[Freesurfer] converting from siemens IMA to mgz
Hi all, I just loaded raw structural scans into one of my subject directories. They are of siemens IMA format and I used the following command: mri_convert -it siemens -ot mgz 001/ 001.mgz I then got the following error: reading from 001/... ERROR: could not parse 001/ ERROR: siemensRead(): 001/ I tried finding similar problems in the threads but nothing yet. Appreciate any help, Binyam Binyam Nardos Cognitive Rehabilitation Research Group Washington University School of Medicine Box # 8505 Forest Park Blvd St. Louis, MO 63108 Office: (314) 454-7795 Fax: (314) 286-1601 The contents of this e-mail message and any attachments are intended solely for the addressee(s) named in this message. This communication is intended to be and to remain confidential and may be subject to applicable physician/patient and/or work product privileges. If you are not the intended recipient of this message, or if this message has been addressed to you in error, please immediately alert the sender by reply e-mail and then delete this message and its attachments. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] converting from siemens IMA to mgz
specify one slice in the series and it will find the rest (not the directory) On Fri, 2 Feb 2007, Binyam Nardos wrote: Hi all, I just loaded raw structural scans into one of my subject directories. They are of siemens IMA format and I used the following command: mri_convert -it siemens -ot mgz 001/ 001.mgz I then got the following error: reading from 001/... ERROR: could not parse 001/ ERROR: siemensRead(): 001/ I tried finding similar problems in the threads but nothing yet. Appreciate any help, Binyam Binyam Nardos Cognitive Rehabilitation Research Group Washington University School of Medicine Box # 8505 Forest Park Blvd St. Louis, MO 63108 Office: (314) 454-7795 Fax: (314) 286-1601 The contents of this e-mail message and any attachments are intended solely for the addressee(s) named in this message. This communication is intended to be and to remain confidential and may be subject to applicable physician/patient and/or work product privileges. If you are not the intended recipient of this message, or if this message has been addressed to you in error, please immediately alert the sender by reply e-mail and then delete this message and its attachments. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] converting from siemens IMA to mgz
Hi Binyam, I think you need to give it the IMA file name, so something like: mri_convert -it siemens -ot mgz 001/file.IMA 001.mgz If that doesn't work there are other options we can try. Jenni On Fri, 2 Feb 2007, Binyam Nardos wrote: Hi all, I just loaded raw structural scans into one of my subject directories. They are of siemens IMA format and I used the following command: mri_convert -it siemens -ot mgz 001/ 001.mgz I then got the following error: reading from 001/... ERROR: could not parse 001/ ERROR: siemensRead(): 001/ I tried finding similar problems in the threads but nothing yet. Appreciate any help, Binyam Binyam Nardos Cognitive Rehabilitation Research Group Washington University School of Medicine Box # 8505 Forest Park Blvd St. Louis, MO 63108 Office: (314) 454-7795 Fax: (314) 286-1601 The contents of this e-mail message and any attachments are intended solely for the addressee(s) named in this message. This communication is intended to be and to remain confidential and may be subject to applicable physician/patient and/or work product privileges. If you are not the intended recipient of this message, or if this message has been addressed to you in error, please immediately alert the sender by reply e-mail and then delete this message and its attachments. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
RE: [Freesurfer] converting from siemens IMA to mgz
thanks Jenni .. I had to change my input file format to siemens_dicom although they were IMAs. It seems to be working now. Binyam Binyam Nardos Cognitive Rehabilitation Research Group Washington University School of Medicine Box # 8505 Forest Park Blvd St. Louis, MO 63108 Office: (314) 454-7795 Fax: (314) 286-1601 The contents of this e-mail message and any attachments are intended solely for the addressee(s) named in this message. This communication is intended to be and to remain confidential and may be subject to applicable physician/patient and/or work product privileges. If you are not the intended recipient of this message, or if this message has been addressed to you in error, please immediately alert the sender by reply e-mail and then delete this message and its attachments. -Original Message- From: Jenni Pacheco [mailto:[EMAIL PROTECTED] Sent: Fri 2/2/2007 10:40 AM To: Binyam Nardos Cc: Freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] converting from siemens IMA to mgz Hi Binyam, I think you need to give it the IMA file name, so something like: mri_convert -it siemens -ot mgz 001/file.IMA 001.mgz If that doesn't work there are other options