Hi,
Coming back with an update from the previous email. I installed it but it tells
me that it cannot be open because of a problem and then I get the above error.
The version is 6.0. Is there a place where I can come with my laptop and see
what is the problem?
Process: prelaunch [1300]
Path:
/Applications/freesurfer/*/segmentSubject.app/Contents/MacOS/prelaunch
Identifier: segmentSubject
Version: 1
Code Type: X86-64 (Native)
Parent Process: ??? [1]
Responsible: prelaunch [1300]
User ID: 501
Date/Time: 2018-10-03 15:47:11.569 -0400
OS Version: Mac OS X 10.13.6 (17G2307)
Report Version: 12
Bridge OS Version: 3.0 (16P375)
Anonymous UUID: C3615BC6-2956-15B2-00D8-9F435B158DB0
Sleep/Wake UUID: 2988BAC2-9FC2-422B-AF82-6F0576A1E894
Time Awake Since Boot: 3200 seconds
System Integrity Protection: enabled
Crashed Thread: 0
Exception Type: EXC_CRASH (SIGABRT)
Exception Codes: 0x0000000000000000, 0x0000000000000000
Exception Note: EXC_CORPSE_NOTIFY
Termination Reason: DYLD, [0x1] Library missing
Application Specific Information:
dyld: launch, loading dependent libraries
Dyld Error Message:
Library not loaded: @rpath/libmwcpp11compat.dylib
Referenced from:
/Applications/freesurfer/*/segmentSubject.app/Contents/MacOS/prelaunch
Reason: image not found
Binary Images:
0x100000000 - 0x100000ff7 +segmentSubject (1)
<BF09BC5D-285F-35DE-BE47-E8F723B03986>
/Applications/freesurfer/*/segmentSubject.app/Contents/MacOS/prelaunch
0x105013000 - 0x10505dacf dyld (551.4)
<8A72DE9C-A136-3506-AA02-4BA2B82DCAF3> /usr/lib/dyld
Kind regards
Eduard
On 10/3/18, 12:00 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
freesurfer-requ...@nmr.mgh.harvard.edu" <freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of freesurfer-requ...@nmr.mgh.harvard.edu> wrote:
Send Freesurfer mailing list submissions to
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To subscribe or unsubscribe via the World Wide Web, visit
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
or, via email, send a message with subject or body 'help' to
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You can reach the person managing the list at
freesurfer-ow...@nmr.mgh.harvard.edu
When replying, please edit your Subject line so it is more specific
than "Re: Contents of Freesurfer digest..."
Today's Topics:
1. Re: Error during decompression of DICOM JPEG compressed
series (Greve, Douglas N.,Ph.D.)
2. Re: Error during decompression of DICOM JPEG compressed
series (Dicamillo, Robert)
3. Re: Error during decompression of DICOM JPEG compressed
series (Greve, Douglas N.,Ph.D.)
4. Mac OS free surfer instalation (Vasile, Eduard)
5. Re: Mac OS free surfer instalation (Hoopes, Andrew)
6. Re: amygdala segmentation atlas influence
(Iglesias Gonzalez, Eugenio)
7. Deadline approaching: PhD in visual perceptual learning at
the Neural Circuits and Cognition lab @ ENI & German Primate
Center G?ttingen (Caspar M. Schwiedrzik)
8. Re: Overlay electric field distribution on pial surface
(Meusen - Klooster, D.C.W.)
9. Re: Overlay electric field distribution on pial surface
(Bruce Fischl)
10. output values of vertices on surface into a textfile
(Sims, Sara A)
----------------------------------------------------------------------
Message: 1
Date: Tue, 2 Oct 2018 17:00:09 +0000
From: "Greve, Douglas N.,Ph.D." <dgr...@mgh.harvard.edu>
Subject: Re: [Freesurfer] Error during decompression of DICOM JPEG
compressed series
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <9b313c16-98ba-9434-e1a9-85febbbd2...@mgh.harvard.edu>
Content-Type: text/plain; charset="utf-8"
Sorry, I meant to change your default shell. That command is being run
using the system() command from inside of a c-program, which undoubtedly
starts your default shell. Just see if it works.
