Re: [Freesurfer] HeadSurface to MEG fiducials
hi Jose, why don't you use MNE for this? MNE is designed to work smoothly with FreeSurfer. http://martinos.org/mne/ Cheers, Alex On Thu, Apr 25, 2013 at 7:35 PM, José Ángel Pineda wrote: > Dear expert, > > I am doing source reconstruction with MEG. > > First, I am corregistering my head surface mesh from the freesurfer > (obtained with mkheadsurf) > to the headshape of the subject obtained with the Polhemus tracking system. > > So I already have one affine transformation (Aff_1) > > The head surface was obtained over the T1 image in voxel native space (not > orig.nii) > > The next step is to apply an affine transformation to the T1 to bring it > into the same coordinates as the headshape (and fiducials). > > Then I apply Aff_1 to the T1 and check the results. I observe there is an > offset displacement between the T1 and the fiducial points. > > I dont know what to do to solve this. I read that as my head surface is in > RAS space I should consider that, but Ive tried to correct this introducing > the affine tranformation matrices that are mentioned on the web for > Coordinates in Freesurfer, but Im not able to correct it. > > Could you please give me any advice? > > Thanks > > Jose > > -- > > José Angel Pineda Pardo > > Center of Biomedical Technology (CTB) > > Parque Científico y Tecnológico de la UPM > > Campus de Montegancedo > > 28223 Pozuelo de Alarcón, Madrid, ES > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] pb reading .annot in matlab/python
hi,
when trying to read the following .annot file:
https://dl.dropboxusercontent.com/u/2140486/annot_pb/left_mc-z.negative.sig.ocn.annot
using the following matlab code:
--
[vertices, label, colortable] =
read_annotation('left_mc-z.negative.sig.ocn.annot');
unique(label)
unique(colortable.table(:, end))
setdiff(colortable.table(:, end), unique(label))
--
there seem to be a discrepancy between the "label" and the last column
of colortable "colortable.table(:, end)"
the script outputs:
--
Reading from version 2
colortable with 7 entries read (originally none)
ans =
0 2244856 3987639 584081611298645
1369813416665710
ans =
2244856 3834223 3987639 584081611298645
1369813416665710
ans =
3834223
--
in other words 0 is in label but not in the colortable. Should I
conclude that 0 is 3834223?
If so what's the proper way of figuring this out?
thanks
Alex
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.
Re: [Freesurfer] pb reading .annot in matlab/python
hi doug,
I thought so. Did I miss something obvious? My version is:
% read_annotation.m
% Original Author: Bruce Fischl
% CVS Revision Info:
%$Author: nicks $
%$Date: 2011/03/02 00:04:12 $
%$Revision: 1.7 $
doc says:
colortable : Column 5 is the structure ID
Each component of the vector has a structureID value.
Why do I get 0 in label if 0 is not in colortable.table(:, end)?
thanks
Alex
On Mon, Aug 26, 2013 at 10:06 PM, Douglas N Greve
wrote:
> Hi Alex, have you looked at the read_annotation help?
> doug
>
>
>
>
> On 08/26/2013 03:37 PM, Alexandre Gramfort wrote:
>> hi,
>>
>> when trying to read the following .annot file:
>>
>> https://dl.dropboxusercontent.com/u/2140486/annot_pb/left_mc-z.negative.sig.ocn.annot
>>
>> using the following matlab code:
>>
>> --
>> [vertices, label, colortable] =
>> read_annotation('left_mc-z.negative.sig.ocn.annot');
>> unique(label)
>> unique(colortable.table(:, end))
>> setdiff(colortable.table(:, end), unique(label))
>> --
>>
>> there seem to be a discrepancy between the "label" and the last column
>> of colortable "colortable.table(:, end)"
>>
>> the script outputs:
>>
>> --
>> Reading from version 2
>> colortable with 7 entries read (originally none)
>> ans =
>> 0 2244856 3987639 584081611298645
>> 1369813416665710
>> ans =
>> 2244856 3834223 3987639 584081611298645
>> 1369813416665710
>> ans =
>> 3834223
>> --
>>
>> in other words 0 is in label but not in the colortable. Should I
>> conclude that 0 is 3834223?