we can try. Jenni On Fri, 2 Feb 2007, Binyam Nardos wrote: > Hi all, > I just loaded raw structural scans into one of my subject directories. They > are of siemens IMA format and I used the following command: > mri_convert -it siemens -ot mgz 001/ 001.mgz > > I then got the following error: > reading from 001/... > ERROR: could not parse 001/ > ERROR: siemensRead(): 001/ > > I tried finding similar problems in the threads but nothing yet. > > Appreciate any help, > Binyam > > > Binyam Nardos > Cognitive Rehabilitation Research Group > Washington University School of Medicine Box # 8505 > Forest Park Blvd > St. Louis, MO 63108 > Office: (314) 454-7795 > Fax: (314) 286-1601 > > > > The contents of this e-mail message and any attachments are intended solely > for the addressee(s) named in this message. This communication is intended to > be and to remain confidential and may be subject to applicable > physician/patient and/or work product privileges. If you are not the intended > recipient of this message, or if this message has been addressed to you in > error, please immediately alert the sender by reply e-mail and then delete > this message and its attachments. > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Variability and randomness in algorithms
Hi, Sorry to dredge up an old thread, I was curious about the details on where randomness is introduced in the following programs (beyond the normal floating points issues): > mris_smooth -seed 1234 > mris_sphere -seed 1234 > mris_fix_topology -seed 1234 > mris_ca_label -seed 1234 I assume that the Segonne, Grimson, and Fischl paper on the genetic algorithm for cortical surface correction applies to mris_fix_topology? Is it also the case that the randomness is injected in other min/maximization-type algorithms in the other functions? > RE: [Freesurfer] variability > Nick Schmansky > Thu, 21 Dec 2006 10:14:12 -0800 > > Valentina, > > The randomization in the algorithms accounts for about a 0.02% change > in thickness results. You can disable randomness (or rather, force > seeding the rng with same number) by including the flag -norandomness > with recon-all. This flag is available in v3.0.4. > > In older versions, do this to disable randomness: create a file called > xopts containing this text: > > mris_smooth -seed 1234 > mris_sphere -seed 1234 > mris_fix_topology -seed 1234 > mris_ca_label -seed 1234 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
RE: [Freesurfer] converting from siemens IMA to mgz
Yea, some siemens scanners/dicom servers produce dicom files with IMA extensions, which fools our software into thinking it is the old ima format. doug On Fri, 2 Feb 2007, Binyam Nardos wrote: thanks Jenni .. I had to change my input file format to siemens_dicom although they were IMAs. It seems to be working now. Binyam Binyam Nardos Cognitive Rehabilitation Research Group Washington University School of Medicine Box # 8505 Forest Park Blvd St. Louis, MO 63108 Office: (314) 454-7795 Fax: (314) 286-1601 The contents of this e-mail message and any attachments are intended solely for the addressee(s) named in this message. This communication is intended to be and to remain confidential and may be subject to applicable physician/patient and/or work product privileges. If you are not the intended recipient of this message, or if this message has been addressed to you in error, please immediately alert the sender by reply e-mail and then delete this message and its attachments. -Original Message- From: Jenni Pacheco [mailto:[EMAIL PROTECTED] Sent: Fri 2/2/2007 10:40 AM To: Binyam Nardos Cc: Freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] converting from siemens IMA to mgz Hi Binyam, I think you need to give it the IMA file name, so something like: mri_convert -it siemens -ot mgz 001/file.IMA 001.mgz If that doesn't work there are other options we can try. Jenni On Fri, 2 Feb 2007, Binyam Nardos wrote: Hi all, I just loaded raw structural scans into one of my subject directories. They are of siemens IMA format and I used the following command: mri_convert -it siemens -ot mgz 001/ 001.mgz I then got the following error: reading from 001/... ERROR: could not parse 001/ ERROR: siemensRead(): 001/ I tried finding similar problems in the threads but nothing yet. Appreciate any help, Binyam Binyam Nardos Cognitive Rehabilitation Research Group Washington University School of Medicine Box # 8505 Forest Park Blvd St. Louis, MO 63108 Office: (314) 454-7795 Fax: (314) 286-1601 The contents of this e-mail message and any attachments are intended solely for the addressee(s) named in this message. This communication is intended to be and to remain confidential and may be subject to applicable physician/patient and/or work product privileges. If you are not the intended recipient of this message, or if this message has been addressed to you in error, please immediately alert the sender by reply e-mail and then delete this message and its attachments. -- Douglas N. Greve, Ph.D. MGH-NMR Center [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] transforms
