
 remove
   non-cortical stuff)
   On Tue, 5 May 2015, Francesca Strappini wrote:

 Thank you so much! I understand what's
 the
 problem and I will make my custom
 ctab file.

 Last question, about the annot files, is
 it
 possible with freesurfer to
 create a mask with the annot or the
 label
 files in which the value 1 is
 assigned to the region and 0 to the rest
 of
 the brain?

 Thanks again!

 Best
 Francesca

 2015-05-05 4:20 GMT+03:00 Nick
 Schmansky, MGH
 ni...@nmr.mgh.harvard.edu:
   Francesca,

   I looked at the files you sent and
 replicated the problem.  It
   is due to
   creating your lh.EKppa.annot file
 using
 FreeSurferColorLUT.txt
   as the
   colortable file.  You should
 create your
 own colortable file,
   which is
   simple to do, and create a new
 .annot
 file using that colortable
   (ie,
   the --ctab option in
 mris_label2annot).

   Here is a simple colortable.txt
 file
 (just a text file) with
   four
   entries, which in this example,
 means
 that you have three
   annotations.
   The first entry must be as it is
 shown,
 ie, 'unknown', as this
   is used
   to automatically 'label' all the
 vertices which do not have a
   .label
   file.

 0  unknown

 25   5  250
 1  mylabel1

 0  92  230
 2  mylabel2
   131
 148 2550
 3  mylabel3

 0   0 2550

   I fixed the code locally so that
 it
 doesn't segfault, and you
   can 

[Freesurfer] Brain Imaging, Built Better: The HCP Course in Hawaii

[Matt Glasser]

To advance the field of brain imaging, the HCP was given the unusual NIH
mandate to devote its first two years to rethinking data acquisition and
analysis methods prior to collecting its core dataset.  The HCP course
provides an excellent opportunity for brain imagers to profit from this
experience by interacting with key HCP investigators in an accessible and
approachable setting.  Among the speakers are David Van Essen (HCP¹s PI),
Steve Smith (FSL), Tom Nichols (brain imaging statistician), Dan Marcus
(XNAT and ConnectomeDB), Robert Oostenveld (FieldTrip), and many others.

We¹ve designed the HCP Course both for folks with considerable brain
imaging experience and for those who are just starting out.  Attendees
will learn how to take advantage of HCP-related advances in data
acquisition, preprocessing, and analysis methods, enhancing their
prospects in an increasingly competitive neuroimaging field.  Highlighted
topics include:

*How to acquire high quality MRI data for use with the HCP¹s cutting-edge
analysis tools.
*How to better answer the question ³Where am I in the brain?² by using the
HCP¹s new standard space and analysis approach‹CIFTI grayordinates‹that
substantially improves spatial localization across subjects and studies.
*How to avoid the erosion of neuroanatomical fidelity caused by
conventional brain imaging analysis methods, instead accurately aligning
cortical areas across subjects and studies and minimizing blurring.
*The first public unveiling of the HCP¹s group average multi-modal
cortical parcellation together with methods for automatically defining
these parcels in individual subjects‹even those with atypical cortical
organization.
*How to perform novel analyses by integrating very high temporal
resolution electrophysiological data (MEG) together with high spatial
resolution MRI in a common analysis framework built around parcellation.

Note that space is limited‹and who doesn¹t want an excuse join us in
Hawaii for an extra week before OHBM? (June 8-12)

See the HCP course website for more details and let us know if you have
any questions (hcpcou...@humanconnectome.org):

http://humanconnectome.org/course-registration/2015/exploring-the-human-con
nectome.php 

Hope to see you in Honolulu,

Matt Glasser.



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Re: [Freesurfer] Quality of surface-based alignment

[Matt Glasser]

What criteria would you use to determine one alignment was better than
another?

Peace,

Matt.

From:  Caspar M. Schwiedrzik cschwie...@mail.rockefeller.edu
Reply-To:  Freesurfer support list freesurfer@nmr.mgh.harvard.edu
Date:  Tuesday, November 4, 2014 at 7:17 AM
To:  Freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu
Subject:  [Freesurfer] Quality of surface-based alignment

Hi Freesurfers, 
I was wondering whether there is a good way to assess post-hoc how well the
alignment between two surfaces was. I wouldn't like to run the alignment
again, but I could, if necessary. I would like to compare this alignment to
a bunch of other alignments to see whether it was worse than the others.
Thanks, Caspar

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Re: [Freesurfer] Overclocking CPU for Freesurfer

[Matt Glasser]

It will just run faster so long as things like memtest86 and prime95 don¹t
have errors.

Peace,

Matt.

From:  Chiu, Bryan (PHTH) bryan.c...@ubc.ca
Reply-To:  Freesurfer support list freesurfer@nmr.mgh.harvard.edu
Date:  Monday, September 29, 2014 at 4:26 PM
To:  freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu
Subject:  [Freesurfer] Overclocking CPU for Freesurfer

Hi, 

Is anyone aware of any issues that arise from overclocking and using
Freesurfer? I was looking to see how much it would speed up recon-all with
OpenMP using a stable overclock.

___
Bryan Chiu
Undergraduate Research Assistant
Aging, Mobility, and Cognitive Neuroscience Lab
Djavad Mowafaghian Centre for Brain Health
Department of Physical Therapy
Faculty of Medicine
University of British Columbia
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Re: [Freesurfer] how to shrink wm surface

[Matt Glasser]

Have a look at mris_make_surfaces.c, this is how I learned about most of
this stuff as the code is pretty well commented (and Bruce telling me
things).

Peace,

Matt.

On 9/12/14, 11:01 PM, Harms, Michael mha...@wustl.edu wrote:


Hi Bruce,
I was wondering if there is info somewhere about what each of those 7 MIN_
and MAX_ variables control regarding the positioning of the white and pial
surfaces?

thanks,
-MH

--
Michael Harms, Ph.D.

---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave.   Tel: 314-747-6173
St. Louis, MO  63110Email: mha...@wustl.edu




On 9/9/14 7:35 AM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote:

Hi Andrea

what is the background image? This is usually either a failure of the
intensity normalization or of the surface deformation/segmentation to
adaptively estimate the underlying intensity distributions of the
gray/white matter. If you look in recon-all.log for that subject you will
find a set of lines like:

setting MIN_GRAY_AT_WHITE_BORDER to 71.1 (was 70)
setting MAX_BORDER_WHITE to 112.0 (was 105)
setting MIN_BORDER_WHITE to 83.0 (was 85)
setting MAX_CSF to 59.1 (was 40)
setting MAX_GRAY to 100.0 (was 95)
setting MAX_GRAY_AT_CSF_BORDER to 77.0 (was 75)
setting MIN_GRAY_AT_CSF_BORDER to 47.2 (was 40)



in your case for example you will probably find that the min_border_white
is too high or tha the max_gray is too low. You can set these using the
expert opts for both mri_segment and mris_make_surfaces.

cheers
Bruce


On Tue, 9 Sep 2014, Andrea
Horváth wrote:

 Dear Freesurfers,


 After running recon-all, the wm surfaces are too close to the pial
surface,
 some gray matter is segmented as white matter as seen in the attached
 picture (red cross: a bigger cortical part is included in the white
matter).

 How can I shrink the wm surface?

 Thank you for your help!

 Andrea










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Re: [Freesurfer] Left and Right Vessels

[Matt Glasser]

Virchow­Robin spaces is another name for those (they are normal in small
amounts, not old strokes, and filled with CSF-like fluid).

Peace,

Matt.

On 8/21/14, 9:23 AM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote:

Hi Mohammed

these are dark regions, usually in inferior pallidum/putamen. There
intensity is different enough from gray matter that having it be a
separate 
class helps us label them more accurately. They could also be lacunae and
not vessels.

cheers
Bruce


On Tue, 19 Aug 2014, Mohammed Goryawala
wrote:

 Hello Freesurfer experts,
 
 In a study I found significant differences in the volume of the left and
 right vessels of the freesurfer atlas.
 
 I wanted to know what regions are included in that ROI and if there are
any
 known functions of these regions.
 
 Thank you
 
 Mohammed Goryawala, PhD
 Miller School of Medicine,
 University of Miami
 
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Re: [Freesurfer] Left and Right Vessels

[Matt Glasser]

I believe their function is to carry blood from one place to another.

Peace,

Matt.

From:  Mohammed Goryawala mgory...@fiu.edu
Reply-To:  Freesurfer support list freesurfer@nmr.mgh.harvard.edu
Date:  Tuesday, August 19, 2014 at 1:55 PM
To:  Freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu
Subject:  [Freesurfer] Left and Right Vessels

Hello Freesurfer experts,

In a study I found significant differences in the volume of the left and
right vessels of the freesurfer atlas.

I wanted to know what regions are included in that ROI and if there are any
known functions of these regions.

Thank you

Mohammed Goryawala, PhD
Miller School of Medicine,
University of Miami
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Re: [Freesurfer] T2-space vs T2-space-FLAIR

[Matt Glasser]

Bruce has said the FLAIR might be a little better for FreeSurfer but it¹s
worse for myelin maps (has less CNR for the myelin, though you can still see
the major areas).  Currently, the T2 and FLAIR flags do exactly the same
thing, so it doesn¹t even matter what flag you use.  I think it depends on
what else you might want to do with the data (i.e. if myelin maps were
important to your study you might go with T2w (like HCP), but if lesion
detection were more important you might go with FLAIR (like biobank).

Peace,

Matt.

From:  Satrajit Ghosh sa...@mit.edu
Reply-To:  Freesurfer support list freesurfer@nmr.mgh.harvard.edu
Date:  Wednesday, July 30, 2014 at 1:01 PM
To:  Freesurfer Mailing List freesurfer@nmr.mgh.harvard.edu
Subject:  [Freesurfer] T2-space vs T2-space-FLAIR

hi bruce,

is there any difference from freesurfer's perspective of using T2-space or
T2-space-flair?

cheers,

satra

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Re: [Freesurfer] T2-space vs T2-space-FLAIR

[Matt Glasser]

Yes we performed both on the same subject in the same session and then
compared the myelin map results.

Peace,

Matt.

From:  Satrajit Ghosh sa...@mit.edu
Reply-To:  Freesurfer support list freesurfer@nmr.mgh.harvard.edu
Date:  Wednesday, July 30, 2014 at 1:53 PM
To:  Freesurfer support list freesurfer@nmr.mgh.harvard.edu
Subject:  Re: [Freesurfer] T2-space vs T2-space-FLAIR

thanks matt,

would like to be sure that your comments in relation to the T2-space-flair
sequence and not the typical clinical TSE-FLAIR. is that the case?

cheers,

satra


On Wed, Jul 30, 2014 at 2:23 PM, Matt Glasser m...@ma-tea.com wrote:
 Bruce has said the FLAIR might be a little better for FreeSurfer but it¹s
 worse for myelin maps (has less CNR for the myelin, though you can still see
 the major areas).  Currently, the T2 and FLAIR flags do exactly the same
 thing, so it doesn¹t even matter what flag you use.  I think it depends on
 what else you might want to do with the data (i.e. if myelin maps were
 important to your study you might go with T2w (like HCP), but if lesion
 detection were more important you might go with FLAIR (like biobank).
 
 Peace,
 
 Matt.
 
 From:  Satrajit Ghosh sa...@mit.edu
 Reply-To:  Freesurfer support list freesurfer@nmr.mgh.harvard.edu
 Date:  Wednesday, July 30, 2014 at 1:01 PM
 To:  Freesurfer Mailing List freesurfer@nmr.mgh.harvard.edu
 Subject:  [Freesurfer] T2-space vs T2-space-FLAIR
 
 hi bruce,
 
 is there any difference from freesurfer's perspective of using T2-space or
 T2-space-flair?
 
 cheers,
 
 satra
 
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Re: [Freesurfer] Convert label file to STL file‏

[Matt Glasser]

It probably thinks the STL file is just a mesh without coloring.

Peace,

Matt.

From:  Mat yuki matsuyuki2...@outlook.jp
Reply-To:  Freesurfer support list freesurfer@nmr.mgh.harvard.edu
Date:  Thursday, July 10, 2014 at 7:19 AM
To:  freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu
Subject:  [Freesurfer] Convert label file to STL file‏

Dear Freesurfer Experts,
 
I'm trying to convert .label file to .stl file.
In more detail of my purpose, I want to get separate stl files of whole
brain. 
Now, I want to make stl files of label files which made from
?h.aparc.a2009s.annot.
 
First, I tried to convert lh.pial to lh.pial.stl, I've got it (this was just
check how mris_convert works).
Second, I copied lh. white file from surf dir into label dir. Then, I runed
next command:
 
cd subjid/label
mris_convert --label lh.bankssts.label bankssts lh.white
lh.bankssts.label.stl
 
And got the error message: ERROR: unknown file annot file type specified for
output: lh.bankssts.label.stl
 
Do you know what could have gone wrong?

Thank you,
Yuki.   
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Re: [Freesurfer] mris_convert to GIFTI misaligned in freeview

[Matt Glasser]

Yes the HCP pipelines have to take care of this as well so that the
surfaces and volume align outside of FreeSurfer.

Peace,

Matt.

On 5/27/14, 8:35 AM, Franz Liem f.l...@psychologie.uzh.ch wrote:

Hi Michael,

I had a similar problem a while ago. Maybe this might help.
http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg31152.html

Best,
Franz

Am 23.05.2014 um 05:38 schrieb Harms, Michael:

 
 Hi,
 I converted a surface to GIFTI
 e.g.,
 mris_convert lh.white lh.white.gii
 
 lh.white and lh.white.gii align when they are both loaded in 'tkmedit'.
 However, they do not align when loaded simultaneously in 'freeview'.
 
 Of possible relevance: When I loaded lh.white.gii into 'freeview', I
got the following message in the terminal:
 Did not find any volume geometry information in the surface
 
 Is this possibly a bug of some sort in the display of GIFTI surfaces
within 'freeview'?
 
 This was all done with FS 5.3.
 
 thanks,
 -MH
 
 -- 
 Michael Harms, Ph.D.
 ---
 Conte Center for the Neuroscience of Mental Disorders
 Washington University School of Medicine
 Department of Psychiatry, Box 8134
 660 South Euclid Ave.  Tel: 314-747-6173
 St. Louis, MO  63110  Email: mha...@wustl.edu
 
  
 
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Healthcare Information or other information of a sensitive nature. If
you are not the intended recipient, be advised that any unauthorized
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contents of this information is strictly prohibited. If you have
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Re: [Freesurfer] problem with pial surface reconstruction using T1 (MPRAGE) and T2 (SPACE) weighted images

[Matt Glasser]

I don’t know if recon-all will pass those flags in or not.  Probably best
to let Bruce take a look.

Peace,

Matt.

On 5/13/14, 7:36 AM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote:

Hi Emil

I would need the entire subject dir plus the T2-space volume

cheers
Bruce
On Tue, 13 May 
2014, Emil H.J. Nijhuis wrote:

 
 Dear Bruce  Matt,
 thank you for your help.
 
 @Bruce: I would be happy to send you the data, just let me know by
e-mail which files you wo
 uld need.
 
 @Matt: Could you please specify the commands for the flags
-nsigma_above and -nsigma_below a
 nd how you would rerun the pipeline? Also what values would be
recommended?
 
