[Freesurfer] tkmedit scripting

thresholds for overlay 1, without any masking? thanks & ahoi Sebastian -- Sebastian Moeller Tel.: 04 21 - 2 18 - 78 38 oder 96 91 Fax.: 04 21 - 2 18 - 90 04 GSM: 01 62 - 3 25 45 59 [EMAIL PROTECTED] AG Kreiter / FB 2 Institut fuer Hirnforschung III Abteilung Theoretische Neurobiol

[Freesurfer] Re: tkmedit scripting

Hi List, sorry for not being able to read, as promised lib/tcl/ tkm_functional.tcl showed how to use it. ahoi Sebastian On Jun 2, 2007, at 9:23 PM, Sebastian Moeller wrote: Hi List, getting into scripting of freesurfer I wonder whether it is possible to script false discovery

[Freesurfer] Re: Freesurfer Digest, Vol 41, Issue 13

er End of Freesurfer Digest, Vol 41, Issue 13 ********** -- Sebastian Moeller Tel.: 04 21 - 2 18 - 78 38 oder 96 91 Fax.: 04 21 - 2 18 - 90 04 GSM: 01 62 - 3 25 45 59 [EMAIL PROTECTED] AG Kreiter / FB 2 Institut fuer Hirnforschung III Abteilung Theoretische Neurobiologie Universitaet Bremen Bioga

[Freesurfer] Re: Freesurfer Digest, Vol 41, Issue 48

This is particularly irksome because the backspace key does not function (and I am forced to cntrl-c to kill the entire session). Are there any solutions for this? Thanks! -- Kevin Teich -- Sebastian Moeller Tel.: 04 21 - 2 18 - 78 38 oder 96 91 Fax.: 04 21 - 2 18 - 90 04 GSM: 01 62 - 3 25

[Freesurfer] what ever happened to spatialsmooth-sess

mplate to "modernize" my scripts thank you very much for the powerful tools as always & ahoi Sebastian -- Sebastian Moeller Tel.: 04 21 - 2 18 - 78 38 oder 96 91 Fax.: 04 21 - 2 18 - 90 04 GSM: 0 15 77 - 1 90 31 41 [EMAIL PROTECTED] AG Kreiter / FB 2 Institut fuer Hirnfo

[Freesurfer] buglet in fast_inorm

ce, 1) = y2(iunder,:); else Ahoi & thanks supplying powerful tools Sebastian -- Sebastian Moeller Tel.: 04 21 - 2 18 - 78 38 oder 96 91 Fax.: 04 21 - 2 18 - 90 04 GSM: 0 15 77 - 1 90 31 41 [EMAIL PROTECTED] AG Kreiter / FB 2 Institut fuer Hirnforschung III Abteilung Theoretisch

[Freesurfer] Re: Freesurfer Digest, Vol 46, Issue 29

___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer End of Freesurfer Digest, Vol 46, Issue 29 ** -- Sebastian Moeller Tel.: 04

[Freesurfer] recommended scan parameters

ot;off-site" Siemens sequences)? I would also be grateful for anybodies input on the matter of "optimising" the raw data for the surface reconstruction, so manual interventions can be minimised. -- Sebastian Moeller Tel.: 04 21 - 2 18 - 78 38 oder 96 91 Fax.: 04 21 - 2 18

Re: [Freesurfer] recommended scan parameters

. Thanks in advance. ahoi Sebastian cheers, Bruce On Tue, 22 Jan 2008, Sebastian Moeller wrote: Dear Experts, after ages of monkey scanning, we recently also included human subjects in our study. I would like to use freesurfer for surface reconstruction, mainly as "canvas&quo

Re: [Freesurfer] recommended scan parameters

ahoi & thanks Sebastian Mike From: Sebastian Moeller <[EMAIL PROTECTED]> Date: Tue, 22 Jan 2008 15:10:15 +0100 To: Bruce Fischl <[EMAIL PROTECTED]> Cc: Mailing Freesurfer List , Andre van der Kouwe <[EMAIL PROTECTED]>, Mike Chee <[EMAIL PROTECTED]> Subj

[Freesurfer] questions regarding freesurfer 4.0.5

framework/ Versions/A/Metadata 0x971f6000 - 0x971fbfff com.apple.CommonPanels 1.2.4 (85) <3b64ef0de184d09c6f99a1a7e77e42be> /System/Library/Frameworks/ Carbon.framework/Versions/A/Frameworks/CommonPanels.framework/Versions/ A/CommonPanels 0x971fc000 - 0x97233fff com.apple.SystemConfigurati