On 10/02/2018 10:36 AM, k3...@free.fr wrote:
> External Email - Use Caution
>
> I am using bash shell but I tried with many others as mentioned in my
first post (zsh, tcsh, csh, sh) and nothing worked so far...
>
>
> ----- Mail original -----
> De: "Douglas N. Greve,Ph.D." <dgr...@mgh.harvard.edu>
> ?: freesurfer@nmr.mgh.harvard.edu
> Envoy?: Mardi 2 Octobre 2018 15:18:14
> Objet: Re: [Freesurfer] Error during decompression of DICOM JPEG
compressed series
>
> What shell are you using? Try using cshell or tcshell to see if it works.
>
> On 10/2/18 4:56 AM, k3...@free.fr wrote:
>> External Email - Use Caution
>>
>> Hi FS team,
>>
>> I am used to run Freesurfer v6.0 on a Ubuntu 18.04 workstation and
everything runs well for most of the subjects that I process so first thanks
for this great tool.
>> I am facing an issue with a JPEG compressed DICOM series that I am not
able to precess, I always get the following error during "mri_convert"
procedure (before calling recon-all), I also wrote the last command that
produces this error:
>>
>> fsdcmdecompress --i freesurfer_18/6858304 --o
/tmp/root.tmp.decompressed.dcm.v1uqEv --jpeg >&
/tmp/root.tmp.decompressed.dcm.v1uqEv.dcmdjpeg.out
>> sh: 1: Syntax error: Bad fd number
>>
>> After some investigations, it looks it is related to the way standard
outputs are redirected to "/tmp/root.tmp.decompressed.dcm.v1uqEv.dcmdjpeg.out"
file (which is missing by the way).
>> It looks like ">&" redirection is not a correct syntax in bash (the
shell I am using), so I tried with others but unfortunately none of them worked
so far (zsh, tcsh, csh, sh).
>>
>> Do you have any recommendation for the way to use "mri_convert" tool? or
any other tool that could convert DICOM to nifty efficiently?
>>
>> Thanks for your feedbacks.
>>
>> Regards,
>> Florent
>>
>> _______________________________________________
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
------------------------------
Message: 2
Date: Tue, 2 Oct 2018 17:43:26 +0000
From: "Dicamillo, Robert" <rdicami...@mgh.harvard.edu>
Subject: Re: [Freesurfer] Error during decompression of DICOM JPEG
compressed series
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <8a4d4b9a-2e49-445a-a616-c74122b3a...@nmr.mgh.harvard.edu>
Content-Type: text/plain; charset="us-ascii"
It may be complaining about >& for redirection. Try using 2>&1 instead.
On Oct 2, 2018, at 4:56 AM, k3...@free.fr<mailto:k3...@free.fr> wrote:
sh: 1: Syntax error: Bad fd number
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Message: 3
Date: Tue, 2 Oct 2018 17:45:13 +0000
From: "Greve, Douglas N.,Ph.D." <dgr...@mgh.harvard.edu>
Subject: Re: [Freesurfer] Error during decompression of DICOM JPEG
compressed series
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <1747fcbd-7c32-9668-3077-20b55c2e3...@mgh.harvard.edu>
Content-Type: text/plain; charset="Windows-1252"
The command is being run from inside of a C-file using the system
command, so there is no way for them to change it
On 10/02/2018 01:43 PM, Dicamillo, Robert wrote:
> It may be complaining about >& for redirection. ?Try using 2>&1 instead.
>
>> On Oct 2, 2018, at 4:56 AM, k3...@free.fr <mailto:k3...@free.fr> wrote:
>>
>> sh: 1: Syntax error: Bad fd number
>
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
------------------------------
Message: 4
Date: Tue, 2 Oct 2018 20:30:34 +0000
From: "Vasile, Eduard" <evas...@mgh.harvard.edu>
Subject: [Freesurfer] Mac OS free surfer instalation
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <9b0bc93c-2256-4e04-bc82-e941136fb...@mgh.harvard.edu>
Content-Type: text/plain; charset="utf-8"
Dear Free Surfer Developers,
I have installed freesurfer on my laptop and followed all steps you
suggested online for a mac computer but freesurfer is still not working. Could
you please assist me in installing it?
