Re: [Freesurfer] Using fieldmap to correct EPI distortions

Hi Reza, On Sep 6, 2014, at 13:47 , Reza Rajimehr r...@nmr.mgh.harvard.edu 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

Re: [Freesurfer] Using fieldmap to correct EPI distortions

Hi Reza, On Sep 6, 2014, at 13:10 , Reza Rajimehr r...@nmr.mgh.harvard.edu 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

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

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 the critical slice. I predict that these will be identical, If so you can

Re: [Freesurfer] Mouse use for tkmedit

Hi Caroline, On Jun 18, 2014, at 18:08 , Caroline Lewis carolineemmale...@gmail.com 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

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

Hi Reza, On Apr 20, 2014, at 14:58 , Reza Rajimehr r...@nmr.mgh.harvard.edu 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

Re: [Freesurfer] Matlab help

Hi Saurabh, On Mar 4, 2014, at 07:56 , Saurabh Thakur srbht...@gmail.com 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.

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

Re: [Freesurfer] tkmedit is not working

Hi again, On Feb 4, 2014, at 14:44 , Saurabh Thakur srbht...@gmail.com wrote: On Tue, Feb 4, 2014 at 6:56 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: ls -l /usr/local/freesurfer/tktools Hi Bruce, I m sending you some result :

Re: [Freesurfer] Installation error

Hi again, On Feb 4, 2014, at 14:57 , Saurabh Thakur srbht...@gmail.com wrote: On Tue, Feb 4, 2014 at 7:15 PM, Sebastian Moeller sebastian.moell...@rwth-aachen.de wrote: tkmedit -f rawavg.mgz Hi Sebastian, //// saurabh

Re: [Freesurfer] Installation error

Saurabh Thakur, On Tue, Feb 4, 2014 at 8:28 PM, Sebastian Moeller sebastian.moell...@rwth-aachen.de wrote: Hi, On Feb 4, 2014, at 15:38 , Saurabh Thakur srbht...@gmail.com wrote: On Tue, Feb 4, 2014 at 7:41 PM, Sebastian Moeller sebastian.moell...@rwth-aachen.de wrote

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 dusanhir...@hotmail.com wrote: Dear Freesurferexperts, I still have the Problem because I can not run the the mris-command to

Re: [Freesurfer] Freesurfer, Matlab and Maverick

Hi Dusan, On Jan 26, 2014, at 15:36 , Douglas Greve gr...@nmr.mgh.harvard.edu 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

[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 sebastian.moell...@rwth-aachen.de Subject: Re: [Freesurfer] Applying two registration matrices Date: January 20, 2014 15:09:45

Re: [Freesurfer] blood hyper-intensity

Hi Colin, On Oct 24, 2013, at 00:24 , Colin Reveley cm...@sussex.ac.uk 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

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

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] 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

Re: [Freesurfer] selxavg3-sess illconditioned error

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 fax: 626-395-8826 German GSM: +49 - 15 77 - 1 90 31 41 mobile: +1-626-325-8598 +1-626-807

Re: [Freesurfer] selxavg3-sess illconditioned error

(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 sebastian.moell...@rwth-aachen.de wrote: Hi Katie, what about just modifying the matlab code that gives the ill-conditioned error? So for free surfer 4.5 you

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

-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 fax: 626-395-8826 German GSM: +49 - 15 77 - 1 90 31 41 mobile

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

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

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

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 sebastian.moell...@rwth-aachen.de wrote: Hi Negar, from your log file: build-stamp.txt: freesurfer-Linux

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

, 2012-12-04 at 12:35 -0800, Sebastian Moeller wrote: Hi Negar, On Dec 4, 2012, at 12:19 , Negar Memarian wrote: Hi Sebastian, Thank you for your reply. The virtual machine that I'm using was built by a friend who also uses FreeSurfer and I copied it entirely onto my computer (a huge

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

(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 PM, Sebastian Moeller sebastian.moell...@rwth-aachen.de wrote: Hi Nick, On Dec 4, 2012, at 14:41

Re: [Freesurfer] p-value too small?