Re: [Freesurfer] questions regarding freesurfer 4.0.5

ry/Frameworks/ CoreServices.framework/Versions/A/Frameworks/Metadata.framework/ Versions/A/Metadata 0x971f6000 - 0x971fbfff com.apple.CommonPanels 1.2.4 (85) <3b64ef0de184d09c6f99a1a7e77e42be> /System/Library/Frameworks/ Carbon.framework/Versions/A/Frameworks/CommonPanels.framework/Versions/

[Freesurfer] Re: Freesurfer Digest, Vol 53, Issue 19

Started at Mon Jul 21 09:32:56 EDT 2008 Ended at Mon Jul 21 09:33:00 EDT 2008 preproc-sess done Any help is appreciated. Thank you. -- Sebastian Moeller Tel.: 04 21 - 2 18 - 78 38 oder 96 91 Fax.: 04 21 - 2 18 - 90 04 GSM: 0 15 77 - 1 90 31 41 [EMAIL PROTECTED] AG Kreiter / FB 2 In

Re: [Freesurfer] Freesurfer Digest, Vol 75, Issue 15

Hi Fred, yu probably checked the following already, but on the off chance you have not... Maybe you have set X11 to 256 color mode? Start X11.app (from /Applications/Utilities) go to the X11 menu, select Preferences..., switch to the tab called output and see what is selected for Colors. If it

[Freesurfer] mri_motion_correct.fsl buglet

ignore if you already fixed this. Many Thanks for your exceptionally nice software... best Sebastian Begin forwarded message: > From: Sebastian Moeller > Date: April 7, 2010 5:28:53 PM PDT > To: Freesurfer Mailing List > Bcc: Sebastian Moeller > Subject: mri_mot

[Freesurfer] tkmedit scripting question

set Button 3 to clone from aux vol I would be happy to hear it. Thanks in advance. Best Sebastian -- Sebastian Moeller telephone: 626-395-6713 fax: 626-395-8826 German GSM: 0 15 77 - 1 90 31 41 moel...@caltech.edu Division of Biology MC 114-96 California Institute of Technology

Re: [Freesurfer] monkey brain recon outputs

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 > prop

[Freesurfer] [fsfast]: temporal overlap of stimuli and concurrent presentation

specifying a TER and have both staggered around the real onset time? I would be happy to receive any pointer. Thanks in advance & best regards Sebastian -- Sebastian Moeller telephone: 626-395-6523 / 626-395-6616 fax: 626-395-8826 German GSM: 0 15 77 - 1 90 31 41 moel...@caltech.edu Divi

Re: [Freesurfer] tkmedit scripting question

lack of them ) are absolutely important. Don't leave any space in > gEditBrush(1,mode) > > The first argument of gEditBrush denotes the brush. 0 means Brush 2 > and 1 means Brush 3. Let us know if it works > > -Krish > > On Jul 28, 2010, at 3:22 PM, Sebastian Moeller wrot

Re: [Freesurfer] [fsfast]: temporal overlap of stimuli and concurrent presentation

high TER would work? or both? I will just go and try both, I guess :) Thank you very much for your help Best Sebastian On Jul 30, 2010, at 8:23 AM, Douglas N Greve wrote: > I have not tried it, but that should work. > > doug > > Sebastian Moeller wrote: >>

Re: [Freesurfer] New v5.0.0 release

he 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 t

Re: [Freesurfer] New v5.0.0 release

Ah, too bad I already switched to snow leopard then ;). Well, I will just continue doing my real work on Linux... (Especially since the macosx build seems 32 bit) Best Sebastian > > n. > > On Mon, 2010-08-16 at 11:35 -0700, Sebastian Moeller wrote: >> Hi Nick,

Re: [Freesurfer] mc-sess in freesurfer 5.0

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 t

Re: [Freesurfer] mc-sess in freesurfer 5.0

e > -frame option. Run with -help to get more info. Ah, super that is a rather simple change to include in my processing stream... (I hope this is all that will be required for v5 :)) Best Sebastian > > doug > > Sebastian Moeller wrote: >> Hi Luis, >&g

Re: [Freesurfer] aligning functionals to anatomicals

ers.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. >> >> >> > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu > Phone N

Re: [Freesurfer] Difficulty running FreeSurfer

s://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the e-mail > contains patient information, please contact the Partners Complian

Re: [Freesurfer] Difficulty running FreeSurfer

Sebastian > > Once more, thank you very much. > > Nisser > > > > > > ------ Original Message -- > Received: Fri, 17 Dec 2010 02:26:28 AM GMT > From: Sebastian Moeller > To: Nisser ali umar > Cc: ryorricks...@gmail.com, Freesurfer@nmr.mgh.

