Re: [Freesurfer] blood hyper-intensity

Hi Colin, On Oct 24, 2013, at 00:24 , Colin Reveley wrote: > Hi - > > I wonder if anyone has experience in dealing with T1 images where there is > hyperintenisty of blood vessels? This looks like receive & transmit surface coil data to me. For MPRAGEs, in my experience, switching t

[Freesurfer] Fwd: Applying two registration matrices

Dear list, I notice I took this off-list for no apparent reason…. Maybe it can be useful.. best Sebastian Begin forwarded message: > From: Sebastian Moeller > Subject: Re: [Freesurfer] Applying two registration matrices > Date: January 20, 2014 15:09:45 GMT+01:00 > T

Re: [Freesurfer] Freesurfer, Matlab and Maverick

Hi Dusan, (I saw your PN earlier but had no idea and hence did not reply). But this has more information, so I try again ;) On Jan 25, 2014, at 02:00 , Dusan Hirjak wrote: > Dear Freesurferexperts, > > I still have the Problem because I can not run the the mris-command to > estimate the gyri

Re: [Freesurfer] Freesurfer, Matlab and Maverick

Hi Dusan, On Jan 26, 2014, at 15:36 , Douglas Greve wrote: > > Hi Dusan, find out where matlab is and add it to your path. Eg, on my mac > matlab is here > > /Applications/MATLAB_R2011b.app/bin/matlab > > In my .cshrc file, I have > set path = ($path /Applications/MATLAB_R2011b.app/bin/matl

Re: [Freesurfer] Installation error

Hi, what happens if you open a terminal and type (without the double quotes): "which tkmedit" "which tkmedit.bin" If your path is set correctly there will something along the lines of (example from my mac): hms-beagle:netperf-wrapper moeller$ which tkmedit /opt/freesurfer-Darwin-lion-stable-pub-

Re: [Freesurfer] tkmedit is not working

Hi again, On Feb 4, 2014, at 14:44 , Saurabh Thakur wrote: > > On Tue, Feb 4, 2014 at 6:56 PM, Bruce Fischl > wrote: > ls -l /usr/local/freesurfer/tktools > > Hi Bruce, > > I m sending you some result : > > //==/// > freesurfer-Linux

Re: [Freesurfer] Installation error

Hi again, On Feb 4, 2014, at 14:57 , Saurabh Thakur wrote: > > On Tue, Feb 4, 2014 at 7:15 PM, Sebastian Moeller > wrote: > tkmedit -f rawavg.mgz > > > Hi Sebastian, > > //// > saurabh@saurabh-

Re: [Freesurfer] tkmedit is not working

S-L502X:~/Downloads/freesurfer$ > > freesurfer-i686-redhat-linux-gnu-stable5-20130513 > > I wil download it one more time. > > and get back to you. > > cheers > Saurabh Thakur, > > > > > > > On Tue, Feb 4, 2014 at 7:26 PM, Bruce Fischl &

Re: [Freesurfer] Installation error

Hi, On Feb 4, 2014, at 15:38 , Saurabh Thakur wrote: > > On Tue, Feb 4, 2014 at 7:41 PM, Sebastian Moeller > wrote: > tkmedit subject1 rawavg.mgz > > Hi Sebastian, > > tkmedit is properly get attached. > tat mea

Re: [Freesurfer] Installation error

mgz" best regards Sebastian > > > cheers > Saurabh Thakur, > > > > > > > On Tue, Feb 4, 2014 at 8:28 PM, Sebastian Moeller > wrote: > Hi, > > > On Feb 4, 2014, at 15:38 , Saurabh Thakur wrote: > > > >

Re: [Freesurfer] Matlab help

Hi Saurabh, On Mar 4, 2014, at 07:56 , Saurabh Thakur wrote: > Hi Markus Gschwind, > > I am using Matlab 7.12.0.635 (R2011a), > > I am not able to read the dicom image neither brain.mgz file nor the surface > file in matlab. > > I have added these file in matlab directory. > > Comment or

Re: [Freesurfer] An overwrite issue with selxavg3-sess

Hi Reza, On Apr 20, 2014, at 14:58 , Reza Rajimehr wrote: > I have done a functional analysis for some contrasts using selxavg3-sess. > In the contrast folders, I have added some files. Now I want to do the > same analysis for some new contrasts. My guess is that selxavg3-sess > computes all th