 I did not find any manual/help files regarding the flags, so it would
be helpful to document
  it.
 
 NB. I found another thread in the maillist which probably relates to
the issue: https://mail
 .nmr.mgh.harvard.edu/pipermail//freesurfer/2013-September/033550.html .
However I could not
 verify this, due to expired dropbox files.
 
 Yours,

  Emil
 
 Probably Emil¹s current example would be best because it is failing in
 your recon-all setup.
 
 Matt.
 
 On 5/9/14, 9:31 AM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote:
 
 Hi Matt
 
 if you can send me an example I'll try to find time to take a look
 Bruce
 On Fri, 9 
 May 2014, Matt Glasser wrote:
 
  Hi Bruce,
  
  For whatever reason, sometimes the T2w surface adjustment will be way
 off.
   Adjusting the -nsigma_above # -nsigma_below # even a little bit
up
 and
  down can get it out of the minimum and make it work, so there might
be a
  bug. 
  
  Peace,
  
  Matt.
  
  From: Emil H.J. Nijhuis emil.nijh...@gmail.com
  Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu
  Date: Friday, May 9, 2014 at 4:53 AM
  To: freesurfer@nmr.mgh.harvard.edu
  Subject: Re: [Freesurfer] problem with pial surface reconstruction
 using T1
  (MPRAGE) and T2 (SPACE) weighted images
  
  Dear Bruce,
  
  thank you for your help.
  
  attached I have put an fslview, tkmedit screen-shot of the T2 image
and
 a tk
  surfer image of lh.woT2.pial.
  
  It appears that without consideration of the T2 this effect does not
 happen.
  
  What would be your recommendation if I would like to keep using the
T2
 weigh
  ted image?
  
  Yours,
   Emil
  
  Hi Emil
  
  how do the surfaces look before you apply the T2 deformation? And
how do
  they look visualized over the T2 instead of the T1?
  
  cheers
  Bruce
  
  On Thu, 8 May 2014, Emil H.J. Nijhuis wrote:
  
  Hi,
  
  I have been using Freesurfer v5.3 to perform surface reconstruct for
1mm
  isotropic T1 (MPRAGE) and T2 (SPACE) weighted images from a Siemens
3T
 Trio
  scanner with a 32-channel head coil. Unfortunately for half of my
 subjects I
  receive an rather odd pial surface artefact, while the 'white'
surfaces
 do
  not suffer from the same issue.
  
  The command line I have used was:
  
  recon-all -all -subjid subjectid -T2  subjectdir/mri/orig/T2.mgz
 -T2pial
  -3T
  
  Are you familiar with this issue and do you have some advice for me?
  
  Thank you very much for your help.
  
  Yours sincerely,
  
   Emil
  
  --
  --
  Emil H.J. Nijhuis, PhD
  Researcher - Division of Diagnostic and Interventional Neuroradiology
  University Hospital Basel
  Petersgraben 4
  CH 4031 Basel Switzerland
  
  
  
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Re: [Freesurfer] problem with pial surface reconstruction using T1 (MPRAGE) and T2 (SPACE) weighted images

[Matt Glasser]

Hi Bruce,

For whatever reason, sometimes the T2w surface adjustment will be way off.
Adjusting the -nsigma_above # -nsigma_below # even a little bit up and
down can get it out of the minimum and make it work, so there might be a
bug.  

Peace,

Matt.

From:  Emil H.J. Nijhuis emil.nijh...@gmail.com
Reply-To:  Freesurfer support list freesurfer@nmr.mgh.harvard.edu
Date:  Friday, May 9, 2014 at 4:53 AM
To:  freesurfer@nmr.mgh.harvard.edu
Subject:  Re: [Freesurfer] problem with pial surface reconstruction using T1
(MPRAGE) and T2 (SPACE) weighted images

Dear Bruce,

thank you for your help.

attached I have put an fslview, tkmedit screen-shot of the T2 image and a
tksurfer image of lh.woT2.pial.

It appears that without consideration of the T2 this effect does not happen.

What would be your recommendation if I would like to keep using the T2
weighted image?

Yours,

 Emil



Hi Emil

how do the surfaces look before you apply the T2 deformation? And how do
they look visualized over the T2 instead of the T1?
cheers
Bruce

On Thu, 8 May 2014, Emil H.J. Nijhuis wrote:
 Hi,
 
 I have been using Freesurfer v5.3 to perform surface reconstruct for 1mm
 isotropic T1 (MPRAGE) and T2 (SPACE) weighted images from a Siemens 3T Trio
 scanner with a 32-channel head coil. Unfortunately for half of my subjects I
 receive an rather odd pial surface artefact, while the 'white' surfaces do
 not suffer from the same issue.
 
 The command line I have used was:
 
 recon-all -all -subjid subjectid -T2  subjectdir/mri/orig/T2.mgz -T2pial
 -3T
 
 Are you familiar with this issue and do you have some advice for me?
 
 Thank you very much for your help.
 
 Yours sincerely,
 
  Emil
 
 --
 --
 Emil H.J. Nijhuis, PhD
 Researcher - Division of Diagnostic and Interventional Neuroradiology
 University Hospital Basel
 Petersgraben 4
 CH 4031 Basel Switzerland
 
 
 
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Re: [Freesurfer] problem with pial surface reconstruction using T1 (MPRAGE) and T2 (SPACE) weighted images

[Matt Glasser]

Probably Emil¹s current example would be best because it is failing in
your recon-all setup.

Matt.

On 5/9/14, 9:31 AM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote:

Hi Matt

if you can send me an example I'll try to find time to take a look
Bruce
On Fri, 9 
May 2014, Matt Glasser wrote:

 Hi Bruce,
 
 For whatever reason, sometimes the T2w surface adjustment will be way
off.
  Adjusting the -nsigma_above # -nsigma_below # even a little bit up
and
 down can get it out of the minimum and make it work, so there might be a
 bug.  
 
 Peace,
 
 Matt.
 
 From: Emil H.J. Nijhuis emil.nijh...@gmail.com
 Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu
 Date: Friday, May 9, 2014 at 4:53 AM
 To: freesurfer@nmr.mgh.harvard.edu
 Subject: Re: [Freesurfer] problem with pial surface reconstruction
using T1
 (MPRAGE) and T2 (SPACE) weighted images
 
 Dear Bruce,
 
 thank you for your help.
 
 attached I have put an fslview, tkmedit screen-shot of the T2 image and
a tk
 surfer image of lh.woT2.pial.
 
 It appears that without consideration of the T2 this effect does not
happen.
 
 What would be your recommendation if I would like to keep using the T2
weigh
 ted image?
 
 Yours,
  Emil
 
 Hi Emil
 
 how do the surfaces look before you apply the T2 deformation? And how do
 they look visualized over the T2 instead of the T1?
 
 cheers
 Bruce
 
 On Thu, 8 May 2014, Emil H.J. Nijhuis wrote:
 
 Hi,
 
 I have been using Freesurfer v5.3 to perform surface reconstruct for 1mm
 isotropic T1 (MPRAGE) and T2 (SPACE) weighted images from a Siemens 3T
Trio
 scanner with a 32-channel head coil. Unfortunately for half of my
subjects I
 receive an rather odd pial surface artefact, while the 'white' surfaces
do
 not suffer from the same issue.
 
 The command line I have used was:
 
 recon-all -all -subjid subjectid -T2  subjectdir/mri/orig/T2.mgz
-T2pial
 -3T
 
 Are you familiar with this issue and do you have some advice for me?
 
 Thank you very much for your help.
 
 Yours sincerely,
 
  Emil
 
 --
 --
 Emil H.J. Nijhuis, PhD
 Researcher - Division of Diagnostic and Interventional Neuroradiology
 University Hospital Basel
 Petersgraben 4
 CH 4031 Basel Switzerland
 
 
 
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sti
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Re: [Freesurfer] using multiple cores

[Matt Glasser]

If you are compiling with clang openmp might not work.

Peace,

Matt.

On 5/2/14, 2:13 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote:

Hi Lukas

sorry, I'm out of my depth on the mac. Perhaps Zeke knows what's going
on? 
Does OpenMP have to be enabled somehow?

Bruce


On Fri, 2 May 2014,
lukas.sch...@ukb.uni-bonn.de wrote:

 Hi Bruce!
 
 I just run: recon-all -s ernie2  -autorecon2 -openmp 4
 
 mri_ca_register  uses 100.9% CPU at most ...
 
 Any idea?  Should I try to recompile FS for the current MacOS release?
If
 so, do I have to take care on special librariwa in order to enable the
 openmp option?
 
 Best wishes,
 
 Lukas
 
 Hi Bruce!
 
 Thanks for the fast response. I used the current stable version 5.3.0.1
 (freesurfer-Darwin-lion-stable-pub-v5.3.0.1).
 So I will try as you have suggested ...
 
 Best wishes,
 
 Lukas
 
  Bruce Fischl Fri, 02 May 2014 05:47:26 -0700
 
  Hi Luke
 
  what version of FS are you running? We see significant speedups. Try
  running top in a unix terminal and seeing if the cpu usage of
  mri_ca_register (during autorecon2, the longest single step) is
morethan
 100%
 
  cheers
  Bruce
 
  On Fri, 2 May 2014, lukas.sch...@ukb.uni-bonn.de wrote:
 
 
   Hi folks!
   
   I try to use -openmp option on an iMAC with 4 cores.
Unfortunately, I
  do not
   see any accelartion when processing a single data set with or
without
  the
   flag -openmp flag set.
  
   recon-all -s ernie_1 -all
  
   leads to ~6,4h processing time.
  
   Unfortunately
   recon-all -s ernie_2 -all -openmp 4
  
   did not change anything. Do I miss anything? Do I have to prepare
my
  system
   in a special way? Or run any scripts in advance?
  
   (System: iMac, 32GbRam,Intel i5, 4 cores, Mac Os 10.9, latest FS
  version)
  
   Best wishes,
  
   Luke
 
 
 
 
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Re: [Freesurfer] Time taken by Freesurfer for processing

[Matt Glasser]

Newer versions also have the ability to run some stages on multiple CPU
cores (with the -openmp cores flag) which speeds certain stages (e.g. in
autorecon2) up considerably.  I'm also sure Bruce wouldn't turn down more
resources to hire the programmers needed to make it faster either!

Peace,

Matt.

On 1/23/14 11:25 AM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote:

Hi Tanya
we have always preferenced minimizing manual interactions over computer
time. It takes so long because of its level of automation and its
completeness. This is also why it is so widely used I assume - because it
generates a comprehensive, accurate and automated morphometric assay of
the 
human brain. Seems like waiting a few extra hours to get something
complete, automated and accurate isn't a big deal.

cheers

Bruce

On Thu, 
23 Jan 2014, Tanya Verma wrote:

 Hi,
 I would like to ask that why does the Freesurfer takes so much time for
 processing particularly autorecon2 ?
 
 Knowing that Freesurfer takes a lot of time for processing, why is it
still
 used widely by researchers ? For segmentation followed by volume
calculation
 , does one has to really wait for hours for the results?
 
 Thank you
 
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Re: [Freesurfer] poor grey/white distinction in superior part of scan

[Matt Glasser]

Some pictures would probably be helpful to know what the issue is.

Peace,

Matt.

From:  Christine Smith cnsm...@ucsd.edu
Date:  Thursday, January 23, 2014 1:05 PM
To:  freesurfer@nmr.mgh.harvard.edu
Subject:  [Freesurfer] poor grey/white distinction in superior part of scan

Hello,

I am emailing to inquire about whether poor grey/white contrast in one part
of a scan (i.e., the posterior and superior part of the scan; ~parietal
cortex) can be addressed. The contrast in other parts of the scan looks good
and freesurfer does a great job of distinguishing white from grey. For the
parietal cortex area the cortex appears very thin. In addition, the entire
brain appears 'white' or bright, even though the brain doesn't look this
bright if you reconstruct it from dicoms.

We have now obtained 4 scans like this, so it isn't just one person with
thinning cortex. 

How can I make an adjustment to only this superior part of the brain and
leave the rest of it alone? Or do I need to make an adjustment to the
intensity early on for the entire scan and then basically start over with
editing? 

Best,
Christine

-- 
Christine N. Smith, Ph.D.
Department of Psychiatry
University of California, San Diego
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[Freesurfer] FW: poor grey/white distinction in superior part of scan

[Matt Glasser]

From:  Christine Smith cnsm...@ucsd.edu
Date:  Thursday, January 23, 2014 3:58 PM
To:  Matt Glasser m...@ma-tea.com
Subject:  Re: [Freesurfer] poor grey/white distinction in superior part of
scan

Please note that the left and right sides of the brain are flipped for
freesurfer vs the dicom picture. Please find attached a dicom picture that
is oriented the same way as freesurfer. Sorry for any confusion.


On Thu, Jan 23, 2014 at 1:56 PM, Christine Smith cnsm...@ucsd.edu wrote:
 Dear Matt, 
 
 Please find attached two pictures. One is of the brain from reconstructed
 dicom files (using AFNI). The other one is a pic from tkmedit of the same
 subject and approximately the same slice of brain. Notice that the freesurfer
 image is very bright. Look at the white matter and pial lines (i.e., cortical
 thickness) in the upper left hand part of the image and see how thin the
 cortex appears. Notice also, that there is very little grey/white contrast in
 this same area in the brain image reconstructed from dicoms.
 
 Please let me know if there are any other pictures you might desire or
 information you might need.
 
 Christine
 
 
 On Thu, Jan 23, 2014 at 11:33 AM, Matt Glasser m...@ma-tea.com wrote:
 Some pictures would probably be helpful to know what the issue is.
 
 Peace,
 
 Matt.
 
 From:  Christine Smith cnsm...@ucsd.edu
 Date:  Thursday, January 23, 2014 1:05 PM
 To:  freesurfer@nmr.mgh.harvard.edu
 Subject:  [Freesurfer] poor grey/white distinction in superior part of scan
 
 Hello,
 
 I am emailing to inquire about whether poor grey/white contrast in one part
 of a scan (i.e., the posterior and superior part of the scan; ~parietal
 cortex) can be addressed. The contrast in other parts of the scan looks good
 and freesurfer does a great job of distinguishing white from grey. For the
 parietal cortex area the cortex appears very thin. In addition, the entire
 brain appears 'white' or bright, even though the brain doesn't look this
 bright if you reconstruct it from dicoms.
 
 We have now obtained 4 scans like this, so it isn't just one person with
 thinning cortex.
 
 How can I make an adjustment to only this superior part of the brain and
 leave the rest of it alone? Or do I need to make an adjustment to the
 intensity early on for the entire scan and then basically start over with
 editing? 
 
 Best,
 Christine
 
 -- 
 Christine N. Smith, Ph.D.
 Department of Psychiatry
 University of California, San Diego
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 to whom it is addressed. If you believe this e-mail was sent to you in error
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 Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail
 was sent to you in error but does not contain patient information, please
 contact the sender and properly dispose of the e-mail.
 
 
 
 -- 
 Christine N. Smith, Ph.D.
 Department of Psychiatry
 University of California, San Diego



-- 
Christine N. Smith, Ph.D.
Department of Psychiatry
University of California, San Diego


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Re: [Freesurfer] Occipital cortex segmentation

[Matt Glasser]

Higher than 1mm resolution helps a lot.  We use 0.7mm isotropic in the HCP.

