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Today's Topics:
1. Re: Setting up Freeview on Ubuntu Linux 18.04: freeview can't
find libpng12 (Tim Sch?fer)
2. field inhomogeneities and eddy current correction evaluation
(Adam Rytina)
3. Re: Setting up Freeview on Ubuntu Linux 18.04: freeview can't
find libpng12 (fsbuild)
4. Issue with BBR and Applying CVS Warps to Diffusion Data
(Austin Patrick)
5. mri_vol2surf produces invalid surface (Shuntaro Aoki)
6. Segmentation problem (Marina Fern?ndez)
7. Full analysis chain without Topology fix, Talairach check?
(HsuD3@mskcc.org)
8. Re: Full analysis chain without Topology fix, Talairach
check? (Bruce Fischl)
9. Job post: full-time research assistant in the lab of Dr.
Emily Finn, Dartmouth College (Emily S. Finn)
----------------------------------------------------------------------
Message: 1
Date: Wed, 26 Feb 2020 18:03:18 +0100 (CET)
From: Tim Sch?fer <ts+ml@rcmd.org>
Subject: Re: [Freesurfer] Setting up Freeview on Ubuntu Linux 18.04:
freeview can't find libpng12
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <1495674409.723727.1582736598420@ox.hosteurope.de>
Content-Type: text/plain; charset="utf-8"
External Email - Use Caution
Hi Tim,
try:
wget http://mirrors.kernel.org/ubuntu/pool/main/libp/libpng/libpng12-0_1.2.54-1ubuntu1_amd64.deb
sudo dpkg -i libpng12-0_1.2.54-1ubuntu1_amd64.deb
More details at https://www.xsmd.org/brain/2019/06/19/freeview-libpng12-so-0-missing-under-lubuntu/
Best,
Tim
--
Dr. Tim Sch?fer
Postdoc Computational Neuroimaging
Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy
University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany
> On February 26, 2020 at 5:36 PM "Harrigan, Timothy P." <Timothy.Harrigan@jhuapl.edu> wrote:
>
>
> External Email - Use Caution
>
> HI,
> I'm setting up freeview on a Linux 18.04 system and running through the instructions in
> https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall
>
> I got through to Example 4: "View the output volumes..." and got the error below.
>
> harritp1@TPHTVB:~/FSSubjects$ freeview
> freeview.bin: error while loading shared libraries: libpng12.so.0: cannot open shared object file: No such file or directory
>
> It looks like I need to either set up an environment variable, or install that specific graphics library. I did an install of the latest version of libpng: i. e. sudo apt-get install -y libpng-dev but that didn't fix the problem.
>
> Have you dealt with this?
>
> Thanks
> Tim
>
>
> Timothy P. Harrigan ScD
> Research and Exploratory Development Division
> Johns Hopkins University Applied Physics Laboratory
> Phone: 240-228-5943
> Cell/Text: 240-280-9444
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
------------------------------
Message: 2
Date: Wed, 26 Feb 2020 18:56:41 +0000
From: Adam Rytina <adam.rytina@outlook.cz>
Subject: [Freesurfer] field inhomogeneities and eddy current
correction evaluation
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<AM0PR0602MB3377830AE274DC1CCD6A42B09AEA0@AM0PR0602MB3377.eurprd06.prod.outlook.com>
Content-Type: text/plain; charset="iso-8859-2"
External Email - Use Caution
Hello all,
how can I evaluate the field inhomogeneities and eddy current correction I performed on my DWI images? Does any metric exist to do so?
Thanks a lot in advance
Regards
Adam
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Message: 3
Date: Wed, 26 Feb 2020 20:50:23 +0100
From: fsbuild <fsbuild@contbay.com>
Subject: Re: [Freesurfer] Setting up Freeview on Ubuntu Linux 18.04:
freeview can't find libpng12
To: freesurfer@nmr.mgh.harvard.edu
Cc: timothy.harrigan@jhuapl.edu
Message-ID: <1582746623.5e56cbff69f8e@trashmail.com>
Content-Type: text/plain; charset="utf-8"
External Email - Use Caution
You also see a list of packages to install on the freesurfer wiki pages under,
https://surfer.nmr.mgh.harvard.edu/fswiki/BuildRequirements
- R.