Hello all, Is there some information on the wiki about the srctoDst voxel-to-voxel transform and the rastoRAas transform? THAnks Chacko. Sucker-punch spam with award-winning protection. Try the free Yahoo! Mail Beta. http://advision.webevents.yahoo.com/mailbeta/features_spam.html ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] transforms
Chacko, There is this page: http://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems and there, open Doug Greve's PowerPoint file, which describes the transforms used within Freesurfer. N. On Fri, 2007-02-02 at 10:49 -0800, Chacko Cherian wrote: > Hello all, > Is there some information on the wiki about the > srctoDst voxel-to-voxel transform and the rastoRAas > transform? > > THAnks > Chacko. > > > > > > Sucker-punch spam with award-winning protection. > Try the free Yahoo! Mail Beta. > http://advision.webevents.yahoo.com/mailbeta/features_spam.html > ___ > 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
[Freesurfer] timecourse overlay
Hi Bruce: Is there a way that I can load the MEG timecourse data on the freesurfer surface? Is it possible that we could get the timecourse waveform for a specific point on the surface? Thanks! Tao ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Re: timecourse overlay
sure, if you save it in the right format. The easiest thing to do would
be to save it as a volume, where the 1st spatial dimension is # of
vertices on the surface, and the last (4th one) is the # of time points
(the 2nd and 3rd would both be 1). Or there are other formats you can save
in if you like, include our "w-file" format. I've attached a matlab file
for writing it.
cheers,
Bruce
On Fri, 2 Feb 2007, T. Song wrote:
Hi Bruce:
Is there a way that I can load the MEG timecourse data on the freesurfer
surface? Is it possible that we could get the timecourse waveform for a
specific point on the surface?
Thanks!
Tao
function err = write_wfile(fname, w, v)
% err = write_wfile(fname, w, )
%
% writes a vector into a binary 'w' file
% fname - name of file to write to
% w - vector of values to be written
% v - 0-based vertex numbers
% (assumes 0 to N-1 if not present or empty).
%
% See also read_wfile.
%
%
% write_wfile.m
%
% Original Author: Doug Greve
% CVS Revision Info:
%$Author: nicks $
%$Date: 2007/01/10 22:55:10 $
%$Revision: 1.2 $
%
% Copyright (C) 2002-2007,
% The General Hospital Corporation (Boston, MA).
% All rights reserved.
%
% Distribution, usage and copying of this software is covered under the
% terms found in the License Agreement file named 'COPYING' found in the
% FreeSurfer source code root directory, and duplicated here:
% https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferOpenSourceLicense
%
% General inquiries: freesurfer@nmr.mgh.harvard.edu
% Bug reports: [EMAIL PROTECTED]
%
err = 1;
if(nargin ~= 2 & nargin ~= 3)
fprintf('USAGE: err = write_wfile(fname, w, ) \n');
return;
end
vnum = length(w) ;
% Handle when v not given or is empty %
if(exist('v') ~= 1) v = []; end
if(isempty(v)) v = [0:vnum-1]; end
% open it as a big-endian file
fid = fopen(fname, 'wb', 'b') ;
if(fid == -1)
fprintf('ERROR: could not open %s\n',fname);
return;
end
fwrite(fid, 0, 'int16') ;
fwrite3(fid, vnum) ;
for i=1:vnum
fwrite3(fid, v(i)) ; % vertex number (0-based)
fwrite(fid, w(i), 'float') ; % vertex value
end
fclose(fid) ;
err = 0;
return
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Re: [Freesurfer] timecourse overlay
If the time course is in the proper format, then you can. It needs to be in one of the "volume" formats, eg mgh or mgh. The number of cols should equal the number of vertices, the number of rows = # of slices = 1, and the 4th dim is time. Then run tksurfer subject hemi surf -timecourse yourfile.mgh doug On Fri, 2 Feb 2007, T. Song wrote: Hi Bruce: Is there a way that I can load the MEG timecourse data on the freesurfer surface? Is it possible that we could get the timecourse waveform for a specific point on the surface? Thanks! Tao ___ 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 [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Re: timecourse overlay
Actually, I think the w file only holds one time point, so that prob
wont work. If you want to go the matlab route, you can do something
like:
mri_convert lh.curv lh.curv.mgh # convert to mgh for a template
then in matalb
f = MRIread('lh.curv.mgh');
f will be a struct
f.vol will be a 4d matrix of size 1 x nverices x 1 x 1
Just change f.vol to your data (packing the time dim appropriately),
then
MRIwrite(f,'yourdata.mgh');
On Fri, 2 Feb 2007, Bruce Fischl wrote:
sure, if you save it in the right format. The easiest thing to do would be to
save it as a volume, where the 1st spatial dimension is # of vertices on the
surface, and the last (4th one) is the # of time points (the 2nd and 3rd
would both be 1). Or there are other formats you can save in if you like,
include our "w-file" format. I've attached a matlab file for writing it.