Re: [Freesurfer] error: can't allocate region / Cannot allocate memory

Hi Vincent, On May 7, 2013, at 23:20 , Vincent Koppelmans wrote: > Dear FreeSurfer experts, > > I am trying to create a template for a longitudinal analysis. For each > subject I have 7 time points. The resolution of the T1 images is > 1.0x0.98x0.98 mm. > > The first step (i.e. the cross-s

Re: [Freesurfer] FreeSurfer v 5.3.0 compatibility with Mac OS X 10.4.11

Hi Max, not speaking for the fressurfer developers, just as a user like yourself... On May 24, 2013, at 00:58 , Swartz, Max wrote: > Hello, > > I am working as a research assistant for the summer with the University of > Cincinnati's Psychiatry department in the Division of Bipolar Disorders

Re: [Freesurfer] very slow analysis with recon-all

Hi Stefano, hi Bruce, sorry to partly high-jack your thread Stafano. In my experience with NHPs I often encounter problems like included cerebellum, so I routinely check the filled.mgz before actually running the surface recon, to confirm that the cerebellum (or other non-white matter) is NOT p

Re: [Freesurfer] FDR Correction of NHP Surface Data

. 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] Phase Encoding Direction and epidewarp.fsl

ent to you in >> error >> but does not contain patient information, please contact the sender and >> properly >> dispose of the e-mail. >> > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail

Re: [Freesurfer] p-value too small?

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

Re: [Freesurfer] p-value too small?

uce the real P value for thiose voxels) as otherwise FDR might not work as expected any more. But I am not looking at the code so I am basically just rambling here... best Sebastian > > Thanks, Caspar > > > > > 2012/11/29 Sebastian Moeller : >> Hi D

Re: [Freesurfer] recon-all unable to make pial and white surfaces

ent > to you in error > but does not contain patient > information, > please contact the > sender and properly > dispose of the e-m

Re: [Freesurfer] recon-all unable to make pial and white surfaces

rsion seems like a no brainer to me, as your failure just takes around 3 minutes to materialize… But I am already at the end of my knowledge here… > > Thank you, > Negar > > On Tue, Dec 4, 2012 at 10:57 AM, Sebastian Moeller > wrote: > Hi Negar, > > fro

Re: [Freesurfer] recon-all unable to make pial and white surfaces

ful that 64b will work, but at the moment i'm > at a loss as to the problem. > > nick > > > > On Tue, 2012-12-04 at 12:35 -0800, Sebastian Moeller wrote: >> Hi Negar, >> >> >> On Dec 4, 2012, at 12:19 , Negar Memarian wrote: >> >>>

Re: [Freesurfer] recon-all unable to make pial and white surfaces

of ram? Please note that I can view images > (tkmedit), I can import images (recon-all -i), it just crashes during > recon-all -all. This is really important for me and I greatly appreciate any > suggestion/idea. > > Best regards, > Negar > > On Tue, Dec 4, 2012 at 3:30

Re: [Freesurfer] Error with fs-fast selxavg3-sess

t; > 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/compliancelin

Re: [Freesurfer] selxavg3-sess illconditioned error

t 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

Re: [Freesurfer] selxavg3-sess illconditioned error

and 4 repetitions of each across the run (which > is the same as all the other runs that are working fine). > > Katie > > On Tue, Feb 19, 2013 at 4:46 PM, Sebastian Moeller > wrote: > Hi Katie, > > what about just modifying the matlab code that gives the ill-c

Re: [Freesurfer] Mouse use for tkmedit

Hi Caroline, On Jun 18, 2014, at 18:08 , Caroline Lewis wrote: > Hi, > > I'm using freesurfer on a mac computer, and therefore my mouse doesn't have a > right click or middle button. Is there an alternative way to make edits in > tkmedit (such as to correct voxels erroneously classified as w

Re: [Freesurfer] success and failure of wm surfaces in (almost) identical structural image

of my wits here, and hope that some of the freesurfer developers can solve this riddle with you. Best Regards Sebastian > > Vincent. > > > On 26.08.2014 16:22, Sebastian Moeller wrote: > >> Hi Vincent hi Melanie, >> please show us the *.orig surfaces on t

Re: [Freesurfer] Using fieldmap to correct EPI distortions

Hi Reza, On Sep 6, 2014, at 13:47 , Reza Rajimehr wrote: > I forgot to mention that I want to use undistorted EPI volumes for the > functional-anatomical registration. Well that is simple then, just undistorted the 3D EPI image you used as template for motion correction and register t

