[Freesurfer] mri_surf2surf to fsaverageX introduces offset

Dear Freesurfers, I tried to map a single subject surface to fsaverageX (for the sake of demonstration lets take fsaverage6). I did the following: mri_surf2surf --hemi lh --srcsubject $s --sval-xyz white --trgsubject fsaverage6 --tval-xyz --tval ./lh.white.ico6 This produces a surface that seems

Re: [Freesurfer] mri_surf2surf to fsaverageX introduces offset

Dear Freesurfers, sorry for the bump, but my message seems to have gone unnoticed. Thanks so much for any ideas. Franz Am 22.08.2013 um 13:37 schrieb Franz Liem: > Dear Freesurfers, > > I tried to map a single subject surface to fsaverageX (for the sake of > demonstration lets tak

Re: [Freesurfer] mri_surf2surf to fsaverageX introduces offset

> coorindates don't change at all. It is surprising that they are as close > as they are. What are you trying to do? > > doug > > > On 08/29/2013 07:41 AM, Franz Liem wrote: >> Dear Freesurfers, >> >> sorry for the bump, but my message seems

Re: [Freesurfer] mri_surf2surf to fsaverageX introduces offset

Hi again, just a clarification. The two surfaces in the image are single subject surfaces (the original lh.white and the transformed lh.white.ico6), not fsaverage6 surfs. Best, Franz Am 30.08.2013 um 09:51 schrieb Franz Liem: > Hi Doug, > > thanks a lot. > I am using Darwin-sno

Re: [Freesurfer] mri_surf2surf to fsaverageX introduces offset

ansfer/outgoing/flat/greve/mri_surf2surf.snowleopard > > note the --tval-xyz requires an argument (give it the orig.mgz) > > doug > > > On 08/30/2013 03:51 AM, Franz Liem wrote: >> Hi Doug, >> >> thanks a lot. >> I am using Darwin-snowleopard and

Re: [Freesurfer] mri_surf2surf to fsaverageX introduces offset

Hi Doug, this gives exactly the same surface as surf2surf followed by mris_convert (i.e. with offset). Thanks, Franz Am 02.09.2013 um 16:50 schrieb Douglas Greve: > > What if you specify the output of surf2surf to be a gii file? > > > On 9/2/13 6:47 AM, Franz Liem wrot

Re: [Freesurfer] mri_surf2surf to fsaverageX introduces offset

x27;ll have to take a > look which could take a while. Depending on what you are doing, it might > not be important. > doug > > > On 9/2/13 2:58 PM, Franz Liem wrote: >> Hi Doug, >> this gives exactly the same surface as surf2surf followed by mris_convert >> (

[Freesurfer] downsampling surface in native space

Dear FS experts, I would like to downsample a subject's white surface to arrive with a smaller number of vertices in order to feed the surface into FSL's surface tracking. I tried to map the fsaverage6 onto the single subject: mri_surf2surf --hemi lh --srcsubject fsaverage6 --sval-xyz white --t

Re: [Freesurfer] downsampling surface in native space

> > On 10/18/2012 07:53 AM, Franz Liem wrote: >> Dear FS experts, >> >> I would like to downsample a subject's white surface to arrive with a >> smaller number of vertices in order to feed the surface into FSL's surface >> tracking.

[Freesurfer] make_face_parcellation ambiguous color table

Dear Freesurfers, I have performed make_face_parcellation on fsaverage (with ic5) (Darwin-leopard-i686-stable-pub-v5.1.0). I read_annotation ed the parcellation into matlab an noticed that while colortable.table has 10242 rows (as expected), length(unique(colortable.table(:,5))) produce

Re: [Freesurfer] make_face_parcellation ambiguous color table

help, Franz Am 25.10.2012 um 18:29 schrieb Douglas N Greve: > Hi Franz, this was noted and addressed a few weeks ago. You can download > a new version here: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mris_make_face_parcellation.linux > doug > > On 10/25/20

Re: [Freesurfer] make_face_parcellation ambiguous color table

Hi Doug, works great. Thanks a lot. Franz Am 26.10.2012 um 22:13 schrieb Douglas N Greve: > Try this one > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mris_make_face_parcellation.mac > > doug > > On 10/26/2012 07:38 AM, Franz Liem wrote: >> Dear Doug,