Kind regards
Eduard
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Message: 5
Date: Tue, 2 Oct 2018 20:35:52 +0000
From: "Hoopes, Andrew" <ahoo...@mgh.harvard.edu>
Subject: Re: [Freesurfer] Mac OS free surfer instalation
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <66754753-6fae-45ce-9dc9-e8360589d...@mgh.harvard.edu>
Content-Type: text/plain; charset="utf-8"
Hi Eduard, we?ll need some more information. What kind of errors are you
running into? Are you trying to download v6.0 or the dev version?
best
Andrew
From: <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of "Vasile,
Eduard" <evas...@mgh.harvard.edu>
Reply-To: FS Help <freesurfer@nmr.mgh.harvard.edu>
Date: Tuesday, October 2, 2018 at 4:31 PM
To: FS Help <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Mac OS free surfer instalation
Dear Free Surfer Developers,
I have installed freesurfer on my laptop and followed all steps you
suggested online for a mac computer but freesurfer is still not working. Could
you please assist me in installing it?
Kind regards
Eduard
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------------------------------
Message: 6
Date: Tue, 2 Oct 2018 20:51:27 +0000
From: "Iglesias Gonzalez, Eugenio" <e.igles...@ucl.ac.uk>
Subject: Re: [Freesurfer] amygdala segmentation atlas influence
To: "Dr Rajendra Morey, M.D." <rajendra.mo...@duke.edu>, Freesurfer
support list <Freesurfer@nmr.mgh.harvard.edu>
Cc: Douglas N Greve <gr...@nmr.mgh.harvard.edu>
Message-ID: <a463f9df-e489-4568-90f7-c7bbf7f34...@ucl.ac.uk>
Content-Type: text/plain; charset="utf-8"
External Email - Use Caution
Thanks, Raj.
I?d argue that, if the volumes of the nuclei were completely driven by the
global volume of the amygdala, e.g., in an extreme case, V_nuc = alpha x
V_whole, then the effect size of the nucleus at hand would be the same as for
the whole amygdala. Whether such effect size is higher or lower than the ?real?
effect size in presence of perfect segmentation? depends on the nucleus ;-)
Doug: any thoughts?
Cheers,
/Eugenio
--
Juan Eugenio Iglesias
ERC Senior Research Fellow
Centre for Medical Image Computing (CMIC)
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/
From: "Dr Rajendra Morey, M.D." <rajendra.mo...@duke.edu>
Date: Monday, 1 October 2018 at 21:53
To: "Iglesias Gonzalez, Eugenio" <e.igles...@ucl.ac.uk>, Freesurfer support
list <Freesurfer@nmr.mgh.harvard.edu>
Subject: RE: [Freesurfer] amygdala segmentation atlas influence
Hi Eugenio
Thanks for your response it is helpful. In the dataset that I just analyzed
with about 375 scans I suspect that the segmentation for some nuclei is heavily
driven by the atlas. This is resulting in relatively low variance in both the
patient group and the control group. The implication is that the between-group
statistical test is overly sensitive and therefore produces higher than the
expected chance of a significant result. Is this a reasonable concern.
The counterargument is that the means of the two groups are closer to each
other than the true means because of a heavy reliance on the atlas. The
implication here is that the between group statistical test is going to be more
conservative than the true difference. Or does it mean the significance of the
test is not affected but that the effect size is artificially low. Let me know
your thoughts!
Thanks
raj
From: Iglesias Gonzalez, Eugenio [mailto:e.igles...@ucl.ac.uk]
Sent: Sunday, September 30, 2018 10:44 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Cc: Dr Rajendra Morey, M.D. <rajendra.mo...@duke.edu>
Subject: Re: [Freesurfer] amygdala segmentation atlas influence
Dear Raj,
A few years ago, we published a paper on how Monte Carlo sampling could be
used to quantify this. Unfortunately, the method was incredibly slow and
difficult to tune, and the performance gain was tiny, so we never put it in
FreeSurfer. But this is a direction I?m still interested in, and which I?m
planning to revisit in the future.