[Freesurfer] spikedet-sess buglet & solution

-- Sebastian Moeller telephone: 626-807-5242 / 626-395-6523 / 626-395-6616 fax: 626-395-8826 German GSM: 0 15 77 - 1 90 31 41 US CDMA: + 1 - 626 - 807 - 5242 moel...@caltech.edu Division of Biology MC 114-96 California Institute of Technology 1200 East California Boulevard CA 91125, Pasadena USA

Re: [Freesurfer] spikedet-sess buglet & solution

hit the download site, before I try to switch over from 4.5. Best Regards Sebastian > > doug > > Sebastian Moeller wrote: >> Dear All I just noticed that spikedet-sess (for both FS 4.5 and 5.0) will >> error out if the mystudy/log directory does not yet exist. I think

Re: [Freesurfer] rotate and reslice anatomical volume

erson 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

Re: [Freesurfer] rotate and reslice anatomical volume

or 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 > di

Re: [Freesurfer] which volume to edit?

nfo/freesurfer > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it is > add

[Freesurfer] tpef question

ults may be inaccurate. RCOND = 1.665831e-43. > In fast_selxavg3 at 212 Warning: Matrix is close to singular or badly scaled. Results may be inaccurate. RCOND = 1.665831e-43. > In fast_selxavg3 at 212 -- Sebastian Moeller telephone: 626-807-5242 / 626-395-6523 / 626-395-6616 fax: 626-

Re: [Freesurfer] tpef question

Hi Doug, sorry for having bothered you before checking closer. Just excluding the offensive run solved my problem... (now off to figuring out how to detect if I want to exclude to many timepoints in a run :)) best Sebastian On Jan 27, 2011, at 11:54 , Sebastian Moeller wrote

Re: [Freesurfer] recon-all taking a really long time

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. -- Sebastian Moeller telephone: +1-626-325-8598 /+1-626-395-6523 / +1-626-395-6616

Re: [Freesurfer] new 'dev' release for Linux rh9, centos4 and

x27; build is not available just yet. Please direct comments or questions to this mailing list. -- Sebastian Moeller Tel.: 04 21 - 2 18 - 97 51 oder 90 95 Fax.: 04 21 - 2 18 - 90 04 GSM: 01 62 - 3 25 45 59 [EMAIL PROTECTED] AG Kreiter / FB 2 Institut fuer Hirnforschung III Abteilung Theoret

[Freesurfer] newbie question regarding pooling (analysis over different sessions)

One more question, is it necessary/helpful to record low-res anatomicals before functional runs to register separate sessions, or is this step avoidable. Regards Sebastian -- Sebastian Moeller Tel.: 04 21 - 2 18 - 97 51 oder 90 95 Fax.: 04 21 - 2 18 - 90 04 GSM: 01 62 - 3 25 45 59 [

[Freesurfer] trouble with seq.info, solved

rotocol name for all variables? Ahoi Sebastian -- Sebastian Moeller Tel.: 04 21 - 2 18 - 97 51 oder 90 95 Fax.: 04 21 - 2 18 - 90 04 GSM: 01 62 - 3 25 45 59 [EMAIL PROTECTED] AG Kreiter / FB 2 Institut fuer Hirnforschung III Abteilung Theoretische Neurobiologie Universitaet Bremen Biogar

[Freesurfer] which version is recommended, and any way to avoid -conform?

nicer way to achieve the use of non-conformed resolution, like doing the -motioncor step of recon-all -autorecon1 manually? Or is the use of the standard process not recommended for monkey data anyway? Regards Sebastian -- Sebastian Moeller Tel.: 04 21 - 2 18 - 97 51 oder 90 95 Fax.: 04 21

[Freesurfer] troubles with monkey brains (inflate)

hooking my data into the recon-all pipe-line. But that fails as I do not have any aseg.mgz (does the segmentation work for monkeys?). So any advice on how to proceed with the processing? Ahoi & Thanks Sebastian -- Sebastian Moeller Tel.: 04 21 - 2 18 - 78 38 oder 96 91 Fax.: 04 21 -

Re: [Freesurfer] troubles with monkey brains (inflate)

running mri_fill manually, supplying the required cc and pons coordinates, but specifying -noaseg sure beats my "do it by hand" approach, by far. Thanks for the impressive automatization work. Ahoi & Thanks Sebastian On Wed, 2006-02-22 at 18:19 +0100, Sebastian Moelle

[Freesurfer] tkregister2 woes

the machine. Any hints besides "don't do that then" ;)? ahoi Sebastian -- Sebastian Moeller Tel.: 04 21 - 2 18 - 78 38 oder 96 91 Fax.: 04 21 - 2 18 - 90 04 GSM: 01 62 - 3 25 45 59 [EMAIL PROTECTED] AG Kreiter / FB 2 Institut fuer Hirnforschung III Abteilu