Peace,

Matt.

From:  Megha K. megha...@gmail.com
Date:  Monday, December 9, 2013 10:23 PM
To:  freesurfer@nmr.mgh.harvard.edu
Subject:  [Freesurfer] Occipital cortex segmentation

Dear Sir/Madam,

I am using freesurfer for 3T MRI analysis of visual cortical thickness in
elderly patients with ophthalmic disease. We are having a bit of trouble
with the accuracy of cortical segmentation in the visual cortex (namely the
pericalcarine region) as the cortex is quite thin in our patients (compared
to controls). You can see in the attached image that whilst there is smooth
cortical segmentation in the peri-calcarine region, the cortex is not
visible to the naked eye.  If you have any ideas on improving accuracy, I
would be very grateful.

Thanks
Megha
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Re: [Freesurfer] T2pial/FLAIRpial processing issues

[Matt Glasser]

To fix the second problem, why not reorient the T2w image so the image axes
are oriented in the way that FreeSurfer expects?

Peace,

Matt.

From:  Martijn Steenwijk martijnsteenw...@gmail.com
Date:  Thursday, November 14, 2013 8:13 AM
To:  freesurfer freesurfer@nmr.mgh.harvard.edu
Cc:  Veronica Popescu v.pope...@vumc.nl, Hugo Vrenken h.vren...@vumc.nl
Subject:  [Freesurfer] T2pial/FLAIRpial processing issues

Dear all,

There seem to be some serious issues with the T2pial / FLAIRpial processing
options provided in the latest versions of FreeSurfer.

First of all, although not clearly documented, T2pial / FLAIRpial processing
does require the FSLDIR to be set (in order to use bbregister with
--init-fsl). If not set,  recon-all will finish just without using the T2 or
FLAIR information. Importantly, no clear warning about this is given
although the user expects that T2/FLAIR has been used for pial surface
refinement. I think this is a very easy source of errors, so it might be a
good idea to just throw an error when FSLDIR is missing and T2pial/FLAIRpial
processing is requested.

Second, if FSLDIR has been set. T2pial/FLAIRpial uses bbregister with FLIRT
initialisation to align the T2 or FLAIR image to orig.mgz. However, we have
some high-res 3DFLAIR data in which this registration (more specifially, the
FLIRT initialisation step of bbregister) seems to fail in more than half of
the cases. Apparently, the FSL initialisation is not capable to change the
orientation such that it fits to the coordinate system used for orig.mgz.
Again, no warning or error is thrown, but the processing just continues with
the wrong registration and without noticing the results will get worse
compared to not using T2 or FLAIR.
Although I know its essential to look at the output data; would it be
possible to put some effort in letting the user know that things got wrong?

As a sidenote; I tried to fix this registration issue, but it seems to be
very complicated using bbregister (other than just inserting my own
registration obtained by using FLIRT to register native FLAIR to native T1,
and subsequently transform the result to Freesurfer space in order to obtain
FLAIR.mgz). 

Best,
Martijn
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Re: [Freesurfer] T2pial/FLAIRpial processing issues

[Matt Glasser]

I think you can do it with mri_convert ­rl.  I don't think it makes sense to
expect FLIRT to get the registration right reliably if the axes are off (in
the HCP Pipelines we definitely don't expect this and make sure all images
are RPI before processing them).

Peace,

Matt.

From:  Martijn Steenwijk martijnsteenw...@gmail.com
Date:  Thursday, November 14, 2013 9:27 AM
To:  Bruce Fischl fis...@nmr.mgh.harvard.edu
Cc:  Veronica Popescu v.pope...@vumc.nl, Hugo Vrenken h.vren...@vumc.nl,
freesurfer freesurfer@nmr.mgh.harvard.edu
Subject:  Re: [Freesurfer] T2pial/FLAIRpial processing issues

Hi Matt, Bruce, 

The problems are indeed a flirt issue, but given that it's programmed with
--init-fsl there is not much flexibility.

However, from a FS point of view, it might be a better and more robust
approach to first register FLAIRraw.mgz to raw.mgz, and then concatenate the
resulting registration with the (header based) registration from raw.mgz to
orig.mgz - instead of trusting the robustness of either registration
algorithms. 

... or, as Matt suggests, fix the image axes appropriately after converting
the FLAIR to mgz, and then run the registration. But I'm not sure how to do
that.

Best,
Martijn  


On Thu, Nov 14, 2013 at 5:53 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu
wrote:
 Hi Martijn
 
 we can print warning and errors if FSLDIR is not set, but the registration
 errros seem to be mostly a flirt issue, no? Have you posted on the FSL list?
 
 Bruce
 
 
 On Thu, 14 Nov 2013, Martijn Steenwijk wrote:
 
 Dear all,
 There seem to be some serious issues with the T2pial / FLAIRpial processing
 options provided in the latest versions of FreeSurfer.
 
 First of all, although not clearly documented, T2pial / FLAIRpial processing
 does require the FSLDIR to be set (in order to use bbregister with
 --init-fsl). If not set,  recon-all will finish just without using the T2 or
 FLAIR information. Importantly, no clear warning about this is given
 although the user expects that T2/FLAIR has been used for pial surface
 refinement. I think this is a very easy source of errors, so it might be a
 good idea to just throw an error when FSLDIR is missing and T2pial/FLAIRpial
 processing is requested.
 
 Second, if FSLDIR has been set. T2pial/FLAIRpial uses bbregister with FLIRT
 initialisation to align the T2 or FLAIR image to orig.mgz. However, we have
 some high-res 3DFLAIR data in which this registration (more specifially, the
 FLIRT initialisation step of bbregister) seems to fail in more than half of
 the cases. Apparently, the FSL initialisation is not capable to change the
 orientation such that it fits to the coordinate system used for orig.mgz.
 Again, no warning or error is thrown, but the processing just continues with
 the wrong registration and without noticing the results will get worse
 compared to not using T2 or FLAIR.
 Although I know its essential to look at the output data; would it be
 possible to put some effort in letting the user know that things got wrong?
  
 
 As a sidenote; I tried to fix this registration issue, but it seems to be
 very complicated using bbregister (other than just inserting my own
 registration obtained by using FLIRT to register native FLAIR to native T1,
 and subsequently transform the result to Freesurfer space in order to obtain
 FLAIR.mgz). 
 
 Best,
 Martijn
 
 
 
 
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Re: [Freesurfer] ERROR: comparison in expression (FS with SGE)

[Matt Glasser]

I think the latest version of FSL has this sorted out (it doesn't change
your machine's POSIXLY_CORRECT setting except briefly in the middle of
fsl_sub).

Peace,

Matt.

From:  chenchunhuichina chenchunhuich...@gmail.com
Date:  Friday, November 1, 2013 2:55 AM
To:  Matt Glasser m...@ma-tea.com
Cc:  free surfer freesurfer@nmr.mgh.harvard.edu
Subject:  ERROR: comparison in expression (FS with SGE)

Dear Matt and freesurfers,
 
I am encounting this old problem, that is, using fsl_sub to launch
FreeSurfer jobs in SGE and get this error message: (standard_in) 2: Error:
comparison in expression
and freesurfer stoped. But running freesurfer without fsl_sub is OK (using
fsl_sub to launch other commonds also fine).
 
Following Matt's message on this problem
https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2012-May/023961.html,
I added a line POSIXLY_CORRECT=0  in fsl_sub under  the line set --
`getopt T:q:a:p:M:j:t:z:N:Fvm:l:s: $*`
which now looks like this
...
set -- `getopt T:q:a:p:M:j:t:z:N:Fvm:l:s: $*`
POSIXLY_CORRECT=0 
...
 
However, the error was still the same, and what's even worse is that seems
the job was launched twice.
 
So can Matt or anybody tell me why? Am I misunderstood Matt's message? or
mybe version differences since Matt's solution came out one year ago?
I am using freesurfer-Linux-centos4_x86_64-stable-pub-v5.2.0, FMRIB Software
Library, Release 5.0 (c) 2012
 
there are two fsLsub
./src/sgeutils/fsl_sub
./bin/fsl_sub
which one should I edit or both?
 
Any help is appreciated, Thank you all!
 
 
2013-11-01 

Chunhui Chen
_
 
State Key Laboratory of Cognitive Neuroscience and Learning
Beijing Normal University
Beijing, China 100875


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Re: [Freesurfer] Major problems with T2-based pial removal

[Matt Glasser]

Also, what kind of T2w sequence is this?  I think we've mostly tested it
with the T2-SPACE (unless Bruce has tested with other things).

Peace,

Matt.

On 9/27/13 12:58 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote:

Hi Michael

that looks pretty bad! What is the resolution of the T2? The T1 that you
overlay on also looks somewhat blurry - what was it?

Bruce


On Fri, 27 Sep 
2013, Michael Waskom wrote:

 Hi, just to make the problem a bit more transparent, I took a second
 screenshot of the slices with the pial surface from the -T2pial run in
red
 and the pial surface from the normal run in
 cyan: https://dl.dropbox.com/s/jv8rcxnq50tdac6/bad_slice_both_pial.png
 
 On Fri, Sep 27, 2013 at 10:37 AM, Michael Waskom mwas...@stanford.edu
 wrote:
   Hi,
 I'm using FS 5.3 and trying to use hires T2-weighted scans to refine
 the pial mesh.
 
 However, I've found that using the T2 is causing rather dramatic
 problems with the pial surface.
 
 I processed the same subject's data with and without the -T2pial
 option. Here are links to a) pial surface image b) slices through the
 volume and c) the recon-all.log:
 
 With -T2pial
 
 https://dl.dropbox.com/s/rtjgplajfptr4xb/bad_surf_withT2.png
 https://dl.dropbox.com/s/d7so5qtujgg8j80/bad_slice_withT2.png
 https://dl.dropbox.com/s/7o00jy014hihrgu/recon_log_withT2.txt
 
 Without -T2pial
 
 https://dl.dropbox.com/s/51y15kogecltfbi/bad_surf_noT2.png
 https://dl.dropbox.com/s/3gps45kp0ngkuli/bad_slice_noT2.png
 https://dl.dropbox.com/s/6jih6f8fh4nwh0k/recon_log_noT2.txt
 
 The release notes for 5.3 claim that the T2 is registered to the T1
 before refining the surface, but I actually can't find any evidence of
 that sequence in the log file. For this subject, the T1 and T2 came
 from different scan sessions, although I have other data where they
 were acquired in the same session that have similar, if less dramatic,
 problems with the pial surface.
 
 Any ideas?
 
 Michael
 
 
 
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Re: [Freesurfer] Major problems with T2-based pial removal

[Matt Glasser]

Someone sent me a different kind of T2w image and it didn't work so well,
so we need to know what kind of image this is.

Peace,

Matt.

On 9/27/13 1:33 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote:

nope, pretty much only with T2-space with and without a flair pulse
On Fri, 
27 Sep 2013, Matt Glasser wrote:

 Also, what kind of T2w sequence is this?  I think we've mostly tested it
 with the T2-SPACE (unless Bruce has tested with other things).

 Peace,

 Matt.

 On 9/27/13 12:58 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote:

 Hi Michael

 that looks pretty bad! What is the resolution of the T2? The T1 that
you
 overlay on also looks somewhat blurry - what was it?

 Bruce


 On Fri, 27 Sep
 2013, Michael Waskom wrote:

 Hi, just to make the problem a bit more transparent, I took a second
 screenshot of the slices with the pial surface from the -T2pial run in
 red
 and the pial surface from the normal run in
 cyan: https://dl.dropbox.com/s/jv8rcxnq50tdac6/bad_slice_both_pial.png

 On Fri, Sep 27, 2013 at 10:37 AM, Michael Waskom
mwas...@stanford.edu
 wrote:
   Hi,
 I'm using FS 5.3 and trying to use hires T2-weighted scans to refine
 the pial mesh.

 However, I've found that using the T2 is causing rather dramatic
 problems with the pial surface.

 I processed the same subject's data with and without the -T2pial
 option. Here are links to a) pial surface image b) slices through the
 volume and c) the recon-all.log:

 With -T2pial
 
 https://dl.dropbox.com/s/rtjgplajfptr4xb/bad_surf_withT2.png
 https://dl.dropbox.com/s/d7so5qtujgg8j80/bad_slice_withT2.png
 https://dl.dropbox.com/s/7o00jy014hihrgu/recon_log_withT2.txt

 Without -T2pial
 
 https://dl.dropbox.com/s/51y15kogecltfbi/bad_surf_noT2.png
 https://dl.dropbox.com/s/3gps45kp0ngkuli/bad_slice_noT2.png
 https://dl.dropbox.com/s/6jih6f8fh4nwh0k/recon_log_noT2.txt

 The release notes for 5.3 claim that the T2 is registered to the T1
 before refining the surface, but I actually can't find any evidence of
 that sequence in the log file. For this subject, the T1 and T2 came
 from different scan sessions, although I have other data where they
 were acquired in the same session that have similar, if less dramatic,
 problems with the pial surface.

 Any ideas?

 Michael



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Re: [Freesurfer] Major problems with T2-based pial removal

[Matt Glasser]

So the T2-SPACE is a variable flip angle sequence that actually has a fair
amount of T1 and MT contrast in it and relatively less T2 contrast.  As a
result, you can clearly see the difference between grey and white matter,
and CSF is not massively brighter than grey and white matter.  If you are
using a different kind of T2w sequence where the distance between CSF
intensity and grey matter intensity is much greater, some of the internal
settings to the -T2pial flag will likely not be optimal.  I don't know if
recon-all allows you to modify those with expert options or not.  Bruce, is
it possible for the user to modify the ­nsigma_above and -nsigma_below flags
for mris_make_surfaces when using -T2pial?

Peace,

Matt.

From:  Michael Waskom mwas...@stanford.edu
Date:  Friday, September 27, 2013 2:20 PM
To:  Matt Glasser m...@ma-tea.com
Cc:  Bruce Fischl fis...@nmr.mgh.harvard.edu,
Freesurfer@nmr.mgh.harvard.edu Freesurfer@nmr.mgh.harvard.edu
Subject:  Re: [Freesurfer] Major problems with T2-based pial removal

Hi Matt,

It's this sequence:
http://cni.stanford.edu/wiki/MR_Protocols#T2_weighted_scans (the 3D T2)

You can click the console screenshots for a closer view of the parameters --
let me know if you need me to track down more info.

mw


On Fri, Sep 27, 2013 at 11:38 AM, Matt Glasser m...@ma-tea.com wrote:
 Someone sent me a different kind of T2w image and it didn't work so well,
 so we need to know what kind of image this is.
 
 Peace,
 
 Matt.
 
 On 9/27/13 1:33 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote:
 
 nope, pretty much only with T2-space with and without a flair pulse
 On Fri,
 27 Sep 2013, Matt Glasser wrote:
 
  Also, what kind of T2w sequence is this?  I think we've mostly tested it
  with the T2-SPACE (unless Bruce has tested with other things).
 
  Peace,
 
  Matt.
 
  On 9/27/13 12:58 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote:
 
  Hi Michael
 
  that looks pretty bad! What is the resolution of the T2? The T1 that
 you
  overlay on also looks somewhat blurry - what was it?
 
