Re: [Freesurfer] mris_pmake on the inflated surface

_ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Rudolph Pienaar, Dr.Eng __ Staff Scientis

Re: [Freesurfer] mris_pmake issue

> Any further ideas? > > Thank you for your help! > > > Best > > > > Am 30.07.2019 um 16:53 schrieb Rudolph Pienaar < > > rudo...@nmr.mgh.harvard.edu>: > > > > > > Apology if this is a repeat email. I used the wrong email addr

Re: [Freesurfer] mri_curvature_stats: -a parameter has no effect and errors (FACES_aroundVertex_reorder: packed / faces mismatch and Segmentation fault)

> > > 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 (4eb35ec) x86_64 x86_64 x86

Re: [Freesurfer] mris_pmake issue

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

Re: [Freesurfer] Curvature in FreeSurfer

> 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. -- Rudolph Pienaar, Dr.Eng / email: rudo...@nmr.mgh

Re: [Freesurfer] Curvature in FreeSurfer

sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -- Rudolph Pienaar, Dr.Eng / email: rudo...@nmr.mgh.harvard.edu MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging 149 (23

Re: [Freesurfer] mris_calc cluster infos

> 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 pat

Re: [Freesurfer] Building from source -- autoconf error

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 >>

Re: [Freesurfer] FreeSurfer Ubuntu Server

6681 - Prédio 32 Térreo - Sala 120 +55 51 33538001 <tel:%2B55%2051%2033538001> 2015-10-01 18:40 GMT-03:00 Rudolph Pienaar <rudolph@gmail.com <mailto:rudolph@gmail.com>>: Yes, FreeSurfer can be installed on Ubuntu without any issues. There is also no functi

Re: [Freesurfer] FreeSurfer Ubuntu Server

f 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 contac

Re: [Freesurfer] Sulc value of given Tal coordinates

celine . 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. > -- Rudolph Pienaar, M.Eng, D.Eng / email: rudo...@nmr.mgh.harvard.edu MGH/MIT/HMS Athinoula A. Martinos C

Re: [Freesurfer] citation for mris_pmake

, 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. -- Rudolph Pienaar, M.Eng, D.Eng / email: rudo

Re: [Freesurfer] mris_pmake update

but does not contain patient information, please contact the sender and properly dispose of the e-mail. -- 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

Re: [Freesurfer] distance comparisons across subjects in fsaverage group sphere

, please contact the sender and properly dispose of the e-mail. -- 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

Re: [Freesurfer] reading colorized labels in tcl file to tksurfer...

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 09:13 AM, Rudolph Pienaar

[Freesurfer] reading colorized labels in tcl file to tksurfer...

internal command... I have looked through the wiki, but didn't immediately see a solution. Help? Best -=R -- 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

Re: [Freesurfer] basic math operations for volume labels?

- 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 someone point me at the correct syntax to use? Thanks, -- Rudolph Pienaar, M.Eng, D.Eng / email: rudo

Re: [Freesurfer] mris_calc recon-all problem

mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- 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] Easiest way to resample a volume..?

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 -- Rudolph Pienaar, M.Eng, D.Eng / email: rudo...@nmr.mgh.harvard.edu MGH/MIT/HMS Athinoula A. Martinos Center

Re: [Freesurfer] Easiest way to resample a volume..?

PM, Rudolph Pienaar wrote: 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 -- Rudolph Pienaar, M.Eng, D.Eng / email: rudo...@nmr.mgh.harvard.edu MGH/MIT

Re: [Freesurfer] Easiest way to resample a volume..?

: Rudolph Pienaar rudo...@nmr.mgh.harvard.edu 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 volume of say 100x100x100 1mm^3 and I'd like to resample it to 300x300x300 0.33mm^3

Re: [Freesurfer] mris_calc erroe in recon-all

://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting Thanks, Stefano ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Rudolph Pienaar, M.Eng, D.Eng / email: rudo...@nmr.mgh.harvard.edu MGH/MIT

Re: [Freesurfer] R: Re: R: Re: mris_calc erroe in recon-all

mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- 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

Re: [Freesurfer] R: Re: mris_calc erroe in recon-all

___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Rudolph Pienaar, M.Eng, D.Eng / email: rudo...@nmr.mgh.harvard.edu MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging

Re: [Freesurfer] mri_convert mgz to nifti

-- 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 mailing list Freesurfer@nmr.mgh.harvard.edu https