[Freesurfer] mri_motion_correct2 woes

is in one "beautiful" example a single run's volume was turned by 90 degrees. Are there any expert options for mri_motion_correct2 to clue it in on the expected scan quality? A before I forget centos4_x86_64-dev20060224 is the version I am trying. Ahoi Sebastian -- Se

[Freesurfer] mri_fix_topology segfaults

Sebastian -- Sebastian Moeller Tel.: 04 21 - 2 18 - 78 38 oder 96 91 Fax.: 04 21 - 2 18 - 90 04 GSM: 01 62 - 3 25 45 59 [EMAIL PROTECTED] AG Kreiter / FB 2 Institut fuer Hirnforschung III Abteilung Theoretische Neurobiologie Universitaet Bremen Biogarten Hochschulring 16a Postfach 33 04

[Freesurfer] mris_fix_topology update

. Error code 4 most likely means (on Linux x86_64) user_mode page_not_found on read. If I can help debug this I would be happy to. Ahoi Sebastian -- Sebastian Moeller Tel.: 04 21 - 2 18 - 78 38 oder 96 91 Fax.: 04 21 - 2 18 - 90 04 GSM: 01 62 - 3 25 45 59 [EMAIL PROTECTED] AG Kreiter / FB

Re: [Freesurfer] mris_fix_topology update

s 4GB Ram and 4GB swap space and addressable space somewhere in the low TB, why is it that it breaks, even if it allocates too_much_memoryTM? Ahoi Sebastian cheers, Bruce On Tue, 28 Feb 2006, Sebastian Moeller wrote: Hi All, some more details to the segfault. The critical progr

Re: [Freesurfer] mris_fix_topology update

Hi Bruce, On 28. Feb 2006, at 16:04 Uhr, Sebastian Moeller wrote: Hi Bruce, On 28. Feb 2006, at 15:20 Uhr, Bruce Fischl wrote: Hi Sebastian, take a look at your surfaces. If it's using that much memory something is probably dramatically wrong. Most likely either the cerebell

Re: [Freesurfer] mri_motion_correct2 woes

work? All the images have the same geometry, I presume? Well yeah I can exclude the offending volume, even though it was scanned with the same parameters and no giant artifacts. Ahoi Sebastian doug Sebastian Moeller wrote: Dear All, I encounter some problems with mri_motion_correct2

Re: [Freesurfer] mri_motion_correct2 woes

Sebastian Moeller wrote: Hi Doug, On 28. Feb 2006, at 16:27 Uhr, Doug Greve wrote: have you looked at all the images to assure that none have any artifacts? I had a relative quick look, without scrutinizing them, they look okay and very similar, but I will redo this. Have you

[Freesurfer] FreeSurferEnv.sh problems

Dear All, my copy of freesurfer-Linux-centos4_x86_64-dev20060224-full contains a small error in the file FreeSurferEnv.sh. In line 155 "export =$MNI_INSTALL_DIR/data" should read "export MNI_DATAPATH=$MNI_INSTALL_DIR/data". Ahoi Sebastian "friend of b

[Freesurfer] mkanalysis-sess.new bug

t sequence names with, e. g. TR4 inside the string. Yeah, most likely this is a case of "don't do that then", but I have way to many sessions with offending sequence names to go rebame them... Ahoi Sebastian -- Sebastian Moeller Tel.: 04 21 - 2 18 - 78 38 oder 96 91 Fax.:

[Freesurfer] Re: mkanalysis-sess.new bug

alysis-sess.new will accept sequence names with, e. g. TR4 inside the string. Yeah, most likely this is a case of "don't do that then", but I have way to many sessions with offending sequence names to go rebame them... Ahoi Sebastian -- Sebastian Moeller Tel.: 04 21 - 2 18 -

[Freesurfer] regarding fsfast in event related mode

resolution with fsfast, and what swiotches should be used? Thanks Sebastian -- Sebastian Moeller Tel.: 04 21 - 2 18 - 78 38 oder 96 91 Fax.: 04 21 - 2 18 - 90 04 GSM: 01 62 - 3 25 45 59 [EMAIL PROTECTED] AG Kreiter / FB 2 Institut fuer Hirnforschung III Abteilung Theoretische Neurobiologie

[Freesurfer] regarding mkanalysis-sess.new and brainmasks

missing conditions versus the possibility to use stable identifiers for loads of conditions used over different days). Ahoi Sebastian -- Sebastian Moeller Tel.: 04 21 - 2 18 - 78 38 oder 96 91 Fax.: 04 21 - 2 18 - 90 04 GSM: 01 62 - 3 25 45 59 [EMAIL PROTECTED] AG Kreiter / FB 2 Institut

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