  Bruce
 
 
  On Fri, 27 Sep
  2013, Michael Waskom wrote:
 
  Hi, just to make the problem a bit more transparent, I took a second
  screenshot of the slices with the pial surface from the -T2pial run
in
  red
  and the pial surface from the normal run in
  cyan: 
 https://dl.dropbox.com/s/jv8rcxnq50tdac6/bad_slice_both_pial.png
 
  On Fri, Sep 27, 2013 at 10:37 AM, Michael Waskom
 mwas...@stanford.edu
  wrote:
Hi,
  I'm using FS 5.3 and trying to use hires T2-weighted scans to refine
  the pial mesh.
 
  However, I've found that using the T2 is causing rather dramatic
  problems with the pial surface.
 
  I processed the same subject's data with and without the -T2pial
  option. Here are links to a) pial surface image b) slices through the
  volume and c) the recon-all.log:
 
  With -T2pial
  
  https://dl.dropbox.com/s/rtjgplajfptr4xb/bad_surf_withT2.png
  https://dl.dropbox.com/s/d7so5qtujgg8j80/bad_slice_withT2.png
  https://dl.dropbox.com/s/7o00jy014hihrgu/recon_log_withT2.txt
 
  Without -T2pial
  
  https://dl.dropbox.com/s/51y15kogecltfbi/bad_surf_noT2.png
  https://dl.dropbox.com/s/3gps45kp0ngkuli/bad_slice_noT2.png
  https://dl.dropbox.com/s/6jih6f8fh4nwh0k/recon_log_noT2.txt
 
  The release notes for 5.3 claim that the T2 is registered to the T1
  before refining the surface, but I actually can't find any evidence
of
  that sequence in the log file. For this subject, the T1 and T2 came
  from different scan sessions, although I have other data where they
  were acquired in the same session that have similar, if less
 dramatic,
  problems with the pial surface.
 
  Any ideas?
 
  Michael
 
 
 
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 it
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 in
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Re: [Freesurfer] Major problems with T2-based pial removal

[Matt Glasser]

I'm sure it was registered to the T1w with BBR, though I don't know the
internals of that in recon-all.  Given that you might only be the second
person to try this with non T2-SPACE T2w images (and I unfortunately had not
told Bruce about my bad experience with this), you can forgive the
FreeSurfer docs for not mentioning it yet. :)

That being said, it isn't guaranteed not to work, you just might have to do
some fiddling with the nsigma parameters to get it to work, as the defaults
for T2-SPACE are probably not good for your images.

Peace,

Matt.

From:  Michael Waskom mwas...@stanford.edu
Date:  Friday, September 27, 2013 10:06 PM
To:  Matt Glasser m...@ma-tea.com
Cc:  Bruce Fischl fis...@nmr.mgh.harvard.edu,
Freesurfer@nmr.mgh.harvard.edu Freesurfer@nmr.mgh.harvard.edu
Subject:  Re: [Freesurfer] Major problems with T2-based pial removal

Hmm, Ok. Thanks Matt.

I still think it's weird that the T2 didn't seem to ever get registered to
the FS volume, but it's not a huge loss if we can't use them. With that
said, it might help to clarify the docs on this point a bit, as it sort of
sounded like any reasonably-sized T2-weighted image would be useful, and I
would have tried to collect a different image if I had known!


On Fri, Sep 27, 2013 at 12:58 PM, Matt Glasser m...@ma-tea.com wrote:
 So the T2-SPACE is a variable flip angle sequence that actually has a fair
 amount of T1 and MT contrast in it and relatively less T2 contrast.  As a
 result, you can clearly see the difference between grey and white matter, and
 CSF is not massively brighter than grey and white matter.  If you are using a
 different kind of T2w sequence where the distance between CSF intensity and
 grey matter intensity is much greater, some of the internal settings to the
 -T2pial flag will likely not be optimal.  I don't know if recon-all allows you
 to modify those with expert options or not.  Bruce, is it possible for the
 user to modify the ­nsigma_above and -nsigma_below flags for
 mris_make_surfaces when using -T2pial?
 
 Peace,
 
 Matt.
 
 From:  Michael Waskom mwas...@stanford.edu
 Date:  Friday, September 27, 2013 2:20 PM
 To:  Matt Glasser m...@ma-tea.com
 Cc:  Bruce Fischl fis...@nmr.mgh.harvard.edu,
 Freesurfer@nmr.mgh.harvard.edu Freesurfer@nmr.mgh.harvard.edu
 Subject:  Re: [Freesurfer] Major problems with T2-based pial removal
 
 Hi Matt,
 
 It's this sequence:
 http://cni.stanford.edu/wiki/MR_Protocols#T2_weighted_scans (the 3D T2)
 
 You can click the console screenshots for a closer view of the parameters --
 let me know if you need me to track down more info.
 
 mw
 
 
 On Fri, Sep 27, 2013 at 11:38 AM, Matt Glasser m...@ma-tea.com wrote:
 Someone sent me a different kind of T2w image and it didn't work so well,
 so we need to know what kind of image this is.
 
 Peace,
 
 Matt.
 
 On 9/27/13 1:33 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote:
 
 nope, pretty much only with T2-space with and without a flair pulse
 On Fri,
 27 Sep 2013, Matt Glasser wrote:
 
  Also, what kind of T2w sequence is this?  I think we've mostly tested it
  with the T2-SPACE (unless Bruce has tested with other things).
 
  Peace,
 
  Matt.
 
  On 9/27/13 12:58 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote:
 
  Hi Michael
 
  that looks pretty bad! What is the resolution of the T2? The T1 that
 you
  overlay on also looks somewhat blurry - what was it?
 
  Bruce
 
 
  On Fri, 27 Sep
  2013, Michael Waskom wrote:
 
  Hi, just to make the problem a bit more transparent, I took a second
  screenshot of the slices with the pial surface from the -T2pial run
in
  red
  and the pial surface from the normal run in
  cyan: 
 https://dl.dropbox.com/s/jv8rcxnq50tdac6/bad_slice_both_pial.png
 
  On Fri, Sep 27, 2013 at 10:37 AM, Michael Waskom
 mwas...@stanford.edu
  wrote:
Hi,
  I'm using FS 5.3 and trying to use hires T2-weighted scans to refine
  the pial mesh.
 
  However, I've found that using the T2 is causing rather dramatic
  problems with the pial surface.
 
  I processed the same subject's data with and without the -T2pial
  option. Here are links to a) pial surface image b) slices through
the
  volume and c) the recon-all.log:
 
  With -T2pial
  
  https://dl.dropbox.com/s/rtjgplajfptr4xb/bad_surf_withT2.png
  https://dl.dropbox.com/s/d7so5qtujgg8j80/bad_slice_withT2.png
  https://dl.dropbox.com/s/7o00jy014hihrgu/recon_log_withT2.txt
 
  Without -T2pial
  
  https://dl.dropbox.com/s/51y15kogecltfbi/bad_surf_noT2.png
  https://dl.dropbox.com/s/3gps45kp0ngkuli/bad_slice_noT2.png
  https://dl.dropbox.com/s/6jih6f8fh4nwh0k/recon_log_noT2.txt
 
  The release notes for 5.3 claim that the T2 is registered to the T1
  before refining the surface, but I actually can't find any evidence
of
  that sequence in the log file. For this subject, the T1 and T2 came
  from different scan sessions, although I have other data where they
  were acquired in the same session that have similar, if less
 dramatic

Re: [Freesurfer] version 2 FS

[Matt Glasser]

Note that this does not apply to HCP-style FreeSurfer runs or the HCP
released data.

Peace,

Matt.

On 9/7/13 8:26 AM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote:

Hi Anupa

it means that for some acquisition types the pial surfaces in 5.2 had
substantial errors. We recommend rerunning with 5.3. Note that this
should 
just involve compute time as all manual interventions will be retained

cheers
Bruce

On 
Sat, 7 Sep 2013, Anupa AV wrote:

 Dear SIr,
 
 I made some analysis based on FS v.2.0.
 Does the Deprecated version means that the results generated by FSv.2
can't
 be published???
 

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[Freesurfer] FW: apply fnirt transformation on a surface

[Matt Glasser]

On 9/2/13 12:02 PM, Glasser, Matthew glass...@wusm.wustl.edu wrote:

Hi Bruce,

Connectome Workbench commandline utilities can do this with FSL warp
fields:

wb_command -surface-apply-warpfield

One needs to use the inverse warp as the warpfield argument and the
forward warp as the -fnirt forward-warp.

Peace,

Matt.

On 9/2/13 11:19 AM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote:

A veritable game of telephone! Thanks Jesper. Matt?

On Mon, 2 Sep 2013, Jesper Andersson wrote:

 Hi guys,
 I didn't think we had any tools for doing that, and said so much on the
FSL
 mailbase. But apparently the WashU people has something that does just
that
 for you. I think the best person to contact about the details is Matt
 Glasser.
 
 J
  
 On 2 Sep 2013, at 15:58, Saad Jbabdi s...@fmrib.ox.ac.uk
  wrote:

   Hi In Probtrackx, this is done internally.
 If you just want to transform the vertex coordinates, then I think
 you'll need to play with the FNIRT source code - I've CC'd Jesper who
 knows better.
 
 Cheers,
 Saad
 
 
 
 On 2 Sep 2013, at 15:56, Bruce Fischl fis...@nmr.mgh.harvard.edu
 wrote:

   you might check on the FSL list. I think I've seen some
   traffic indicating that there are some tools for doing
   this. I'l cc Saad as he might know

   cheers
   Bruce
 

   On Mon, 2 Sep 2013, Douglas Greve wrote:

 Hi Shani, I don't think you can apply a FNIRT
 transform to a surface.
 doug
 On 9/2/13 8:20 AM, Shani Ben Amitay wrote:
  Dear freesurfer people,
 Any idea whether I can apply transformation
 that was calculated by fsl
 fnirt on the white/pial surfaces calculated
 using the freesurfer
 stream?
 Thanks!
 Shani
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   the sender and properly
   dispose of the e-mail.
 
 
 
 --
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 University of Oxford, FMRIB Centre
 
 JR Hospital, Headington, OX3 9DU, UK
 (+44)1865-222466  (fax 717)
 www.ndcn.ox.ac.uk/team/researchers/saad-jbabdi
 
 
 



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Re: [Freesurfer] issue with pial surface in orbitofrontal cortex

[Matt Glasser]

Hard to fix if that is the receive field and you don't have another image
like a T2w to remove it with.  Perhaps mri_normalize can be tuned to
improve this with expert options as the white matter that is being
correctly segmented appears to be darker as well.

Peace,

Matt.

On 5/17/13 9:30 AM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote:

Hi Caspar

yes, that might help. There are expert opts for this. Sorry, I have
almost no experience analyzing monkey brains at .5mm, so I'm really not
sure what to advise you. Perhaps one of the other people on list who have
done a bunch can comment?
Bruce
On Fri, 17 May 2013, Caspar M. Schwiedrzik wrote:

 Hi Bruce,
 I tried adding control points in the white matter in that region,
 however, it does not seem to fix the issue. Also, the brainmask.mgz
 does not seem to exclude this part of the brain, so that is not the
 problem either.
 I am attaching another screenshot (horizontal 119) to illustrate the
problem.
 White matter pixel values range from the high 80ies to 100 in this
area.
 Included grey matter pixel values are in the low 80ies.
 Excluded grey matter pixel values range from the low 60ies to low 70ies.

 Would it make sense to re-run mri_segment with a different threshold?
 Thanks, Caspar



 2013/5/16 Bruce Fischl fis...@nmr.mgh.harvard.edu:
 Hi Caspar

 is the closest white matter captured by the white surface? What is the
 intensity of voxels there? If  110 you could try putting control
points in
 them and seeing if that helps (that is, in the closest voxels that are
 entirely white matter).


 Bruce

 On Thu, 16 May 2013, Caspar M. Schwiedrzik wrote:

 Hi Bruce,
 ok.
 But in theory, what would you recommend to get around the darkening
 issue? Unfortunately, I do not have a field map available for this
 data set.
 Or should I not expect to get a pial surface in this area since the
 white matter is not discernable?
 There are five slices without clear white matter (original voxel size
 0.5x0.5x0.5 mm).
 Thanks, Caspar

 2013/5/16 Bruce Fischl fis...@nmr.mgh.harvard.edu:

 Hi Caspar

 if it's primate I don't think I'm going to be able to help - you'll
need
 someone more familiar with primate anatomy

 sorry
 Bruce
 On Thu, 16 May 2013, Caspar M.
 Schwiedrzik wrote:

 Hi Bruce and Matt,
 yes, it is primate data. I just dropped an archive on your FTP
server
 in transfer/incoming.
 Thanks!
 Caspar

 2013/5/16 Matt Glasser m...@ma-tea.com:

 Is the brain extraction removing that part of the brain?  Do you
know
 where the OFC ends and olfactory bulb begins?

 Peace,

 Matt.

 On 5/16/13 11:43 AM, Caspar M. Schwiedrzik
 cschwie...@mail.rockefeller.edu wrote:

 Hi!
 I am failing to get a proper pial surface in orbitofrontal cortex.
 See attached screenshot.
 This is NHP data, processed with version 4.5.
 I am not sure how to proceed here, as there is no clear with
matter.
 Any advice would be appreciated.
 Thanks!
 Caspar
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 e-mail
 contains patient information, please contact the Partners
Compliance
 HelpLine at
 http://www.partners.org/complianceline . If the e-mail was sent
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Re: [Freesurfer] issue with pial surface in orbitofrontal cortex

[Matt Glasser]

Your line continuation isn't working for some reason?  Type the command
line all on one line and see if that fixes the problem.

Matt.

On 5/17/13 1:37 PM, Caspar M. Schwiedrzik
cschwie...@mail.rockefeller.edu wrote:

set threshold = `echo 7/10 | bc -l`
set segment_options = -v -fillv -fillbg -wlo 104 -ghi 118  -whi 140
-n 4 -p $threshold -keep

mri_segment ${segment_options} \
-i brain.mgz -seg wm.mgz

filling ventricles
filling basal ganglia
using white lolim = 104.0
using gray hilim = 118.0
using white hilim = 140.0
running border classification 4 times
preserving editing changes in output volume...
using 70% threshold
mri_read(): couldn't determine type of file
mri_segment: could not read source volume from .700
-i: Command not found


2013/5/17 Bruce Fischl fis...@nmr.mgh.harvard.edu:
 Hi Caspar

 can you include the command line and all the output?


 Bruce
 On Fri, 17 May 2013, Caspar M. Schwiedrzik wrote:

 filling ventricles
 filling basal ganglia
 using white lolim = 104.0
 using gray hilim = 118.0
 using white hilim = 140.0
 running border classification 4 times
 preserving editing changes in output volume...
 using 70% threshold
 mri_read(): couldn't determine type of file /.../.700
 mri_segment: could not read source volume from .700
 ../mri/brain.mgz: Permission denied

 if I add a -i to the input volume, it says flag not recognized.
 to get a floating point number into my tcsh script, I am using `echo
 7/10 | bc -l`

 according to this previous discussion on the mailing list, there
 should be a fix available somewhere:
 
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg18824.html

 Thanks, Caspar

 2013/5/17 Bruce Fischl fis...@nmr.mgh.harvard.edu:

 and what happens? Can you send the full screen output?