Re: [Freesurfer] Using fieldmap to correct EPI distortions

Hi Reza, On Sep 6, 2014, at 13:10 , Reza Rajimehr wrote: > Hi, > > I have a basic question, but the answer can be useful for others as well. > > I am doing a customized preprocessing of monkey functional data in FS-FAST > v5.3. After motion correction and before functional-anatomical > regist

[Freesurfer] mri_convert -conform issue

vox2ras matrices. Shouldn't tkrvox2ras also be updated? And if not why :) ? Best Sebastian -- Sebastian Moeller telephone: +1-626-325-8598 /+1-626-395-6523 / +1-626-395-6616 fax: 626-395-8826 German GSM: +49 - 15 77 - 1 90 31 41 mobile: +1-626-325-8598 +1-62

[Freesurfer] Fwd: mri_convert -conform issue

current orientation. Sorry for the confusion best Sebastian Begin forwarded message: > From: Sebastian Moeller > Date: August 29, 2011 17:10:20 PM PDT > To: "freesurfer@nmr.mgh.harvard.edu List" , > Douglas N Greve > Bcc: Sebastian Moeller > Subject

Re: [Freesurfer] Process monkey data

Line > 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

Re: [Freesurfer] Fw: wm surface does not follow wm.mgz

oes not contain patient information, please contact the sender and > > properly > > dispose of the e-mail. > > > > > > > > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.n

Re: [Freesurfer] Fw: wm surface does not follow wm.mgz

). Well in my laptops screen it works well enough. But this is really irrelevant as the orig surface does not include this bit of cortex, so the value of 1 does not hurt there… Best Sebastian > > Thank you! > Leon > > From: Sebastian Moeller > To: Leo

[Freesurfer] Re: Freesurfer Digest, Vol 56, Issue 20

followed the instruction for creating the qdec table, loaded the data in successfully and requested an analysis with two continuous variance. The following is the final output before it crashes because it cannot allocate memory. I have the maximum memory in my machine. What can I do? -- Seb

[Freesurfer] 4.3.0 macosx leopard mri_normalize segfaults

fault 4) optionally include the subject's /script/recon-all.log See also: http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting Any idea, what I can do? -- Sebastian Moeller telephone: 626-395-6713 German GSM: 0 15 77 - 1 90 31 41 moel...@caltech.edu Division of Biology MC 114-96

[Freesurfer] mri_normalization, what do the command line switches do?

ether there is any reasoning to use the -monkey parameter here. (Since the full recon takes a while, doing trial and error here is a bit less attractive) Thank you very much in advance for any insight, aloha Sebastian -- Sebastian Moeller telephone: 626-395-6713 German GSM: 0 15

[Freesurfer] tksurfer question

scripts? Please let me know... ahoi Sebastian -- Sebastian Moeller telephone: 626-395-6713 German GSM: 0 15 77 - 1 90 31 41 moel...@caltech.edu Division of Biology MC 114-96 California Institute of Technology 1200 East California Boulevard CA 91125, Pasadena USA

[Freesurfer] Re: Freesurfer Digest, Vol 63, Issue 35

tkmedit does? It doesn't need to be included within FreeSurfer but it would be better if it could handle the .mgz format. Regards, Falk -- Sebastian Moeller telephone: 626-395-6713 German GSM: 0 15 77 - 1 90 31 41 moel...@caltech.edu Division of Biology MC 114-96 California Institut

[Freesurfer] new release?

alert the users. Thanks for developing & supplying these great tools -- Sebastian Moeller telephone: 626-395-6713 German GSM: 0 15 77 - 1 90 31 41 moel...@caltech.edu Division of Biology MC 114-96 California Institute of Technology 1200 East California Boulevard CA 91125, Pasadena

[Freesurfer] Re: Freesurfer Digest, Vol 63, Issue 48

-autorecon2-wm \ -subjid ${tmp_subj} \ -cc-crs ${CC_string} \ -pons-crs ${PONS_string} \ -noaseg \ -xopts-use Thanks in advance, Regards, Falk I hope this helps Sebastian -- Sebastian Moeller teleph

[Freesurfer] Re: Freesurfer Digest, Vol 63, Issue 50

targ_dir}/register.dat endif # auto registration supposedly requires same session anatomicals... #autoreg-sess –sf sessid –df sesspar # last line follows... -- Sebastian Moeller telephone: 626-395-6713 German GSM: 0 15 77 - 1 90 31 41 moel

Re: [Freesurfer] Freesurfer Digest, Vol 66, Issue 9

tenv doublebufferflag 0, which also did not work. > > Thanks, > > Corinna > > On Wed, Aug 5, 2009 at 1:05 PM, Sebastian Moeller > > wrote: > Hi Guang, > > if I recall correctly "the sliver problem" stems from the use of an > incompatible libGL.