On Feb 26, 2020, at 12:03, Tim Sch?fer <ts+ml@rcmd.org> wrote: External Email - Use Caution Hi Tim,try: wget http://mirrors.kernel.org/ubuntu/pool/main/libp/libpng/libpng12-0_1.2.54-1ubuntu1_amd64.debsudo dpkg -i libpng12-0_1.2.54-1ubuntu1_amd64.debMore details at https://www.xsmd.org/brain/2019/06/19/freeview-libpng12-so-0-missing-under-lubuntu/Best,Tim--Dr. Tim Sch?ferPostdoc Computational NeuroimagingDepartment of Child and Adolescent Psychiatry, Psychosomatics and PsychotherapyUniversity Hospital Frankfurt, Goethe University Frankfurt am Main, GermanyOn February 26, 2020 at 5:36 PM "Harrigan, Timothy P." <Timothy.Harrigan@jhuapl.edu> wrote: External Email - Use Caution HI,I'm setting up freeview on a Linux 18..04 system and running through the instructions inhttps://surfer.nmr.mgh..harvard.edu/fswiki/DownloadAndInstallI got through to Example 4: "View the output volumes..." and got the error below.harritp1@TPHTVB:~/FSSubjects$ freeviewfreeview.bin: error while loading shared libraries: libpng12.so.0: cannot open shared object file: No such file or directoryIt looks like I need to either set up an environment variable, or install that specific graphics library. I did an install of the latest version of libpng: i. e. sudo apt-get install -y libpng-dev but that didn't fix the problem.Have you dealt with this?ThanksTimTimothy P. Harrigan ScDResearch and Exploratory Development DivisionJohns Hopkins University Applied Physics LaboratoryPhone: 240-228-5943Cell/Text: 240-280-9444_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Message: 4
Date: Wed, 26 Feb 2020 20:50:17 +0000
From: Austin Patrick <patrick4@wisc.edu>
Subject: [Freesurfer] Issue with BBR and Applying CVS Warps to
Diffusion Data
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <35AB0017-CE6B-465D-AF07-819D222844DB@wisc.edu>
Content-Type: text/plain; charset="utf-8"
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Dear All,
I have used CVS to align around 180 scans to a single, representative subject. I have then used BBR to align the mean b0 image to register the diffusion data to the native space T1 and then apply CVS warps; however, the resulting aligned images for calculated maps from the DWIs are very poor with a great deal of heterogeneity, especially at the boundary but also within white matter. The coefficient of variation of the mean b0 BB registered to the T1 is around 30% globally (excluding the edges of the brain) and 40% or greater for FA. I have reviewed the initial rigid registration of the b0s to the T1s for gross misalignment and found that FLIRT performed pretty well and didn?t fail for any of my subjects and didn?t require manual adjustment; however, the result of after applying the CVS warps is quite poor. The data T1s are 1mm (MPnRAGE) and the b0s are at 2mm. The DWIs were corrected for eddy currents, Gibbs? ringing, rician noise, and B0 distortions and look pretty great. The DWIs are 70x180x180 at 2mm isotropic and the T1s are 256x256x256 at 1mm isotropic. Are there any suggestions for this issue? I have tried re-aligning the DTI parameter maps to the b0s before applying the CVS warps (although they should be in the same space) and I have tried using both the ?t2 and ?dti, as well as with/out the ?fsl-init flag. Is bbregister shifting the origin for the images at all? Any help would be appreciated.
Cheers,
-Austin
--
Austin M. Bazydlo, MS
PhD Candidate
Dept. of Medical Physics
University of Wisconsin-Madison
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Message: 5
Date: Thu, 27 Feb 2020 18:49:30 +0900
From: Shuntaro Aoki <aoki.shuntaro.6n@kyoto-u.ac.jp>
Subject: [Freesurfer] mri_vol2surf produces invalid surface
To: freesurfer@nmr.mgh.harvard.edu
Message-ID:
<CAA-kdDdWxd5LFf7kzrd0eU54-2C8xFeNjp9JQRoKJ8358aXwUQ@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"
External Email - Use Caution
Dear mailing list,
I was trying to convert a volume image to a freesurfer surface (as
gii) with `mri_vol2surf` for visualization, but ended up with invalid
surface data (i.e., a file not loadable by freeview).
What I did was:
---
% mri_vol2surf --version
stable5
% mri_vol2surf --src ./sample_volume.nii.gz --regheader sample-sub
--hemi lh --out ./sample_vol2surf_lh.gii
---
Here, `sample_volume.nii.gz` is a volume image (such as a statistical
map) registered to an individual reference T1w image of subject
`sample-sub`, which was the input of recon-all for the subject.
