[Freesurfer] converting IMA files

Hello, I am a Freesurfer newbie trying to use the mri_convert command to convert IMA format files to either nii or nifti1 format files. Whenever I run the command I get an error at the very end saying that it failed to write (please see below for the exact output error that was displayed). Any hel

Re: [Freesurfer] converting IMA files

Hi Doug, I have plenty of disk space available. I am currently running freesurfer-Darwin-leopard-ppc-stable-pub-v5.0.0. Best, Lisa On Fri, Oct 8, 2010 at 11:10 AM, Douglas N Greve wrote: > Are you running out of disk space? What version of FS are you using? > > doug > >

Re: [Freesurfer] converting IMA files

Any suggestions? Best, Lisa __ On Fri, Oct 8, 2010 at 11:14 AM, Lisa F. Akiyama wrote: > Hi Doug, > > I have plenty of disk space available. > I am currently running freesurfer-Darwin-leopard-ppc-stable-pub-v5.0.0. > > > Best, > Lisa &

[Freesurfer] Source matrix with zero determinant

: Loading volume 001.mgz > > Couldn't read the anatomical volume. > > Tkmedit couldn't read the volume you specified. > This could be because the image format wasn't recognized, > or it couldn't find the proper header, > or the

Re: [Freesurfer] Source matrix with zero determinant

l-to-ras determinant 0 ras to voxel transform: mat = NULL! MatrixFree: NULL mat POINTER! Thank you. Best, Lisa ______ Lisa F. Akiyama Research Study Assistant Institute for Learning & Brain Sciences (I-LABS) University of Washington P Please consider the environment bef

Re: [Freesurfer] Source matrix with zero determinant

#x27;t 0, recon-all -autorecon1 should work? Thanks. Best, Lisa ______ Lisa F. Akiyama Research Study Assistant Institute for Learning & Brain Sciences (I-LABS) University of Washington P Please consider the environment before printing this e-mail. On Fri, Oct 2

Re: [Freesurfer] Source matrix with zero determinant

Hi Doug, Thanks for the tips. I will look into putting all the slices into one volume. Best, Lisa __ Lisa F. Akiyama Research Study Assistant Institute for Learning & Brain Sciences (I-LABS) University of Washington P Please consider the environment before prin

[Freesurfer] talairach.xfm and talairach_avi

Hello, Are there any documentations on the details of the talairach_avi command and the 3x4 matrix (talairach.xfm) output? Thank you. Best, Lisa Akiyama __ Lisa F. Akiyama Research Study Assistant Institute for Learning & Brain Sciences (I-LABS) Universit

Re: [Freesurfer] talairach.xfm and talairach_avi

Linear_Transform = >1.055506230.03465762 -0.08214028 -3.92954969 >0.023125341.039396760.38879746 -13.37033176 >0.00010875 -0.351719381.10944259 -10.23139286* * > * *Thank you. Best, Lisa __________ Lisa F. Akiyama Research Study Assistant I

[Freesurfer] Using another atlas besides "talaraich" (mni305)?

Hi FreeSurfers, Is it possible to tranform a MRI to an atlas that is not "talairach" (MNI305 atlas) using the talairach_avi command or using another command in FreeSurfer? Thank you. Best, Lisa ______ Lisa F. Akiyama Research Study Assistant Institute fo

Re: [Freesurfer] talairach.xfm and talairach_avi

Hi Martin, Thanks for the detailed explanation! I think I've got it down now. Best, Lisa __ Lisa F. Akiyama Research Study Assistant Institute for Learning & Brain Sciences (I-LABS) University of Washington P Please consider the environment before printi

[Freesurfer] Run skullstrip only?

beneficial for preparing the MRIs for skullstripping. I've attached the snapshot of brainmask.mgz to this email. Thanks in advance. Best, Lisa __ Lisa F. Akiyama Research Study Assistant Institute for Learning & Brain Sciences (I-LABS) University of Washington

Re: [Freesurfer] Run skullstrip only?

