Re: [Freesurfer] Complex value color scales.
There color wheel only works for complex, and there's currently no way to pass an arbitrary color map. We realize how annoying this is, though, and a future version of our surface viewer won't have this limitation. On Fri, 2007-03-23 at 16:38 -0500, Greg Appelbaum wrote: > Thanks for the info Kevin. The angle function is quite revealing. As it > happens I am looking at EEG data, which likely wasn't in mind in the > functional development of FreeSurfer. > > Might I also ask if you (the general FreeSurfer 'you') know if it's possible > to pass a 'wheel' scale bar to non-complex data? Or generally how to pass > in an arbitrary color map? > > Thanks again > > Greg > > > On 3/22/07 4:27 PM, "Kevin Teich" <[EMAIL PROTECTED]> wrote: > > > > >> I am trying to display phase information on the cortical surface using > >> tksurfer, > >> but am running into problems with the scale bar. Specifically when > >> plotting > >> scalar values using a complex color scale (e.g. RYGB Wheel), I am getting > >> nice > >> looking (continulus) cortical maps, with the correct scale values, but the > >> color bar is showing up inconsistent (two colors). Is there any way to > >> correct > >> this problem, or access the actual color values being projected to the > >> cortical > >> mesh? > > > > Unfortunately, the scale bar isn't really meant to be used with the > > complex color wheel. There is no way to get a nice legend for the color > > wheel. However, if you select View->Information->Angle, you can see the > > actual value that is being passed into the color function, so you can > > mouseover a color on the surface and see what value is mapped to it. I > > know it's not great, but maybe it will help a bit. > > > > > -- Kevin Teich ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Complex value color scales.
Thanks for the info Kevin. The angle function is quite revealing. As it happens I am looking at EEG data, which likely wasn't in mind in the functional development of FreeSurfer. Might I also ask if you (the general FreeSurfer 'you') know if it's possible to pass a 'wheel' scale bar to non-complex data? Or generally how to pass in an arbitrary color map? Thanks again Greg On 3/22/07 4:27 PM, "Kevin Teich" <[EMAIL PROTECTED]> wrote: > >> I am trying to display phase information on the cortical surface using >> tksurfer, >> but am running into problems with the scale bar. Specifically when plotting >> scalar values using a complex color scale (e.g. RYGB Wheel), I am getting >> nice >> looking (continulus) cortical maps, with the correct scale values, but the >> color bar is showing up inconsistent (two colors). Is there any way to >> correct >> this problem, or access the actual color values being projected to the >> cortical >> mesh? > > Unfortunately, the scale bar isn't really meant to be used with the > complex color wheel. There is no way to get a nice legend for the color > wheel. However, if you select View->Information->Angle, you can see the > actual value that is being passed into the color function, so you can > mouseover a color on the surface and see what value is mapped to it. I > know it's not great, but maybe it will help a bit. > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Re: Freesurfer Digest, Vol 37, Issue 21
Not being Roland and al...
On 23. Mar 2007, at 18:49 Uhr, [EMAIL PROTECTED]
wrote:
Message: 2
Date: Thu, 22 Mar 2007 15:18:05 -0400 (EDT)
From: Bruce Fischl <[EMAIL PROTECTED]>
Subject: Re: [Freesurfer] Re: Freesurfer Digest, Vol 37, Issue 16
To: Paul Aparicio <[EMAIL PROTECTED]>
Cc: freesurfer@nmr.mgh.harvard.edu
Message-ID:
<[EMAIL PROTECTED]>
Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed
no, definitely don't use COR. I think you can use mri_convert -i[ijk]s.
Rudolph: can you elaborate on how to do this?
here is what I use to accomplish this (in a csh script):
set targ_dir = /path/to/your/input_volumes
set targ_file_name = example.mgz
set conformed_vol = the_name_of_the_volume_with_faked_resolution.mgz
mri_convert -i ${targ_dir}/${targ_file_name} -o
${targ_dir}/${conformed_vol} -iis 1 -ijs 1 -iks 1
CAVEAT this expects isometric input scans, otherwise it gets a bit more
elaborate...:
this is what I used in the days of non-isometric scanning. It will
express all resolutions as multiples of the minmum so that resampling
later (by running mri_convert -cm ...) will do something reasonable.
You still have to make sure, that you have <= 256 voxels per
dimension...
ahoi & hope it helps
Sebastian
# silly script to follow...##
#! /bin/csh!
