[Freesurfer] gca atlas creation
Dear FreeSurfer expertsHapp new year to all of you, and thanx for all your help along the past 2012.I would like to make some questions regardins a new atlas creation1) In a first step before mri_ca_train I did use mri_ca_normalize to normalize my FS_MNI152average subject to the JHU.ICBMtracts.1mm.mgz but this create an empty norm.mgz, is this normal? whean I saw that the norm.mgz was empty I decide to create all the files by:recon-all -s My_MNI152_avg -autorecon1 -autorecon2-inflate1, that create all files as normally does with my every other subjects; Then I run mri_ca_train, using as -mask the brain.mgz, as -T1 the norm.mgz created during recon-all, directed to my FS_MNI251average subject, and as -parc_dir JHU.ICBMtracts.1mm..mgz; as result got the .gca and a mgh fileI use the load_gca.m to check the .gca created, but get the next error message:"version 5 in file $JHU.ICBMtracts_12_2012.gca incorrect - not a known gca file"2) Is there any way to check at the gca file created? just to make myself sure that everything is placed in the right way3) And lastly, Which is the next step to parcellate the WM of all my subjects as the new atlas? Can I use this gca file with mris_ca_label? or some other tool will be better?Many thanks in advanced,Gabriel. ___ 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] about ROI
Dear experts I has obtained the ROI by analysis, I want to obtain the label of this ROI, whether has the command to direct keep label, not drawing this ROI? thanks! Bo Xiang___ 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] gca atlas creation
Hi Gabriel what are you trying to achieve? There's no point in building a gca from a single average subject. The gca is typically built be compiling statistics across many subjects. Not sure if you need the answers any longers but (1) you can view the gca with freeview as it if were an image file (append #0 and #1 for viewing different "frames", in this case that denotes max probability label and mean intensity of that label). (2) the norm.mgz definitely shouldn't be empty, and (3) yes, mri_ca_label would be the right tool cheers Bruce On Wed, 2 Jan 2013, Gabriel Gonzalez Escamilla wrote: > Dear FreeSurfer experts > > Happ new year to all of you, and thanx for all your help along the past 2012. > > I would like to make some questions regardins a new atlas creation > > 1) In a first step before mri_ca_train I did use mri_ca_normalize to > normalize my FS_MNI152average subject > to the JHU.ICBMtracts.1mm.mgz but this create an empty norm.mgz, is this > normal? > whean I saw that the norm.mgz was empty I decide to create all the files by: > recon-all -s My_MNI152_avg -autorecon1 -autorecon2-inflate1, that create all > files as normally does with > my every other subjects; > > Then I run mri_ca_train, using as -mask the brain.mgz, as -T1 the norm.mgz > created during recon-all, > directed to my FS_MNI251average subject, and as -parc_dir > JHU.ICBMtracts.1mm..mgz; as result got the .gca > and a mgh file > I use the load_gca.m to check the .gca created, but get the next error > message: > "version 5 in file $JHU.ICBMtracts_12_2012.gca incorrect - not a known gca > file" > 2) Is there any way to check at the gca file created? just to make myself > sure that everything is placed > in the right way > > 3) And lastly, Which is the next step to parcellate the WM of all my subjects > as the new atlas? Can I use > this gca file with mris_ca_label? or some other tool will be better? > > > Many thanks in advanced, > Gabriel. > > ___ 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] fscalc / mris_calc problem
Fred, You can try an updated mris_calc for the mac found here: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/macos-leopard-intel/ Nick On Mon, 2012-12-31 at 13:21 +0200, Rudolph Pienaar wrote: > Hi Fred -- > > I'm currently traveling and have limited internet connectivity. I'll be back > at the office later in the week and will take a look then. > > In the meantime, has this ever worked for you previously? I know that older > versions of 'mris_calc' were somewhat particular about filename lengths and > filename conventions, and you might be seeing the same bug here... > > Best > -=R > > Sent from my iPad > > On Dec 28, 2012, at 7:50, Fred Lado wrote: > > > Hi FreeSurfer Gurus, > > I am having difficulty invoking the 'upl' and 'lrl' operations in > > mris_calc. The following is the message I get for 'upl': > > > > /usr/local/freesurfer/bin/fscalc rh.dat.mgh upl 20 --o tmp.mgh > > > > freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0 > > Darwin Fred-Lados-MacBook-Pro.local 12.2.0 Darwin Kernel Version 12.2.0: > > Sat Aug 25 00:48:52 PDT 2012; root:xnu-2050.18.24~1/RELEASE_X86_64 x86_64 > > mri_convert rh.dat.mgh ./tmpdir.fscalc.5004/tmp.mgh > > mri_convert rh.dat.mgh ./tmpdir.fscalc.5004/tmp.mgh > > $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ > > reading from rh.dat.mgh... > > TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 > > i_ras = (-1, -0, 0) > > j_ras = (-0, -1, 0) > > k_ras = (-0, -0, -1) > > writing to ./tmpdir.fscalc.5004/tmp.mgh... > > -- > > mris_calc -o ./tmpdir.fscalc.5004/tmp.mgh ./tmpdir.fscalc.5004/tmp.mgh upl > > 20 > > Unknown operation upl failed. > > > > No such file or directory > > > > Fred Lado, MD PhD > > Director, Neurology Service - Moses & North Divisions > > Director, EEG Laboratory > > Associate Clinical Professor of Neurology > > Montefiore Medical Center > > 718-920-8499 office > > 718-324-3730 fax > > email: ladof...@gmail.com > > > > > > > > > > > > > > > > > > > > ___ > > 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 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] FW: how to obtain MRI coordinates of scalp surface points marked in tksurfer
HI, I created a scalp surface mesh with mkheadsurf. I need to mark or select some scalp surface points and obtain their MRI coordinates. That is, if my MRI is 256-cubed I need the (ix,iy,iz) MRI voxel coordinates closest to the scalp mesh point I mark, where these run from 1 to 256 (or 0-255 if you must). The tksurfer display shows several types of floating point coordinates, but they assume an origin in the center of the head somewhere. If I knew the MRI coordinates of this origin I could calculate the original MRI. Thanks, -Jeff ___ 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] FW: how to obtain MRI coordinates of scalp surface points marked in tksurfer
Hi Jeff The coordinate conversions are documented on our wiki. Or you could do the marking in tkmedit or freeview which will show you voxel and surface RAS coords. There might also be an option to view them in tksurfer too, I can't remember (view->information or something like that) Cheers Bruce On Jan 2, 2013, at 7:43 PM, Jeff Eriksen wrote: > HI, > > I created a scalp surface mesh with mkheadsurf. I need to mark or select some > scalp surface points and obtain their MRI coordinates. That is, if my MRI is > 256-cubed I need the (ix,iy,iz) MRI voxel coordinates closest to the scalp > mesh point I mark, where these run from 1 to 256 (or 0-255 if you must). The > tksurfer display shows several types of floating point coordinates, but they > assume an origin in the center of the head somewhere. If I knew the MRI > coordinates of this origin I could calculate the original MRI. > > Thanks, > -Jeff > > ___ > 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.