. But I am not looking at the code so I am basically just rambling here... best Sebastian Thanks, Caspar 2012/11/29 Sebastian Moeller sebastian.moell...@rwth-aachen.de: Hi Doug, hi Caspar, which matlab version are you using? We had some issues in the past that some

Re: [Freesurfer] p-value too small?

/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Sebastian Moeller telephone: +1-626-325-8598 /+1-626-395-6523 / +1-626-395-6616 fax: 626-395

Re: [Freesurfer] Phase Encoding Direction and epidewarp.fsl

, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Sebastian Moeller telephone: +1-626-325-8598 /+1-626

Re: [Freesurfer] FDR Correction of NHP Surface Data

/listinfo/freesurfer -- 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 +1-626-807-5242 US CDMA: +1-626-807-5242 moel...@caltech.edu Division of Biology MC 114

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

contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -- Sebastian Moeller

Re: [Freesurfer] Process monkey data

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 fax: 626-395-8826 German GSM: +49 - 15 77 - 1 90 31 41 mobile: +1-626-325-8598 +1-626-807

[Freesurfer] mri_convert -conform issue

the 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 +1-626-807

[Freesurfer] Fwd: mri_convert -conform issue

the current orientation. Sorry for the confusion best Sebastian Begin forwarded message: From: Sebastian Moeller sebastian.moell...@rwth-aachen.de Date: August 29, 2011 17:10:20 PM PDT To: freesurfer@nmr.mgh.harvard.edu List freesurfer@nmr.mgh.harvard.edu, Douglas N Greve gr

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

. -- 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 +1-626-807-5242 US CDMA: +1-626-807-5242 moel...@caltech.edu Division of Biology MC 114-96 California Institute

[Freesurfer] tpef question

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: 626-395-8826 German GSM: 0 15 77 - 1 90 31 41 mobile: +1-626-325-8598 US CDMA

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] which volume to edit?

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. -- Sebastian Moeller telephone: 626-807-5242 / 626-395-6523 / 626-395-6616 fax

Re: [Freesurfer] rotate and reslice anatomical volume

://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: 626-807-5242 / 626-395-6523 / 626-395-6616 fax: 626-395-8826 German GSM: 0 15

Re: [Freesurfer] rotate and reslice anatomical volume

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

Re: [Freesurfer] spikedet-sess buglet solution

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 that would be easy to fix by including

[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] Difficulty running FreeSurfer

-- Original Message -- Received: Fri, 17 Dec 2010 02:26:28 AM GMT From: Sebastian Moeller sebastian.moell...@rwth-aachen.de To: Nisser ali umar nisser...@usa.net Cc: ryorricks...@gmail.com, Freesurfer@nmr.mgh.harvard.edu, Obisesan Thomas O tobise...@howard.edu Subject: Re: [Freesurfer

Re: [Freesurfer] Difficulty running FreeSurfer

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. -- Sebastian Moeller telephone: 626-807-5242 / 626-395-6523 / 626-395-6616 fax: 626-395-8826

Re: [Freesurfer] aligning functionals to anatomicals

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

Re: [Freesurfer] mc-sess in freesurfer 5.0

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, On Nov 28, 2010, at 16:48 , Luis Lafer-Sousa wrote

Re: [Freesurfer] mc-sess in freesurfer 5.0

/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: 626-395-6523 / 626-395-6616 fax: 626-395-8826 German GSM: 0 15 77 - 1 90 31 41 US CDMA: + 1 - 626 - 807

Re: [Freesurfer] New v5.0.0 release

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: 626-395-6523 / 626-395-6616 fax: 626-395-8826 German GSM: 0 15 77 - 1

Re: [Freesurfer] New v5.0.0 release

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, pretty cool. It looks like

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

with a 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: Dear fellow Surfers

Re: [Freesurfer] monkey brain recon outputs

/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: 626-395-6523 / 626-395-6616 fax: 626-395-8826 German GSM: 0 15 77 - 1 90 31 41 moel...@caltech.edu