Cheers,
/Eugenio
--
Juan Eugenio Iglesias
ERC Senior Research Fellow
Centre for Medical Image Computing (CMIC)
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/
From:
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
on behalf of Emily K Clarke <ek...@duke.edu<mailto:ek...@duke.edu>>
Reply-To: Freesurfer support list
<freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Wednesday, 26 September 2018 at 15:15
To: "freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>"
<freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Cc: "Dr Rajendra Morey, M.D."
<rajendra.mo...@duke.edu<mailto:rajendra.mo...@duke.edu>>
Subject: [Freesurfer] amygdala segmentation atlas influence
External Email - Use Caution
Hello all,
I have run the amygdala segmentation in my datasets to obtain volumes of
nuclei. I am aware from the fswiki that the volumes should be interpreted with
caution because of the reliance on the atlas. When running FS, is there a way
to get some metric about how much the segmentation relied on the atlas relative
information from the T1 being segmented. If this metric is not available to the
user, is some version of it calculated by the software and therefore available
internally. Thanks in advance for your help!
raj
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Message: 7
Date: Wed, 3 Oct 2018 09:29:09 +0200
From: "Caspar M. Schwiedrzik" <cschwie...@mail.rockefeller.edu>
Subject: [Freesurfer] Deadline approaching: PhD in visual perceptual
learning at the Neural Circuits and Cognition lab @ ENI & German
Primate Center G?ttingen
To: "Freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<ca+bx-385pvrzpmrk0ynf584jih+wqzivew8qqv0rktgtbtx...@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"
External Email - Use Caution
The European Neuroscience Institute in G?ttingen (ENI-G) Germany, a
partnership between the University Medical Center G?ttingen and the
Max-Planck-Society, is seeking a
*Ph.D. student *
About us:
The Neural Circuits and Cognition lab of Caspar Schwiedrzik at the European
Neuroscience Institute (ENI-G) and the German Primate Center
<http://www.dpz.eu/de/startseite.html> (DPZ) in G?ttingen, Germany is
looking for an outstanding PhD student interested in studying the neural
basis of perceptual learning in vision. The project investigates neural
mechanisms of learning and perception at the level of circuits and single
cells, utilizing functional magnetic resonance imaging (fMRI) in
combination with electrophysiology and behavioral testing in humans and
non-human primates. It is funded by an ERC Starting Grant (Acronym VarPL;
?Specificity or generalization? Neural mechanisms for perceptual learning
with variability?). The PhD student?s project will focus on developing new
perceptual learning paradigms and investigating the neural basis of
perceptual learning in humans using fMRI. In addition, the PhD student will
cooperate with other lab members on parallel electrophysiological and fMRI
experiments as well as comparative research exploring the same questions in
non-human primates.
The lab seeks to understand the cortical basis and computational principles
of perception and experience-dependent plasticity in the macaque and human
brain (see http://www.eni-g.de/groups/neural-circuits-and-cognition). To
this end, we use a multimodal approach including fMRI-guided
electrophysiological recordings in non-human primates and fMRI and ECoG in
humans. The PhD student will play a key role in our research efforts in
this area. The lab is located at the ENI (http://www.eni-g.de) and the DPZ (
http://www.dpz.eu), which are interdisciplinary research centers with
international faculty and students pursuing cutting-edge research in
neuroscience. The PhD student will have access to a new imaging center
<http://www.dpz.eu/en/infocenter/> with a dedicated 3T research scanner,
electrophysiology, and behavioral setups.