 On Fri, 17 May 2013, Caspar M. Schwiedrzik wrote:

 mri_segment \
 -v \
 -fillv \
 -fillbg \
 -wlo 104 \
 -ghi 118 \
 -whi 140 \
 -n 4 \
 -keep \
 brain.mgz wm.mgz

 The pial surface in the rest of the brain is ok, it is only the
 orbitofrontal/piriform cortex that is problematic. I now wanted to
add
 -p 0.7.

 Caspar


 2013/5/17 Bruce Fischl fis...@nmr.mgh.harvard.edu:


 what is your command line? You are probably better off setting
gray_hi,
 gray_low, wm_hi, wm_low, etc...

 Bruce
 On Fri, 17 May 2013, Caspar M. Schwiedrzik wrote:

 When I try to specify a different threshold using -p, mri_segment
 reads in the threshold as the input volume.
 I tried specifying the input with -i (as explained here:


 
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg18826.
html),
 but now it does not recognize the -i flag.
 Caspar


 2013/5/17 Matt Glasser m...@ma-tea.com:



 Hard to fix if that is the receive field and you don't have
another
 image
 like a T2w to remove it with.  Perhaps mri_normalize can be tuned
to
 improve this with expert options as the white matter that is being
 correctly segmented appears to be darker as well.

 Peace,

 Matt.

 On 5/17/13 9:30 AM, Bruce Fischl fis...@nmr.mgh.harvard.edu
 wrote:

 Hi Caspar

 yes, that might help. There are expert opts for this. Sorry, I
have
 almost no experience analyzing monkey brains at .5mm, so I'm
really
 not
 sure what to advise you. Perhaps one of the other people on list
who
 have
 done a bunch can comment?
 Bruce
 On Fri, 17 May 2013, Caspar M. Schwiedrzik wrote:

 Hi Bruce,
 I tried adding control points in the white matter in that
region,
 however, it does not seem to fix the issue. Also, the
brainmask.mgz
 does not seem to exclude this part of the brain, so that is not
the
 problem either.
 I am attaching another screenshot (horizontal 119) to illustrate
 the
 problem.
 White matter pixel values range from the high 80ies to 100 in
this
 area.
 Included grey matter pixel values are in the low 80ies.
 Excluded grey matter pixel values range from the low 60ies to
low
 70ies.

 Would it make sense to re-run mri_segment with a different
 threshold?
 Thanks, Caspar



 2013/5/16 Bruce Fischl fis...@nmr.mgh.harvard.edu:



 Hi Caspar

 is the closest white matter captured by the white surface?
What is
 the
 intensity of voxels there? If  110 you could try putting
control
 points in
 them and seeing if that helps (that is, in the closest voxels
that
 are
 entirely white matter).


 Bruce

 On Thu, 16 May 2013, Caspar M. Schwiedrzik wrote:

 Hi Bruce,
 ok.
 But in theory, what would you recommend to get around the
 darkening
 issue? Unfortunately, I do not have a field map available for
 this
 data set.
 Or should I not expect to get a pial surface in this area
since
 the
 white matter is not discernable?
 There are five slices without clear white matter (original
voxel
 size
 0.5x0.5x0.5 mm).
 Thanks, Caspar

 2013/5/16 Bruce Fischl fis...@nmr.mgh.harvard.edu:




 Hi Caspar

 if it's primate I don't think I'm going to be able to help -
 you'll
 need
 someone more familiar with primate anatomy

 sorry
 Bruce
 On Thu, 16 May 2013, Caspar M.
 Schwiedrzik wrote:

 Hi

Re: [Freesurfer] using T2* weighted scans to assist with dura stripping in a GE scanner?

[Matt Glasser]

Gordon Xu who helped us set up the protocol reminded me of the following:

The main benefit of the readout PF is to reduce echo spacing, hence less
blurring in the slice direction. The side benefit is that it also reduces
the minimum TE, hence less dropout. However, you do give up some SNR at
the high spatial frequency as Souheil mentioned. There are two senarios of
this, a) the SNR is adequate, you only lose some SNR due to less sampling,
b) if the SNR is borderline or worse, in addition to losing SNR you also
lose some spatial resolution in the readout direction as the other side of
the high spatial frequency k-space is less reliable.

I remember we did pilot acquisition with and without asymmetric echo in
two subjects. You looked at the images and you either liked the one with
asymmetric echo because of less blurring or at least indifferent between
the two. So I assume with the Siemens 32ch coil we are in senario a)
above.


If I had to guess, we probably went with the readout partial fourier to
reduce the dropout regions in the gradient echo MPRAGE and didn't see an
obvious loss in resolution.

Peace,

Matt.

On 5/13/13 1:03 PM, Inati, Souheil (NIH/NIMH) [E]
souheil.in...@nih.gov wrote:

Hi Matt,

Thanks for the link.

Reading on pages 29-31, I am struck by the complexity of the procedure.
Not to say that it doesn't work, or that the single T1w image free-surfer
stuff is simple :-), on the contrary, it's just that I was expecting to
see something about an optimization that used both images, rather than
something based on the T1w image followed by an exclusion criterion based
on the T2w image.  Anyway, works better than without.

Minor question on the acquisition of the anatomicals:
- Why are you using partial fourier in the read direction?  You're
throwing away a lot of SNR at the high spatial frequencies, seems a shame
to go to 0.7mm and then do that.

Cheers,
Souheil

On May 12, 2013, at 10:54 PM, Matt Glasser m...@ma-tea.com wrote:

 This is available online now:
 
 http://authors.elsevier.com/sd/article/S1053811913005053
 
 
 On 5/7/13 3:10 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote:
 
 actually Matt Glasser points out that a brief description is in his
paper
 that is coming out soon, and there is also some description in Andre's
 multi-echo mprage paper
 Bruce
 On Tue, 7 May 2013, Inati, Souheil (NIH/NIMH) [E]
 wrote:
 
 thanks :-)
 
 On May 7, 2013, at 3:28 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu
 wrote:
 
 no, of course not :)
 
 On Tue, 7 May 2013, Inati, Souheil (NIH/NIMH) [E]
 wrote:
 
 Hi Bruce,
 
 Out of curiosity and for reference for my users, do you have a paper
 on the T2 or FLAIR assisted segmentation?
 
 Cheers,
 Souheil
 
 -
 
 Souheil Inati, PhD
 Staff Scientist
 FMRI Facility
 NIMH/NIH/DHHS
 souheil.in...@nih.govmailto:souheil.in...@nih.gov
 
 
 
 
 On May 7, 2013, at 2:24 PM, Bruce Fischl
 fis...@nmr.mgh.harvard.edumailto:fis...@nmr.mgh.harvard.edu
wrote:
 
 Hi Katie
 
 I'm really not sure. These days I would recommend a highres (e.g.
1mm
 isotropic) FLAIR if you can get one, or T2 if not. The T2* can help,
 but
 it's pretty noisy in brain.
 
 cheers
 Bruce
 
 On Tue, 7 May 2013, Katie Surrence wrote:
 
 Dear Freesurfer gurus,
 
 At the course, André van der Kouwe mentioned in his morphometry
 methods talk that T2* weighted contrast from
 MEMPRAGE could be used to further seperate dura from cortex, as also
 discussed in this paper:
 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2408694/.  We have a GE
 scanner in our lab.  The internet suggests
 that a Multi-echo FSPGR/FGRE exists.  Would this be the analog?
 Would it work the same way?  Could you also
 use these images with the mris_make_surfaces command?
 
 Thanks very much for your insight -- and I enjoyed the course!
 
 /Katie Surrence
 
 --
 Research Coordinator
 Social Cognition Laboratory
 New York State Psychiatric Institute
 
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 the e-mail
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Re: [Freesurfer] using T2* weighted scans to assist with dura stripping in a GE scanner?

[Matt Glasser]

This is available online now:

http://authors.elsevier.com/sd/article/S1053811913005053


On 5/7/13 3:10 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote:

actually Matt Glasser points out that a brief description is in his paper
that is coming out soon, and there is also some description in Andre's
multi-echo mprage paper
Bruce
On Tue, 7 May 2013, Inati, Souheil (NIH/NIMH) [E]
wrote:

 thanks :-)

 On May 7, 2013, at 3:28 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu
wrote:

 no, of course not :)

 On Tue, 7 May 2013, Inati, Souheil (NIH/NIMH) [E]
 wrote:

 Hi Bruce,

 Out of curiosity and for reference for my users, do you have a paper
on the T2 or FLAIR assisted segmentation?

 Cheers,
 Souheil

 -

 Souheil Inati, PhD
 Staff Scientist
 FMRI Facility
 NIMH/NIH/DHHS
 souheil.in...@nih.govmailto:souheil.in...@nih.gov




 On May 7, 2013, at 2:24 PM, Bruce Fischl
fis...@nmr.mgh.harvard.edumailto:fis...@nmr.mgh.harvard.edu wrote:

 Hi Katie

 I'm really not sure. These days I would recommend a highres (e.g. 1mm
 isotropic) FLAIR if you can get one, or T2 if not. The T2* can help,
but
 it's pretty noisy in brain.

 cheers
 Bruce

 On Tue, 7 May 2013, Katie Surrence wrote:

 Dear Freesurfer gurus,

 At the course, André van der Kouwe mentioned in his morphometry
methods talk that T2* weighted contrast from
 MEMPRAGE could be used to further seperate dura from cortex, as also
discussed in this paper:
 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2408694/.  We have a GE
scanner in our lab.  The internet suggests
 that a Multi-echo FSPGR/FGRE exists.  Would this be the analog?
Would it work the same way?  Could you also
 use these images with the mris_make_surfaces command?

 Thanks very much for your insight -- and I enjoyed the course!

 /Katie Surrence

 --
 Research Coordinator
 Social Cognition Laboratory
 New York State Psychiatric Institute

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Re: [Freesurfer] Advice on integrating FSL\'s BET with recon-all

[Matt Glasser]

Those pipelines will hopefully be available publicly this summer.  The
relevant code is this though:

recon-all -i input image -subjid $SubjectID -sd $SubjectDIR -motioncor
-talairach -nuintensitycor -normalization
mri_convert input brain extracted image
$SubjectDIR/$SubjectID/mri/brainmask.mgz --conform
mri_em_register -mask $SubjectDIR/$SubjectID/mri/brainmask.mgz
$SubjectDIR/$SubjectID/mri/nu.mgz
$FREESURFER_HOME/average/RB_all_2008-03-26.gca
$SubjectDIR/$SubjectID/mri/transforms/talairach_with_skull.lta
mri_watershed -T1 -brain_atlas
$FREESURFER_HOME/average/RB_all_withskull_2008-03-26.gca
$SubjectDIR/$SubjectID/mri/transforms/talairach_with_skull.lta
$SubjectDIR/$SubjectID/mri/T1.mgz
$SubjectDIR/$SubjectID/mri/brainmask.auto.mgz
cp $SubjectDIR/$SubjectID/mri/brainmask.auto.mgz
$SubjectDIR/$SubjectID/mri/brainmask.mgz
recon-all -subjid $SubjectID -sd $SubjectDIR -autorecon2 ­autorecon3

Basically,  you make mri_em_register give a more accurate registration (this
is typically what fails when you get a bad brain extraction from FreeSurfer
in my experience), and then use FreeSurfer's own very nice brain extraction
algorithm with the better registration to get the final brain mask.

Peace,

Matt.

From:  lukas.sch...@ukb.uni-bonn.de
Date:  Sunday, April 28, 2013 4:21 AM
To:  freesurfer@nmr.mgh.harvard.edu
Subject:  Re: [Freesurfer] Advice on integrating FSL\'s BET with recon-all

Hi Matt!

Refering to an older mail from  06 Mar 2013  I would be also interested to
integrate BET-results for the initial registration step.  Using the -B
option in BET I get very robust results.

You recommend: ... using the BET extracted image instead of the image with
skull for the initial registration step, and then you can use mri_watershed
on the original image...

How can this be implemented practically? Are the HCP protocols / pipelines
you mentioned later available for the research community?

Many thanks in advance,

Luke

Matt Glasser 
http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.eduq=from:
%22Matt+Glasser%22  Wed, 06 Mar 2013 16:09:44 -0800
http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.eduq=date:
20130306 

I would check the mri_em_register registrations of the step that
immediately precedes mri_watershed (and produces
talairach_with_skull.lta).  We found that most of the variability and
failures occurred in this step, and mri_watershed itself is a very robust
brain extraction algorithm when it is given an accurate registration (my
experience with BET is that it is probably not the best tool for getting
very accurate brainmasks and sometimes takes away too much). I would
recommend using the BET extracted image instead of the image with skull
for the initial registration step, and then you can use mri_watershed on
the original image and get good results every time.  This is the type of
strategy we use in the HCP Pipelines (except we use something more robust
than BET for the initial mask).

Note that the talairach registration (done by the -talairach step with
the talairach_avi tool) has nothing to do with the registration that
precedes brain extraction.  Perhaps it should is more robust and should be
used, but the affine would have to be converted to the correct format.

Peace,

Matt.

On 3/6/13 3:53 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote:

you can use

mri_convert -rl ...

to reslice the output of bet so that it has the same geometry as the rest
of our stream

cheers
Bruce

On Wed, 6 Mar 2013, Winter, Warren wrote:

 Hi again,
 We have had some suboptimal results from FreeSurfer's skullstripping
algorithm, even after iteratively trying different
 watershed thresholds and after checking the quality of Talairach
registration.  The results are pretty good, but often leave
 some dura matter and bits of neck behind whose higher intensity values,
I believe, may end up skewing recon-all's later
 estimation of the range of intensity values within grey matter, and
consequently compromising the accuracy of pial surface
 estimation.
 
 FSL's BET, however, seems to do a better job of extracting the brain,
at least for our dataset.  So, I was wondering if I
 might be able to skip over mri_watershed and feed autorecon2 and
autorecon3 a brainmask.mgz file created using BET.  I tried
 this procedure:
 
 
 1) mri_convert path/to/T1dcm T1.nii.gz
 2) bet T1.nii.gz BET_brainmask.nii.gz -A
 3) mri_convert BET_brainmask.nii.gz BET_brainmask.mgz
 4) recon-all -s subjid -autorecon1 -noskullstrip
 5) mv BET_brainmask.nii.gz ./subjid/mri/brainmask.mgz
 6) recon-all -s subjid -autorecon2 -autorecon3
 
 And I got this error message, right after normalization2:
 
 
 #@# Mask BFS Tue Mar  5 22:52:05 EST 2013
 
/net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/20
12_bet/mri
 
  mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz
 
 threshold mask volume at 5
 ERROR: dimension mismatch between source and mask
 Linux rc-thunderball 3.2.21-mosix #1 SMP Mon Jul 2 08:55:48 EDT

Re: [Freesurfer] Incorporating (high resolution) T2- and FLAIR volumes

[Matt Glasser]

I find the T2w image works well for removing dura and blood vessels, but
I'm not sure FLAIR would work for T1w/T2w myelin mapping because of what
would happen to the ratio near the pial surface.