The command completed without errors:
---
srcvol = ./sample_volume.nii.gz
srcreg unspecified
srcregold = 0
srcwarp unspecified
surf = white
hemi = lh
reshape = 0
interp = nearest
float2int = round
GetProjMax = 0
INFO: float2int code = 0
Done loading volume
Computing registration from header.
Using /home/share/data/fmri/freesurfer/subjects/sample-sub/mri/orig.mgz
as target reference.
Reading surface
/home/share/data/fmri/freesurfer/subjects/sample-sub/surf/lh.white
Done reading source surface
Mapping Source Volume onto Source Subject Surface
1 0 0 0
using old
Done mapping volume to surface
Number of source voxels hit = 31055
Writing to ./sample_vol2surf_lh.gii
Dim: 155685 1 1
---
Then I tried to open the resulting surface `sample_vol2surf_lh.gii`
with freeview (ver 1.0 build 2013-05-13) but it failed, saying "Failed
to load Surface".
I also got the following shell output:
---
mriseadGIFTIfile: mris is NULL! found when parsing file
/home/mu/aoki/work/surf_sphere/sample_vol2surf_lh.gii
MRISread failed
mriseadGIFTIfile: mris is NULL! found when parsing file
/home/mu/aoki/work/surf_sphere/sample_vol2surf_lh.gii
---
The output of `mris_info` is:
---
% mris_info sample_vol2surf_lh.gii
==================================================
gifti_image struct
version = 1.0
numDA = 1
gim->meta nvpairs struct, len = 3 :
nvpair: 'UserName' = 'aoki'
nvpair: 'Date' = 'Thu Feb 27 17:32:40 2020'
nvpair: 'gifticlib-version' = 'gifti library version 1.09, 28 June, 2010'
gim->labeltable giiLabelTable struct, len = 0 :
--------------------------------------------------
gim->darray[0] giiDataArray struct
intent 0 = NIFTI_INTENT_NONE
datatype 16 = NIFTI_TYPE_FLOAT32
ind_ord 1 = RowMajorOrder
num_dim = 1
dims = 155685, 0, 0, 0, 0, 0
encoding 3 = GZipBase64Binary
endian 2 = LittleEndian
ext_fname =
ext_offset = 0
darray->meta nvpairs struct, len = 0 :
data = <set>
nvals = 155685
nbyper = 4
numCS = 0
darray->ex_atrs nvpairs struct, len = 0 :
--------------------------------------------------
gifti_image struct
swapped = 0
compressed = 1
-- darray totals: 1 MB
gim->ex_atrs nvpairs struct, len = 0 :
==================================================
---
I checked matching between voxels in the input volume and the surface
with the output of --srchit option and found the registration was
fine.
I also tried mgh output but got another invalid file.
---
% mris_info sample_vol2surf_lh.mgh
ERROR: MRISread: file 'sample_vol2surf_lh.mgh' has 0 vertices!
Probably trying to use a scalar data file as a surface!
No such file or directory
---
I would appreciate any advice on this.
Regards,
Shuntaro
--
----------------------------------------
Shuntaro C. Aoki, Ph.D.
Program-specific Researcher
Neuroinformatics group
Graduate School of Informatics
Kyoto University
s_aoki@i.kyoto-u.ac.jp
----------------------------------------
------------------------------
Message: 6
Date: Thu, 27 Feb 2020 10:56:10 +0100
From: Marina Fern?ndez <marina.fdez.alvarez@gmail.com>
Subject: [Freesurfer] Segmentation problem
To: freesurfer@nmr.mgh.harvard.edu
Message-ID:
<CAALjZme941HDGik=ECskGVA+4qwZd9omrfRUYqSU02HURbDAuw@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"
External Email - Use Caution
Dear Freesurfeer experts,
After running the recon-all, a part of the temporal lobe of one subject was
removed.
I used the watershed algorithm to be less agressive in the skull stripping
step:
recon-all -skullstrip -wsthresh 35 -clean-bm -no-wsgcaatlas -subjid sub_001
And the problem was solved in the brainmask.mgz volume because I can see
the temporal lobe completely, but the surfaces are still displaced. In
order to correct the surfaces I used the white matter edit tool but there
is no change after correcting WM and running the recon-all -autorecon2-wm
-autorecon3. I also used control points and but the following error was
shown in the terminal when I run the recon-all -autorecon2-cp -autorecon3:
recon-all -s sub_001 existed with errors
I detected that there are very high values in the white matter of this part
of the temporal lobe (even 132), maybe it has something to do. What can I
do to solve the problem with this subject?
Thank you very much in advance.
Best regards,
Marina.
