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__
Staf
at 17:33 +0200, Sebastian Strauss wrote:
> External Email - Use Caution
>
> Dear Rudolph,
> Thank you for following up.
> I changed flags and tried it again with this command line:
>
> mris_pmake --subject cvs_avg35_inMNI152_temp --hemi lh --
> surfaceF
aces are open and have edges?
>
>
> 1) FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-
> v6.0.0-2beb96c
> 2) Platform: SUSE Linux Enterprise Server 12 SLES 12 SP 1
> 3) uname -a: Linux hpcl5004 3.12.74-60.64.40-default #1 SMP Wed May
> 10 05:07:16 UTC 2017 (
Apology if this is a repeat email. I used the wrong email address in my
reply. I was one of the original
authors of `mris_pmake` although it's been (quite) a few years now. I
do remember that at some point the CLI changed, and given the FS
release cycle it took a while for this to make it into pro
> b) yes, it means that the fold is "sharper" at least in one direction
>
I want to underscore Bruce's point. Higher mean curvature could mean
that folds are sharper. It does not mean that there are necessarily more
folds.
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nformation, please contact the sender and properly
dispose of the e-mail.
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MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging
149 (2301) 13th Street, Charlestown, MA 02129 USA
_
s 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 s
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.or
ng it from source in your environment.
HTH
-=R
On 10/02/2015 10:53 AM, Bruno LAD wrote:
Thanks for you reply, Rudolph.
We have a cluster environment in our university, and the best Ubuntu
version to us for now is Ubuntu 12.04 (in a closest future we will
update to a newer version, but not now...).
I
il 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
&g
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 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 n
tion, 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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don't think you will be able to draw the geodesic distance in the
> ribbon in 3D as it will cut across imaging planes unpredictably. If you
> want the true within-subject geodesic distance there are tools for doing
> this (I think it was part of Mukund Balasubramanian's Ph
rh.G_occipital_sup.label ; labl_set_color 3 255 255 45
labl_load rh.G_oc-temp_med-Lingual.label ; labl_set_color 4 255 255 60
On 4/4/14, 15:50 , Douglas N Greve wrote:
>
> You can use mris_label2annot to create an annotation and then control
> the colors via the ctab
> doug
>
> On 04/03/2014
fer internal command... I have
looked through the wiki, but didn't immediately see a solution.
Help?
Best
-=R
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MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging
149 (2301) 13th Str
ote:
> As far as I can tell - and I may very well be using incorrect syntax -
> mris_calc needs volumes as inputs and does not accept labels. Does
> mris_calc accept label files as inputs, for instance in a command like:
> "mris_calc roi2.label and roi3.label"? If so, could s
t; Thanks,
>>
>> Eli
>>
>> Eli Johnson
>> Research Assistant, Track-On
>> UCL Institute of Neurology, Box 104 Queen Square, London, WC1N 3BG
>> Tel:+44(0)207 242 0038
>>
>>
>>
>> ___
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&g
elp.xml.html
>
> Jon
>
> - Original Message -
> From: "Rudolph Pienaar"
> To: freesurfer@nmr.mgh.harvard.edu
> Sent: Wednesday, October 16, 2013 2:36:37 PM
> Subject: [Freesurfer] Easiest way to resample a volume..?
>
> Hi all --
>
> I have a volu
Perfect! That worked :-)
Thanks
On 10/16/13 16:03 , Juan Eugenio Iglesias wrote:
> Hi Rudolph,
> yes, you can use mri_convert with the flag -vs 0.33 0.33 0.33
> You might want to play with -rt as well to switch from linear to cubic
> resampling.
> Cheers,
> /Euge
Hi all --
I have a volume of say 100x100x100 1mm^3 and I'd like to resample it to
300x300x300 0.33mm^3.
What's the easiest way to do this? Will 'mri_convert' do the trick?