ENI-G is engaged in experimental molecular and cellular research on the
central and peripheral nervous systems as well as cognitive and systems
neurosciences research. ENI is part of the University Medical Center
G?ttingen and associated with the Max Planck Society. The University
Medical Center G?ttingen is a tertiary care center. Its 7,400 employees
work in over 65 departments and facilities to provide top-quality patient
care, excellent research and modern teaching facilities. G?ttingen provides
a vibrant and stimulating neuroscience community with a strong background
in computational as well as experimental neurosciences. The PhD student
will have the opportunity to join one of the fourteen programs of the
G?ttingen Graduate School for Neurosciences, Biophysics, and Molecular
Biosciences (http://www.ggnb.uni-goettingen.de).
Your profile:
The position will be available starting in November 2018 with an initial
appointment for 3 years and a salary according to 50% TVL-13. Candidates
should have a degree (master, diploma or equivalent) in a relevant field
(e.g., neuroscience, psychology, biology), and ideally prior experience in
fMRI, strong quantitative, programming, and experimental skills, and share
a passion for understanding the neural basis of visual perception and its
plasticity. Interested candidates should send their curriculum vitae, a
description of their scientific interest and the names and contact
information of up to two references who are able to comment on your
academic background and who agreed to be contacted to
c.schwiedr...@eni-g.de,
preferably before *October 10th, 2018*, but later expressions of interest
will be considered until the position is filled. A good command of English
is a requirement, but fluency in German is not essential.
Please apply by 10.10.2018 to:
Universit?tsmedizin G?ttingen
European Neuroscience Institute G?ttingen
Neural Circuits and Cognition Lab
Dr. Caspar Schwiedrzik
Grisebachstr. 5
37077 G?ttingen
Germany
Tel.: +49-(0)551-39-61371
E-Mail: c.schwiedr...@eni-g.de
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Message: 8
Date: Wed, 3 Oct 2018 13:00:59 +0000
From: "Meusen - Klooster, D.C.W." <d.c.w.kloos...@tue.nl>
Subject: Re: [Freesurfer] Overlay electric field distribution on pial
surface
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<94d6e99297013f46990eeba320449f6184311...@xserver30a.campus.tue.nl>
Content-Type: text/plain; charset="us-ascii"
External Email - Use Caution
Ah, I see now that my configure screen is clipped, so I can click on all
the options but I cannot actually apply them... What are the options for
-colortable? If I have those, I can play with the visualization from the
command line but I cannot find them.
Thank you in advance.
Best,
Debby
________________________________________
Van: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] namens Meusen - Klooster, D.C.W.
[d.c.w.kloos...@tue.nl]
Verzonden: dinsdag 2 oktober 2018 17:37
Aan: Freesurfer support list
Onderwerp: Re: [Freesurfer] Overlay electric field distribution on pial
surface
External Email - Use Caution
Yes, I made a (pretty stupid) mistake in the coregistration. The overlay is
working perfectly now. Only for the visualization, is it possible to set my
colorbar from 1 (blue) to approx 200 (red)? Can I get rid of the 'double' color
bars for positive (red) and negative (blue) values?
Thank you in advance.
Best,
Debby
________________________________________
Van: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] namens Douglas Greve
[dgr...@mgh.harvard.edu]
Verzonden: maandag 17 september 2018 17:04
Aan: freesurfer@nmr.mgh.harvard.edu
Onderwerp: Re: [Freesurfer] Overlay electric field distribution on pial
surface
Did you look at the results of the registration to make sure that they
are ok? But you probably don't need to run the registration anyway since
the surfaces are in the T1.mgz space anyway. How are you verifying that
the efield is properly aligned to the T1.mgz? Is it also 1mm^3 and
256^3? Does it have the same vox2ras matrix as the T1.mgz? use mri_info
--vox2ras T1.mgz Dep48_DLPFC_normE_CORRECTED.nii
On 9/17/18 8:42 AM, Meusen - Klooster, D.C.W. wrote:
> External Email - Use Caution
>
> Dear Prof. Fischl,
>
> Sorry for the lack of clarity. I used bbregister to generate a
registration.dat file. I used simnibs to calculate the Efield distribution and
this has the option to convert the Efield mesh files to .nii files. So I
registered the high resolution T1 (from simnibs, that aligns with the Efield)
to the original T1 data. Consecutively, I used tksurfer to visualize.
