Re: [Freesurfer] QDEC 5.0 with data from 4.x recon-all data

[Manabu Kubota]

Hi,

 I'm interested in this issue.
 If I use a former FreeSurfer version (ver. 4.x)  for all the
preprocessing of each data and apply the new QDEC in FreeSurfer ver.
5.0.0 JUST to make analyses easier (say, use of mri_glmfit-sim),
do I have to specify both FreeSurfer ver. 4.x and FreeSurfer 5.0.0 (or
QDEC ver 1.4) in the methodological section of research manuscripts?
Or is it enough to mention FreeSurfer ver. 4.x (and mri_glmfit-sim)
for the analyses?

 Best regards,

 Manabu

 Graduate school of medicine,
 Kyoto University

2010/10/1 Nick Schmansky ni...@nmr.mgh.harvard.edu:
 yes, you may use v5 qdec with prior processed data.

 n.


 On Thu, 2010-09-30 at 21:04 +0200, Christian Scheel wrote:
 Dear Mira,

 I posted a similar question some days ago. It seems to be possible to
 use the new qdec version for the group analysis for data that has been
 processed and cached with version 4.x (at least 4.05 and newer).

 Check this posting in the mailing archive:
 http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg15166.html

 Best wishes,
 Christian


 ---
 Christian Scheel
 University of Cologne
 Department of Psychiatry






 Am 30.09.2010 20:45, schrieb Mira Michelle Raman:
  Hi,
 I was wondering if it were possible/advisable to use data processed and 
  cached using earlier versions of FreeSurfe with the new 5.0 QDEC, since it 
  has enhanced capabilities.
 
  Sincerely,
  Mira
 
  Mira Michelle Raman
  Scientific Programmer
  Center for Interdisciplinary Brain Sciences Research
  Stanford University
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-- 
久保田　学　KUBOTA Manabu
kubot...@kuhp.kyoto-u.ac.jp
Department of Neuropsychiatry
Graduate School of Medicine, Kyoto University
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Re: [Freesurfer] squashed ascii coordinates of flattened patch

[Bruce Fischl]

Hi Eyal,

you need to make your axes square in matlab to unsquash it. Not sure what 
the other vertices are though. There is some code around that removes 
orphan vertices (ones that have no valid neighbors)

cheers
Bruce



On Fri, 1 Oct 
2010, Eyal Dechter wrote:

 Hi, I'm trying to get the coordinates of vertices on a flattened patch that
 I've cut out of an inflated surface using tksurfer in fs 4.5.0. I save the
 patch, use mris_flatten, and then mris_convert -p. However, the coordinates
 I'm getting render the patch somewhat distorted and I'm wondering how I can
 recover the original geometry. Loading the ascii file back into tksurfer
 results in the correct geometry, so is there some distortion that tksurfer
 accounts for when loading up a patch. At the link below I've put a screen
 shot of the ascii coordinates plotted (ignore the black line) and the flat
 patch as it looks in tksurfer. I've also put the patch files I'm using. Note
 how the patch seems squashed.

 http://web.mit.edu/~edechter/Public/

 After saving the patch I run:

 mris_flatten -w 10 patch_file patch_file.flat
 mris_convert -p patch_file.flat patch_file.flat.asc


 Also, there are a number of extraneous random vertices that show up in the
 ascii files. They are speckled around the patch in the left hand plot. What
 are these? And how do I get rid of them?

 Thanks,
 Eyal Dechter

 --
 edech...@mit.edu
 Kanwisher Lab
 MIT

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