[Freesurfer] Patch x y z

Hello, read_patch (patch_name) gives x,y and z values. Are these vertex RAS? Thank you. Hiroyuki ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-

[Freesurfer] sup temporal plane 3-D view (Neuroimage 2006)

Dear Freesurfer, I am impressed with 3d-view of the supra temporal lobe in your Neuroimage(2006) paper (fig2). I am also trying to create such 3d view of supra temporal plane. If you could tell me the procedure to create it, that would be greatly appreciated. Thanks. Hiroyuki Oya __

[Freesurfer] Oblique slices with pial and white matter surface

Dear all, I'd like to make serial oblique slices with pial surface resampled into the slice. Would it be possible to do this with tkmedit ? Any suggestion would be appreciated. Hiroyuki ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu http

[Freesurfer] white matter mask

Hello All, I'd like to create mask of white matter. Would it be possible to use white matter surface to do this? Tx. Hhiroyuki ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] Conform to 0.8mm

Dear Experts, We obtain structural MPRAGE T1 with 0.8 x 0.8 x 1.0mm voxel size (3 volumes). Is is possible to conform the volume to 0.8mm for all the processing (recon-all)? Thank you very much. Hiroyuki ___ Freesurfer mailing list Freesurfer@nmr.mgh

[Freesurfer] Conform to 0.8mm

Dear Experts, We obtain structural MPRAGE T1 with 0.8 x 0.8 x 1.0mm voxel size (3 volumes). Is is possible to conform the volume to 0.8mm for all the processing (recon-all)? Thank you very much. Hiroyuki ___ Freesurfer mailing list Freesurfer@nmr.mg

[Freesurfer] anat2exf.reg.dat

Deal all, A basic question. What is the first 3raws in anat2exf.reg.dat ? Many thanks. Hiroyuki ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] Voxel correspondence from Functional to Structural

Dear Experts, I would like to find the voxel correspondence from FSL functional volume (tstat volume) to FSL structural volume (orig.mgz) in a subject explicitly. Is it enough to use anat2exf.reg.dat transformation matrix (I have already processed functional data with reg-feat2anat)? Thank

[Freesurfer] tkmedit : Functional RAS to Functional index

Hello Experts, Transformation from Volume RAS to Functional RAS is done with anat2exf.reg.dat. But how does tkmedit calculate Functional index from Functional RAS ? Thank you in advance. Hiroyuki ___ Freesurfer mailing list Freesurfer@nmr.mgh.harva

[Freesurfer] Lose Keyboard

Dear all, I am running freesurfer 4.5 on Ubuntu9.10(64bit). Is anybody experiencing " lost keyboard " problem? I cannot put any number in tkmedit and tksurfer using keyboard. Thank you. Hiroyuki ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.

[Freesurfer] Smoothing BOLD on the surface

Dear Experts, I would like to first analyze the BOLD response without smoothing in the functional volume, and apply smoothing on the surface and map it. Would this be possible? Thank you in advance. Hiroyuki ___ Freesurfer mailing list Freesurfer@n

[Freesurfer] RAS to Vertex Index

Dear EXPERTS, I have a coordinate set (RAS) in a volume and would like to map those coordinates in a surface of same subjects. Is there a good way to convert Volume RAS to vertex index directly rather than searching with mouse? Thank you. Hiroyuki ___

[Freesurfer] Tiff images created by tksurfer

Hello tksurfer can save multiple surface renderings of the brain as 600 x600 tiff formatted images. If anybody can tell me the relationship between center of the image and the brain, that would be appreciated. Thank you very much. Hiroyuki ___ Free

[Freesurfer] Vertex values

Dear Experts, Is it possible to import surface vertex index and corresponding values into Matlab? Thank you very much . Hiroyuki ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] Vol index to Talairach

Dear experts, I like to find Tarairach and MNI coordinate from volume index (data has been already processed with recon-all) off line using Matlab. Which transform should I use to find it ? Thank you. Hiroyuki ___ Freesurfer mailing list Freesurfer

[Freesurfer] Color Scale in tksurfer

Dear All, How can I use my own color scale in tksurfer overlay? Thank you in advance? Hiroyuki ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] Color scale in tksurfer

Dear All, How can I use my own color scale in tksurfer overlay? Thank you in advance? Hiroyuki ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] mri_vol2surf

In mri_vol2surf , is it still valid to set -fwhm value less than 1? Thank you. Hiroyuki ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is inten