>> If so what's the proper way of figuring this out?
>>
>> thanks
>> Alex
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> The information in this e-mail is intended only for the person to whom it is
> addressed. If you believe this e-mail was sent to you in error and the e-mail
> contains patient information, please contact the Partners Compliance HelpLine
> at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] pb reading .annot in matlab/python
hi Doug,
I am sorry but I still don't get it.
If:
label vector lookup of annotation values for
corresponding vertex index.
and label contains some 0 and 0 is not a valid id in colortable.table(:, 5)
what should I do with my vertices whose label is 0?
thanks
Alex
On Mon, Aug 26, 2013 at 11:52 PM, Douglas N Greve
wrote:
> ah, the newer version has a lot more info. See if this answers your question
> doug
>
> help read_annotation
> NAME
>
> function [vertices, label, colortable] = ...
> read_annotation(filename [,
> verbosity])
>
> ARGUMENTS
> INPUT
> filenamestring name of annotation file to read
>
> OPTIONAL
> verbosity int if true (>0), disp running output
> + if false (==0), be quiet and do
> not
> + display any running output
>
> OUTPUT
> verticesvector vector with values running from 0 to
> + size(vertices)-1
> label vector lookup of annotation values for
> + corresponding vertex index.
> colortable struct structure of annotation data
> + see below
>
> DESCRIPTION
>
> This function essentially reads in a FreeSurfer annotation file
> and returns structures and vectors that together
> assign each index in the surface vector to one of several
> structure names.
>
> COLORTABLE STRUCTURE
>
> Consists of the following fields:
> o numEntries: number of entries
> o orig_tab: filename of original colortable file
> o struct_names: cell array of structure names
> o table:n x 5 matrix
> Columns 1,2,3 are RGB values for struct color
> Column 4 is a flag (usually 0)
> Column 5 is the structure ID, calculated from
> R + G*2^8 + B*2^16 + flag*2^24
>
> LABEL VECTOR
>
> Each component of the vector has a structureID value. To
> match the structureID value with a structure name, lookup the row
> index of the structureID in the 5th column of the colortable.table
> matrix. Use this index as an offset into the struct_names field
> to match the structureID with a string name.
>
> PRECONDITIONS
>
> o must be a valid FreeSurfer annotation file.
>
> POSTCONDITIONS
>
> o will be an empty struct if not embedded in a
> FreeSurfer annotation file.
>
>
> On 08/26/2013 05:35 PM, Alexandre Gramfort wrote:
>>
>> hi doug,
>>
>> I thought so. Did I miss something obvious? My version is:
>>
>> % read_annotation.m
>> % Original Author: Bruce Fischl
>> % CVS Revision Info:
>> %$Author: nicks $
>> %$Date: 2011/03/02 00:04:12 $
>> %$Revision: 1.7 $
>>
>> doc says:
>>
>> colortable : Column 5 is the structure ID
>>
>> Each component of the vector has a structureID value.
>>
>> Why do I get 0 in label if 0 is not in colortable.table(:, end)?
>>
>> thanks
>> Alex
>>
>> On Mon, Aug 26, 2013 at 10:06 PM, Douglas N Greve
>> wrote:
>>>
>>> Hi Alex, have you looked at the read_annotation help?