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

that by 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 Division

Re: [Freesurfer] tkmedit scripting question

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 wrote: Aloha fellow surfers, I am trying to script a few steps of my

[Freesurfer] tkmedit scripting question

to 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

[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 sebastian.moel...@lur.rwth-aachen.de Date: April 7, 2010 5:28:53 PM PDT To: Freesurfer Mailing List freesurfer@nmr.mgh.harvard.edu

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

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

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

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,

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

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 sebastian.moel...@lur.rwth-aachen.de wrote: Hi Paige, I ran

Re: [Freesurfer] tkregister2 problems

be 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, at 7:16 AM, Douglas N Greve wrote: Hmmm, da

Re: [Freesurfer] tkregister2 problems

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, I am a happy user of freesurfer

[Freesurfer] tkregister2 problems

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 California Institute

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

[Freesurfer] unpacksdcm/mri_convert question

the 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: 626-395-6713

[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, now

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

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

® is up to 70% faster. Now good news travels really fast. Try it now. -- 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

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

/freesurfer4.4.0/lib/tcl/fsgdfPlot.tcl Reading /home/freesurfer4.4.0/lib/tcl/tkUtils.tcl Successfully parsed tksurfer.tcl reading white matter vertex locations... I also tried setenv doublebufferflag 0, which also did not work. Thanks, Corinna On Wed, Aug 5, 2009 at 1:05 PM, Sebastian Moeller

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

\ -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 telephone: 626-395-6713 German GSM: 0

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

... #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...@caltech.edu Division of Biology MC 114-96 California Institute of Technology 1200 East California Boulevard CA 91125, Pasadena USA

[Freesurfer] new release?

to 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 USA

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

volumes like 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

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

brain.unmasked.mgz. Again I am interested to learn whether 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

[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] 4.3.0 macosx leopard mri_normalize segfaults

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 California

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

, 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? -- Sebastian Moeller Tel.: 04 21 - 2 18 - 90 96 Fax.: 04

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

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 Institut fuer Hirnforschung III Abteilung Theoretische Neurobiologie Universitaet Bremen Biogarten Hochschulring 16a

Re: [Freesurfer] questions regarding freesurfer 4.0.5

??? (???) /usr/lib/ libobjc.A.dylib 0x - 0x1780 libSystem.B.dylib ??? (???) /usr/lib/ libSystem.B.dylib -- 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

[Freesurfer] questions regarding freesurfer 4.0.5

/A/SystemConfiguration 0xfffe8000 - 0xfffebfff libobjc.A.dylib ??? (???) /usr/lib/ libobjc.A.dylib 0x - 0x1780 libSystem.B.dylib ??? (???) /usr/lib/ libSystem.B.dylib -- 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

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

Re: [Freesurfer] recommended scan parameters

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 freesurfer@nmr.mgh.harvard.edu, Andre van der Kouwe [EMAIL PROTECTED], Mike Chee [EMAIL PROTECTED] Subject: Re

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

@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 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

[Freesurfer] buglet in fast_inorm

(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 Theoretische Neurobiologie Universitaet

[Freesurfer] what ever happened to spatialsmooth-sess

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 Hirnforschung III Abteilung Theoretische

[Freesurfer] Re: 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 Biogarten Hochschulring 16a

[Freesurfer] tkmedit scripting

the 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 Neurobiologie

[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] 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 Hirnforschung III Abteilung

[Freesurfer] unpacksdcmdir multiple volume protocols

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 -- Sebastian Moeller Tel.: 04 21 - 2

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

[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 -- Sebastian Moeller Tel

[Freesurfer] 3.0.4: some remarks

on this 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] 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

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

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 Hochschulring 16a

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

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: [Freesurfer] parameters for N3 correction

[Freesurfer] Re: N3 options

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 Moeller wrote

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

;). And 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] newbie question event-related

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.: 04 21 - 2 18 - 90 04 GSM: 01 62

[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 freesurfer@nmr.mgh.harvard.edu

[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

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