Re: [Freesurfer] labels to lobes

___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- 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

Re: [Freesurfer] labels to lobes

28, 2013, at 10:47 AM, Rudolph Pienaar wrote: After a conventional FS run you can do the following: $mri_annotation2label --subject subj --hemi hemi --lobesStrict hemi.lobesStrict.annot Which will create an annotation file hemi.lobesStrict.annot containing the lobar labels. To extract

Re: [Freesurfer] labels to lobes

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, Rudolph Pienaar wrote: It looks

Re: [Freesurfer] mris_pmake

://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- 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

Re: [Freesurfer] Downsampling/decimating overlays (not surfaces)

Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- 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

Re: [Freesurfer] fscalc / mris_calc problem

1 root wheel 5903448 May 26 2011 /usr/local/freesurfer/bin/mris_calc.old Not sure what I'm missing, any suggestions? -Fred -- 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

Re: [Freesurfer] fscalc / mris_calc problem

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

Re: [Freesurfer] mris_pmake options

, thank you, Octavian. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Rudolph Pienaar, M.Eng, D.Eng / email: rudo...@nmr.mgh.harvard.edu MGH/MIT/HMS Athinoula A. Martinos

Re: [Freesurfer] pial mesh decimation...

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, -- Rudolph Pienaar, M.Eng, D.Eng / email: rudo...@nmr.mgh.harvard.edu

Re: [Freesurfer] Ubuntu 11.10 64 bit

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 -- Rudolph Pienaar, M.Eng, D.Eng / email: rudo...@nmr.mgh.harvard.edu MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical

[Freesurfer] Re-generating spherical surfaces...

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 Pienaar, M.Eng, D.Eng

Re: [Freesurfer] FreeSurfer Ubuntu 11.10

Please verify your base system bitness. Best -=R -- 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 mailing

Re: [Freesurfer] Downsampling pial surfaces and mapping output to fsaverage6

) use sphere.reg, which has ~15 vertices. Many thanks, Christine ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Rudolph Pienaar, M.Eng, D.Eng / email: rudo

Re: [Freesurfer] End-of-line detection in text file

lf 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/crossplatform/texteol.html -- Rudolph Pienaar, M.Eng, D.Eng / email: rudo

Re: [Freesurfer] End-of-line detection in text file

in single quotes. I see that my copy-paste in the earlier email somehow lost the quotes. If you have a file called file1.txt and want to do the cr/lf sub and save to file2.txt, the exact command is sed 's/0xd/xoa/' file1.txt file2.txt HTH -- Rudolph Pienaar, M.Eng, D.Eng / email: rudo

Re: [Freesurfer] End-of-line detection in text file

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. -- Rudolph Pienaar, M.Eng, D.Eng / email: rudo...@nmr.mgh.harvard.edu MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging 149 (2301

Re: [Freesurfer] FW: Question on mris_pmake

___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Rudolph Pienaar, M.Eng, D.Eng / email: rudo...@nmr.mgh.harvard.edu MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging 149

Re: [Freesurfer] mris_pmake error

-=R -- 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 mailing list Freesurfer@nmr.mgh.harvard.edu https

Re: [Freesurfer] mris_pmake error

, Stephan ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Rudolph Pienaar, M.Eng, D.Eng / email: rudo...@nmr.mgh.harvard.edu MGH/MIT/HMS Athinoula A. Martinos Center

Re: [Freesurfer] mris_pmake error

-- 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 mailing list Freesurfer@nmr.mgh.harvard.edu https

Re: [Freesurfer] mris_calc problem

/listinfo/freesurfer -- 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 mailing list Freesurfer

Re: [Freesurfer] (no subject)

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 -- Rudolph Pienaar, M.Eng

Re: [Freesurfer] fscalc size mismatch error

a size mismatch, i.e. len(input1)!=len(input2) Any suggestions? Thanks, Corinna ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Rudolph Pienaar, M.Eng, D.Eng / email

Re: [Freesurfer] distance between two points along cortical surface

--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. -- Rudolph Pienaar, M.Eng, D.Eng / email: rudo...@nmr.mgh.harvard.edu MGH/MIT/HMS

Re: [Freesurfer] Distance between two points along cortical

/freesurfer -- 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 mailing list Freesurfer@nmr.mgh.harvard.edu https

Re: [Freesurfer] cortical thickness curvature index

___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Rudolph Pienaar, M.Eng, D.Eng / email: rudo...@nmr.mgh.harvard.edu MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical

Re: [Freesurfer] [New release] - iSurf Brainview 2.1.0

/MZStore.woa/wa/viewSoftware?id=381072423mt=8 Cheers Pedro Paulo Jr. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Rudolph Pienaar, M.Eng, D.Eng / email: rudo