>>> doug
>>>
>>>
>>>
>>>
>>> On 08/26/2013 03:37 PM, Alexandre Gramfort wrote:
>>>>
>>>> hi,
>>>>
>>>> when trying to read the following .annot file:
>>>>
>>>>
>>>> https://dl.dropboxusercontent.com/u/2140486/annot_pb/left_mc-z.negative.sig.ocn.annot
>>>>
>>>> using the following matlab code:
>>>>
>>>> --
>>>> [vertices, label, colortable] =
>>>> read_annotation('left_mc-z.negative.sig.ocn.annot');
>>>> unique(label)
>>>> unique(colortable.table(:, end))
>>>> setdiff(colortable.table(:, end), unique(label))
>>>> --
>>>>
>>>> there seem to be a discrepancy between the "label" and the last column
>>>> of colortable "colortable.table(:, end)"
>>>>
>>>> the script outputs:
>>>>
>>>> --
>>>> Reading from version 2
>>>> colortable with 7 entries read (originally none)
>>>> ans =
>>>> 0 2
Re: [Freesurfer] pb reading .annot in matlab/python
hi doug, this helps thanks. A next question is why can we have in the colortable a structureID that has no corresponding vertex with this label? In my example it was 3834223 but I get the same thing with "fsaverage/label/lh.aparc.annot" that has a 3294840 structureID not present in the label array. thanks Alex On Tue, Aug 27, 2013 at 6:32 PM, Douglas N Greve wrote: > > I think the 0s represent "unknown" areas. In this case, vertices that were > not part of any cluster. Does that make sense? > doug > > > > > On 08/27/2013 07:47 AM, Alexandre Gramfort wrote: >> >> hi Doug, >> >> I am sorry but I still don't get it. >> >> If: >> >> label vector lookup of annotation values for >> corresponding vertex index. >> >> and label contains some 0 and 0 is not a valid id in colortable.table(:, >> 5) >> what should I do with my vertices whose label is 0? >> >> thanks >> Alex >> >> >> >> On Mon, Aug 26, 2013 at 11:52 PM, Douglas N Greve >> wrote: >>> >>> ah, the newer version has a lot more info. See if this answers your >>> question >>> doug >>> >>> help read_annotation >>>NAME >>> >>> function [vertices, label, colortable] = ... >>> read_annotation(filename [, >>> verbosity]) >>> >>>ARGUMENTS >>>INPUT >>> filenamestring name of annotation file to read >>> >>>OPTIONAL >>> verbosity int if true (>0), disp running >>> output >>> + if false (==0), be quiet and >>> do >>> not >>> + display any running output >>> >>>OUTPUT >>> verticesvector vector with values running from >>> 0 to >>> + size(vertices)-1 >>> label vector lookup of annotation values for >>> + corresponding vertex index. >>> colortable struct structure of annotation data >>> + see below >>> >>>DESCRIPTION >>> >>> This function essentially reads in a FreeSurfer annotation file >>> and returns structures and vectors that together >>> assign each index in the surface vector to one of several >>> structure names. >>> >>>COLORTABLE STRUCTURE >>> >>> Consists of the following fields: >>> o numEntries: number of entries >>> o orig_tab: filename of original colortable file >>> o struct_names: cell array of structure names >>> o table:n x 5 matrix >>> Columns 1,2,3 are RGB values for struct color >>> Column 4 is a flag (usually 0) >>> Column 5 is the structure ID, calculated from >>> R + G*2^8 + B*2^16 + flag*2^24 >>> >>>LABEL VECTOR >>> >>> Each component of the vector has a structureID value. To >>> match the structureID value with a structure name, lookup the >>> row >>> index of the structureID in the 5th column of the >>> colortable.table >>> matrix. Use this index as an offset into the struct_names field >>> to match the structureID with a string name. >>> >>>PRECONDITIONS >>> >>> o must be a valid FreeSurfer annotation file. >>> >>>POSTCONDITIONS >>> >>> o will be an empty struct if not embedded in a >>>FreeSurfer annotation file. >>> >>> >>> On 08/26/2013 05:35 PM, Alexandre Gramfort wrote: >>>> >>>> hi doug, >>>> >>>> I thought so. Did I miss something obvious? My version is: >>>> >>>> % read_annotation.m >>>> % Original Author: Bruce Fischl >>>> % CVS Revision Info: >>>> %$Author: nicks $ >>>> %$Date: 2011/03/02 00:04:12 $ >>>> %$Revision: 1.7 $ >>>> >>>> doc says: >>>> >>>> colortable : Column 5 is the structure ID >>>> &g
