[Freesurfer] bug: tkmedit - image view
Hi all, I'm Flavio, doctorate student at Fluminense University from Brazil. I would like to report a bug with tkmedit. I'm using Ubuntu distribution, kernel release 2.6.27.11 (32-bits). I have installed FreeSurfer version freesurfer-Linux-centos4-stable-pub-v4.2.0. My video card is a ATI Radeon 9600Pro. I'm using ATI/AMD FGLRX device driver on Linux. When I start tkmedit (eg. tkmedit bert orig.mgz), the coronal session image is displayed. But, when I move the mouse (eg. to select the sagittal view on tkmedit menu), the image disappear. The display window may be minimized and I can't view the image anymore. When I try maximizing image window, the image is displayed until I move the mouse. Then, it is disappeared again. Does anyone have a doubt? I would appreciate any help. Thank you, Flavio. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Outline files convert
Hi All, I've got from IBSR (Internet Brain Segmentation Repository) MR images and their subcortical structures segmented manually. The segmented images are saved in Outline (.OTL) format. How could I convert from .OTL to .IMG or .NII (Analyze) format using mri_convert? Are there any examples? I would appreciate any help. There are one image to each of image slice, as shown bellow: IBSR_01_seg_18.otl IBSR_01_seg_46.otl IBSR_01_seg_73.otl IBSR_01_seg_100.otl IBSR_01_seg_19.otl IBSR_01_seg_47.otl IBSR_01_seg_74.otl IBSR_01_seg_101.otl IBSR_01_seg_20.otl IBSR_01_seg_48.otl IBSR_01_seg_75.otl IBSR_01_seg_102.otl IBSR_01_seg_21.otl IBSR_01_seg_49.otl IBSR_01_seg_76.otl IBSR_01_seg_103.otl IBSR_01_seg_22.otl IBSR_01_seg_4.otl IBSR_01_seg_77.otl IBSR_01_seg_104.otl IBSR_01_seg_23.otl IBSR_01_seg_50.otl IBSR_01_seg_78.otl IBSR_01_seg_105.otl IBSR_01_seg_24.otl IBSR_01_seg_51.otl IBSR_01_seg_79.otl IBSR_01_seg_106.otl IBSR_01_seg_25.otl IBSR_01_seg_52.otl IBSR_01_seg_7.otl IBSR_01_seg_107.otl IBSR_01_seg_26.otl IBSR_01_seg_53.otl IBSR_01_seg_80.otl IBSR_01_seg_108.otl IBSR_01_seg_27.otl IBSR_01_seg_54.otl IBSR_01_seg_81.otl IBSR_01_seg_109.otl IBSR_01_seg_28.otl IBSR_01_seg_55.otl IBSR_01_seg_82.otl IBSR_01_seg_10.otl IBSR_01_seg_29.otl IBSR_01_seg_56.otl IBSR_01_seg_83.otl IBSR_01_seg_110.otl IBSR_01_seg_2.otl IBSR_01_seg_57.otl IBSR_01_seg_84.otl IBSR_01_seg_111.otl IBSR_01_seg_30.otl IBSR_01_seg_58.otl IBSR_01_seg_85.otl IBSR_01_seg_112.otl IBSR_01_seg_31.otl IBSR_01_seg_59.otl IBSR_01_seg_86.otl IBSR_01_seg_113.otl IBSR_01_seg_32.otl IBSR_01_seg_5.otl IBSR_01_seg_87.otl IBSR_01_seg_114.otl IBSR_01_seg_33.otl IBSR_01_seg_60.otl IBSR_01_seg_88.otl IBSR_01_seg_115.otl IBSR_01_seg_34.otl IBSR_01_seg_61.otl IBSR_01_seg_89.otl IBSR_01_seg_116.otl IBSR_01_seg_35.otl IBSR_01_seg_62.otl IBSR_01_seg_8.otl IBSR_01_seg_117.otl IBSR_01_seg_36.otl IBSR_01_seg_63.otl IBSR_01_seg_90.otl IBSR_01_seg_118.otl IBSR_01_seg_37.otl IBSR_01_seg_64.otl IBSR_01_seg_91.otl IBSR_01_seg_119.otl IBSR_01_seg_38.otl IBSR_01_seg_65.otl IBSR_01_seg_92.otl IBSR_01_seg_11.otl IBSR_01_seg_39.otl IBSR_01_seg_66.otl IBSR_01_seg_93.otl IBSR_01_seg_120.otl IBSR_01_seg_3.otl IBSR_01_seg_67.otl IBSR_01_seg_94.otl IBSR_01_seg_12.otl IBSR_01_seg_40.otl IBSR_01_seg_68.otl IBSR_01_seg_95.otl IBSR_01_seg_13.otl IBSR_01_seg_41.otl IBSR_01_seg_69.otl IBSR_01_seg_96.otl IBSR_01_seg_14.otl IBSR_01_seg_42.otl IBSR_01_seg_6.otl IBSR_01_seg_97.otl IBSR_01_seg_15.otl IBSR_01_seg_43.otl IBSR_01_seg_70.otl IBSR_01_seg_98.otl IBSR_01_seg_16.otl IBSR_01_seg_44.otl IBSR_01_seg_71.otl IBSR_01_seg_99.otl IBSR_01_seg_17.otl IBSR_01_seg_45.otl IBSR_01_seg_72.otl IBSR_01_seg_9.otl Thank you, Flavio ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Transform orig.mgz image to native space
Hi Hii, I'm beginner Freesurfer user. I segmented brain subcortical structures using Freesurfer (recon-all). The process was concluded ok. How could I convert aseg.mgz and orig.mgz back to native space? I've tried "mri_convert orig.mgz orig.nii -ot nii --apply_inverse_transform transforms/talairach.xfm", but didn't work. Anyone could help me? I would appreciate any suggestion. Thank you, Flávio. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Re: Transform orig.mgz image to native space