# run number from the dicom file zero padded to three digits
set run = 008
# number of the first dicom file to contain data for this run (actually
any dicom file for a run should do'?)
set first_dicom = 34840259
# the session to work on
set session_dir = 050610Lupo
set dicom_dir = 06131042
set user_id = moeller
# where does the dicom data live
set src_dir = /space/data/raw_data/20${session_dir}/
set src_file = $src_dir/$first_dicom
# where to put the cor files
set targ_base_dir =
/space/data/${user_id}/cooked/anatomicals/$session_dir/mri
mkdir $targ_base_dir
# the next one has to match the run number from the dicom information...
set targ_dir = $targ_base_dir/orig
# get the dimensions (read from unpack.log)
# let's do it like freesurfer does (no error checkin though)
set first_two_dims = `mri_probedicom --i $src_file --t 28 30`
# tag 28 30 is of form 0.453125\0.453125, so split the critter at the
back slash
#echo $first_two_dims
set first_dim = `echo "$first_two_dims" | awk '{split($0, a, "\\");
print a[1]}'`
#echo $first_dim
set second_dim = `echo "$first_two_dims" | awk '{split($0, a, "\\");
print a[2]}'`
#echo $second_dim
# the slice resolution either in tag 18 50 or 18 88
set third_dim = `mri_probedicom --i $src_file --t 18 50`
#echo $third_dim
# get the shortest dimension, all this requires gnu bc to be installed
set min_dim = `echo "min = $first_dim; if (min > $second_dim) { min =
$second_dim }; if (min > $third_dim) { min = $third_dim }; min" | bc
-l`
set iis = `echo "scale=6; $first_dim / $min_dim" | bc -l`
set ijs = `echo "scale=6; $second_dim / $min_dim" | bc -l`
set iks = `echo "scale=6; $third_dim / $min_dim" | bc -l`
#for unpacking at raw resolution
mri_convert -i $src_file -o $targ_dir -it siemens_dicom -ot mgh #-iis
$iis -ijs $ijs -iks $iks
#end of script...
###
--
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
Postfach 33 04 40
28359 Bremen
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[Freesurfer] Question about mri_surfcluster
Dear FreeSurfer Gurus I have two questions about surfcluster that I would appreciate some help with 1. What 'connectivity radius' is used in surfcluster? It seems to be hardwired, because I can't find a flag to specify it. By connectivity radius I do not mean the minimum cluster size that of course can be specified, but the minimum distance in mm that two vertexes can be within in order to be considered part of the same cluster on the surface. If this value is low, then clusters are probably defined as cases of adjacent vertexes (perhaps within 1 edge distance?), but I could see uses for changing this parameter so that 'adjacency' would be defined somewhat more liberally (especially in cases when smoothing is low). SUMA's surfclust has the -rad option that achieves this (["Maximum distance between an activated node and the cluster to which it belongs.Distance is measured on the surface's graph (mesh)"] and I was wondering if FreeSurfer has this option. If not, does anyone know what the hard coded value is? Knowing it will help choosing smoothing parameters on the surface. 2. When seeing the textual results of surfcluster, it is indeed very useful to see the Max T, cluster size and number of nodes in cluster. But, for purposes of some permutation algorithms, it would be extremely useful to be able to know the mean T value in each cluster. This enables calculating the *mass* of each cluster, defined roughly as the number of vertexes multiplied by the mean T value (Bullmore, 1999). This lets one normalize for T values, and define 'reliable' clusters are those that pass a certain mass, independent of their size.. Would it be possible to get the mean T value in each cluster as an output from surfcluster? Obviously one could script a utility that for each cluster, computes its mean T by cross referencing the cluster-tagged output with the T value of each vertex (pivot table by cluster), BUT, getting the mean cluster T directly from surfcluster would be a great feature. Thank you for your time and patience, Best, Uri ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] maximum number of ROI in atlas
Hello, I am modifying the 35-entries atlas by subdividing some parcels into N rois. Is there any limitation of the number of regions in an Atlas? Or an annotation file? Because when I have more than 300 region of interest in the atlas, the display of some region failed (gray) and the corresponding label became none. Do you know why? Leila ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Parts of tempral lobes not included
Hi Bruce: I appreciate if you could suggest how to intervene manually to fix this topology error - parts of superior & middle temporal regions not included in orig surface but included in brainmask & wm.mgz. Any suggestions is much appreciated. Thanks, Deepa. -- Deepa Ramasamy, MD Research Assistant Buffalo Neuroimaging Center The Jacobs Neurological Institute 100 High St. Buffalo, NY 14203 Work: 716-859-7038 E-Mail: [EMAIL PROTECTED] ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