[Freesurfer] Fwd: Freesurfer Digest, Vol 66, Issue 9

Reading /home/m047599/freesurfer-install/freesurfer/lib/tcl/ > > > > > fsgdfPlot.tcl > > > > > Reading /home/m047599/freesurfer-install/freesurfer/lib/tcl/ > > > > > tkUtils.tcl > > > > > Successfully parsed tksurfer.tcl > > > >

Re: [Freesurfer] Freesurfer Digest, Vol 67, Issue 72

Aloha, tksurfer is extremely picky about the underlaying opengl libraries, many do not work at all. People had dofferent degrees of success updating the graphic drivers on their computers to the most recent versions their hardware maker saupplies (if I recall correctlt especially with nvid

[Freesurfer] selxavg3-sess questions

Hi List, hi Doug, I just started to use freesurfer 4.5.0 for functional data (before I only used 3.0.5). Now I see that the whole analysis workflow has changed from mkanalysis-sess.new -> selxavg-sess -> mkcontrast-sess -> stxgrinder-sess to mkanalyss-sess -> mkcontrast-sess -> selxavg3-sess, n

[Freesurfer] unpacksdcm/mri_convert question

xstart, ystart and zstart are wrong for nii as unpack target). In both cases does the unpack log give 96 as FOV. Is this something to be alarmed about? Should I send example DICOMS? Best Regards & many thanks for the great tools Sebastian -- Sebastian Moeller telephone: 626-395-

Re: [Freesurfer] Freesurfer Digest, Vol 72, Issue 25

Hi Tamara, neuroecon is not ia64 but x86_64, that is you binaries will probanbly never run on this cluster no matter the permissions. You can just ask the neuroecon support people (help-...@caltech.edu) to install 4.5.0 under /share/apps. In addition to actually use freesurfer on this system (s

[Freesurfer] tkregister2 problems

is issue, so please let me know what I can do to help. best regards & thanks for all the cool tools in freesurfer 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 Califor

Re: [Freesurfer] tkregister2 problems

float the resulting .nii float has the reported problem. All the data is from a v17 TIM trio maybe there is something wonky in the headers... Anything I should try to figure this out? Best Sebastian > > doug > > Sebastian Moeller wrote: >> Dear Freesurfer Experts,

Re: [Freesurfer] tkregister2 problems

much nicer though :) Thanks for looking into this Sebastian On Feb 22, 2010, at 11:15 AM, Douglas N Greve wrote: > OK, I can replicate with this data. Let me see what's going on. > > Sebastian Moeller wrote: >> Hi Doug, >> >> On Feb 19, 2010, a

Re: [Freesurfer] Freesurfer Digest, Vol 73, Issue 52

Hi Paige, I ran into a similar problem a few months ago. Freesurfer 3.0.5 could not read data from a TIM trio with numaris B17. I solved this by transplanting (copying) a number of files from freesurfer 4.4.0 (the recent one at the time) into 3.0.5. unpacsdcmdir, mri_convert and a few more, tha

Re: [Freesurfer] Freesurfer Digest, Vol 73, Issue 52

e, I can do that. If that's > not possible, I'd prefer to transplant files; multiple operational versions > of software does get confusing, but that would also work as a last resort. > > Thanks, > Paige > > On Fri, Mar 19, 2010 at 3:10 PM, Sebastian Moeller >

Re: [Freesurfer] Freesurfer Digest, Vol 73, Issue 56

Hi Janani, I seem to recall that newer distributions (and judging from your kernel it is a rather new distribution) come with libtiff.so.4 instead of libtiff.so.3. My solution to this problem so far just was to symlink libtiff.so.4 to libtiff.so.3. (Just go in the directory where the library li

Re: [Freesurfer] Freesurfer Digest, Vol 74, Issue 13

Hi Krishna, how does your brainmask look? In my experience, if you use bet to create a brainmask for monkeys, occasionally the brain center is positioned to far posterior. This seems to cause to a loss of frontal gray & white matter in the brainmask. That in turn, would "crop" these parts away