>
> bbregister --s Dep48_T1_origANAT --mov
/home/debby/Desktop/FigModPap_Depr48/fs_HeadmeshDep48_origT1/mri/T1.mgz --reg
/home/debby/Desktop/FigModPap_Depr48/register_AnatSimnToAnatOrig.dat --t1
>
> tksurfer FigModPap_Depr48 lh pial -sdir /home/debby/Desktop -overlay
/home/debby/Desktop/FigModPap_Depr48/Dep48_DLPFC_normE_CORRECTED.nii
-overlay-reg
/home/debby/Desktop/FigModPap_Depr48/register_AnatSimnToAnatOrig.dat -fthresh
-2 -fmid 150
>
> Best,
> Debby
> ________________________________________
> Van: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] namens Bruce Fischl
[fis...@nmr.mgh.harvard.edu]
> Verzonden: zaterdag 15 september 2018 17:21
> Aan: Freesurfer support list
> Onderwerp: Re: [Freesurfer] Overlay electric field distribution on pial
surface
>
> Hi Debby
>
> you need to give us a lot more information. What commands did you use to
> sample the field onto the surface? What was the output of those commands?
> Note that tksurfer is deprecated, so I wouldn't worry about how it looks
>
> cheers
> Bruce
>
>
> On Sat, 15 Sep 2018, Meusen - Klooster, D.C.W. wrote:
>
>> External Email - Use Caution
>>
>> Dear all,
>> I am studying transcranial magnetic stimulation (TMS) and would like to
nicely visualize my TMS
>> induced electric fields over a pial surface, preferably using Freesurfer
to stay in line with my
>> other images. I have a .nii file of the electric field distribution,
registered to T1, representing
>> field strengths in every voxel. Visualization in freeview looks okay,
but visualization using
>> tksurfer does not really give the right results (most of the brain is
yellow... no field
>> distribution visible). I guess something goes wrong in the setting of
the colorbar. Preferably I
>> would like to see the field strengths (min:max) in a blue-red
colorscheme. Can anybody tell me how
>> to accomplish this?
>> Thank you very much in advance.
>> Best,
>> Debby
>>
>>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________
Freesurfer mailing list
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Message: 9
Date: Wed, 3 Oct 2018 09:38:45 -0400 (EDT)
From: Bruce Fischl <fis...@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Overlay electric field distribution on pial
surface
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Cc: Ruopeng Wang <rpw...@nmr.mgh.harvard.edu>
Message-ID:
<alpine.lrh.2.20.1810030938280.20...@gate.nmr.mgh.harvard.edu>
Content-Type: text/plain; charset=US-ASCII; format=flowed
there may be a keyboard shortcut for "apply". Maybe return? Can't you
resize the window?
On Wed, 3 Oct 2018, Meusen - Klooster, D.C.W. wrote:
> External Email - Use Caution
>
> Ah, I see now that my configure screen is clipped, so I can click on all
the options but I cannot actually apply them... What are the options for
-colortable? If I have those, I can play with the visualization from the
command line but I cannot find them.
> Thank you in advance.
> Best,
> Debby
> ________________________________________
> Van: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] namens Meusen - Klooster, D.C.W.
[d.c.w.kloos...@tue.nl]
> Verzonden: dinsdag 2 oktober 2018 17:37
> Aan: Freesurfer support list
> Onderwerp: Re: [Freesurfer] Overlay electric field distribution on pial
surface
>
> External Email - Use Caution
>
> Yes, I made a (pretty stupid) mistake in the coregistration. The overlay
is working perfectly now. Only for the visualization, is it possible to set my
colorbar from 1 (blue) to approx 200 (red)? Can I get rid of the 'double' color
bars for positive (red) and negative (blue) values?
> Thank you in advance.