Best
-=R
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MGH/MIT/HMS Athinoul
t; recon-all -s SUBJECTS_DIR exited with ERRORS at Thu Sep 12 08:25:31
> > CEST 2013
> >
> > For more details, see the log file
> >
> /Applications/freesurfer/subjects/subject_prova/Con28/SUBJECTS_DIR/scripts/recon-all.log
> > To report a problem, see
> > http:
king on input filetype sizes,
> > > I found a size mismatch, i.e. len(input1)!=len(input2)
> > >
> > > Darwin iMac-di-Stefano.local 12.4.0 Darwin Kernel Version 12.4.0: Wed
> > > May 1 17:57:12 PDT 2013; root:xnu-2050.24.15~1/RELEASE_X86_64 x86_64
> > >
> &
t_prova/Con28/SUBJECTS_DIR/scripts/recon-all.log
> To report a problem, see
> http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>
>
> Thanks,
>
>
>
> Stefano
>
>
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149 (2301) 13th Street, Charlestown, MA 02129 USA
v5.0.0 is too old. I'd suggest grabbing the current 5.1.0 build and
then just using the 'mri_annotation2label' from that.
On Thu Feb 28 12:17:02 2013, Sudhin A. Shah wrote:
> freesurfer-Linux-centos4_x86_64-stable-pub-v5.0.0
>
>
> On Feb 28, 2013, at 12:12 PM, Rud
a workaround?
>
> On Feb 28, 2013, at 10:47 AM, Rudolph Pienaar wrote:
>
>> After a conventional FS run you can do the following:
>>
>> $>mri_annotation2label --subject --hemi --lobesStrict
>> .lobesStrict.annot
>>
>> Which will create an annotation
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ppreciated.
>
> Andrew
>
>
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around.
>
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t; -rwxr-xr-x 1 root wheel 5936512 Aug 13 19:53
> /usr/local/freesurfer/bin/mris_calc
> -rwxr-xr-x 1 root wheel 5903448 May 26 2011
> /usr/local/freesurfer/bin/mris_calc.old
>
> Not sure what I'm missing, any suggestions?
> -Fred
>
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Hi Fred --
I'm currently traveling and have limited internet connectivity. I'll be back at
the office later in the week and will take a look then.
In the meantime, has this ever worked for you previously? I know that older
versions of 'mris_calc' were somewhat particular about filename lengths
xels along an axis.
>> When doing
>> mris_calc -o out.mgz binF2.mgz add binF1.mgz,
>> the binF2 is shifted.
>>
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MGH/MIT/HMS Athinoula A. Martinos Center
?
Yes. Look in the 'options.txt' file and make sure that the
'b_labelFileSave' flag is set to '1'. The name of the output file can
be set with the 'labelFile' setting.
> Your insight is very important,
> thank you,
> Octavian.
>
>
>
>
Good afternoon,
I am new to freesurfer - is it possible to auto-segment the Amygdala into
sub-regions?
Thank you for your time,
Marc
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You can also use 'mris_decimate' and its companion, 'mris_decimate_gui'...
On 05/31/12 17:05, Gonzalo Rojas Costa wrote:
> Hi:
>
>How can I do a decimation to 1 polygons aprox to the pial surface ?...
>
>Sincerely,
>
>
--
Ru
xml.so.1
(And this is just an example. I don't remember which odd library might
have had issues -- it wasn't libxml, but the general fix is the same).
Best
-=R
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MGH/MIT/HMS Athinoula A. Martinos Center for Biomedi
On 01/22/12 22:21, Jesse Bledsoe wrote:
> I second Octavian's question. Does anyone know how FreeSurfer runs on
> Ubuntu 11.10?
Works fine on both 11.04 and 11.10.
Best
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MGH/MIT/HMS Athinoula A. Martinos
Hi all --
If I make changes to a subject's ?h.smoothwm, how do I re-generate the
?h.sphere surfaces? I'd like to reduce the number of mesh vertices using
'mris_decimate' on a given hemisphere, and then (re)generate a
corresponding spherical surface.
Thanks
--
Rudolph P
ped
Please verify your base system "bit"ness.
Best
-=R
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MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging
149 (2301) 13th Street, Charlestown, MA 02129 USA
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Frees
vertices.
Many thanks,
Christine
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On 11/9/11 09:49 , Rudolph Pienaar wrote:
>
> sed 's/0xd/xoa/' file1.txt > file2.txt
>
sed 's/0xd/x0a/' file1.txt > file2.txt
Oops... critical typo.