cheers,
Bruce
On Fri, 2 Feb 2007, T. Song wrote:
Hi Bruce:
Is there a way that I can load the MEG timecourse data on the freesurfer
surface? Is it possible that we could get the timecourse waveform for a
specific point on the surface?
Thanks!
Tao
--
Douglas N. Greve, Ph.D.
MGH-NMR Center
[EMAIL PROTECTED]
Phone Number: 617-724-2358
Fax: 617-726-7422
In order to help us help you, please follow the steps in:
surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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Re: [Freesurfer] Re: timecourse overlay
oops, you're right. Anders wrote another format for multiple time points,
but I can't seem to find it. The volume is the best way to go these
days though.
Bruce
On Fri, 2 Feb 2007, Doug Greve
wrote:
Actually, I think the w file only holds one time point, so that prob
wont work. If you want to go the matlab route, you can do something
like:
mri_convert lh.curv lh.curv.mgh # convert to mgh for a template
then in matalb
f = MRIread('lh.curv.mgh');
f will be a struct f.vol will be a 4d matrix of size 1 x nverices x 1 x 1
Just change f.vol to your data (packing the time dim appropriately),
then
MRIwrite(f,'yourdata.mgh');
On Fri, 2 Feb 2007, Bruce Fischl wrote:
sure, if you save it in the right format. The easiest thing to do would be
to save it as a volume, where the 1st spatial dimension is # of vertices on
the surface, and the last (4th one) is the # of time points (the 2nd and
3rd would both be 1). Or there are other formats you can save in if you
like, include our "w-file" format. I've attached a matlab file for writing
it.
cheers,
Bruce
On Fri, 2 Feb 2007, T. Song wrote:
Hi Bruce:
Is there a way that I can load the MEG timecourse data on the freesurfer
surface? Is it possible that we could get the timecourse waveform for a
specific point on the surface?
Thanks!
Tao
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[Freesurfer] total brain volume
I would like to calculate total brain volume (defined as: total white, gray, and subcortical altogether). Should I take the BrainSegVol and minus out cerebellum and ventricles, or add the white and gray matter volumes from mris_anatomical_stats (it seems I remember hearing that white matter from mris_anatomical_stats is not reliable)? Thanks. -Derin ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] total brain volume
Hi Derin, the aseg labeling of cortical gm is not that accurate - the surfaces are quiet a bit more so. We have a new tool for generating the estimate of the gm and wm volume from the surfaces called mris_volume and mris_wm_volume. I think Doug or Nick has integrated it into the dev version of recon-all. cheers, Bruce On Fri, 2 Feb 2007, Derin Cobia wrote: I would like to calculate total brain volume (defined as: total white, gray, and subcortical altogether). Should I take the BrainSegVol and minus out cerebellum and ventricles, or add the white and gray matter volumes from mris_anatomical_stats (it seems I remember hearing that white matter from mris_anatomical_stats is not reliable)? Thanks. -Derin ___ 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
Re: [Freesurfer] total brain volume
Bruce, So if I downloaded the dev version of the program I could use it to get the volumes from subjects processed with 3.0.3? And would adding these volumes together generate the total volume I'm looking for (including subcoritical)? Thanks! -Derin > Hi Derin, > > the aseg labeling of cortical gm is not that accurate - the surfaces are > quiet a bit more so. We have a new tool for generating the estimate of the > gm and wm volume from the surfaces called mris_volume and mris_wm_volume. > I > think Doug or Nick has integrated it into the dev version of recon-all. > > cheers, > Bruce > > > On Fri, 2 Feb 2007, Derin Cobia wrote: > >> I would like to calculate total brain volume (defined as: total white, >> gray, and subcortical altogether). Should I take the BrainSegVol and >> minus out cerebellum and ventricles, or add the white and gray matter >> volumes from mris_anatomical_stats (it seems I remember hearing that >> white >> matter from mris_anatomical_stats is not reliable)? Thanks. >> >> -Derin >> >> >> ___ >> 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 > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] total brain volume
