Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30088 discussions

Manual segmentation to volume
by Benjamin Ineichen 20 Dec '19

20 Dec '19

External Email - Use Caution Dear Freesurfer experts, I have a manual segmentation of a certain brain feature done in Freeview. I want to pool these segmentations from different subjects to create some kind of a heat map/probability map. In order to do this, I assume I need to convert my segmentation to a volume first (In my case the Talairach space); hence, I tried: mri_label2vol --seg example.mgz --temp talairach.xfm --o seg_talairach --reg example_orig.mgz the example_orig.mgz would correspond to the original T1 which I used to do the segmentation. But this gives me the error message: ERROR: could not determine type of talairach.xfm ERROR: reading talairach.xfm header Where is the problem? Many thanks! /Ben

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Creating a label from overlapping cluster results
by cody samth 20 Dec '19

20 Dec '19

External Email - Use Caution Hi, I was wondering if there is any automated command/method to create a new label that consists of the overlap of two labels? I've run two whole brain analyses with different predictors and have regions where the clusters from each analysis overlap. I'm interested in creating a label for visualization purposes and to extract cortical data in these regions of overlap. Thanks, Cody

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Re: [Freesurfer] Conversion fMRI volumes to surface
by Marina Fernández 19 Dec '19

19 Dec '19

External Email - Use Caution Thanks Doug. I created the surface with the command line that I sent you (mri_vol2surf ...) and then, I run that command that you sent me (tkregisterfv...) but I have the following error when freeview is trying to load the file: 'Failed to load MRI /.../4d_inputBOLD.nii'. I discard that the problem is not with the EPI file because when I load only the 4d_inputBOLD.nii there is no problem. I guess that the problem is the register.dat. What do you think I should do? Best regards, Marina.

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Pial surface does not follow the gray/csf boundary
by Ardesch, D.J. 19 Dec '19

19 Dec '19

External Email - Use Caution Dear FreeSurfers, I’m trying to create surface reconstructions for some small monkey scans (about half the size of a rhesus macaque). The white surfaces look fine, but I can’t seem to get the pial surfaces to extend properly to the edge of the gray matter. Is there a way to ‘force’ the mris_make_surfaces command to place the pial surface along a certain voxel intensity or intensity gradient? As I understand it, mris_make_surfaces takes the ?h.orig surface and extends it into the gray matter until it finds the gray matter/csf boundary. I’ve therefore tried to edit the brain.finalsurfs.mgz and brainmask.mgz volumes such that all white matter voxels have an intensity of 110 and all other brain voxels have an intensity of 80, and added some smoothing to create an intensity gradient, but this did not make a difference. The gray matter surface is still placed about 1/5th of the way between the gray/white boundary and the gray/csf boundary. Adding a T2 scan did not help either. My setup is the following: * FreeSurfer v6.0.0 * MacOS 10.14.6 * Running FreeSurfer with the -hires flag (voxel size is 0.25 mm isotropic) With some manual editing I’ve been able to complete all pipeline steps until the surface reconstruction, except the topology fixing because it created large inaccuracies in the occipital lobe (including the topology fixing step did not solve the problem either). Any help would be greatly appreciated! With kind regards, Dirk Jan

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(no subject)
by Nader Razmara 19 Dec '19

19 Dec '19

External Email - Use Caution Hi experts I use freesurfer vm 5.3 on oracle vb 6 with 8 GB ram. When i use mri_cvs_register as: mri_cvs_register --mov subjid --mni or mri_cvs_register --mov subjid --template subjid in both cases it stops in step 2 by diffrent errors. I asked zollei this problem and she sujest that it is ram problem. My question is: If it is true. How many ram this command needs? Thanks Nader Phd student in medical engineering Alzheimer research project

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Project functional region into white matter
by Corinna Bauer 18 Dec '19

18 Dec '19

External Email - Use Caution Hello all, I have a series of functionally-defined ROI volumes (.nii format) that I'd like to project into the white matter to then be used for tractography. So far the vols have been brought from cvs_avg35 space into subject space from using mri_vol2vol and the corresponding m3z file. This was followed by mri_vol2vol using the registration from bbregister to get the functional regions into diffusion space. I have done this for the ROIs in their original GM volume, but would now like to also have corresponding WM volumes for tractography. What is the best way to go about doing this? Thanks, Corinna

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Transform LIA orientation to RAS
by Marina Fernández 18 Dec '19

18 Dec '19

External Email - Use Caution Dear Freesurfer experts, How can I transform an EPI-surface with LIA orientation to RAS orientation? Thank you in advance. Best regards, Marina.

2 1

Re: [Freesurfer] Conversion fMRI volumes to surface
by Marina Fernández 18 Dec '19

18 Dec '19

External Email - Use Caution Thank you Doug/Bruce. We would like to project our AFNI preprocessed EPI scans (T1-registration, motion correction, linear regression, but unsmoothed) to Freesurfer cortical surfaces in order to obtain one file containing 250 (number of dynamics) EPI-cortical surfaces in the native space. For this, we are using the following command: mri_vol2surf --mov '4d_inputBOLD.nii' --reg 'register.dat' --hemi '[l/r]h' --projfrac 0.5 --interp nearest --o 'output.nii' Is that correct? As our EPI scans were previously registered with AFNI to T1 (that it is in FS space), I guess that bbregister is not required, right? Thank you in advance. Best wishes, Marina.

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FA index greater than 1
by Benxamin varela lópez 18 Dec '19

18 Dec '19

External Email - Use Caution Dear freesurfer experts I am a beginner in DWI data processing and my question may be absurd, if so, I apologize in advance. I am using TRACULA for the analysis of my DWI data. Reviewing the outputs of the statistics for the FA index I realized that some of these are greater than 1. Considering that FA oscillates between the values 0-1, how is this possible? I send to you in attached the .txt with the average FA values for the Forceps Minor where the "anomalous" values can be observed. Thanks in advance Best regards Benxamín

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using different Freesurfer versions for cross-sectional & longitudinal processing
by Morgan Botdorf 18 Dec '19

18 Dec '19

External Email - Use Caution Dear Freesurfer Experts, We have child data that was previously processed cross-sectionally using version 5.1. We are now interested in looking at the data longitudinally. Can the longitudinal processing stream in version 6.0 be used on data that was processed cross-sectionally using 5.1? Or is it better that we reprocess the data using 6.0. We appreciate any help you can provide! Thank you, Morgan Botdorf, M.S. Doctoral Candidate Neurocognitive Development Lab University of Maryland, College Park mbotdorf(a)terpmail.umd.edu Office: 301.405.5922

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