Hi Doug, I'm trying to skull strip in order to do something outside of freesurfer. Thanks - I will try running mri_watershed. Best, Lisa __ Lisa F. Akiyama Research Study Assistant Institute for Learning & Brain Sciences (I-LABS) University of Washingt

[Freesurfer] Saving individual slices within a nifti file

Hello, Is there a way to individually save slices within a nifti file in the nifti format using the mri_convert command? Thank you. Best, Lisa __ Lisa F. Akiyama Research Study Assistant Institute for Learning & Brain Sciences (I-LABS) University of Washingt

Re: [Freesurfer] Saving individual slices within a nifti file

=0.00, flip angle=0.00 i_ras = (1, 0, 0) j_ras = (0, 1, 0) k_ras = (0, 0, 1) writing to /usr/local/freesurfer/subjects/mni305_minc/average_305_test_slice0.nii... Could you guide me on what I am doing wrong? Thanks. Best, Lisa __ Lisa F. Akiyama Research Study Assistant

Re: [Freesurfer] Saving individual slices within a nifti file

Hi Doug, Thanks for the tips. It is working now. Best, Lisa __ Lisa F. Akiyama Research Study Assistant Institute for Learning & Brain Sciences (I-LABS) University of Washington Portage Bay Building, BOX 357988 Seattle, WA 98195-7988 U.S.A. E-mail: lris...@uw

[Freesurfer] mri_convert batch conversion of ima files

.2 2010/08/10 19:11:50 greve Exp $ > reading from 393-2-4.ima... > rows = 256 > cols = 256 > TR=11.40, TE=4.40, TI=300.00, flip angle=15.00 > i_ras = (-0, -1, -0) > j_ras = (-0, 0, -1) > k_ras = (-1, 0, 0) > writing to kh4.nii... > __ Lisa F

Re: [Freesurfer] mri_convert batch conversion of ima files

x_s = -0., y_s = -1., z_s = 0., c_s = -10.2740 INFO: set hdr.hist.orient to 'transverse unflipped' ______ Lisa F. Akiyama Research Study Assistant Institute for Learning & Brain Sciences (I-LABS) University of Washington E-mail: lris...@uw.edu P Pl

Re: [Freesurfer] mri_convert batch conversion of ima files

Hi Doug, Alright. I'll try doing that. Thanks for the information. Best, Lisa __ Lisa F. Akiyama Research Study Assistant Institute for Learning & Brain Sciences (I-LABS) University of Washington Portage Bay Building, BOX 357988 Seattle, WA 98195-7988 U.S.

[Freesurfer] mri_head

0 0.00 0.00 c ras = -4.403150 -14.970646 -10.273973 det(xyz_ras) = -1.00 ras_good_flag = 1 brightness = 1 subject_name = path_to_t1 = fname_format = __ Lisa F. Akiyama Research Study Assistant Institute for Learning & Brain Sciences (I-LABS) Univ

Re: [Freesurfer] mri_head

Hi Doug, These are pretty old ima files. I tried out mri_probe_ima and it worked! Thank you! Best, Lisa __ Lisa F. Akiyama Research Study Assistant Institute for Learning & Brain Sciences (I-LABS) University of Washington E-mail: lris...@uw.edu P Please cons

[Freesurfer] Trying to run recon-all on old raw data

U/Linux > recon-all -s A_H exited with ERRORS at Mon Dec 13 14:34:21 PST 2010 Does anyone know how to resolve this issue? Thank you. Best, Lisa ______ Lisa F. Akiyama Research Study Assistant Institute for Learning & Brain Sciences (I-LABS) University of W

Re: [Freesurfer] Trying to run recon-all on old raw data

subject. Attached is the tag information listed in a text file. (I've deleted subject's personal info) Thank you. Best, Lisa ______ Lisa F. Akiyama Research Study Assistant Institute for Learning & Brain Sciences (I-LABS) University of Washington P Pleas

Re: [Freesurfer] Trying to run recon-all on old raw data

Hi Bruce, MIPAV did allow me to save it in other formats like Nifti and Analyze, but it only created corrupted files. Thanks. Best, Lisa __ Lisa F. Akiyama Research Study Assistant Institute for Learning & Brain Sciences (I-LABS) University of Washington P Pl