Re: [Freesurfer] inter vertex distance

. thanks for your help. YUMI ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Rudolph Pienaar, M.Eng, D.Eng / email: rudo...@nmr.mgh.harvard.edu MGH/MIT/HMS Athinoula

Re: [Freesurfer] 3D view in freeview

) 643-7340 ma...@nmr.mgh.harvard.edu ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Rudolph Pienaar, M.Eng, D.Eng / email: rudo...@nmr.mgh.harvard.edu MGH/MIT/HMS Athinoula

Re: [Freesurfer] 3D view in freeview

it? Thanks, Marco -Original Message- From: Rudolph Pienaar [mailto:rudo...@nmr.mgh.harvard.edu] Sent: Wednesday, November 17, 2010 10:06 AM To: Marco Loggia Cc: 'freesurfer' Subject: Re: [Freesurfer] 3D view in freeview Try using 'mris_decimate_gui' -- if you pass it a --decimationLevel

Re: [Freesurfer] saving snapshots with white background

/freesurfer -- 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 mailing list Freesurfer@nmr.mgh.harvard.edu

Re: [Freesurfer] Creating annotation file for lobar regions...

, 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, I'd like to have a ?h.lobar.annot with corresponding lobar.annot.ctab. Apologies

[Freesurfer] Creating annotation file for lobar regions...

... a quick google didn't reveal anything. Many thanks -=R -- 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

Re: [Freesurfer] Thickness values for every voxel

access to the values of thickness for each voxel / point in the mesh? Thank you, Ana Catarino ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Rudolph

Re: [Freesurfer] number of vertices per hemisphere using mri_glmfit

list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- 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

Re: [Freesurfer] Circle around vertex

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,

Re: [Freesurfer] dual boot OS

___ 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 Rudolph

Re: [Freesurfer] Freesurfer installation on Ubuntu desktop or server?

the desktop version and add whatever additional servers I might need afterwards -- you'll be up and running FS a lot quicker. -- 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

Re: [Freesurfer] installing on ubuntu

in both cases, when you're done unpacking, simply type: 'exit' so that you are no longer the 'root' user and return to being 'fatima'. HTH -=R -- 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

Re: [Freesurfer] installing on ubuntu

an error along the lines of 'libtiff.so.3 not found' -- 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

Re: [Freesurfer] installing on ubuntu

Matt Glasser wrote: I assume you meant sudo ln -s /usr/lib/libtiff.so.4 /usr/lib/libtiff.so.3 Yes - thanks! -- 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

Re: [Freesurfer] freesurfer in Ubuntu 8.1 or 9.04

___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- 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

Re: [Freesurfer] averaging mgz files

Douglas N Greve wrote: or mri_concat or fscalc.fsl or 'mris_calc'... ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] FreeSurfer backgrouund color

to white? Thanks, Attila ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Rudolph Pienaar, M.Eng, D.Eng

Re: Fw: [Freesurfer] Anatomical stats for fsaverage

(ROI Surface): 0.59023 mm^2 ... -- 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 mailing list

Re: [Freesurfer] smooth sulc on only part of the surface one more time

, 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 0.01 would create lh.sulc.neg.bin.f with values of 0 and 0.01... -- Rudolph Pienaar, M.Eng, D.Eng / email: rudo

Re: [Freesurfer] A problem about average curvature value

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 mailing list Freesurfer

Re: [Freesurfer] cortical thickness value of each pixel

/) ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- 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

Re: [Freesurfer] A question about cortical foldings

/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Rudolph Pienaar, M.Eng, D.Eng / email: rudo...@nmr.mgh.harvard.edu MGH

Re: [Freesurfer] one more question about curvature

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. -- Rudolph Pienaar, M.Eng, D.Eng / email: rudo

Re: [Freesurfer] aparc-stats wth curv-file as input?

