Re: [Freesurfer] TRACULA Preprocessing Error

Hi Ameen - diffusion_recons/elmo.2005 should have the freesurfer recon of the T1 data and diffusion_tutorial/elmo.2005 should have the diffusion data. Can you confirm if this was in what you downloaded? Thanks! a.y From: freesurfer-boun...@nmr.mgh.harvard.edu o

Re: [Freesurfer] medial wall metric file

External Email - Use Caution Yes, a label or roi metric file of 0 and 1s (preferably 0s for the medial wall vertices) for that can be converted to workbench format. Jim On Jan 28, 2020 5:42 PM, "Greve, Douglas N.,Ph.D." wrote: Attention: This email originated from outside the

Re: [Freesurfer] Cortical segmentation error

External Email - Use Caution Sorry for the very late reply and not explaining the problem well in the first place. I would still appreciate your assistance if possible. Like some other threads that are on the archive, I was experiencing the problem where the pial surface wasn't get

Re: [Freesurfer] Extract specific LGI and Volume values

External Email - Use Caution Thank you for your response. I used longitudinal pipeline for my data set with two time points and calculated the LGI differences between them. Then I created the label based on significant clusters which showed in QDEC. I tried to load the label on sub

Re: [Freesurfer] medial wall metric file

Do you mean you want a binary mask of the medial wall? You can create a mask of the cortical label (?h.cortex.label) with mri_label2label You can then invert that with something like fscalc lh.cortex.mask.mgz not -o lh.medialwall.mask.mgz On 1/28/2020 6:31 PM, Alexopoulos, Dimitrios wrote:

[Freesurfer] medial wall metric file

External Email - Use Caution Is there a freesurfer file that contains metric info that delineates the medial wall in the native surface output for an individual? It appears to be associated with the ?lh.aparc.annot file (below). I'd like to be able to export the medial wall metric

[Freesurfer] TRACULA Preprocessing Error

External Email - Use Caution Hi Freesurfer Developers, I downloaded the Freesurfer tutorial data to run the TRACULA tutorial, and encountered a number of issues: 1. When running trac-all, I get the following error: trac-all -prep -c $TUTORIAL_DATA/diffusion_tutorial/dmrirc.tutor

Re: [Freesurfer] recon-all errors - mri_segstats and mri_relabel_hypointensities

Hi Laurel if a subject dir already exists recon-all will exit unless you specify -force. Alternatively you can try using the -make all flag, which should rerun only the steps that are needed (assuming the reboot didn't happen e.g. in the middle of writing a file) cheers Bruce On Tue, 28 Jan

Re: [Freesurfer] recon-all errors - mri_segstats and mri_relabel_hypointensities

External Email - Use Caution Hi Doug, Thanks for looking over that file. It is the correct recon-all file for one of the problem brains. I discovered that there was a system reboot of some sort when the recon-all was processing for these problem brains, so that is likely what c

Re: [Freesurfer] help: fs-fast group level analysis per run

External Email - Use Caution Thanks Dr. Greve. We've made our script available on github for anyone who may be interested! https://github.com/MolecularImagingLab/fMRI_scripts -- Rami Hamati, MSc. Royal's Institute of Mental Health Research Molecular Imaging Laboratory (MIL) 114

Re: [Freesurfer] what is the argument for arguments for symmetric Geometric Transfer Matrix and two-compartment model (Meltzer Method) in the PETsurfer ?

External Email - Use Caution Thank your very much Douglas for the information. Much appreciated. On Tue, Jan 28, 2020 at 1:12 PM Greve, Douglas N.,Ph.D. < dgr...@mgh.harvard.edu> wrote: > The symmetric GTM is the default (the non-sym is not implemented). > > I highly recommend

Re: [Freesurfer] what is the argument for arguments for symmetric Geometric Transfer Matrix and two-compartment model (Meltzer Method) in the PETsurfer ?

The symmetric GTM is the default (the non-sym is not implemented). I highly recommend that you don't use melzter (which is why I did not have docs for it:). But if you must run it, add --melzter BinThresh MaskThresh nDilations BinThresh is used to create a binary mask by thresholding the WM+GM t

Re: [Freesurfer] Extract specific LGI and Volume values

I cannot see anything wrong with the label. How did you create it? Are you sure that the label belongs to the same subject's surface that you loading it onto? On 1/26/2020 12:10 AM, Tien Pham wrote: External Email - Use Caution Thank you for your e-mail. Yes, of course. I send the label

Re: [Freesurfer] Flag for recon-all to output aparc2005 labels (freesurfer 6.0)

Not sure, we have not been using that flag in a while. When you look at the volume in freeview, you can see what the code is by clicking on a voxel. You can change the offset by including --base-offset XXX to mri_aparc2aseg, On 1/24/2020 2:40 PM, Grodin, Erica wrote: External Email - U

Re: [Freesurfer] recon exited with errors

Have you looked at your images to confirm that there is nothing really wrong? Look at orig.mgz, brain.mgz, and aseg.auto_noCCseg.mgz On 1/21/2020 11:02 AM, Desel, Tenzin wrote: Hello FreeSurfer Developers, I'm attempting to run recon-all after unpacking data. It is exiting with errors - mri_cc

Re: [Freesurfer] Reconstruction editing

I think that is going to be tough. Maybe you can edit the wm.mgz so that the orig surface starts in the right place. I don't think control points are going to work very well On 1/21/2020 10:31 AM, Jane Tseng wrote: External Email - Use Caution Dear Freesurfer experts, I would like to

Re: [Freesurfer] Recommendation for CFT and CWT FreeSurfer analysis

Hi, sorry for the delay. On 1/10/2020 1:42 PM, Martin Juneja wrote: External Email - Use Caution Dear Dough, Thanks for your reply. Below, I am summarizing my concerns from previous emails: Q1. I was wondering which of the following two options is better than the other (or neither may