Re: [Freesurfer] pb reading .annot in matlab/python
> For aparc, that is the corpus callosum. It just means that it was in the > color table when the annotation file was created. It is not necessary > that it be in the annotation itself. Can you ignore it? now that I have your approval to ignore it yes :) thanks all clear. Alex ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] recon-all issue (CSF seg as gray matter)
Hi, after running recon-all on many datasets without any manual intervention, it looks like I finally have to. As you can see in : https://dl.dropboxusercontent.com/u/2140486/Screen%20Shot%202013-08-28%20at%2013.16.52.png the CSF is segmented as gray matter while white+gray matters are merged. what's my best option to fix this? thanks Alex ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Downsampling/decimating overlays (not surfaces)
hi, what we do with MEG in the MNE package is indeed store downsampled overlays (that actually have a temporal dimension). More specifically we store the values e.g. only at the vertices of the ico5 subdivision and store the ico 5 vertex indices and overlay values. Then to display them on the high resolution freesurfer surface we basically use a smoothing/diffusion process to fill the missing values. For this downsampling to be valid you'll need to make sure the data are smooth enough in order to avoid aliasing. let me know if you need more details hope this helps, Alex On Thu, Jan 24, 2013 at 3:47 AM, Bruce Fischl wrote: > Hi Nicola > > I think this gets done in the MEG analysis stream, but perhaps Matti > (ccd) can comment. > cheers > BruceOn Thu, 24 Jan 2013, Nicola Toschi wrote: > >> Hello list, >> >> is there a quick way to decimate an overlay /while respecting surface >> geomery)? I am looking to downsample by about a factor 100. >> >> Alternatively, I know I can use mris_decimate to downsample a surface, but I >> would have to project my highres overlays onto the downsampled surface >> (which may not be straightforward). >> >> Thanks a lot in advance, >> >> Nicola >> >> PS apologies for the repost - my subject line was incorrect the first time >> around. >> >> > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the e-mail > contains patient information, please contact the Partners Compliance HelpLine > at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Fwd: Freesurfer Digest, Vol 98, Issue 29
hi all, @bruce : I've just given a try your own binaries in ~fischl/dev/freesurfer/bin/ and it worked fine. It looks like a bug has been fixed since the last stable release. Alex On Tue, Apr 24, 2012 at 10:44 PM, Andrew C Yourich wrote: > Sadly, I haven't been able to determine the problem yet. I have tested the > exact command that was suggested in both the Mac 5.1.0 version as well as the > Windows/Ubuntu 5.1.0 virtual machine version, and neither have seemed to > expand correctly when viewed in freeview. I won't have access to a machine > running Linux natively until tomorrow. A colleague who runs Freesurfer 5.0 > and 5.1.0 on a Linux machine is going to work with me to test if he has this > issue as well. > > Do you know if there have been any changes to the code of the mris_expand > binary since 4.0.2? If not, we may try using the mris_expand from that > version on the recon-all results from a 5.1.0 segmentation to see if the > issue truly is the expand binary or not. > > Any other suggestions you all have would be appreciated. > > Thanks, > Andrew > > From: Alexandre Gramfort [gramf...@nmr.mgh.harvard.edu] > Sent: Tuesday, April 24, 2012 3:24 PM > To: Andrew C Yourich > Subject: Fwd: Fwd: Freesurfer Digest, Vol 98, Issue 29 > > hi, > > have you fixed your problem? I still don't manage to make it work… > > thanks > Alex > > -- Forwarded message -- > From: Alexandre Gramfort > Date: Mon, Apr 23, 2012 at 7:10 PM > Subject: Re: Fwd: Freesurfer Digest, Vol 98, Issue 29 > To: Bruce Fischl > Cc: Nick Schmansky , ayour...@uab.edu, > Krish Subramaniam , Ruopeng Wang > > > >> not sure about the mac, I'll cc Nick, Krish and Ruopeng so that they can >> answer. > > could be due to my update of XCode this morning but things work fine > with freeview -f lh.white -v ../mri/T1.mgz > on my mac with lion. sorry for the noise > >> I built my own in ~fischl/dev/freesurfer/bin/freeview. Sure, put the >> surfaces somewhere I can look at them and I'll take a look > > see the files in : > > /homes/6/gramfort/cluster/work/data/MNE-sample-data/subjects/fsaverage/surf/lh.white.expanded > > that's the sample data we use for MNE. > > the log: > > $ mris_expand -thickness lh.white 0.5 lh.white.expanded > using distance as a % of thickness > expanding surface lh.white by 50.0% of thickness and writing it to > lh.white.expanded > reading thickness... > ending sse = 4485.856144 > nrounds = 6 > writing expanded surface to lh.white.expanded... > writing group avg surface area 822 cm^2 into surface file > surface expansion took 27 minutes and 15 seconds. > > Alex > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the e-mail > contains patient information, please contact the Partners Compliance HelpLine > at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Freeview chrash
Dear Ruopeng, to reproduce the problem with : MatrixMultiply: m2 is null! and the seg fault. $source /usr/local/freesurfer/nmr-stable51-env $cd ~gramfort/cluster/work/data/MNE-sample-data/subjects $setenv SUBJECTS_DIR $PWD $freeview -f sample/surf/lh.inflated if you cannot access this folder you can get it at: /cluster/fusion/sample_data/MNE-sample-data-processed.tar.gz Hope this helps, Alex On Wed, May 2, 2012 at 3:43 PM, Ruopeng Wang wrote: > Would it be possible to send us the surface file that caused the crash? > So that we can replicate the problem? > > Thanks, > Ruopeng > > On 5/2/12 9:35 AM, Focke, Niels wrote: >> Dear experts, >> >> I have experienced some problems with freeview. When loading a surface (both >> for my locally generated surfaces as well as for "bert" surfaces) the program >> exits (progress bar at approx. 10%) with this message: >> >> MatrixMultiply: m2 is null! >> >> The problem happens both for command line loading and GUI loading. Volume >> loading/viewing works fine. >> >> Has anyone had a similar problem? Or (even better) has a fix available? >> >> Version information: >> >> FREESURFER_HOME: /tools/freesurfer/live >> >> Build stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 >> >> RedHat release: CentOS release 5.7 (Final) >> >> Kernel info: Linux 2.6.18-274.el5 x86_64 >> >> >> Many thanks, >> >> >> Niels >> >> >> __ >> >> Dr. Niels Focke >> Klinische Neurophysiologie >> UMG - Universitätsmedizin Göttingen >> >> >> >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the e-mail > contains patient information, please contact the Partners Compliance HelpLine > at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Freeview chrash
> Alex, since you're in the Martinos center, can you try source the dev > version just to see if the same problem exists? I just tried after sourcing /usr/local/freesurfer/nmr-dev-env and got the same segfault with MatrixMultiply: m2 is null! I tried on the machine: megmix Alex ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] load multiple overlays with different colors
Hi Kathy,
subprocess.check_output
was introduced in python 2.7. You use 2.6
I recommend to upgrade if possible.
Otherwise we need to fix this
Alex
On Fri, May 4, 2012 at 3:44 PM, keepmoon wrote:
> Dear Michael,
>
> I try to install Python and Pysurfer following the instructions
> (using easy_install -U pysurfer and additional packages usingEPD). It
> didn't show error during the install process. Now I want to test it.