Cheers -=R -- 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 mailing list Freesurfer@nmr.mgh.harvard.edu

Re: [Freesurfer] getting vertex numbers

': $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 -- Rudolph Pienaar, M.Eng, D.Eng / email: rudo...@nmr.mgh.harvard.edu MGH/MIT/HMS Athinoula A. Martinos

Re: [Freesurfer] qdec ?h.sulc

' files contain information about curvatures, and the 'sulc' files contain information about displacement. HTH -=R -- 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

Re: [Freesurfer] Top Quartile of Active Voxels

-- 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 threshold -- top25pc.mgz will contain only the voxels in someVolume.mgz with intensities greater than or equal to threshold. -=R -- Rudolph Pienaar

Re: [Freesurfer] shell choice

use bash is there any significant reason not to? You can use 'bash' as your conventional shell without any ill-effect FreeSurfer-wise. I myself use bash and not tcsh. Remember, of course, to just source the bash-script equivalent setup scripts (i.e. SetUpFreeSurfer.sh)... HTH -=R -- Rudolph

Re: [Freesurfer] absolute curvature values for vertex-wise comparison

Since this is only in the 'dev' tree, let me know if you'd like a binary. -=R -- 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

Re: [Freesurfer] mris_calc

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 input hack that

Re: [Freesurfer] 6 direction mgh gradient sequence

? 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 -- Rudolph Pienaar, M.Eng, D.Eng / email: [EMAIL PROTECTED] MGH/MIT

[Freesurfer] FI and sulc -- how are they related?

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 derived from the topology

[Freesurfer] creating intermediate surfaces

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 -- Rudolph Pienaar, M.Eng, D.Eng / email: [EMAIL PROTECTED] MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging 149 (2301) 13th

Re: [Freesurfer] version for windows- a simple tool

this. 2GB is really the minimum to be comfortable. Hope this helps... Cheers -=R -- 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

Re: [Freesurfer] apple leopard 64 bit

running the Tiger binaries on 64 Leopard for a while now. Everything works fine. -=R -- 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

[Freesurfer] Convert from {png,jpg} -- dicom

-- 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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https

Re: [Freesurfer] Folding Index question (fwd)

if you'd like the current dev version. Cheers -=R -- 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 ___ Freesurfer mailing list

Re: [Freesurfer] OpenGL

in the process table...? What command line syntax (including arguments do you use)? At the very least, you should get a surfer.log and error.log file in the directory from which you launch any of the graphical apps... Do these even appear? -=R -- Rudolph Pienaar, M.Eng, D.Eng / email: [EMAIL

Re: [Freesurfer] Keyboard Mapping (up arrow)

the way FreeSurfer sets the PATH environment variable so that it picks up your system readline-aware tclsh first, and not the FreeSurfer bundled tclsh. FWIW, I have used the second approach successfully, so it can and does work. -=R -- Rudolph Pienaar, M.Eng, D.Eng / email: [EMAIL PROTECTED

Re: [Freesurfer] freesurfer in cygwin

programs on Windows. Although 'cygwin' allows you to run UNIX-like programs on Windows, these programs have to be specifically compiled on Windows for 'cygwin'. Your best way to run FreeSurfer is on Linux or on Mac OS X. Cheers -=R -- Rudolph Pienaar, M.Eng, D.Eng / email: [EMAIL PROTECTED] MGH/MIT

Re: [Freesurfer] System requirements

, the best case would be to get dedicated Linux (or Mac OS X) machines to use FreeSurfer. Cheers -=R -- 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

Re: [Freesurfer] ROI Curvature

The subject to process hemi Hemisphere to process curvFile Curvature file to process (does not affect the Gaussian / mean stats). Cheers -=R -- Rudolph Pienaar, M.Eng, D.Eng / email: [EMAIL PROTECTED] MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging 149 (2301) 13th Street

Re: [Freesurfer] mgz conversion

and version. If you have a RedHat (or related) distro (like Fedora, CentOS, Mandrake), you can also type more /etc/issue to provide details on the distribution itself. -- Rudolph Pienaar, M.Eng, D.Eng / email: [EMAIL PROTECTED] MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging 149

Re: [Freesurfer] mgz conversion

you downloaded the gsl rpm files. Say you downloaded them to /tmp: cd /tmp Now install them with rpm -Uhv *.rpm and you'll see a short report as each rpm is installed. You should be all set now. Good luck, -=R -- Rudolph Pienaar, M.Eng, D.Eng / email: [EMAIL PROTECTED] MGH

Re: [Freesurfer] using Freesurfer with external storage media

to Windows and have full read/write access to such a partitions. See: http://www.fs-driver.org/index.html Cheers -=R -- 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

Re: [Freesurfer] mris_convert help

On Friday 11 March 2005 13:24, Bruce Fischl wrote: the output surface has to have the extension .asc . Thanks, that fixed it. Cheers --R -- Rudolph Pienaar, M.Eng, D.Eng / email: [EMAIL PROTECTED] MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging 149 (2301) 13th Street

Re: [Freesurfer] Making a patch of area A

) into account. --R -- 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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu