Hi Bruce,
Thanks for the reply. So I will do recon-all -talairach for all subjects
using version 4.30 and obtain the new eTIV, keeping the segmentation and
surface data unchanged. Is that the correct way? And can someone please help
me with problem #1?
Thanks,
Zheng Hui
On 8/4/09 20:51, "Bruce
It's probably the case that it's badly scaled (eg, the age regressor is
10 or 100 times the other regressors). Try dividing the age by 10 or 100.
doug
Lusineh Gharapetian wrote:
Hello,
I'm trying to use the mri_glmfit function but keep running into the
same error.
I am using the FSGD forma
Hello,
I'm trying to use the mri_glmfit function but keep running into the same
error.
I am using the FSGD format and have set up my fsgd file according to the
tutorial instructions:
" GroupDescriptorFile 1
Title mci_age_BNTchange
Class Male
Class Female
VariablesAge BNTchang
Jamie,
The script would contains lines like this:
set SUBJECTS=(subj1 subj2 subj3 subj4)
set ONE_SUBJECT=(subj3)
When rebuilding the atlas of 40 subjects on our cluster, where each
subject gets its own node, it takes about 2 days. so on a single
machine, about 80 days.
Nick
On Wed, 2009-0
John,
I'm glad to see someone checks these! I had to upload a new version of
4.3.0 a couple days after it was first released, because some files
pertaining to aparcstats2table and asegstats2table were missing. But I
forgot to upload the md5sum.txt file, which I have just done. The
md5sums you c
Falk,
Because the -hires switch disables the use the atlas during the skull-
strip step, skull-stripping is more subject to stripping too much or too
little brain (which is why use of the atlas was introduced). See this
tutorial for ways to correct badly stripped skull:
http://surfer.nmr.mgh.har
Hi Jamie,
SUBJECTS should specify all the subjects you want to put in the atlas (all
the manually labeled ones).
cheers
Bruce
On Wed, 8 Apr 2009, Jamie Hanson wrote:
so that it just runs the command locally. note that this script submits
multiple subjects to multiple nodes, so if you have
> so that it just runs the command locally. note that this script submits
> multiple subjects to multiple nodes, so if you have 30 subjects, and you
> dont use a cluster, it will take much much much longer to complete.
Hi Nick-
I am working on that script right now. One quick question about this
Mishkin,
This will create what you want:
cd subj/label
mri_annotation2label --subject subj \
--hemi lh \
--annotation aparc \
--seg lh.aparc.mgh
replacing subj and lh with appropriate.
then type:
mris_convert -c ./lh.aparc.mgh \
../surf/lh.white \
lh.aparc.asc
and the output file (l
Jamie,
Included in the $FREESURFER_HOME/bin directory is a script called
'rebuild_gca_atlas.csh' that we use to rebuild our atlas. You will need
to read and understand this script as some edits to it will need to be
made. It contains descriptive text within the file.
The script is intended to
run
yum list | grep vtk | grep png
Sent from my Nokia phone @E71
-Msg original-
De: Derin Cobia
Enviada: 08/04/2009 15:56:27
Assunto: [Freesurfer] libvtkpng.so.5.2 missing?
We're running subjects under the new 4.3.0 version (CentOS 4
platform), and are experiencing the following erro
We're running subjects under the new 4.3.0 version (CentOS 4
platform), and are experiencing the following error during the
cortical ribbon mask stage:
#...@# Cortical ribbon mask Wed Apr 8 07:12:20
Actually, the --statsfile switch makes more sense. I'll maintain that
backwards compatibility towards --stats too.
So, NMR center users should have the update as early as tomorrow
( where they can specify either --stats or --statsfile
) and others should get it in our next stable release.
Hi Tori
the --statsfile option is now --stats i.e use --stats name> That in conjuction with --subdir will work.
I'll update the documentation ( which still says --statsfile and is
wrong... sorry! )let me know how it goes.
Thanks
Krish
On Apr 8, 2009, at 10:36 AM, Victoria Williams wrote:
Hello,
I am having a bit of trouble using asegstats2table. I have tried using
different versions of this command and if only I could combine the two, it
would work perfectly. I am trying to compile wmparc stats for about 160
subjects.
Unlike the new aparcstats2table, asegstats2table seems to
Hello,
I am having a problem downloading the latest version of freesurfer 4.3.
On 2 separate servers on 2 separate days I get the same md5sum which does not
match the md5sums listed in the md5sum file in the downloads section.
your md5s
29450bd531d94909cc858384551d43b0
freesurfer-Linux-c
Hi Nick,
First I wanted to give you a little bit of feedback. I'm still processing
one volume with .6mm which is working perfectly fine until now. The skull
stripping was done really well and no manual intervention was needed. I'm
currently running autorecon3 and will have a look at the final resu
Hi Zheng,
I'll leave 2 for Nick. As for 1, we don't use the tal very much, and a
bad tal will not affect your thickness estimates. The newer versions
rarely have a bad tal since we changed over to Avi Synder's code (which
also fixes the problems we had with eTIV). You can manually correct it
Hi all,
I have two problems here.
1. talairach.xfm
By browsing through the mailing list, it seems that talairach.xfm was
not used much in the recon-all process which is quite different from the
table given at
https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllFilesVsSteps. We did find
many su
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