Instructions for T1w/T2w myelin mapping are available here:
http://brainvis.wustl.edu/wiki/index.php/Caret:MyelinMaps

One starts with FreeSurfer outputs.

Bruce: do you guys have an unsmoothed group average grey/white map?  We
could do a quick comparison on fsaverage if you guys were interested.

Peace,

Matt.

On 3/28/13 7:45 AM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote:

1a) You would do this after running recon-all on the T1-weighted image.
It 
will only adjust the surfaces, not the segmentation. Something like
recon-all -T2pial path to flair

1b) this will work with either, but in my experience the FLAIR helps more
to distinguish dura from gm

2) Yes. The standard aseg will label them and we have some custom tools
that are more accurate if you have other image contrasts. I don't think
they are quite distributed yet, but perhaps Doug can comment.

3) Sure, this isn't too hard.  David Salat has published using the
gray/white ratio as an interesting biomarker and the techniques would be
pretty similar. I think Matt mostly used FreeSurfer for his analysis, but
perhaps he can comment on the particulars

cheers
Bruce


On Thu, 28 Mar 2013, lukas.sch...@ukb.uni-bonn.de wrote:

 
 Hi FreeSurfer experts!
 
 We have isotropic T1/T2 and FLAIR volumes for a larger cohort.  It
would be
 fine to use the T2 / FLAIR volumes to improve the segmentation and to
 perform a couple additional analyses using FS. This leads to the
following
 questions:
 
 1) How do I incorporate T2/Flair volumes into the recon all processing
 stream?
 
 a) Would it be like:  recon-all bert -all -T2 /luke/xyz/007-T2.nii ?
 
 b) What is expected to get the better results regarding the pial
surface:
 FLAIR or T2? (both are at 1x1x1mm)
 
 2) Is there any module in FS to detect white matter lesions?
 
 3) How can I perform myelin mapping using the ratio method (T1w/T2w)?
Or do
 I have to switch to Caret?
 
 Many thanks in advance for your help and advice!
 
 Best wishes,
 
 Luke
 
 
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Re: [Freesurfer] Very different results between 5.1.0 and 5.2.0

[Matt Glasser]

Do the surfaces look correct in these regions?  You might post some
screenshots of subjects who have a big difference between 5.1 and 5.2 with
the 5.1 and 5.2 white and pial surfaces on volume slices that highlight
the difference.  Without this kind of info, its hard to know which was
more correct, 5.1 or 5.2.

Peace,

Matt.

On 3/18/13 5:13 PM, Ritobrato Datta rida...@mail.med.upenn.edu wrote:

I concur. I have seen similar results in primary visual cortex from ~40
subjects. While fs 5.1 estimated mean thickness in the range of 1.5 to
1.9 in V1, fs 5.2 is giving me V1 thickness in the range of 2 to 2.3.

Ritobrato Datta, Ph.D.
Post Doctoral Researcher
Department of Neurology
University of Pennsylvania School of Medicine
3rd Floor, Room 312
3710 Hamilton Walk (Goddard Laboratories)
Philadelphia, PA 19104-6241
email - rida...@mail.med.upenn.edu
 

- Original Message -
From: Daniel Yang yung-jui.y...@yale.edu
To: freesurfer@nmr.mgh.harvard.edu
Sent: Mon, 18 Mar 2013 17:44:44 -0400 (EDT)
Subject: [Freesurfer] Very different results between 5.1.0 and 5.2.0

Dear FreeSurfer Experts,

I ran FreeSurfer 5.1.0 and FreeSurfer 5.2.0 on identical set of 161
subjects, and I'm interested in rh_superior_temporal_sulcus_thickness in
particular.

Previously, the mean thickness is 2.24 mm in 5.1.0; now it is 3.28 mm in
5.2.0. They are significantly different, t(160) = 56.71.

The correlation between the two versions is r = .33

Is this something possible?? I can't see what went wrong in my procedures.

Thanks!
Daniel

--
Yung-Jui Daniel Yang, PhD
Postdoctoral Researcher
Yale Child Study Center
New Haven, CT
(203) 737-5454

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Re: [Freesurfer] Caret to Freesurfer

[Matt Glasser]

She wants to go from Caret to FreeSurfer, rather than from FreeSurfer to
Caret, which is what I do.

Kara, I believe we are meeting tomorrow to discuss the options for this?

I don't know anything about the FreeSurfer longitudinal pipeline, but it
would take going through the pipeline and finding all of the inputs needed
and converting them or generating them.  I think the main goal here is to
use the longitudinal surface registration.

Matt.

On 3/14/13 8:04 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote:

Hi Kara

I think the answer is yes as there are people at Wash U that do this
routinely. Maybe Matt Glasser or someone else can chime in?

cheers
Bruce


On Thu, 14 Mar 2013, Ellspermann, Kara wrote:

 I am new to Freesurfer, and I am trying to input/process preterm infant
 brain data (ultimately attempting longitudinal registration). I already
have
 surfaces generated from Caret, as well as the original T1/T2 images.  My
 question is: Does anything exist to take processed data from Caret into
 Freesurfer?  If not, is there a good way to process the T1/T2 images in
 Freesurfer despite the differences in contrast and intensity (and
anatomy)? 
 
 Thank you in advance for your advice,
 Kara
 
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Re: [Freesurfer] Advice on integrating FSL's BET with recon-all

[Matt Glasser]

I would check the mri_em_register registrations of the step that
immediately precedes mri_watershed (and produces
talairach_with_skull.lta).  We found that most of the variability and
failures occurred in this step, and mri_watershed itself is a very robust
brain extraction algorithm when it is given an accurate registration (my
experience with BET is that it is probably not the best tool for getting
very accurate brainmasks and sometimes takes away too much). I would
recommend using the BET extracted image instead of the image with skull
for the initial registration step, and then you can use mri_watershed on
the original image and get good results every time.  This is the type of
strategy we use in the HCP Pipelines (except we use something more robust
than BET for the initial mask).

Note that the talairach registration (done by the -talairach step with
the talairach_avi tool) has nothing to do with the registration that
precedes brain extraction.  Perhaps it should is more robust and should be
used, but the affine would have to be converted to the correct format.

Peace,

Matt.

On 3/6/13 3:53 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote:

you can use

mri_convert -rl ...

to reslice the output of bet so that it has the same geometry as the rest
of our stream

cheers
Bruce

On Wed, 6 Mar 2013, Winter, Warren wrote:

 Hi again,
 We have had some suboptimal results from FreeSurfer's skullstripping
algorithm, even after iteratively trying different
 watershed thresholds and after checking the quality of Talairach
registration.  The results are pretty good, but often leave
 some dura matter and bits of neck behind whose higher intensity values,
I believe, may end up skewing recon-all's later
 estimation of the range of intensity values within grey matter, and
consequently compromising the accuracy of pial surface
 estimation.
 
 FSL's BET, however, seems to do a better job of extracting the brain,
at least for our dataset.  So, I was wondering if I
 might be able to skip over mri_watershed and feed autorecon2 and
autorecon3 a brainmask.mgz file created using BET.  I tried
 this procedure:
 
 
 1) mri_convert path/to/T1dcm T1.nii.gz
 2) bet T1.nii.gz BET_brainmask.nii.gz -A
 3) mri_convert BET_brainmask.nii.gz BET_brainmask.mgz
 4) recon-all -s subjid -autorecon1 -noskullstrip
 5) mv BET_brainmask.nii.gz ./subjid/mri/brainmask.mgz
 6) recon-all -s subjid -autorecon2 -autorecon3
 
 And I got this error message, right after normalization2:
 
 
 #@# Mask BFS Tue Mar  5 22:52:05 EST 2013
 
/net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/20
12_bet/mri
 
  mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz
 
 threshold mask volume at 5
 ERROR: dimension mismatch between source and mask
 Linux rc-thunderball 3.2.21-mosix #1 SMP Mon Jul 2 08:55:48 EDT 2012
x86_64 x86_64 x86_64 GNU/Linux
 
 recon-all -s 2012_bet exited with ERRORS at Tue Mar  5 22:52:06 EST 2013
 
 
 I'm guessing that the dimensions of norm.mgz and aseg.mgz didn't match
those of brainmask.mgz, resulting during normalization2
 in a mismatch between brain.mgz and brainmask.mgz.  Does that seem
right, and is there a possible workaround?
 
 Thank you!
 
 Warren
 
 --
 Warren Winter
 Research Coordinator
 Boston Children's Hospital
 Sheridan Laboratory of Cognitive Neuroscience
 Division of Developmental Medicine
 1 Autumn Street, AU 650
 Boston, MA 02215
 857-218-5224
 
 
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Re: [Freesurfer] High resolution fMRI and resolution of anatomical scans

[Matt Glasser]

I'd collect highres T1w as well and then refine the 1mm surfaces using that.

Peace,

Matt.

From:  SHAHIN NASR sha...@nmr.mgh.harvard.edu
Date:  Monday, February 25, 2013 1:39 PM
To:  Freesurfer freesurfer@nmr.mgh.harvard.edu, Bruce Fischl
fis...@nmr.mgh.harvard.edu, Doug Greve gr...@nmr.mgh.harvard.edu
Subject:  [Freesurfer] High resolution fMRI and resolution of anatomical
scans

Hi,
We are planning to collect high resolution functional MRI for a group of
subjects with voxel size smaller than 1 mm. For these subjects, we already
have reconstructed anatomical scans with 1 mm voxel size. The question is,
do we need to re-collect anatomical scans for these subjects with smaller
voxel size (e.g. 0.5 x 0.5 x 0.5) or we can still use the old anatomical
data for co-registration with freesurfer.

P.S.: We usually analyze our subjects in native space but technically we can
do this in fsaverage space.  So, we only need this co-registration for
pre-processing and mapping fMRI data to fsaverage space.

Regards


-- 
Shahin Nasr

PhD in Cognitive Neuroscience
Martinos Imaging Center, MGH
Harvard Medical School
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Re: [Freesurfer] unusually long running time in autorecon2

[Matt Glasser]

I've noticed this at well when something goes wrong before mri_cc.  It gets
stuck in some kind of infinite loop.  You might check that the linear and
nonlinear registration worked correctly.

Peace,

Matt.

From:  Dawei Liu ldw70...@gmail.com
Date:  Wednesday, February 20, 2013 10:49 AM
To:  freesurfer@nmr.mgh.harvard.edu
Subject:  [Freesurfer] unusually long running time in autorecon2


Dear Freesurfer experts,
 
I am running autorecon2 using Freesurfer verion 5.1.0 on Linux. For some
subjects, it looks that the pipeline stucked in the middle of  mri_cc and
keeps running for days (without any error message). Last time when it
occurred I thought it may be caused by some hardware-related problem, so I
killed these jobs and re-launched recon-all -autorecon2 on a different
machine. Now these jobs have been running for over 40 hours and they are
still running. Do you know why they take so long? For your reference,  I
copied the most recent processing information below:
 
mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta
/Experiments/20120801.SubjectOrganized_Results/20121213_RAW_T1_ONLY/0057_344
79/mri/transforms/cc_up.lta 0057_34479
 
will read input aseg from aseg.auto_noCCseg.mgz
writing aseg with cc labels to aseg.auto.mgz
will write lta as 
/Experiments/20120801.SubjectOrganized_Results/20121213_RAW_T1_ONLY/0057_344
79/mri/transforms/cc_up.lta
reading aseg from 
/Experiments/20120801.SubjectOrganized_Results/20121213_RAW_T1_ONLY/0057_344
79/mri/aseg.auto_noCCseg.mgz
reading norm from 
/Experiments/20120801.SubjectOrganized_Results/20121213_RAW_T1_ONLY/0057_344
79/mri/norm.mgz
24076 voxels in left wm, 23641 in right wm, xrange [73, 130]
searching rotation angles z=[65 79], y=[-54 -40]
searching scale 1 Z rot 75.6  global minimum found at slice 103.0, rotations
(-50.09, 68.60)
final transformation (x=103.0, yr=-50.093, zr=68.597):
0.234  -0.931  -0.280   230.831;
0.597   0.365  -0.714   75.219;
0.767  -0.000   0.642   3.440;
0.000   0.000   0.000   1.000;
 
Thanks in advance for your help!
 
Dawei
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Re: [Freesurfer] How can I get 300 dpi resolution or about when saving tiff files in tksurfer?

[Matt Glasser]

Perhaps you can maximize the tksurfer window on a large monitor, take a
whole screen screenshot, and then in a photo editing program: decrease the
physical size of the image (in mm or inches) while not decreasing the
matrix size.  You can do this in photoshop in Image  Image Size  And
then change the document size until the resolution is 300.  This will
increase the DPI to make nice figures.  What Bruce suggests will just
upsample the image (without adding detail), which is not what journals
have in mind when they ask for 300dpi figures.  Keep in mind that the
document size is the printable size, so your image will get smaller on the
printed page when you do this.  Often, figures have multiple panels and if
you take each panel as a full screen image on a large monitor and then
reduce the size you will have more than 300dpi to spare in the end result.
 

Peace,

Matt.

On 12/6/12 3:22 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote:

Hi Knut
the tiffs written by tksurfer are 600x600 regardless of what DPI you set.
You can change the dpi with convert (or photoshop), but it won't change
the 
# of pixels.

cheers
Bruce


On Thu, 6 Dec 2012, Knut J Bjuland wrote:


   How can I get 300 dpi resolution or about when saving tiff files in
 tksurfer?
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Re: [Freesurfer] Tool for incorporating T2-SPACE data in pial surface recons?

[Matt Glasser]

If you get an MPRAGE and T2-SPACE you can make myelin maps too.
FreeSurfer's final surface placement benefits a lot from high resolution
images (less than 1mm) and you can still get good SNR with when you use
32-channel coils.  

Peace,

Matt.

On 11/20/12 4:41 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote:

Yes, definitely. The t2-space flair is a big help



On Nov 20, 2012, at 5:40 PM, Watson, Christopher
christopher.wat...@childrens.harvard.edu wrote:

 Hi Bruce,
 So would you recommend acquiring a T2 in addition to an
(ME)MPRAGE/SPGR? i.e. is it worth squeezing another acquisition into a
protocol?
 
 Chris
 
 From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl
[fis...@nmr.mgh.harvard.edu]
 Sent: Tuesday, November 20, 2012 3:01 PM
 To: Winter, Warren
 Cc: freesurfer@nmr.mgh.harvard.edu
 Subject: Re: [Freesurfer] Tool for incorporating T2-SPACE data in pial
surface recons?
 
 Hi Warren
 
 yes, it will be part of the upcoming 5.2 release, hopefully in Dec. It
 will use either a FLAIR or T2 (ideally T2-SPACE for either one)
 
 cheers
 Bruce
 On Tue, 20
 Nov 2012, Winter, Warren wrote:
 
 Hi all,
 
 Back in January and October Bruce mentioned that he had under
development some scripts designed to utilize T2-SPACE images for better
pial surface reconstruction in the presence of dura -- I was just
wondering if any of that is ready for trial?
 
 Thanks!
 