>
> In Terminal I typed:
>
> Pysurfer fsaverage lh infalted
> then it shows following:
>
> Traceback (most recent call last):
> File "/usr/local/bin/pysurfer", line 5, in
> pkg_resources.run_script('pysurfer==0.3', 'pysurfer')
> File
> "/Library/Python/2.6/site-packages/setuptools-0.6c11-py2.6.egg/pkg_resources.py",
> line 489, in run_script
>
> File
> "/Library/Python/2.6/site-packages/setuptools-0.6c11-py2.6.egg/pkg_resources.py",
> line 1207, in run_script
> # we assume here that our metadata may be nested inside a "basket"
> File
> "/Library/Python/2.6/site-packages/pysurfer-0.3-py2.6.egg/EGG-INFO/scripts/pysurfer",
> line 9, in
> from surfer._commandline import parser
> File
> "/Library/Python/2.6/site-packages/pysurfer-0.3-py2.6.egg/surfer/__init__.py",
> line 1, in
> from io import Surface
> File
> "/Library/Python/2.6/site-packages/pysurfer-0.3-py2.6.egg/surfer/io.py",
> line 3, in
> from subprocess import check_output
> ImportError: cannot import name check_output
>
>
>
> This means I didn't install successfully or where is wrong? The computer
> that I use is MacBook.
>
>
> Thanks for your help!
>
> Kathy
>
>
>
>
>
> On Wed, May 2, 2012 at 6:32 PM, Michael Waskom wrote:
>>
>> Hi,
>>
>> If you're somewhat handy with Python, you can use PySurfer for this.
>> See this example:
>> http://pysurfer.github.com/auto_examples/plot_fmri_conjunction.html
>>
>> Best,
>> Michael
>>
>> On Wed, May 2, 2012 at 7:51 AM, keepmoon
>> wrote:
>> > Dear all,
>> >
>> > I search my question before I post it. I did find similar questions, but
>> > didn't find answer. I want to overlay two files with different colors.
>> > For
>> > example, one is sig1.mgh from cortical thickness, the other is sig2.mgh
>> > from
>> > area. I want to use tksurfer overlaying them with three colors: red is
>> > significant regions of thickness; blue is significant regions of area;
>> > green
>> > is overlap significant regions of thickness and area.
>> >
>> > I tried to use the following command:
>> >
>> > tksurfer fsaverage lh inflated -annot aparc.annot -fthresh 2 -overlay
>> > sig1.mgh -overlay sig2.mgh
>> >
>> > It just can display sig1.mgh or sig2.mgh, but can't display two
>> > together. In
>> > addition, I don't know how to control overlap and other regions color.
>> >
>> > Anyone knows how to do this?
>> >
>> > Any help will be appreciated!
>> >
>> > Thanks in advance!
>> >
>> > Kathy
>> >
>> > ___
>> > Freesurfer mailing list
>> > Freesurfer@nmr.mgh.harvard.edu
>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> >
>> >
>> > The information in this e-mail is intended only for the person to whom
>> > it is
>> > addressed. If you believe this e-mail was sent to you in error and the
>> > e-mail
>> > contains patient information, please contact the Partners Compliance
>> > HelpLine at
>> > http://www.partners.org/complianceline . If the e-mail was sent to you
>> > in
>> > error
>> > but does not contain patient information, please contact the sender and
>> > properly
>> > dispose of the e-mail.
>> >
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> The information in this e-mail is intended only for the person to whom it is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] load multiple overlays with different colors
hi,
this problem has been reported and fixed.
You should install the latest hot fit with:
https://github.com/nipy/PySurfer/zipball/master
then do from the folder:
python setup.py install
HTH
Alex
On Sat, May 5, 2012 at 10:09 PM, keepmoon wrote:
> Hi Michael and Alex,
>
> Thanks for your suggestion about my question!
>
> I am trying to install Pysurfer to solve my problem (load multiple
> overlays with different colors). I have already installed all the software
> following the instruction (three software (1) epd-7.2-2-macosx-i386.dmg; (2)
> setuptools-0.6c11-py2.7.egg (md5); (3) python-2.7.3-macosx10.3.dmg).