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Message: 7
Date: Thu, 27 Feb 2020 15:50:06 +0000
From: HsuD3@mskcc.org
Subject: [Freesurfer] Full analysis chain without Topology fix,
Talairach check?
To: freesurfer@nmr.mgh.harvard.edu
Cc: aristopm@mskcc.org
Message-ID: <93368702701d461eab5147a0eccc3b82@mskcc.org>
Content-Type: text/plain; charset="iso-8859-1"
External Email - Use Caution
Dear Freesurfers,
I am attempting to run the full reconstruction in Freesurfer on several hundred patient images with diseased areas of the brain.
Without skipping any steps of the analysis chain, I am able to complete the full reconstruction for about 50% of said patients. When the analysis is able to complete, the disease sites are generally not included in the white or gray segmentation labels, which is ideal for my use case. However, when the disease is far from the cortical surface, it generally results in a large topological defect. (In other cases, the Talairach check fails.) I would like to know, does it really make sense to try to analyze the images with a "real" topological defect, and if so, how to accomplish it?
I have tried to run the reconstruction with flags "-nofix" and "-notal-check" to accept an imperfect Talairach transform and avoid crashes trying to fix these unfixable topological defects. Unfortunately, the step "mris_autodet_gwstats" which comes after "mris_sphere", seems to look for a file "surf/lh.orig.premesh" which is not found, causing a crash. From what I can understand, that file is produced by the so-called old topology fix [1], so it would imply that a full analysis chain is not supported if you eschew topology-fixing. Is this a feature, or do you recommend modifying the logic of the script to work around it? This is as far as I got, but I suppose there may be steps later in the analysis chain that will also look for files only produced if the topology fix runs.
For your information, I am currently using the nightly build from February 12 for CentOS7, and I am amenable to switching to an older or newer build. Thank you for taking the time to help me.
Best regards,
Dylan Hsu, Ph.D
Memorial Sloan-Kettering Cancer Center
[1] <https://github.com/freesurfer/freesurfer/tree/dev/scripts#L3128-L3139> https://github.com/freesurfer/freesurfer/blob/6044b3df08de93c15e4b44807349f21d9e4bc794/scripts/recon-all#L3128-L3139
=====================================================================
Please note that this e-mail and any files transmitted from
Memorial Sloan Kettering Cancer Center may be privileged, confidential,
and protected from disclosure under applicable law. If the reader of
this message is not the intended recipient, or an employee or agent
responsible for delivering this message to the intended recipient,
you are hereby notified that any reading, dissemination, distribution,
copying, or other use of this communication or any of its attachments
is strictly prohibited. If you have received this communication in
error, please notify the sender immediately by replying to this message
and deleting this message, any attachments, and all copies and backups
from your computer.
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Message: 8
Date: Thu, 27 Feb 2020 11:11:18 -0500 (EST)
From: Bruce Fischl <fischl@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Full analysis chain without Topology fix,
Talairach check?
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Cc: aristopm@mskcc.org
Message-ID:
<alpine.LRH.2.21.2002271110350.25524@door.nmr.mgh.harvard.edu>
Content-Type: text/plain; charset="iso-8859-1"
Hi Dylan
I think you could probably do a recon without topology fixing although of
course the spherical mapping will then be multi-valued. It will take a bit
of hacking at recon-all to get it to work though as it is not a use-case
that we explicitly support.
cheers
Bruce
On Thu, 27 Feb 2020,
HsuD3@mskcc.org wrote:
>
> ????????External Email - Use Caution????????
>
> Dear Freesurfers,
>
>
> I am attempting to run the full reconstruction in?Freesurfer on several
> hundred patient images with diseased areas of the brain.
>
> Without skipping any steps of the analysis chain,?I am able to complete the
> full reconstruction?for about 50% of said patients. When the analysis is
> able to complete, the disease sites are generally not included in the white
> or gray segmentation labels, which is ideal for my use case. However, when
> the disease is far from the cortical surface, it generally?results?in a
> large topological defect. (In other cases, the Talairach check fails.)?I
> would like to know, does it really?make sense to try to analyze the images
> with a "real" topological defect, and if so, how to accomplish it?
>
>
> I have tried to run the reconstruction with flags "-nofix" and
> "-notal-check" to accept an imperfect Talairach transform and avoid crashes
> trying to fix these unfixable topological defects. Unfortunately, the step
> "mris_autodet_gwstats" which comes after "mris_sphere", seems to look for a
> file "surf/lh.orig.premesh" which is not found, causing a crash. From what I
> can understand, that file is produced by the?so-called old topology fix?[1],
> so it would imply that a?full analysis chain is not supported if you
> eschew?topology-fixing.?Is this a feature, or do you recommend modifying
> the?logic of the script to work around it? This is as far as I got, but?I
> suppose there may be steps later in the analysis chain that will also look
> for files only produced if the topology fix runs.
