[Freesurfer] memprage processing steps?

External Email - Use Caution Hi! I was wondering whether there is an overview / walkthrough for all the steps involved when working with MEMPRAGE? I am thinking dcmunpack, mri-concat / mri_average, flags for recon-all, mris_make_surfaces, etc. Any pointers would be appreciated. Th

Re: [Freesurfer] memprage processing steps?

Hi Caspar I think you just compute the rms across the echoes and give it to recon-all. I suppose the -mprage flag could help cheers Bruce On Thu, 23 Aug 2018, Caspar M. Schwiedrzik wrote: External Email - Use Caution Hi! I was wondering whether there is an overview / walk

[Freesurfer] Extract Cortical Thickness Values from ROI.nii

External Email - Use Caution Dear all, I've just completed the recon -all command and I would like to extract Cortical thickness values in subject space at vertex level (without any sort of normalization). Could you please give me an insight on how to do it? Thanks in advance D

Re: [Freesurfer] questions about hippocampus subfield error

External Email - Use Caution Hi Shize, Does recon-all complete when you run it without the hippocampal subfield flag? It doesn’t look like an error in the subfield module to me … Cheers, /Eugenio -- Juan Eugenio Iglesias ERC Senior Research Fellow Centre for Medical Image Computi

Re: [Freesurfer] questions about hippocampus subfield error

External Email - Use Caution Hi Eugenio, Yes, If I run without the hippocampal subfield flag. Recon-all complete without any error. So I am confused what is wrong with this. Thank you Shize 在 2018-08-24 00:02:32，"Iglesias Gonzalez, Eugenio" 写道： External Email -

Re: [Freesurfer] Extract Cortical Thickness Values from ROI.nii

Hi Dave if recon-all is done it will produce two files named lh.thickness and rh.thickness, which are scalar maps with a thickness value at each vertex cheers Bruce On Thu, 23 Aug 2018, Davide Momi wrote: External Email - Use Caution Dear all,  I've just completed the re

[Freesurfer] Low resolution voxels of T1-weighted data (FreeSurfer)

External Email - Use Caution Hi FS experts, I came across this post https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2013-June/031245.html by Dr. Bruce Fischl, where it is mentioned that "*You won't be able to analyze the data unless **it is T1-weighted with voxels that are <

Re: [Freesurfer] Low resolution voxels of T1-weighted data (FreeSurfer)

Hi Martin yes, 1.3mm is probably fine and even 1.5 might work. It is really an empircal question. We have done a ton of 1.3mm, so that response was overly conservative. Bruce On Thu, 23 Aug 2018, Martin Juneja wrote: External Email - Use Caution Hi FS experts, I came ac

Re: [Freesurfer] PSIR to refine pial surface?

Hi Chris can you send us an example image? I haven't seen one cheers Bruce On Thu, 16 Aug 2018, Vriend, Chris wrote: External Email - Use Caution Dear Freesurfers,     In our centre we acquire T1 MPRAGE scans and phase-sensitive inversion recovery (PSIR) scans. Becaus

[Freesurfer] converting a color lookup table in csv to freesurfer format (.ctab)

External Email - Use Caution Hello, How can I convert a csv color lookup table to freesurfer format (.ctab)? My end goal is to use it to perform partial volume correction for an atlas/segmentation different from default freesurfer atlas. The atlas has a color lookup table however,

Re: [Freesurfer] questions about hippocampus subfield error

External Email - Use Caution Thanks! Can you please send us the log of the hippocampal subfield segmentation? It should be in the same directory as the recon-all log. Cheers, /E Juan Eugenio Iglesias Centre for Medical Image Computing (CMIC) University College London http:/

Re: [Freesurfer] questions about hippocampus subfield error

External Email - Use Caution Hi Juan Thank you for your kindly help. Attached is the log file with error. I am not sure if this is the file for hippocampus subfield segmentation. Thank you very much Shize 在 2018-08-24 05:08:35，"Iglesias Gonzalez, Eugenio" 写道： E