>
>
>
> Now I test Pysurfer using command:
>
> Pysurfer fsaverage lh inflated
>
> It doesn’t work. The error is:
>
>
>
> % pysurfer fsaverage lh inflated
>
> Traceback (most recent call last):
>
> File "/Library/Frameworks/Python.framework/Versions/2.7/bin/pysurfer",
> line 5, in
>
> pkg_resources.run_script('pysurfer==0.3', 'pysurfer')
>
> File
> "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/setuptools-0.6c11-py2.7.egg/pkg_resources.py",
> line 489, in run_script
>
> File
> "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/setuptools-0.6c11-py2.7.egg/pkg_resources.py",
> line 1207, in run_script
>
> File
> "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/pysurfer-0.3-py2.7.egg/EGG-INFO/scripts/pysurfer",
> line 9, in
>
> from surfer._commandline import parser
>
> File
> "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/pysurfer-0.3-py2.7.egg/surfer/__init__.py",
> line 2, in
>
> from viz import Brain, TimeViewer
>
> File
> "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/pysurfer-0.3-py2.7.egg/surfer/viz.py",
> line 19, in
>
> from enthought.traits.api import (HasTraits, Range, Int, Float, \
>
> ImportError: No module named enthought.traits.api
>
>
>
> Then I tried to install enthought.traits.api.
>
> % easy_install enthought.traits.api
>
> Searching for enthought.traits.api
>
> Reading http://pypi.python.org/simple/enthought.traits.api/
>
> Couldn't find index page for 'enthought.traits.api' (maybe misspelled?)
>
> Scanning index of all packages (this may take a while)
>
> Reading http://pypi.python.org/simple/
>
> No local packages or download links found for enthought.traits.api
>
> error: Could not find suitable distribution for
> Requirement.parse('enthought.traits.api')
>
>
>
> I didn’t find suitable answer to this question. Could you give me some
> suggestions?
>
>
>
> Thanks
>
>
>
> Kathy
>
>
>
>
>
>
>
>
>
> On Wed, May 2, 2012 at 6:32 PM, Michael Waskom wrote:
>>
>> Hi,
>>
>> If you're somewhat handy with Python, you can use PySurfer for this.
>> See this example:
>> http://pysurfer.github.com/auto_examples/plot_fmri_conjunction.html
>>
>> Best,
>> Michael
>>
>> On Wed, May 2, 2012 at 7:51 AM, keepmoon
>> wrote:
>> > Dear all,
>> >
>> > I search my question before I post it. I did find similar questions, but
>> > didn't find answer. I want to overlay two files with different colors.
>> > For
>> > example, one is sig1.mgh from cortical thickness, the other is sig2.mgh
>> > from
>> > area. I want to use tksurfer overlaying them with three colors: red is
>> > significant regions of thickness; blue is significant regions of area;
>> > green
>> > is overlap significant regions of thickness and area.
>> >
>> > I tried to use the following command:
>> >
>> > tksurfer fsaverage lh inflated -annot aparc.annot -fthresh 2 -overlay
>> > sig1.mgh -overlay sig2.mgh
>> >
>> > It just can display sig1.mgh or sig2.mgh, but can't display two
>> > together. In
>> > addition, I don't know how to control overlap and other regions color.
>> >
>> > Anyone knows how to do this?
>> >
>> > Any help will be appreciated!
>> >
>> > Thanks in advance!
>> >
>> > Kathy
>> >
>> > ___
>> > Freesurfer mailing list
>> > Freesurfer@nmr.mgh.harvard.edu
>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> >
>> >
>> > The information in this e-mail is intended only for the person to whom
>> > it is
>> > addressed. If you believe this e-mail was sent to you in error and the
>> > e-mail
>> > contains patient information, please contact the Partners Compliance
>> > HelpLine at
>> > http://www.partners.org/complianceline . If the e-mail was sent to you
>> > in
>> > error
>> > but does not contain patient information, please contact the sender and
>> > properly
>> > dispose of the e-mail.
>> >
>
>
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