[Freesurfer] Sulci

Dear All, Looking at pial surface, sulci looks wider than those of the actual brain. Is there any parameter to be tuned? Does watershed threshold have any effect on the pial surface estimation ? Hiroyuki ___ Freesurfer mailing list Freesurfer@nmr.mg

[Freesurfer] Talairach afd error

Dear all, recon-all failed at the talairach stage. ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0., pval=0. < threshold=0.0050) Linux hiroyuki-desktop 2.6.32-24-generic #42-Ubuntu SMP Fri Aug 20 14:21:58 UTC 2010 x86_64 GNU/Linux In what circumst

[Freesurfer] [Fwd: Re: Talairach afd error]

--- Begin Message --- can you post these to the list so others can answer? Did you check the talairach.xfm with either tkmedit or tkregister2? On Fri, 3 Sep 2010, Oya, Hiroyuki wrote: Hi Bruce, Bringing up the image with tkmedit, directions are correct. And I have not done any process in

Re: [Freesurfer] Talairach afd error

t; On Fri, 3 Sep 2010, Oya, Hiroyuki wrote: > > > Hi Bruce, > > > > Bringing up the image with tkmedit, directions are correct. > > And I have not done any process in Analyze format. > > > > Thank you. > > > > > > > > > >

[Freesurfer] tksurfer

Dear all, Can tksurfer load both hemispheres at once from command line input? Hiroyuki ___ 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

Re: [Freesurfer] Patch x y z

If I have vertices for making a new patch, is there any command line tool for this? Hiroyuki -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: 03 October 2013 16:01 To: Oya, Hiroyuki Cc

[Freesurfer] Different freesurfer version

Hello Is it fine to process the anatomical data in v4.5 and analyze the results in v5.1? Thanks, Hiroyuki Notice: This UI Health Care e-mail (including attachments) is covered by the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521, is confidential an

[Freesurfer] freeview RAS

Dear Sir, When I view a brain volume (e.x., orig.mgz) with freeview and tkmedit, RAS coordinate differs. Why? Thank you. Hiroyuki Notice: This UI Health Care e-mail (including attachments) is covered by the Electronic Communications Privacy Act, 18 U.S.C. 251

[Freesurfer] mri_ca_register error

Hello , I am running recon-all with -cm switch and getting following error. Is there any workaround? Without -cm switch , recon-all completes all the processing just fine. Thank you. Hiroyuki mri_ca_register -invert-and-save transforms/talairach.m3z mri passed volume size is different fro

[Freesurfer] Bad vertex in mris_flatten

Dear sir, Mris_flatten could not be completed due to the fact that only one bad vertex was found in the patch. Is there any quick way to correct the vertex? Thank you. Hiroyuki Notice: This UI Health Care e-mail (including attachments) is covered by the Elec

[Freesurfer] surface normals

Dear Sir, Can the surface normals be loaded in matlab? Is there a code for that and what variable should I look at in surf dir? Thank you. HIroyuki Notice: This UI Health Care e-mail (including attachments) is covered by the Electronic Communications Privacy A

[Freesurfer] selxavg3-sess error

Hi I got an error while running selxavg3-sess, "cannot find AFNI command 3dvolreg".(In ubuntu v11.). Any help would be appreciated. Hiroyuki Notice: This UI Health Care e-mail (including attachments) is covered by the Electronic Communications Privacy Act, 1

Re: [Freesurfer] selxavg3-sess error

I have not set path for afni. After setting the correct path, that runs fine. From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Oya, Hiroyuki (UI Health Care) Sent: 30 March 2012 07:53 To: freesurfer@nmr.mgh.harvard.edu Subject

[Freesurfer] -cm switch error

Hello When I run recon-all with -cm switch, that generates error as follows: /* mri passed volume size is different from the one used to create M3D data ERROR: mri_ca_register with non-zero status 0 */ Without -cm switch, recon-all completes all processing without error. Any help would be appre

[Freesurfer] read data mri_vol2surf

Hello Is it possible to load the outputs of mri_vol2surf with matlab? Thank you. Hiroyuki ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-m

[Freesurfer] surfsace of specific broadman's area

Dear all, I like to create a surface rendering restricted to some area (selected from aparc.annot.a2009s.ctab files)? Any suggestion would be appreciated. Best, Hiroyuki Notice: This UI Health Care e-mail (including attachments) is covered by the Electronic Co

[Freesurfer] find corresponding coordinates of verteces

Dear all, Is it possible to find the coordinates (ras and MNI) of every vertex points on a surface in matlab? Thank you. Hiroyuki Notice: This UI Health Care e-mail (including attachments) is covered by the Electronic Communications Privacy Act, 18 U.S.C. 25