The native data has (0.449219, 0.449219, 0.45) mm size and (512, 512, 356) voxels. The orig.mgz has (256, 256, 256) voxels. I would like to transform orig.mgz back to native data coordinates. Best Regards, Flavio. --- On Tue, 5/26/09, Bruce Fischl wrote: From: Bruce Fischl Subject: Re: Transform orig.mgz image to native space To: "Flavio Seixas" Cc: freesurfer@nmr.mgh.harvard.edu, t...@nmr.mgh.harvard.edu, gr...@nmr.mgh.harvard.edu Date: Tuesday, May 26, 2009, 5:56 PM the data should already be in the native space, not talairach. cheers, Bruce On Tue, 26 May 2009, Flavio Seixas wrote: > Hi Hii, > > I'm beginner Freesurfer user. I segmented brain subcortical structures using > Freesurfer (recon-all). The process was concluded ok. How could I convert > aseg.mgz and orig.mgz back to native space? I've tried "mri_convert orig.mgz > orig.nii -ot nii --apply_inverse_transform transforms/talairach.xfm", but > didn't work. Anyone could help me? I would appreciate any suggestion. > > Thank you, > Flávio. > > > > > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Re: Transform orig.mgz image to native space
Works. Thank you ! Flavio. --- On Tue, 5/26/09, Nick Schmansky wrote: From: Nick Schmansky Subject: Re: [Freesurfer] Re: Transform orig.mgz image to native space To: "Flavio Seixas" Cc: "Bruce Fischl" , "Freesurfer Mailing List" , t...@nmr.mgh.harvard.edu, "Doug Greve" Date: Tuesday, May 26, 2009, 6:12 PM try: mri_convert orig.mgz -rl rawavg.mgz orig.nii On Tue, 2009-05-26 at 18:10 -0700, Flavio Seixas wrote: > The native data has (0.449219, 0.449219, 0.45) mm size and (512, 512, > 356) voxels. The orig.mgz has (256, 256, 256) voxels. I would like to > transform orig.mgz back to native data coordinates. > > Best Regards, > Flavio. > > > --- On Tue, 5/26/09, Bruce Fischl wrote: > > From: Bruce Fischl > Subject: Re: Transform orig.mgz image to native space > To: "Flavio Seixas" > Cc: freesurfer@nmr.mgh.harvard.edu, t...@nmr.mgh.harvard.edu, > gr...@nmr.mgh.harvard.edu > Date: Tuesday, May 26, 2009, 5:56 PM > > the data should already be in the native space, not talairach. > > cheers, > Bruce > > On Tue, 26 May 2009, Flavio Seixas wrote: > > > Hi Hii, > > > > I'm beginner Freesurfer user. I segmented brain subcortical > structures using Freesurfer (recon-all). The process was > concluded ok. How could I convert aseg.mgz and orig.mgz back > to native space? I've tried "mri_convert orig.mgz orig.nii -ot > nii --apply_inverse_transform transforms/talairach.xfm", but > didn't work. Anyone could help me? I would appreciate any > suggestion. > > > > Thank you, > > Flávio. > > > > > > > > > > > > > > ___ > 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] Brain cortical structures segmentation - comparison of hippocampal volumes
My name is Flavio, student at Universidade Federal Fluminense. I research image segmentation methods applied to brain cortical structures segmentation. I've compared against the hippocampal region got from FIRST-FSL to Freesurfer, using the same magnetic resonance (MR) image. The FSL is a neuroimage analysis tool developed by FMRI group from Oxford. I found out a great volume difference between segmentations. Despite different automated image analysis tool, I was expecting a higher volume overlap index when comparing the same brain structure from the same MR image. I got about 25% volume overlap. Is there any "recon-all" flag that I can use in conjunction with entire process so as to get better volume overlap? I would appreciate any suggestion. Thank you in advance, Flavio. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Estimated total incranial volume
Dear All, In addition to eTIV based on Tailarach transform matrix (see Buckner et al. paper), is there other estimated total intracranial volume method, for example, using the BET2 (brain extraction tool)? Thank you in advance, Flavio ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