you would need to add in whatever subcortical components you wanted to include, as they are excluded from the wm volume On Fri, 2 Feb 2007, Derin Cobia wrote: Bruce, So if I downloaded the dev version of the program I could use it to get the volumes from subjects processed with 3.0.3? And would adding these volumes together generate the total volume I'm looking for (including subcoritical)? Thanks! -Derin Hi Derin, the aseg labeling of cortical gm is not that accurate - the surfaces are quiet a bit more so. We have a new tool for generating the estimate of the gm and wm volume from the surfaces called mris_volume and mris_wm_volume. I think Doug or Nick has integrated it into the dev version of recon-all. cheers, Bruce On Fri, 2 Feb 2007, Derin Cobia wrote: I would like to calculate total brain volume (defined as: total white, gray, and subcortical altogether). Should I take the BrainSegVol and minus out cerebellum and ventricles, or add the white and gray matter volumes from mris_anatomical_stats (it seems I remember hearing that white matter from mris_anatomical_stats is not reliable)? Thanks. -Derin ___ 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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] total brain volume
I have not implemented it in recon-all yet. doug On Fri, 2 Feb 2007, Bruce Fischl wrote: you would need to add in whatever subcortical components you wanted to include, as they are excluded from the wm volume On Fri, 2 Feb 2007, Derin Cobia wrote: Bruce, So if I downloaded the dev version of the program I could use it to get the volumes from subjects processed with 3.0.3? And would adding these volumes together generate the total volume I'm looking for (including subcoritical)? Thanks! -Derin Hi Derin, the aseg labeling of cortical gm is not that accurate - the surfaces are quiet a bit more so. We have a new tool for generating the estimate of the gm and wm volume from the surfaces called mris_volume and mris_wm_volume. I think Doug or Nick has integrated it into the dev version of recon-all. cheers, Bruce On Fri, 2 Feb 2007, Derin Cobia wrote: I would like to calculate total brain volume (defined as: total white, gray, and subcortical altogether). Should I take the BrainSegVol and minus out cerebellum and ventricles, or add the white and gray matter volumes from mris_anatomical_stats (it seems I remember hearing that white matter from mris_anatomical_stats is not reliable)? Thanks. -Derin ___ 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 ___ 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 [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] input registration matrix
Hello All, After making changes using tkregister2 the input registration matrix changes.IS there an 'optimum' input registration matrix that i should try to get.I notice that the closer the values(last column of the input reg matrix) are to zero the better the outcome. Thanks in advance. Chacko. Now that's room service! Choose from over 150,000 hotels in 45,000 destinations on Yahoo! Travel to find your fit. http://farechase.yahoo.com/promo-generic-14795097 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] some questions about volumes of aseg, .aparc, .aparc.2005s
.Bold { font-weight: bold; }
.Title { font-weight: bold; font-size: 18px; color: #cc3300; }
.Code { border: #8b4513 1px solid; padding-right: 5px; padding-left: 5px;color:
#66; font-family: 'Courier New' , Monospace;background-color: #ff9933; }
Dear Freesurfer experts.
I have some questions about calculated volumes by freesurfer.
1. Are the volumes in aseg, .aparc, .aparc.2005s absolute volumes measured in
naive space
or volumes measured after spatial normalization.
2. How much accurate the volumes (hippocampus, amygdala, thalamus, insula,
precentral, etc)
in aseg, .aparc, .aparc.2005s. And they are verified?
3. Are the volumes in lh(or rh).aparc gray matter volumes?
4. What is meaning G_*, and S_* in lh(or rh).aparc.a2005s?
5. How can I separately see the strucures of .aparc, .aparc.2005s in pial
surface rendering?
Woo Suk, Tae Ph.D
Seoul, Korea
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