> Best,
> Debby
> ________________________________________
> Van: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] namens Douglas Greve
[dgr...@mgh.harvard.edu]
> Verzonden: maandag 17 september 2018 17:04
> Aan: freesurfer@nmr.mgh.harvard.edu
> Onderwerp: Re: [Freesurfer] Overlay electric field distribution on pial
surface
>
> Did you look at the results of the registration to make sure that they
> are ok? But you probably don't need to run the registration anyway since
> the surfaces are in the T1.mgz space anyway. How are you verifying that
> the efield is properly aligned to the T1.mgz? Is it also 1mm^3 and
> 256^3? Does it have the same vox2ras matrix as the T1.mgz? use mri_info
> --vox2ras T1.mgz Dep48_DLPFC_normE_CORRECTED.nii
>
>
> On 9/17/18 8:42 AM, Meusen - Klooster, D.C.W. wrote:
>> External Email - Use Caution
>>
>> Dear Prof. Fischl,
>>
>> Sorry for the lack of clarity. I used bbregister to generate a
registration.dat file. I used simnibs to calculate the Efield distribution and
this has the option to convert the Efield mesh files to .nii files. So I
registered the high resolution T1 (from simnibs, that aligns with the Efield)
to the original T1 data. Consecutively, I used tksurfer to visualize.
>>
>> bbregister --s Dep48_T1_origANAT --mov
/home/debby/Desktop/FigModPap_Depr48/fs_HeadmeshDep48_origT1/mri/T1.mgz --reg
/home/debby/Desktop/FigModPap_Depr48/register_AnatSimnToAnatOrig.dat --t1
>>
>> tksurfer FigModPap_Depr48 lh pial -sdir /home/debby/Desktop -overlay
/home/debby/Desktop/FigModPap_Depr48/Dep48_DLPFC_normE_CORRECTED.nii
-overlay-reg
/home/debby/Desktop/FigModPap_Depr48/register_AnatSimnToAnatOrig.dat -fthresh
-2 -fmid 150
>>
>> Best,
>> Debby
>> ________________________________________
>> Van: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] namens Bruce Fischl
[fis...@nmr.mgh.harvard.edu]
>> Verzonden: zaterdag 15 september 2018 17:21
>> Aan: Freesurfer support list
>> Onderwerp: Re: [Freesurfer] Overlay electric field distribution on pial
surface
>>
>> Hi Debby
>>
>> you need to give us a lot more information. What commands did you use to
>> sample the field onto the surface? What was the output of those commands?
>> Note that tksurfer is deprecated, so I wouldn't worry about how it looks
>>
>> cheers
>> Bruce
>>
>>
>> On Sat, 15 Sep 2018, Meusen - Klooster, D.C.W. wrote:
>>
>>> External Email - Use Caution
>>>
>>> Dear all,
>>> I am studying transcranial magnetic stimulation (TMS) and would like to
nicely visualize my TMS
>>> induced electric fields over a pial surface, preferably using
Freesurfer to stay in line with my
>>> other images. I have a .nii file of the electric field distribution,
registered to T1, representing
>>> field strengths in every voxel. Visualization in freeview looks okay,
but visualization using
>>> tksurfer does not really give the right results (most of the brain is
yellow... no field
>>> distribution visible). I guess something goes wrong in the setting of
the colorbar. Preferably I
>>> would like to see the field strengths (min:max) in a blue-red
colorscheme. Can anybody tell me how
>>> to accomplish this?
>>> Thank you very much in advance.
>>> Best,
>>> Debby
>>>
>>>
>>
>> _______________________________________________
>> 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 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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>
>
------------------------------
Message: 10
Date: Wed, 3 Oct 2018 15:48:09 +0000
From: "Sims, Sara A" <sno...@uab.edu>
Subject: [Freesurfer] output values of vertices on surface into a
textfile
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <3f08dd7f-df68-4f2c-8f8e-867d7a8a6...@uab.edu>
Content-Type: text/plain; charset="utf-8"
External Email - Use Caution
Hello!
I would like to output the location and value of each vertex on a surface
to a text file. How could I go about doing this?
Thanks,
Sara Sims
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End of Freesurfer Digest, Vol 176, Issue 3
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