 Warren
 
 --
 Warren Winter
 Research Coordinator
 Boston Children's Hospital
 Sheridan Laboratory of Cognitive Neuroscience
 Division of Developmental Medicine
 1 Autumn Street, AU 650
 Boston, MA 02215
 857-218-5224
 
 
 ___
 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
 
 
 The information in this e-mail is intended only for the person to whom
it is
 addressed. If you believe this e-mail was sent to you in error and the
e-mail
 contains patient information, please contact the Partners Compliance
HelpLine at
 http://www.partners.org/complianceline . If the e-mail was sent to you
in error
 but does not contain patient information, please contact the sender and
properly
 dispose of the e-mail.
 
 
 

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Re: [Freesurfer] Tool for incorporating T2-SPACE data in pial surface recons?

[Matt Glasser]

If you make a T1 map you can use that to look at differences in myelin
content, but I don't know all of the ways to calculate T1 or if you could
get that from only two flip angles.  Two images with roughly the same
contrast won't work for the ratio method.  You need to have opposite
contrast.

Also I'm not sure how a FLAIR would be better than a T2-SPACE.

Peace,

Matt.

From:  Satrajit Ghosh sa...@mit.edu
Date:  Tuesday, November 20, 2012 5:51 PM
To:  Matt Glasser m...@ma-tea.com
Cc:  Watson, Christopher christopher.wat...@childrens.harvard.edu,
Winter, Warren warren.win...@childrens.harvard.edu,
freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu
Subject:  Re: [Freesurfer] Tool for incorporating T2-SPACE data in pial
surface recons?

hi 

matt: could you generate the myelin maps say from two flash scans at
different flip angles?

bruce: if one had a choice between an mprage + t2 flair and 2 flash scans at
5/20 flip angles, what would be your recommendation?

cheers,

satra

On Tue, Nov 20, 2012 at 6:35 PM, Matt Glasser m...@ma-tea.com wrote:
 If you get an MPRAGE and T2-SPACE you can make myelin maps too.
 FreeSurfer's final surface placement benefits a lot from high resolution
 images (less than 1mm) and you can still get good SNR with when you use
 32-channel coils.
 
 Peace,
 
 Matt.
 
 On 11/20/12 4:41 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote:
 
 Yes, definitely. The t2-space flair is a big help
 
 
 
 On Nov 20, 2012, at 5:40 PM, Watson, Christopher
 christopher.wat...@childrens.harvard.edu wrote:
 
  Hi Bruce,
  So would you recommend acquiring a T2 in addition to an
 (ME)MPRAGE/SPGR? i.e. is it worth squeezing another acquisition into a
 protocol?
 
  Chris
  
  From: freesurfer-boun...@nmr.mgh.harvard.edu
 [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl
 [fis...@nmr.mgh.harvard.edu]
  Sent: Tuesday, November 20, 2012 3:01 PM
  To: Winter, Warren
  Cc: freesurfer@nmr.mgh.harvard.edu
  Subject: Re: [Freesurfer] Tool for incorporating T2-SPACE data in pial
 surface recons?
 
  Hi Warren
 
  yes, it will be part of the upcoming 5.2 release, hopefully in Dec. It
  will use either a FLAIR or T2 (ideally T2-SPACE for either one)
 
  cheers
  Bruce
  On Tue, 20
  Nov 2012, Winter, Warren wrote:
 
  Hi all,
 
  Back in January and October Bruce mentioned that he had under
 development some scripts designed to utilize T2-SPACE images for better
 pial surface reconstruction in the presence of dura -- I was just
 wondering if any of that is ready for trial?
 
  Thanks!
 
  Warren
 
  --
  Warren Winter
  Research Coordinator
  Boston Children's Hospital
  Sheridan Laboratory of Cognitive Neuroscience
  Division of Developmental Medicine
  1 Autumn Street, AU 650
  Boston, MA 02215
  857-218-5224
 
 
  ___
  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
 
 
  The information in this e-mail is intended only for the person to whom
 it is
  addressed. If you believe this e-mail was sent to you in error and the
 e-mail
  contains patient information, please contact the Partners Compliance
 HelpLine at
  http://www.partners.org/complianceline . If the e-mail was sent to you
 in error
  but does not contain patient information, please contact the sender and
 properly
  dispose of the e-mail.
 
 
 
 
 ___
 Freesurfer mailing list
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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] Tool for incorporating T2-SPACE data in pial surface recons?

[Matt Glasser]

Hi Bruce,

Can you get good FLAIRs at 0.7mm isotropic?

The fluid thing makes sense for surface reconstruction, but I think it
would mess up myelin maps if someone also wanted to do that using the
ratio method.  If the CSF is now dark and you divide the dark CSF in the
T1w with dark CSF in the T2w, you would get unpredictable results in the
partial volume region along the edge.

Thanks,

Matt.

On 11/20/12 6:27 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote:

Hi Satra

the T1 maps accomplish much of what the ratio does - it gets rid of
receive bias effects. I'm not really sure which is better. They are about
the same amount of scan time.

The advantage of including the flair inversion pulse in the T2 space is
that it nulls fluid and lets intensities by monotonically decreasing
moving 
outwards from the gray/white boundary. This makes partial volume effects
less of a problem. Dura is also pretty much totally absent from the FLAIR
and in the prelim data that we've processed having the FLAIR images lets
the surface recover from pretty much all mistakes in which dura is
included 
in the pial surface.

cheers
Bruce



On Tue, 20 Nov 2012, Matt Glasser wrote:

 If you make a T1 map you can use that to look at differences in myelin
 content, but I don't know all of the ways to calculate T1 or if you
could
 get that from only two flip angles.  Two images with roughly the same
 contrast won't work for the ratio method.  You need to have opposite
 contrast.
 
 Also I'm not sure how a FLAIR would be better than a T2-SPACE.
 
 Peace,
 
 Matt.
 
 From: Satrajit Ghosh sa...@mit.edu
 Date: Tuesday, November 20, 2012 5:51 PM
 To: Matt Glasser m...@ma-tea.com
 Cc: Watson, Christopher christopher.wat...@childrens.harvard.edu,
 Winter, Warren warren.win...@childrens.harvard.edu,
 freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu
 Subject: Re: [Freesurfer] Tool for incorporating T2-SPACE data in pial
 surface recons?
 
 hi 
 matt: could you generate the myelin maps say from two flash scans at
 different flip angles?
 bruce: if one had a choice between an mprage + t2 flair and 2 flash
scans at
 5/20 flip angles, what would be your recommendation?
 
 cheers,
 
 satra
 
 On Tue, Nov 20, 2012 at 6:35 PM, Matt Glasser m...@ma-tea.com wrote:
   If you get an MPRAGE and T2-SPACE you can make myelin maps too.
   FreeSurfer's final surface placement benefits a lot from high
   resolution
   images (less than 1mm) and you can still get good SNR with when
   you use
   32-channel coils.

   Peace,

   Matt.

   On 11/20/12 4:41 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu
   wrote:

   Yes, definitely. The t2-space flair is a big help
   
   
   
   On Nov 20, 2012, at 5:40 PM, Watson, Christopher
   christopher.wat...@childrens.harvard.edu wrote:
   
Hi Bruce,
So would you recommend acquiring a T2 in addition to an
   (ME)MPRAGE/SPGR? i.e. is it worth squeezing another
   acquisition into a
   protocol?
   
Chris

From: freesurfer-boun...@nmr.mgh.harvard.edu
   [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce
   Fischl
   [fis...@nmr.mgh.harvard.edu]
Sent: Tuesday, November 20, 2012 3:01 PM
To: Winter, Warren
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Tool for incorporating T2-SPACE
   data in pial
   surface recons?
   
Hi Warren
   
yes, it will be part of the upcoming 5.2 release, hopefully
   in Dec. It
will use either a FLAIR or T2 (ideally T2-SPACE for either
   one)
   
cheers
Bruce
On Tue, 20
Nov 2012, Winter, Warren wrote:
   
Hi all,
   
Back in January and October Bruce mentioned that he had
   under
   development some scripts designed to utilize T2-SPACE images
   for better
   pial surface reconstruction in the presence of dura -- I was
   just
   wondering if any of that is ready for trial?
   
Thanks!
   
Warren
   
--
Warren Winter
Research Coordinator
Boston Children's Hospital
Sheridan Laboratory of Cognitive Neuroscience
Division of Developmental Medicine
1 Autumn Street, AU 650
Boston, MA 02215
857-218-5224
   
   
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
   
   
   
___
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The information in this e-mail is intended only for the
   person to whom

Re: [Freesurfer] Tool for incorporating T2-SPACE data in pial surface recons?

[Matt Glasser]

You can correct the readout distortion with a field map.  The main
residual is just signal loss in the gradient echo image.

Peace,

Matt.

On 11/20/12 7:22 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote:

sure. Note that whichever you do it's absolutely critical to bandwidth
and readout match them so there is no differential distortion between the
contrast types
Bruce
On Tue, 20 Nov 2012, Satrajit Ghosh wrote:

 thanks matt and bruce. this is very helpful.
 cheers,
 
 satra
 
 On Tue, Nov 20, 2012 at 7:53 PM, Bruce Fischl
fis...@nmr.mgh.harvard.edu
 wrote:
   yes, that's probably true. The FLAIR we use is just a T2-SPACE
   scan with an inversion pulse to put CSF at the null point, so if
   you can get T2-space at .7 you should be able to get FLAIR
   (although you do burn some SNR with the inversion)

   On Tue, 20 Nov 2012, Matt Glasser wrote:

 Hi Bruce,

 Can you get good FLAIRs at 0.7mm isotropic?

 The fluid thing makes sense for surface
 reconstruction, but I think it
 would mess up myelin maps if someone also wanted to
 do that using the
 ratio method.  If the CSF is now dark and you divide
 the dark CSF in the
 T1w with dark CSF in the T2w, you would get
 unpredictable results in the
 partial volume region along the edge.

 Thanks,

 Matt.

 On 11/20/12 6:27 PM, Bruce Fischl
 fis...@nmr.mgh.harvard.edu wrote:

   Hi Satra

   the T1 maps accomplish much of what the
   ratio does - it gets rid of
   receive bias effects. I'm not really
   sure which is better. They are about
   the same amount of scan time.

   The advantage of including the flair
   inversion pulse in the T2 space is
   that it nulls fluid and lets intensities
   by monotonically decreasing
   moving
   outwards from the gray/white boundary.
   This makes partial volume effects
   less of a problem. Dura is also pretty
   much totally absent from the FLAIR
   and in the prelim data that we've
   processed having the FLAIR images lets
   the surface recover from pretty much all
   mistakes in which dura is
   included
   in the pial surface.

   cheers
   Bruce
 
 

   On Tue, 20 Nov 2012, Matt Glasser wrote:

 If you make a T1 map you can
 use that to look at
 differences in myelin
 content, but I don't know
 all of the ways to calculate
 T1 or if you
 could
 get that from only two flip
 angles.  Two images with
 roughly the same
 contrast won't work for the
 ratio method.  You need to
 have opposite
 contrast.

 Also I'm not sure how a
 FLAIR would be better than a
 T2-SPACE.

 Peace,

 Matt.

 From: Satrajit Ghosh
 sa...@mit.edu
 Date: Tuesday, November 20,
 2012 5:51 PM
 To: Matt Glasser
 m...@ma-tea.com
 Cc: Watson, Christopher
 christopher.wat...@childrens.harvard.edu,
 Winter, Warren
 warren.win...@childrens.harvard.edu,
 freesurfer@nmr.mgh.harvard.edu
 freesurfer@nmr.mgh.harvard.edu
 Subject: Re: [Freesurfer]
 Tool for incorporating
 T2-SPACE data in pial
 surface recons?

 hi
 matt: could you generate the
 myelin maps say from two
 flash scans at
 different flip angles?
 bruce: if one had a choice
 between an mprage + t2 flair
 and 2 flash
 scans at
 5/20 flip angles, what would
 be your recommendation?

 cheers,

 satra

 On Tue, Nov 20, 2012 at 6:35
 PM, Matt Glasser

Re: [Freesurfer] bad acquisition and noise problem.

[Matt Glasser]

Are you using a 32-channel coil?  It looks like B1- receive field
inhomogeneity to me.

Peace,

Matt.

From:  youngmin huh ymin1...@gmail.com
Date:  Monday, November 12, 2012 10:22 PM
To:  Bruce Fischl fis...@nmr.mgh.harvard.edu,
freesurfer@nmr.mgh.harvard.edu
Subject:  Re: [Freesurfer] bad acquisition and noise problem.

Hi,
3D SPGR sequences were used. (TR=22, TE=4, thickness=1.4, FOV=240*240,
FA=40)
If the artifacts are due to B0 distortion, I wonder how I can fix it.

Thanks,
Youngmin Huh



2012/11/12 Bruce Fischl fis...@nmr.mgh.harvard.edu
 Can you give us the acquisition details? I suspect this is not noise, but
 rather B0 distortion.
 what is the acquisition? And what bandwidth?
 
 
 On Nov 8, 2012, at 2:53 AM, youngmin huh ymin1...@gmail.com wrote:
 
  Dear all,
 
  I'm working with some images, and they have so much noises on temporal
 areas.
  I just ran recon2, but not sure if they'll be segmented properly.
  Does anyone have a recommendation for dealing with it?
  I wonder if there is any flag or option for this occasion.
  I would appreciate any comments or help.
  I attached an example.
 
  Thanks,
 
  Youngmin Huh
  temporal_001.jpg
 
 
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Re: [Freesurfer] (no subject)

[Matt Glasser]

What are the units of that measure?

 

Thanks,


Matt.

 

  _  

From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas Greve
Sent: Sunday, August 12, 2012 9:25 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] (no subject)

 

The values are in the ?h.sulc file
doug

On 8/12/12 10:12 PM, Hugh Pemberton wrote: 

Hi, 

 

How can I get sulcal depth measurements from Freesurfer? 

 

Cheers,

Hugh






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Re: [Freesurfer] Ribbon

[Matt Glasser]

Hi Bruce,

He just needs the grey matter part of a typical ribbon.mgz volume.  He lost
some of his recon-all folder.  

Peace,

Matt.

-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl
Sent: Sunday, July 08, 2012 12:17 PM
To: Colin Reveley
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Ribbon

Hi Colin

what is the representation you want in the end? You can also fill the 
interior of the surfaces using mris_fill then do some boolean algebra on 
the results of e.g. the white and pial interiors.

cheers
Bruce


On Sun, 8 Jul 2012, Colin Reveley wrote:

 Hi - I need to make a ribbon volume. I have all the necessary surfaces,
but
 I'm lacking an aseg.mgz because the data is monkey. I saw one guy on the
 list had success by just calling his orig.mgz aseg.mgz. I tried that, and
it
 calculated the left right pial and white distances. Men sadly it
segfaulted.
 The program mri_ribbon will give me separate left and white gm ribbons. I
 combined those, coloured them 3 and 42 and did my level best to fill the
wm
 with the right values, but some bits are wrong.
 
 What I'm actually trying to do is use matt glassers myelin mapping in
caret.
 other things could be wrong than my ribbon estimate.
 
 If anyone has an idea how to make a good ribbon  without aseg I'd
appreciate
 it. Please bear in mind I may be missing much of what one gets when one
runs
 recon-all. I have thickness, curv, surfaces, filled.mgz, pretesselstion
 wm.mgz not so much else. The filled.mgz doesn't fill all non cortex the
way
 the bert ribbon does, so it's not that useful.
 