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MGH/MIT/HMS Athinoula A. Martino
On 11/9/11 09:36 , Ed Gronenschild wrote:
> Hi Rudolph,
>
> I used TextEdit. On a Mac with OS version earlier than OS10.6
> this problem didn't occur. With TextEdit it is not possible to save
> as UNIX format.
> Thanks for the trick to use sed.
>
> Ed
>
I&#
y convert your old-style
Mac text file to a new style file with:
sed s/x0d/x0a/ old-b-vec-file> new-b-vec-file
This replaces the '0x0d' (10 in hex) characters in the file with '0x0a'
(13 in hex).
For more details, see:
http://www.peterbenjamin.com/seminars
On 10/25/11 17:38 , Steph Bickel wrote:
> Hi Rudolph and Bruce,
>
> thanks for your responses.
>
> rudolph, your example works great. just 2 questions:
> what dimension is the total path cost in the mris_pmake output?
> is there a way to input a file with several vertex poi
Then
> I had the message as above. What might be the problem? (It seems as if
> multiple terminal instances share the socket port number)
>
> *2)*How can I get interhemispheric distances between visual areas across
> hemispheres?
>
> Ryu
>
> PhD student
>
On 10/25/11 10:57 , Steph Bickel wrote:
> Hi Rudolph,
>
> thanks for your speedy response.
> I want to get distance along vertices (the surface) between two vertex
> points.
OK -- 'mris_pmake' works for this. Say you have a subject called 'test'
and you want
eesurfer functions.
>
> I am using freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 on ubuntu
> 11.04.
>
> Any help is much appreciated.
>
> thanks,
>
> Stephan
>
>
>
>
>
>
>
>
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list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
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>
on input filetype sizes,
> I found a size mismatch, i.e. len(input1)!=len(input2)
>
> Any suggestions?
>
> Thanks,
> Corinna
>
>
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--mpmOverlay euclidean --mpmProg pathFind --mpmArgs
startVertex:1,endVertex:3
Note, that this is *not* the geodesic, but is very close. The path is
constrained to run along the surface mesh, so will in general be
slightly longer than the geodesic.
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Rudolph Pienaar, M.Eng, D.Eng /
hese two point along cortical
> surface (not direct distance). Does FS report this kind of distance? Any
> suggestion will be very appreciated.
>
> Aize
>
>
>
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&
; reading input white surface
>> /usr/local/freesurfer/subjects/subject1/surf/rh.white...
>> structure is "rh.cortex.label"
>> number of vertices = 158401
>> total surface area = 102285 mm^2
>> total gray matter volume = 291519 mm^3
>> average cortical t
woa/wa/viewSoftware?id=381072423&mt=8
> <http://itunes.apple.com/WebObjects/MZStore.woa/wa/viewSoftware?id=381072423&mt=8>
>
> Cheers
>
> Pedro Paulo Jr.
>
>
>
>
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more than a year or so, so it does need some handholding to run.
-=R
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MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging
149 (2301) 13th Street, Charlestown, MA 02129 USA
__
; fsaverage surface with freesurfer. thanks for your help.
>
> YUMI
>
>
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It's in the 'dev' tree. You'll have to source the nmr-dev environment
On 11/17/10 10:24 , Marco Loggia wrote:
> Thanks Rudolph.
>
> I don't seem to have that command in my path... I take it is not in the
> standard FreeSurfer distribution (version 5) availabl
;s Hospital
>
> HarvardMedicalSchool
>
> CNYBuilding 120, suite101E
>
> Charlestown, Massachusetts02129
>
> Phone: (617) 643-7267
>
> Fax: (617) 643-7340 ma...@nmr.mgh.harvard.edu
>
>
>
> _______
> Freesurfer mailing li
s 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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ard.edu
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>
>
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149 (2301) 13th Street, Charlestown, MA 02129 USA
___
doug
>
>
> On Thu, 20 May 2010, Rudolph Pienaar wrote:
>
>> Hi all --
>>
>> Is there a simple way to create an annotation for
>> frontal/temporal/occipital/parietal lobes based off the ?h.aparc.annot
>> files in a FS 'label' dir? Ideally speaking
come up before... a quick google didn't
reveal anything.