[Freesurfer] mri_motion_correct.fsl buglet

Dear Freesurfers, I just tried to use mri_motion_correct.fsl with the -tmpdir and -nocleanup options. Since I currently average around 10 to 16 mprage volumes per subject (NHPs) I want to look at the variance in addition to the average. And it seemed simplest to just keep the co-registered vol

Re: [Freesurfer] regarding mkanalysis-sess.new and brainmasks

= " line, so user error on my part. Redid an analysis right now, and the end result with -taumax 20 has way less significant activation outside the brain proper. Thanks for the explanation. Ahoi Sebastian Sebastian Moeller wrote: Hi All, as the subject line rev

[Freesurfer] yakview ttrouble

o call to se_text(gca,ud), with the following construct: if (gcf == ud.hThisYakFig), set_text(gca,ud); end Oh yeah zooming does not really work, but I did not investigate further One more thing though, what to use -v1 or -v2? Ahoi & thanks Sebastian -- Sebastian Moeller Tel.: 04

[Freesurfer] (no subject)

urn this sucker so that it works with mgz? #TODO: normalize with control points... Cut and pas

[Freesurfer] two short questions, (flat maps, paint-sess)

be really happy to learn more about this variable. Ahoi & Thanks in Advance 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 Th

[Freesurfer] regarding slice timing

any way. 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 Neurobiologie Universitaet Bremen Biogarten Hochschulring 16a

Re: [Freesurfer] regarding slice timing

ation points for the model in time? Anyway thanks for the pointer, I will test stc-sess to see whether it improves my analysis. Thnaks for the help & Ahoi Sebastian doug Sebastian Moeller wrote: Dear fellow FreeSurfers, does anybody know how to account for interleaved slice acquis

[Freesurfer] Re: Freesurfer Digest, Vol 28, Issue 15

the linux machine try to install freenx. Combined with nomachine's (www.nomachine.it) client software freesurfer remote controlling works down to adsl speeds, where X11 over ssh long lost its usability. Ahoi Sebastian Many thanks for any advice. -- Sebastian Moeller Tel.: 04 21

[Freesurfer] mkbrainmask-sess

Hi All, just a quick note to let you know that 3.0.2's (centos4 x86_64) mkbrainmask-sess does not really parse the "-run nth" parameter it specifies in its help text. Haven't found time to implement a fix yet, but it is a minor issue anyway... Ahoi Sebastian

[Freesurfer] mkbrainmask-sess

the label "parse_args:" and the command "goto parse_args_return". 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 Abteil

[Freesurfer] mri_normalize -conform question

e before running mri_normalize. Just a nit, specifying "-v" some where else than at the end of the commandline easily produces segmentation faults (probably because -v is "overloaded" to also expect Gx Gy Gz arguments? the help is a bit terse) Ahoi Sebastian -- Sebast

[Freesurfer] Re: Freesurfer Digest, Vol 28, Issue 32

ux recon-all exited with ERRORS at Sun Jun 25 15:43:11 CDT 2006 -- 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 Br

Re: [Freesurfer] mri_normalize -conform question

running a full mri_convert --conform on my input file before running mri_normalize. Just a nit, specifying "-v" some where else than at the end of the commandline easily produces segmentation faults (probably because -v is "overloaded" to also expect Gx Gy Gz arguments? the h

Re: [Freesurfer] mri_normalize -conform question

iploads of control points, and getting the wm.mgz into good shape). So unfortunatelly, I will have to stick to cheating about the resolution :(. Ahoi & thanks Sebastian Bruce On Mon, 26 Jun 2006, Sebastian Moeller wrote: Hi Bruce, On 26. Jun 2006, at 02:30 Uhr, Bruce Fisch

Re: [Freesurfer] mri_normalize -conform question

uot; to get to the help while other fs tools use either "-h" or gnuish "--help", maybe you might want to consider to consolidate to one uniform command line switch? But I digress... ahoi Sebastian Bruce On Mon, 26 Jun 2006, Sebastian Moeller wrote: Hi Bruce

Re: [Freesurfer] mkbrainmask-sess

Sebastian doug Sebastian Moeller wrote: Hi List, to follow up my mail from several days ago, all mkbrainmask-sess (v3.0.2 centos4 x86_64) really needs to be able to select the run from which to take the run-number are the following lines: case "-run" set run = $argv[1]; shift;

