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
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
(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
/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 centos6_x86_64.
What I am trying to do is to use the white surface as seed
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 wrote:
Dear Doug,
thank you
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 to have gone unnoticed.
Thanks so much for any ideas.
Franz
Am 22.08.2013 um 13:37
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-snowleopard
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 take fsaverage6). I
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 10/25/2012 10:33 AM, Franz Liem
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,
thanks for the quick response
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)))
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
: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.
I tried to map the fsaverage6 onto the single subject:
mri_surf2surf --hemi lh
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
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 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
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 problem (I don't have a solution,
though. My coding skills are quite
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.
Thank you very much for your replies.
Prit, I ran you modified_bvecs. This resulted in zeros
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 file from scratch with osx' TextEdit
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:
does your flip4fsl
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 flip4fsl my fake file the the numbers after the decimal point are
missing in the output
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
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 with the bvecs
file at the -prep stage.
After dtifit is started an error massage occurs: Error: bvecs and bvals don't
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