Many thanks
-=R
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> Freesurfer mailing list
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>
>
>
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Yes -- that's exactly right. The '--discrete' is also the default so doesn't
need to be specified. The '--continuous' uses the old curvature engine.
You will notice that each engine option results in slightly different curvature
values.
Sent via BlackBerry from T-Mobile
-Original Message
Sorry -- appended the wrong version of 'mris_display.
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149 (2301) 13th Street, Charlestown, MA 02129 USA
function [hf, hp, av_filtered] = mris_display(astr
Bruce Fischl wrote:
(2) Import that surface onto Matlab and visualize it there.
There is such a visualizer in the 'dev' tree of FreeSurfer -- called
'mris_display'. I've appended the relevant m files -- just save to a dir
on your MatLAB path.
-=R
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>
> Many thanks,
>
> Stefan
>
>
>
>
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Hi Martin --
There is an app in the development tree, 'mris_pmake' that can be used
to generate fixed-radius regions about arbitrary vertices. It's
scriptable, so you can feed it a list of vertex indices to build
circular ROIs about.
It should be available in the 5.0 release of FreeSurfer, but
install Linux as a dual boot operating system as
> opposed to what I currently have, which is an emulator?
>
> Thanks,
> Fatima
>
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bably the problem. I remember experimenting with intensity gradients
applied across the wm volumes, but don't think any results were
satisfactory for the 'pial' surfaces.
If you'd like more info, feel free to ping me directly.
Regards
-=R
(*) perhaps 'definitely' is to
Basu
>
> Cell : 425 638 2936
> Home: 206 257 0174
>
>
>
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ther than different kernel
optimizations there's little difference.
Personally, I'd install the desktop version and add whatever additional
servers I might need afterwards -- you'll be up and running FS a lot
quicker.
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Rudolph Pienaar, M.Eng, D.Eng / email: rudo...@nmr.mgh.har
but we use 'sudo'
instead of 'su', and you can use your password and not the 'root' password:
$>sudo bash
Password:
#>cd /usr/local
#>tar xzvf
/home/fatima/Desktop/freesurfer-Linux-centos4-stable-pub-v4.3.1-full.tar
in both
Matt Glasser wrote:
> I assume you meant sudo ln -s /usr/lib/libtiff.so.4 /usr/lib/libtiff.so.3
Yes - thanks!
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any
FreeSurfer GUI type apps. If you forget to do it, you'll simply get an
error along the lines of 'libtiff.so.3 not found'
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ncerely,
>
>
>
> Gonzalo Rojas Costa
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>
>
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Douglas N Greve wrote:
or mri_concat or fscalc.fsl
or 'mris_calc'...
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$>mris_calc -o combined.mgz vol1.mgz add vol2.mgz
(i.e. combined.mgz = vol1.mgz + vol2.mgz)
--Original Message--
From: xfore...@ucla.edu
Sender: freesurfer-boun...@nmr.mgh.harvard.edu
To: 'Freesurfer Mailing List'
Subject: [Freesurfer] merging 2 .mgz files?
Sent: Jun 29, 2009 16:57
Dear
rom
black to white?
Thanks,
Attila
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rtex Area (ROI Surface): 0.59023 mm^2
...
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Rudolph Pienaar, M.Eng, D.Eng / email: rudo...@nmr.mgh.harvard.edu
MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging
149 (2301) 13th Street, Charlestown, MA 02129 USA
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Freesurf
positive values unchanged, and replaced all the original negative values
with '1'. Of course, you can set the bin value in 'lh.sulc.neg.bin' to
whatever you'd like by first multiplying it by the desired value:
$>mris_calc -o lh.sulc.neg.bin.f lh.sulc.neg.bin mul
(http://www.cgu.edu.tw/ic/)
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Rudolph Pienaar, M.Eng, D.Eng / email: rudo...@nmr.mgh.harvard.edu
MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging
149 (2301) 13th Str
27; and
save to 'lh.abs.curv'.
--
Rudolph Pienaar, M.Eng, D.Eng / email: rudo...@nmr.mgh.harvard.edu
MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging
149 (2301) 13th Street, Charlestown, MA 02129 USA
___
Freesurfer
Zhangyuanchao wrote:
By the way, could you recommend me relevant papers that calculates the
following indices :
Check the Freesurfer wiki... Our papers on "curvature methodologies" as
well as "wavelet decomposition" have pdfs available.