>
>
> For your information, I am currently?using the nightly build from February
> 12 for?CentOS7, and I am amenable to switching to an older or newer build.
> Thank you for taking the time to help me.
>
>
> Best regards,
>
> Dylan Hsu, Ph.D
>
> Memorial Sloan-Kettering Cancer Center
>
>
> [1]?https://github.com/freesurfer/freesurfer/blob/6044b3df08de93c15e4b44807
> 349f21d9e4bc794/scripts/recon-all#L3128-L3139
>
>
>
> =====================================================================
>
> Please note that this e-mail and any files transmitted from
> Memorial Sloan Kettering Cancer Center may be privileged, confidential,
> and protected from disclosure under applicable law. If the reader of
> this message is not the intended recipient, or an employee or agent
> responsible for delivering this message to the intended recipient,
> you are hereby notified that any reading, dissemination, distribution,
> copying, or other use of this communication or any of its attachments
> is strictly prohibited. If you have received this communication in
> error, please notify the sender immediately by replying to this message
> and deleting this message, any attachments, and all copies and backups
> from your computer.
>
>
>
------------------------------
Message: 9
Date: Thu, 27 Feb 2020 16:58:23 +0000
From: "Emily S. Finn" <Emily.S.Finn@dartmouth.edu>
Subject: [Freesurfer] Job post: full-time research assistant in the
lab of Dr. Emily Finn, Dartmouth College
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<MN2PR03MB492862DB8380B3C244C21FB5C0EB0@MN2PR03MB4928.namprd03.prod.outlook.com>
Content-Type: text/plain; charset="windows-1252"
External Email - Use Caution
Dear Freesurfer users,
The laboratory of Dr. Emily Finn in the Department of Psychological and Brain Sciences at Dartmouth College is seeking a full-time Research Assistant for a targeted start date of July 2020. The research of the lab focuses on individual differences in brain activity and connectivity, and how these relate to behavior. Some key questions are: How do our intrinsic traits bias our perceptions and judgments, and how is this reflected in patterns of brain activity? Why might different people arrive at different interpretations of the same experience? Our research combines behavioral, neuroimaging and computational modeling techniques to study individual differences in cognition, especially under rich, dynamic, ?naturalistic? stimulation such as watching movies or listening to stories. This position is especially well-suited for individuals planning to apply for a PhD in cognitive neuroscience or psychology. The position would be for an initial 1 year, with an ability to renew up to 2 additional years thereafter based on performance. Preference will be given to applicants who are willing to stay at least two years. Questions may be directed to Emily Finn (emily.s.finn@dartmouth.edu). For full consideration, please apply by March 13, 2020.
Position Purpose
Plays a crucial role in helping to set up the lab as well as conduct experiments. The Research Assistant?s role will involve administrative tasks, such as purchases, participant recruitment, ethics applications, organizing files, and setting up meetings. Conducts research, including designing experiments, collecting data, analyzing data, and writing papers, with the aim of completing an independent research project by the end of their time. The Research Assistant will learn techniques in programming, functional MRI brain scanning, and in-person and online behavioral experimentation.
Required Qualifications
- Bachelor?s degree with a major in psychology, neuroscience, cognitive science, computer science, biology, or a similar field
- Previous experience in one or more laboratory methods, procedures and techniques as well as the equipment and instruments, e.g., fMRI data acquisition, eye-tracking, behavioral experimentation
- Ability to work independently and apply critical thinking and sound judgment
- Excellent organizational and time management skills
- Knowledge of software for writing and presentation (e.g., Microsoft Office), and online scientific literature search engines
Preferred Qualifications
- Two years of relevant laboratory/ research experience during undergraduate
- General programming and computational skills for data analysis (e.g., Python, MATLAB, R)
- Experience with neuroimaging analysis software (e.g., AFNI, SPM, FSL) and experiment creation (e.g., PsychoPy, Psychtoolbox)
- Experience working with human participants
For more information or to apply: https://searchjobs.dartmouth.edu/postings/53845
--
Emily S. Finn, PhD
Assistant Professor, beginning July 2020
Psychological & Brain Sciences
Dartmouth College
esfinn.github.io<http://esfinn.github.io>
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