Re: [Freesurfer] wmparc/white matter problems?

Can you load and examine the aseg.mgz, {lh.rh}.ribbon.mgz? How do they look in that area? Ryan Muetzel wrote: Hi Doug, The images are attached. Thanks again for your help! -Ryan On Dec 6 2007, Doug Greve wrote: Can you send a pic? Ryan Muetzel wrote: Hello, We are running Freesurf

Re: [Freesurfer] retinotopy help

Did you check the registration? anisha narula wrote: Hello, I am carrying a retinotopy analysis and not getting good flattened images. When I view the slices using the sliceview-sess -sf sessid -df sessdir -analysis rtopy -c eccen -map h -slice h command, there is apparent activation the reg

Re: [Freesurfer] ROI labels for geometry vertices

Hi Sergey, In matlab you you can use read_annotation.m: function [vertices, label, colortable] = read_annotation(filename) % [vertices, label, colortable] = read_annotation(annotfilename.annot) % % vertices expected to be simply from 0 to number of vertices - 1; % label is the vector of annotati

[Freesurfer] ROI labels for geometry vertices

Hi, Please, help me to find out how to extract information I need. For each vertex in the geometry of the cortical surface I want an additional label that tells me which ROI this vertex belongs to. I extract all geometrical information using: mne_read_surfaces in matlab. This, however, doe

Re: [Freesurfer] mri_convert and VB15

This was fixed in the most recent minor stable release. doug Jason Webster wrote: Hello, After upgrading our scanner software to VB15A, we began receiving the following error from mri_convert when running unpacksdcmdir: ERROR: incorreclty formatted version string syngo MR B15 found in dicom

Re: [Freesurfer] mris_register

Hi XJ, if you specify -n 0 I think it will not run the nonlinear. cheers, Bruce On Fri, 7 Dec 2007, XJ Kang wrote: Hi, I am trying to register the spheres to the template. The current version of mris_register may have some nonlinear local deformation of the gyral and sulcal structure. Anyw

[Freesurfer] mris_register

Hi, I am trying to register the spheres to the template. The current version of mris_register may have some nonlinear local deformation of the gyral and sulcal structure. Anyway I can specify the "rigid alignment" only? I didn't find the option for linear alignment only after checking the options

[Freesurfer] mri_convert and VB15

Hello, After upgrading our scanner software to VB15A, we began receiving the following error from mri_convert when running unpacksdcmdir: ERROR: incorreclty formatted version string syngo MR B15 found in dicom tag 18,1020 (len = 3 != 6) Numaris Version: syngo MR B15 Maj = -1073750848, Min=-1073771

Re: [Freesurfer] Recon-all failing at CA Reg

Hi Caroline, can you replicate this problem? Does it always happen for this subject? If so, please send me the data and I'll fix it. Bruce On Fri, 7 Dec 2007, Caroline Chapman wrote: Hi Bruce and all, Thank you for your help. Bill Monaco emailed and let me know that this happened to him

Re: [Freesurfer] Recon-all failing at CA Reg

Hi Bruce and all, Thank you for your help. Bill Monaco emailed and let me know that this happened to him as well. He suggested running the '-autorecon2 -autorecon3' flags on this subject (as opposed to the 'recon-all -all'), and this worked for me! However, here is the end of the recon-all.

[Freesurfer] buglet in fast_inorm

Dear fellow freesurfers, using FreeSurfer 3.0.5 and 4.0.1, I can make fast_inorm.m (as called by inorm) die, with otherwise innocently looking inputs. The syndrom is that if my fist slice contains only one iunder voxel twf_under (see 3.0.5's line 88 of fast_inorm.m) is initialised as scalar