Re: [Freesurfer] mri_normalize -conform question

oes the dev build go on the web every day? Bruce On Mon, 26 Jun 2006, Sebastian Moeller wrote: Hi Bruce, On 26. Jun 2006, at 16:15 Uhr, Bruce Fischl wrote: it should - consider it a bug. On a related note, is there an easy way to convince mri_info to just spit out the type (UCHAR FLOA

[Freesurfer] tksurfer/suse 10.1 troubles

SE 9.3 (all OSs 64bit linux). I am downloading 3.0.3 ATM to see whether this was fixed. If any of you have any advise I am keen to hear it ;). 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 PROTECT

[Freesurfer] Re: tksurfer/suse 10.1 troubles

installed the latest nvidia driver package on the server in question short of the actual kernel module (as I use X over ssh, so the console machine uses its kernel module). I hope this helps to fix the problem. ahoi Sebastian On 30. Jun 2006, at 12:56 Uhr, Sebastian Moeller wrote:

Re: [Freesurfer] Re: tksurfer/suse 10.1 troubles

ebastian On 30. Jun 2006, at 12:56 Uhr, Sebastian Moeller wrote: Hi List, running freesurfer (centos 4 x86_64 3.0.2 pub full under SuSE 10.1 (had to upgrade from 9.3 because of stability issues)) I get the following Error while trying to run surf-sess (over ssh tunneled X11): surfer: ### GL

Re: [Freesurfer] Re: tksurfer/suse 10.1 troubles

t display of the colorscalebar no longer enforces a tksurfer crash, joy. Thank you very much. Ahoi Sebastian Thanks, Nick On Fri, 2006-06-30 at 21:25 +0200, Sebastian Moeller wrote: Hi Nick, On 30. Jun 2006, at 16:01 Uhr, Nick Schmansky wrote: Sebastian, Hi! The 'glutInit

[Freesurfer] scuba and macosx 10.3.9

Hi All, on my trusty iBook (10.3.9) trying to run scuba (from the 3.0.1 panther version) crashes the X-server (well Xquartz the windowmanager dies, taking the whole X11 with it). Will try 3.0.3. ahoi Sebastian -- Sebastian Moeller Tel.: 04 21 - 2 18 - 78 38 oder 96 91 Fax.: 04 21

[Freesurfer] macosx 10.3.9 and scuba 3.0.3

Hi All, just tried 3.0.3 panther, scuba still crashes and takes X11 with it. 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

[Freesurfer] howto cut "canonical" occipital patches?

alcarine sulcus, but how about the temporal lobe (I really would like to keep FFA and the STS if possible...). Thanks in advance & 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 Krei

Re: [Freesurfer] howto cut "canonical" occipital patches?

occipital patch doesn't contain STS, and probably not FFA either. The whole-hemi patch does, but requires more cuts. Bruce On Fri, 7 Jul 2006, Sebastian Moeller wrote: Hi All, I recently finished the surface transform of my first human brain with freesurfer. (All I had to do was run reco

[Freesurfer] trouble using inorm-sess

.3 Linux-centos4_x86_64-pub, Matlab 7.1 x86_64, running suse Linux 10.1 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 The

[Freesurfer] question about h_NNN.dat volumes

value from the h-offset volume result in percent of total? 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 Neurobiologie

[Freesurfer] Re: question about h_NNN.dat volumes

e eresvar per whole model (or for each real timepoint of the model, but I digress), but what is really inside of the odd timepoints of the h-volumes then? ahoi Sebastian On 11. Jul 2006, at 12:07 Uhr, Sebastian Moeller wrote: Hi Doug, hi List, I got a question regarding the h volu

[Freesurfer] Re: question about h_NNN.dat volumes

Sebastian doug Sebastian Moeller wrote: Hi Doug, hi List, I got a question regarding the h volumes inside the analysis sub directories. The content of those file are the regression coefficients for each voxel (XY planes) for each condition (Z stack). Supposedly those estimates are corr

[Freesurfer] newbie question event-related

and even taummax in mkanalysis)? So far any nicorr value I used produced errors on the way... I would be delighted for any pointer of how to properly convinve fs-fast to analyse my data ;). Ahoi & thanks Sebastian -- Sebastian Moeller Tel.: 04 21 - 2 18 - 78 38 oder 96 91 Fax.:

[Freesurfer] Re: Freesurfer Digest, Vol 30, Issue 26

Hi Doug, On 28. Aug 2006, at 23:55 Uhr, [EMAIL PROTECTED] wrote: Date: Mon, 28 Aug 2006 17:53:30 -0400 From: Doug Greve <[EMAIL PROTECTED]> Subject: [Freesurfer] Re: newbie question event-related To: Sebastian Moeller <[EMAIL PROTECTED]> Cc: Freesurfer Mailing List Message

Re: [Freesurfer] Re: Freesurfer Digest, Vol 30, Issue 26

thing more? One more question, when is the FIR design the better choice than the gammafit design (if that question has an easy answer at all)? Ahoi & Thanks again Sebastian Sebastian Moeller wrote: Hi Doug, On 28. Aug 2006, at 23:55 Uhr, [EMAIL PROTECTED] wrote: Date: Mon, 28

N3 options (was: [Freesurfer] parameters for N3 correction)

urface coil users out there... ahoi & sorry -- 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 Hochsc

Re: N3 options (was: [Freesurfer] parameters for N3 correction)

t;specimens" to get any comments. ahoi Sebastian On Fri, 3 Nov 2006, Sebastian Moeller wrote: Hi List, On 3. Nov 2006, at 19:48 Uhr, [EMAIL PROTECTED] wrote: Message: 10 Date: Fri, 03 Nov 2006 13:48:18 -0500 From: Nick Schmansky <[EMAIL PROTECTED]> Subject: Re: [Fre

[Freesurfer] Re: N3 options

t for us? Make sure to make backups of your current versions of recon-all and mri_nu_correct.mni :). Wahoo, I am impressed, that was fast; that works for me and is much nicer than my unconditional hack to always set those parameters. thanks & ahoi Sebastian doug Sebastian Moel

Re: N3 options (was: [Freesurfer] parameters for N3 correction)

pointers how to improve the quality are welcome. ahoi Sebastian On Fri, 3 Nov 2006, Sebastian Moeller wrote: Hi Bruce, On 3. Nov 2006, at 20:33 Uhr, Bruce Fischl wrote: do you mean single channel surface coils? Can you get decent surfaces out of that kind of data??? Well, yes

[Freesurfer] feature wish for tkregister/tkmedit

of my speciemens into the ftp drop last week, any idea how to improve the quality of the recon/surface extraction? 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

[Freesurfer] 3.0.4: some remarks

list. aloha Sebastian - cut me - #!/bin/sh LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${FSLDIR}/lib export LD_LIBRARY_PATH $FSLDIR/bin/fslview_exe $@ -- cut me - -- 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

[Freesurfer] surface coil intensity normalisation and 3.0.4

$XOptsFile`; and then replace the original line 521, now line 522 with the following: --o nu.mgz --n $NuIterations $xopts) (basically this adds "$xopts to the creation of cmd"). then it works like it expected. Thanks for all the tools & the support Sebastian -- Sebastia

Re: [Freesurfer] surface coil intensity normalisation and 3.0.4

Sebastian Nick On Tue, 2006-12-12 at 02:54 +0100, Sebastian Moeller wrote: Hi Doug, hi list, recently you implemented a version of mri_nu_correct.mni for me that allows for better settings for surface coil recordings. I dragged your change from 3.0.3 into 3.0.4 and just now realised, that

[Freesurfer] unpacksdcmdir & multiple volume protocols

uot;--in_orientation" thing later on the .img works like a charm, I am now puzzled whether this is the right behaviour. I am more than willing to test anything out or send test images if that helps... Anyway, thanks for the nice tools and the great support Ahoi Sebastian -- Sebas

[Freesurfer] Re: Freesurfer Digest, Vol 37, Issue 15

___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer End of Freesurfer Digest, Vol 37, Issue 15 ********** -- Sebastian Moeller Tel.: 04 21 - 2 18 - 78 38 oder 96 91 Fa

[Freesurfer] Re: Freesurfer Digest, Vol 37, Issue 21

-l` set ijs = `echo "scale=6; $second_dim / $min_dim" | bc -l` set iks = `echo "scale=6; $third_dim / $min_dim" | bc -l` #for unpacking at raw resolution mri_convert -i $src_file -o $targ_dir -it siemens_dicom -ot mgh #-iis $iis -ijs $ijs -iks $iks #end of script... #

[Freesurfer] tkmedit question

guess that does not really matter. ahoi & thanks for supplying these nice & powerful tools 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 Hirnforsc

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