 Thanks,
 
 Colin
 



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Re: [Freesurfer] ERROR: comparison in expression (FS with SGE)

[Matt Glasser]

Rather one unsets it like this:

unset POSIXLY_CORRECT

Peace,

Matt.

-Original Message-
From: Matt Glasser [mailto:m...@ma-tea.com] 
Sent: Friday, May 18, 2012 12:47 PM
To: 'freesurfer@nmr.mgh.harvard.edu'
Subject: RE: [Freesurfer] ERROR: comparison in expression (FS with SGE)

Another note on this:

Apparently, getopt (used in fsl_sub) doesn't work correctly when this flag
is not set to 1 (it picks op a lot of options it shouldn't).  Thus, instead
of commenting out the flag, it is better to set it to zero after the 

set -- `getopt T:q:a:p:M:j:t:N:n:Fvm:l: $*`

Line.  Then one gets the best of both worlds.  

Peace,

Matt.

-Original Message-
From: Matt Glasser [mailto:m...@ma-tea.com] 
Sent: Thursday, March 22, 2012 5:36 PM
To: 'freesurfer@nmr.mgh.harvard.edu'
Subject: RE: [Freesurfer] ERROR: comparison in expression (FS with SGE)

I'm dredging this 2 year old post up for the benefit of Google and anyone
else who wonders about the cause of this.  It is a non-fatal error (for
FreeSurfer, but perhaps not other things) that is caused by having set the
variable:

POSIXLY_CORRECT=1

It causes bc (on Debian/Ubuntu) systems to fail when making comparisons
like:

echo '3.5  2.5' | bc -l

I am guessing (because this is what I was doing) that the poster was using
fsl_sub to launch FreeSurfer jobs in SGE.  fsl_sub sets this flag for some
reason, but commenting it out seems not to cause any problems.

Peace,

Matt.

-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Xue, Feng
Sent: Sunday, March 14, 2010 1:37 PM
To: Bruce Fischl
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] ERROR: comparison in expression (FS with SGE)

Thanks! I would check them later.

On Mon, Mar 15, 2010 at 1:24 AM, Bruce Fischl
fis...@nmr.mgh.harvard.edu wrote:
 if it was a syntax error then recon-all wouldn't have finished, so I'm not
 sure what's going on. You should visually inspect the surfaces and
 segmentations to make sure they are all ok.

 cheers,
 Bruce

 On Mon, 15 Mar 2010, Xue, Feng wrote:

 Sorry, I didn't notice that the reply address was not the list, I've
 done re-post it.

 Is there any method to check whether it is ok? For SGE, it might only
 write errors to dot e files instead of warnings.

 It seemed like a shell syntax error, however, I don't have that
 experience to check the recon-all script.

 On Sun, Mar 14, 2010 at 11:24 PM, Bruce Fischl
 fis...@nmr.mgh.harvard.edu wrote:

 can you post this to the list? There are others better qualified to say
 what's going on. But if everything finished ok is there really a
problem?
 Maybe this is just a warning?
 On Sun, 14 Mar 2010, Xue, Feng wrote:

 Hi Bruce,

 Thanks for your reply. The recon-all.log said it finished without
 error. please find the whole scripts root in the attachment.
 I'm also running a raw testing with one subject and without
SGEMaybe
 I can report the result the day after tomorrow.

 BTW, I found in my 64bit Debian nodes, I repeated got the error as
below
 (standard_in) 2: Error: comparison in expression
 but in 32bit, I met both.

 for the GMail security restriction, I changed recon-all.cmd in the
 attachment to recon-all.cmds.

 On Sat, Mar 13, 2010 at 11:58 PM, Bruce Fischl
 fis...@nmr.mgh.harvard.edu wrote:

 what does the recon-all.log say? Did the recon finish correctly? Does
 this
 happen if you just run it on the command line?
 Bruce

 On Sat, 13 Mar 2010, Xue, Feng wrote:

 Dear Bruce  FS experts,

 Please forgive my re-post, for I havn't got any response from last
 post.
 I do appreciate if anyone could give me a hint or suggestion.

 ++

 We are running freesurfer with Sun GridEngine. Currently, we
 repeatedly got this error in SGE's job error log file on some data
 when doing recon_all:

 $ cat recon_xf.e437
 (standard_in) 2: Error: comparison in expression
 $ cat recon_xf.e431
 (standard_in) 2: comparison in expression

 I also checked the recon-all-status.log file, but not error was
found.

 Has anyone met this problem? Is it critical?
 Thanks in advance.

 --
 Best Regards

 Xue, Feng Phd. candidate
 Major in Developmental Cognitive Neuroscience

 National Key Laboratory of Cognitive Neuroscience and Learning
 Beijing Normal University
 Beijing, China. 100875
 Tel: +86-13810154455
 web: http://psychbrain.bnu.edu.cn
 ==
 Welcome to MuDuo JinSheng BBS @ Beijing Normal University
 telnet://bbs.mdjs.org
 http://bbs.mdjs.org
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 is
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 e-mail
 contains patient information, please contact the Partners Compliance

Re: [Freesurfer] ERROR: comparison in expression (FS with SGE)

[Matt Glasser]

Another note on this:

Apparently, getopt (used in fsl_sub) doesn't work correctly when this flag
is not set to 1 (it picks op a lot of options it shouldn't).  Thus, instead
of commenting out the flag, it is better to set it to zero after the 

set -- `getopt T:q:a:p:M:j:t:N:n:Fvm:l: $*`

Line.  Then one gets the best of both worlds.  

Peace,

Matt.

-Original Message-
From: Matt Glasser [mailto:m...@ma-tea.com] 
Sent: Thursday, March 22, 2012 5:36 PM
To: 'freesurfer@nmr.mgh.harvard.edu'
Subject: RE: [Freesurfer] ERROR: comparison in expression (FS with SGE)

I'm dredging this 2 year old post up for the benefit of Google and anyone
else who wonders about the cause of this.  It is a non-fatal error (for
FreeSurfer, but perhaps not other things) that is caused by having set the
variable:

POSIXLY_CORRECT=1

It causes bc (on Debian/Ubuntu) systems to fail when making comparisons
like:

echo '3.5  2.5' | bc -l

I am guessing (because this is what I was doing) that the poster was using
fsl_sub to launch FreeSurfer jobs in SGE.  fsl_sub sets this flag for some
reason, but commenting it out seems not to cause any problems.

Peace,

Matt.

-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Xue, Feng
Sent: Sunday, March 14, 2010 1:37 PM
To: Bruce Fischl
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] ERROR: comparison in expression (FS with SGE)

Thanks! I would check them later.

On Mon, Mar 15, 2010 at 1:24 AM, Bruce Fischl
fis...@nmr.mgh.harvard.edu wrote:
 if it was a syntax error then recon-all wouldn't have finished, so I'm not
 sure what's going on. You should visually inspect the surfaces and
 segmentations to make sure they are all ok.

 cheers,
 Bruce

 On Mon, 15 Mar 2010, Xue, Feng wrote:

 Sorry, I didn't notice that the reply address was not the list, I've
 done re-post it.

 Is there any method to check whether it is ok? For SGE, it might only
 write errors to dot e files instead of warnings.

 It seemed like a shell syntax error, however, I don't have that
 experience to check the recon-all script.

 On Sun, Mar 14, 2010 at 11:24 PM, Bruce Fischl
 fis...@nmr.mgh.harvard.edu wrote:

 can you post this to the list? There are others better qualified to say
 what's going on. But if everything finished ok is there really a
problem?
 Maybe this is just a warning?
 On Sun, 14 Mar 2010, Xue, Feng wrote:

 Hi Bruce,

 Thanks for your reply. The recon-all.log said it finished without
 error. please find the whole scripts root in the attachment.
 I'm also running a raw testing with one subject and without
SGEMaybe
 I can report the result the day after tomorrow.

 BTW, I found in my 64bit Debian nodes, I repeated got the error as
below
 (standard_in) 2: Error: comparison in expression
 but in 32bit, I met both.

 for the GMail security restriction, I changed recon-all.cmd in the
 attachment to recon-all.cmds.

 On Sat, Mar 13, 2010 at 11:58 PM, Bruce Fischl
 fis...@nmr.mgh.harvard.edu wrote:

 what does the recon-all.log say? Did the recon finish correctly? Does
 this
 happen if you just run it on the command line?
 Bruce

 On Sat, 13 Mar 2010, Xue, Feng wrote:

 Dear Bruce  FS experts,

 Please forgive my re-post, for I havn't got any response from last
 post.
 I do appreciate if anyone could give me a hint or suggestion.

 ++

 We are running freesurfer with Sun GridEngine. Currently, we
 repeatedly got this error in SGE's job error log file on some data
 when doing recon_all:

 $ cat recon_xf.e437
 (standard_in) 2: Error: comparison in expression
 $ cat recon_xf.e431
 (standard_in) 2: comparison in expression

 I also checked the recon-all-status.log file, but not error was
found.

 Has anyone met this problem? Is it critical?
 Thanks in advance.

 --
 Best Regards

 Xue, Feng Phd. candidate
 Major in Developmental Cognitive Neuroscience

 National Key Laboratory of Cognitive Neuroscience and Learning
 Beijing Normal University
 Beijing, China. 100875
 Tel: +86-13810154455
 web: http://psychbrain.bnu.edu.cn
 ==
 Welcome to MuDuo JinSheng BBS @ Beijing Normal University
 telnet://bbs.mdjs.org
 http://bbs.mdjs.org
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 The information in this e-mail is intended only for the person to whom
 it
 is
 addressed. If you believe this e-mail was sent to you in error and the
 e-mail
 contains patient information, please contact the Partners Compliance
 HelpLine at
 http://www.partners.org/complianceline . If the e-mail was sent to you
 in
 error
 but does not contain patient information, please contact the sender
and
 properly
 dispose of the e-mail.













-- 
Best Regards

Xue, Feng Phd. candidate
Major in Developmental Cognitive

Re: [Freesurfer] Freesurfer 1mm Isotropic standard and the Future

[Matt Glasser]

Yes, I have a modified script working.  For the white surface, the
essentials are the same as Bruce's script but it has some additional stuff
(e.g register T2w to T1w), and I call it in the middle of the recon-all
rather than at the end.  For the pial surface, I have done some more
complicated stuff, which I'd love to talk to Bruce about some more some
time. :)

Peace,

Matt.

-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl
Sent: Tuesday, May 15, 2012 7:29 AM
To: Michael Waskom
Cc: FreeSurfer
Subject: Re: [Freesurfer] Freesurfer 1mm Isotropic standard and the Future

you need to call mris_make_surfaces directly. It's a bit complicated as you 
need to intensity normalize and register the hires volume to the surfaces 
first. I have an example script if anyone is interested, but no one has 
used it yet but me I don't think (unless Matt Glasser has gotten his 
version working, which on second thought he probably has)

On Mon, 14 
May 2012, Michael Waskom wrote:

 Hi Bruce,
 Is there a flag for this on recon-all?  Or do you need to use
 mri_make_surfaces directly?
 
 Best,
 Michael
 
 On Mon, May 14, 2012 at 2:09 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu
 wrote:
   Hi Joshua

   yes, we already have upgraded mris_make_surfaces to take higher
   res data
   and refine the surfaces with it. Haven't tried it on the aseg
   yet, but if
   you upload a sample dataset I could see how hard it is.

   cheers
   Bruce
   On Mon, 14 May 2012,
   Joshua Lee wrote:

Dear Freesurfers,
   
Over the last years, MR imaging technology hasimproved such
   that sub 1-mm
isotropic scans can be obtained with good signal to noise
   characteristics.
For example, our lab uses 0.7mm isotropic structural MR
   images. I understand
that the Freesurfer pipeline will up-sample these to 1mm
   isotropic, but it
seems a shame that so much information is left unused which
   could be used to
improve the accuracy of sub-cortical and cortical
   segmentation. My question
is whether there are any plans at Freesurfer to change the
   reference
standard resolution from 1mm isotropic, or provide another
   solution that can
help researchers make the most of your technology.
   
Sincerely,
   
   
Joshua
-
Joshua
   
   
   
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 The information in this e-mail is intended only for the person to whom
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 e-mail
 contains patient information, please contact the Partners Compliance
 HelpLine at
 http://www.partners.org/complianceline . If the e-mail was sent to you
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[Freesurfer] Edit Aseg with Surfaces

[Matt Glasser]

Is there a way to adjust the grey and white matter of the aseg automatically
based on the surfaces?  

 

Thanks,


Matt.

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Re: [Freesurfer] Freesurfer 1mm Isotropic standard and the Future

[Matt Glasser]

I'd be interested to hear how this goes too.

Thanks,

Matt.

-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl
Sent: Monday, May 14, 2012 4:09 PM
To: Joshua Lee
Cc: FreeSurfer
Subject: Re: [Freesurfer] Freesurfer 1mm Isotropic standard and the Future

Hi Joshua

yes, we already have upgraded mris_make_surfaces to take higher res data 
and refine the surfaces with it. Haven't tried it on the aseg yet, but if 
you upload a sample dataset I could see how hard it is.

cheers
Bruce
On Mon, 14 May 2012, 
Joshua Lee wrote:

 Dear Freesurfers,
 
 Over the last years, MR imaging technology hasimproved such that sub 1-mm
 isotropic scans can be obtained with good signal to noise characteristics.
 For example, our lab uses 0.7mm isotropic structural MR images. I
understand
 that the Freesurfer pipeline will up-sample these to 1mm isotropic, but it
 seems a shame that so much information is left unused which could be used
to
 improve the accuracy of sub-cortical and cortical segmentation. My
question
 is whether there are any plans at Freesurfer to change the reference
 standard resolution from 1mm isotropic, or provide another solution that
can
 help researchers make the most of your technology.
 
 Sincerely,
 
 
 Joshua
 -
 Joshua
 
 

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contains patient information, please contact the Partners Compliance
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Re: [Freesurfer] white matter hyper intensities

[Matt Glasser]

Hi Greg,

I would say there are a variety of possible confounds for cortical thickness
(e.g. changes in cortical myelin content, changes in the closeness of
opposition between grey matter and the dura from brain atrophy), but that
wouldn't be one of the ones I would think of.  White matter hyperintensities
tend to be most visible in T2w images (especially FLAIR), and not so much in
T1w images (in fact, they might actually make T1w images darker).  They also
tend to be in deep white matter away from the cortex.  

The insula tends to be a hard place to reconstruct surfaces because the
white matter is thin and not very bright (and has the grey matter claustrum
interposed between the external and extreme capsules).  A difference in the
white matter or claustrum could well create a problem reconstructing the
surface there, but I wouldn't expect a white matter hyperintensity there.  

Peace,

Matt.

-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Gregory Kirk
Sent: Wednesday, April 04, 2012 11:47 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] white matter hyper intensities

a collaborator just got a grant review that claimed 
















There's a possibility that changes in cortical thickness in
the insula might be a consequence of lesions (MR-hyperintensities) in the
white
matter.


i would think that white matter hyper intensities would tend to enhance
freesurfers ability
to detect the white matter/grey matter boundary rather than cause an error.


any comments as to the correctness of my thinking would be appreciated.


thank you


greg

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