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Rudolph Pienaar, M.Eng,
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eared to
curvature-type files):
$>mris_curvature_stats
If you have the ROI in a FS label file:
$>mris_curvature_stats -l
will limit the stats analysis only to the .
If you just want simple stats (mean, std, etc), you can also try:
$>mris_calc stats
Cheers
-=R
--
Rudo
ess" greater than 1.5, and store in 'lh.filter':
$>mris_curvature_stats --highPassFilter 1.5 --filterLabel lh.filter
MySubj lh thickness
will create a label file, 'lh.filter' containing a list of all vertices
whose "thickness" value exceeds 1.5
-=R
i,
i.e. curving "up". Areas with negative curvature are colored green, and
correspond to curves pointing "down", i.e. gyri.
So, in a nutshell, the difference is that the 'curv' files contain information
about curvatures, and the 'sulc' files contain information
>mris_calc someVolume.mgz stats
--> will dump min/max/mean/std data
Based on the range max-min determine the 25% threshold, then:
$>mris_calc -o top25pc.mgz someVolume.mgz gte
--> top25pc.mgz will contain only the voxels in someVolume.mgz with
intensities greater than or equal to .
-
reeSurfer.sh)...
HTH
-=R
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Rudolph Pienaar, M.Eng, D.Eng / email: [EMAIL PROTECTED]
MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging
149 (2301) 13th Street, Charlestown, MA 02129 USA
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Freesurfer@
output ', so
$>mris_calc --output rh.curv.abs rh.curv abs
Since this is only in the 'dev' tree, let me know if you'd like a binary.
-=R
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Rudolph Pienaar, M.Eng, D.Eng / email: [EMAIL PROTECTED]
MGH/MIT/HMS Athinoula A.
On Fri, 31 Oct 2008, Bruce Fischl wrote:
Hi Rudolph,
we store things like thickness in 'volume' formats these days - the volumes
are nvertices x 1 x 1. Not sure why it didn't work, I would have thought it
would.
Errr... I think nonetheless the problem might be the
mris_calc currently only works with flat curvature files (eg ?h.curv, ?h.sulc,
?h.area, ?h.thickness, etc) and not on volumes.
--Original Message--
From: Akram Bakkour
Sender: [EMAIL PROTECTED]
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] mris_calc
Sent: Oct 31, 2008 20:13
H
but ended up with the same problem.
>
> Is anyone having the similar problem?
>
Are you running any compiz desktop effects (wobbly windows, fade animations,
etc.)? I've had similar problems with Ubuntu 8.04 and FreeSurfer tools if
compiz effects were activated. If they are active,
> Dear Rudolph Pienaar,
> could you please tell me if the Folding index and the sulc are in a way
> correlated?
> thank you
Hi David -
This question does not really have a simple yes or no answer, mostly because
each measures different features. These features are both deri
t at 13. Any
> suggestions?
>
Try this:
1 1 0
1 -1 0
0 1 1
0 -1 1
1 0 1
-1 0 1
Has worked for me, but your mileage may vary.
Cheers
-=R
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Rudolph Pienaar, M.Eng, D.Eng / email: [EM
Hi all -
Is there a way to create "intermediate" surfaces in FreeSurfer? By
intermediate I mean "some fraction" between gray/white and pial.
Cheers
-=R
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Rudolph Pienaar, M.Eng, D.Eng / email: [EMAIL PROTECTED]
MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Ima
irach_afd: Talairach
> Transform:FAILED Does someone know how to solve the problem?
> Thanks for help,
>
> Yuan
--
Rudolph Pienaar, M.Eng, D.Eng / email: [EMAIL PROTECTED]
MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging
149 (2301) 13th S
r) or 10.5 (leopard)
* has at the very least 1GB of RAM, although I'd not recommend this. 2GB is
really the minimum to be comfortable.
Hope this helps...
Cheers
-=R
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Rudolph Pienaar, M.Eng, D.Eng / email: [EMAIL PROTECTED]
MGH/MIT/HMS Athinoula A. Martinos C
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