Re: [Freesurfer] mris_convert to GIFTI misaligned in freeview

Hi Michael, I had a similar problem a while ago. Maybe this might help. http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg31152.html Best, Franz Am 23.05.2014 um 05:38 schrieb Harms, Michael: > > Hi, > I converted a surface to GIFTI > e.g., > mris_convert lh.white lh.white.gii >

[Freesurfer] mris_make_face_parcellation

Dear Freesurfers, I have some questions regarding mris_make_face_parcellation (and possibly found one error in the .tri file). (I am working with freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0). I would like to make a high res parcellation of several subjects and used ic3.tri. Parcels should

Re: [Freesurfer] mris_make_face_parcellation

rry > Bruce > > > On Thu, 26 Jan 2012, Franz Liem wrote: > >> Dear Freesurfers, >> >> I have some questions regarding mris_make_face_parcellation (and possibly >> found one error in the .tri file). >> (I am working with freesurfer-Darwin-leopard-i68

[Freesurfer] tracula bvecs problem

Dear Freesurfers. I am trying to run trac-all on one subject and have a problem with the bvecs file at the -prep stage. After dtifit is started an error massage occurs: Error: bvecs and bvals don't have the same number of entries. I checked the dmri/bvals and dmri/bvecs. There seems to be a prob

Re: [Freesurfer] tracula bvecs problem

hment). I don't really get how this printf & awk command works. Any comments are very much appreciated. Franz bvecs Description: Binary data Am 05.07.2011 um 15:19 schrieb Franz Liem: > Dear Freesurfers. > > I am trying to run trac-all on one subject and have a problem

Re: [Freesurfer] tracula bvecs problem

s has something to do with the file's carriage return. I then produced >> a new bvecs file by manually typing values into a new text file. Now awk >> '{ print $1 }' bvecs delivers one column with 33 lines. >> >> >> Nevertheless, the bvecs output of flip

Re: [Freesurfer] tracula bvecs problem

? I could not find any files that had > 33 lines among your attachments so I'm not sure what your input files look > like. > > Thanks, > a.y > > On Tue, 5 Jul 2011, Franz Liem wrote: > >> Hello again. >> >> I dug into the code and could locate the

Re: [Freesurfer] tracula bvecs problem

ne I can only > read the first 3 lines of the file. This was probably courtesy of excel. > Can you try using dos2unix on the files or saving them in another program? > > a.y > > On Wed, 6 Jul 2011, Franz Liem wrote: > >> Hi Priti and Anastasia. >> >> Tha

Re: [Freesurfer] tracula bvecs problem

does your flip4fsl convert this file correctly (with the numbers after the decimal point)? Thank you, Franz Am 06.07.2011 um 18:06 schrieb Anastasia Yendiki: > > Yes! > > On Wed, 6 Jul 2011, Franz Liem wrote: > >> Hi Anastasia, >> thank you. I created this

Re: [Freesurfer] tracula bvecs problem

bvecs_bvecs_onezero3decpoint1_western_out Description: Binary data bvecs_faketutorial Description: Binary data Am 06.07.2011 um 19:48 schrieb Anastasia Yendiki: > > I'd need the nifti file to run flip4fsl. Can you try it on your data? > > On Wed, 6 Jul 2011, Franz Liem wrote: > &

Re: [Freesurfer] tracula bvecs problem

t sgn*$n}'` and '{print $n}'` ? Thank you very much, Franz Am 06.07.2011 um 21:32 schrieb Anastasia Yendiki: > > I'm attaching what I get when I run it. Only the trailing zeros are missing. > > On Wed, 6 Jul 2011, Franz Liem wrote: > >> If i flip4

Re: [Freesurfer] tracula bvecs problem

quot;en_US" LC_ALL="en_US" Now the bvec rotation and correction works fine. Is your setting en_US or another format (e.g. en_US.ISO8859-1, en_US.ISO8859-15, en_US.US-ASCII, en_US.UTF-8)? Anastasia and Priti, thank you for your time. Best, Franz Am 06.07.2011 um 21:32 schrieb A