[Freesurfer] Longitudinal Pipeline

Hi All, Is it standard practice to conduct test when corrections are made in freesurfer for subcortical structure volumes? Also, are you able to analyse data acquired (1.5T - time point one) with time-point two (3T) in the longitudinal pipeline? Thanks Theo

Re: [Freesurfer] Medial Surface Problem

Hi Bruce, That's fine, thanks very much. Bronwyn Overs Research Assistant Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia M 0411 308 769 T +61 2 9399 1883 [ http://neura.edu.au/ | neura.edu.au  ] [

[Freesurfer] mri_vol2surf: visualising the edges at projfrac 0.1 - 0.5

Hi Freesurfer Team, Is there a way to visualise the sampling edges across a range of projfrac values (0.1 (closer to WM) - 0.5) and overlay them onto PET data? Any suggestions are greatly appreciated. Thanks. Best Wishes, Elijah  ___ Freesurfer

[Freesurfer] Surface area of a define volume projection on cortical surface

Dear Freesurfer's experts, Given the well known size of a voxel I would like to know the equivalent surface area once projected on the white fsaverage cortical surface. Could anyone give me a proper way of computing this ? Best regards, Matthieu ___

[Freesurfer] Applying an affine transformation to a surface

Hello In a very similar situation to a post I found in the Freesurfer archive, I have low-resolution (3T) and high-resolution scans (7T) of the same subject - and would like to put the surfaces from the low-resolution scan into the space of the hi-res data. The instructions from the previous

Re: [Freesurfer] Libnetcdf.so.6 error during mris_make_surfaces

Hello Lisa, Can you provide me with the contents of your FREESURFER_HOME/build-stamp.txt file On 06/12/2017 05:44 PM, Lisa Kramarenko wrote: > Hi, > > I am getting the following error when my HCP pipelines come to the > mris_make surfaces step: > > mris_make_surfaces: error while loading

Re: [Freesurfer] Merging outputs of mri_label2vol across hemi

Hi Doug, After resampling the aparc annotation into the functional native space, the LUT values no longer correspond to the correct regions. A screenshot is attached here: http://i.imgur.com/HNIgrKI.png The values for the labels range from 1 - 35 only. The command is mri_label2vol --annot

[Freesurfer] Longitudinal Pipeline

Hi All, Is it standard practice to conduct reliability when corrections are made in freesurfer for subcortical structure volumes? Also, are you able to analyse data acquired (1.5T - time point one) with time-point two (3T) in the longitudinal pipeline? Thanks Theo

Re: [Freesurfer] Medial Surface Problem

thanks Bronwyn I got them. It will take a bit for us to get to as this is in the long stream and we have a new postdoc who will be taking it over. cheers Bruce On Tue, 13 Jun 2017, Bronwyn Overs wrote: Hi Bruce, Sure, files have been dropped again. Kind regards, Bronwyn Overs Research

Re: [Freesurfer] Merging outputs of mri_label2vol across hemi

Great! Many thanks, Doug. Best Wishes, Elijah  On 13 June 2017 at 07:05:13, Douglas Greve (gr...@nmr.mgh.harvard.edu) wrote: You can try mri_concat seg1.nii.gz seg2.nii.gz --sum --o seg.nii.gz This will work if there are no overlapping voxels. If there are, you'll have to do something like

Re: [Freesurfer] Merging outputs of mri_label2vol across hemi

You can try mri_concat seg1.nii.gz seg2.nii.gz --sum --o seg.nii.gz This will work if there are no overlapping voxels. If there are, you'll have to do something like mri_mask seg1.nii.gz seg2.nii.gz seg1-masked.nii.gz then use the masked in the mri_concat command On 6/11/17 11:18 AM,

Re: [Freesurfer] difference in T1 and T2 resolution

can you send the log file? On 6/11/17 10:08 PM, John Anderson wrote: In the log file the error was: ERROR: MultiRegistration::loadMovables: images have different voxel sizes. Currently not supported, maybe first make conform? Debug info: size(1) = 1, 1, 1 size(0) = 0.7, 0.7, 0.8