[Freesurfer] error message recon-all

Hi, I keep getting this error message when running, or trying to run, recon-all. I suspect there is a file somewhere indicating that this subject has been run before. But all that is in the directory 3002 is dicom images. What is wrong? [LMR in subjects/DTI ] recon-all -subjid 3002 -i 3002/1.dcm

[Freesurfer] How to split frames from .mhg files?

Dear FreeSurfer Experts, I have a .mgh file which contains thickness data for 200 subjects in fsaverage space, so it has 200 frames. When I convert this file to ascii format it only converts the first frame. So I either need to split the .mgh file to single frame files and then convert to ascii or

Re: [Freesurfer] How to split frames from .mhg files?

Hi Ray this should do the trick: mri_convert -nth 10 all_frames.mgz frame10.mgz or mri_convert all_frames.mgz#10 frame10.mgz note that the second syntax should be accepted by most of our tools cheers Bruce On Thu, 22 Jan 2015, Ray Razlighi wrote: Dear FreeSurfer Experts, I have a .mgh

[Freesurfer] aquisition_parameters_echo time

Dear FS Experts, In this paper http://jmbe.bme.ncku.edu.tw/index.php/bme/article/viewFile/1558/939 the authors explained the effects of b-Value and Echo Time on Magnetic Resonance Diffusion Tensor Imaging but they didn't say what is the recommended range for the echo time that we should use.

Re: [Freesurfer] error message recon-all

Hi Lars you have to give recon-all some directive telling it what to do (-all, -autorecon1, -autorecon2, -autorecon3). cheers Bruce On Thu, 22 Jan 2015, Lars M. Rimol wrote: Hi, I keep getting this error message when running, or trying to run, recon-all. I suspect there is a file

Re: [Freesurfer] standardized community affiliation vector

You would have to get a connectivity matrix (either from someone who has analyzed the data, or from analysis that you do yourself). Even still, there won't be a standard because: * there are different ways of measuring connectivity (probabilistic vs. deterministic tractography; resting-state

Re: [Freesurfer] Problem with a recon edit

Hi Celine, Yes that's right, a value of 0 is treated differently than a value of 1 in the wm.mgz. Drawing with Recon Edit uses a value of 255 and erasing uses 1. When you reprocess the edited case with recon-all, whenever there is a 1 in the wm volume it knows that you specifically changed

Re: [Freesurfer] using -cw256 as default is good?

I think it should be ok, but I have not tested it extensively. On one data set the two commands gave the same result. doug On 01/22/2015 12:48 PM, Daniel Ferreira wrote: Dear experts, Could you please help me with my previous comment (see below)? Thanks so much Daniel Ferreira Dear

Re: [Freesurfer] Problem with a recon edit

Thanks Lee, I am testing it right now. Just to be sure, it means that a value of 1 in the wm.mgz volume would be treated differently from a value of 0? I did not touch the wm.mgz volume in those regions because I didn't see anything to delete, but it is interesting to know that even if the sulci

[Freesurfer] lost volume geometry information using read_surf.m and write_surf.m

Dear all, while working in Matlab with modified surfaces I came along the following problem: After reading a surface file in Matlab with read_surf.m and saving it again (unmodified) using write_surf.m the entries are the same, as expected. However, the visualisation of these (same) surfaces in

[Freesurfer] using -cw256 as default is good?

Dear experts, Could you please help me with my previous comment (see below)? Thanks so much Daniel Ferreira Dear experts, We are processing a dataset that gives us this error quite often: ERROR! FOV=300.000 256 Include the flag -cw256 with recon-all! Inspect orig.mgz to ensure the head

Re: [Freesurfer] mri_cnr and bash

Dear Dr. Greve, dear Dr. Fischl would something like this work? set cnr = `mri_cnr $SUBJECTS_DIR/$subject/surf $SUBJECTS_DIR/$subject/mri/norm.mgz | grep total | awk '{print $4}'` echo $subject $cnr yourfile Unfortunately it doesnt. I was trying to modify the paths, but got always