[Freesurfer] Research Position

Hi Freesurfers, I wanted to bring to the attention of recent graduates a research assistant position in my lab. Briefly, the position entails the application and transfer of your proficiency with FreeSurfer in the acquisition and analysis of fMRI data collected from healthy adults. More detail

[Freesurfer] selxavg3-sess problem: SVD input matrix contains NaN

Hi, I'm attempting an inaugural run through the FS pipeline on some event-related data collected over 6 runs. I'm not sure if this makes any difference, but the experiment is self-paced, and the events are of varying duration (it's a lexical decision task, and participants can take up to 4 secon

[Freesurfer] preproc-sess error opening tmp brain_mask

I was hoping the developers might be able to help with a problem I'm having with a sub-step of preproc-sess. I executed the following: preproc-sess -s FS_T1_501 -surface self lhrh -fwhm 6 -per-run -fsd bold In the relevant output, I see mktemplate-sess completed, followed by a call to mkbra

Re: [Freesurfer] preproc-sess error opening tmp brain_mask

on another dataset (but on another workstation, but neither were those two binaries to be found on that workstation). Is your /tmp space full? On 04/15/2016 12:54 PM, Mcnorgan, Christopher wrote: > > I was hoping the developers might be able to help with a problem I'm > having with

[Freesurfer] ERROR: DOF=0 in call to mri_glmfit by preproc-sess

Hi, First, thanks to Doug Greve for helping me isolate my previous problem, which turns out to have resulted from a conflicting fsl installation. Now that that's resolved, I'm having a problem on a first-level analysis. In preparation for calling selxavg3-sess, I am running preproc-sess on an

Re: [Freesurfer] ERROR: DOF=0 in call to mri_glmfit by preproc-sess

?That seems to have been the problem: Running the data through Slicer as suggested elsewhere fixed the slice time code, but then saved only a single frame of the 4D data. I had been poking around the file header looking for a corresponding field, not suspecting that it was a calculated value and

[Freesurfer] External Regressor of Interest in FS-FAST

The references to external regressors in mkanalysis-sess are a little sparse on how I would go about analyzing a continuous regressor: I have a mixed design experiment: TaskBlock1 Rest TaskBlock2 Rest … TaskBlockN Rest x6 Runs Within each block are jittered events (5 of condition A, 5 of conditi

[Freesurfer] mri_glmfit error (mri_reshape number of elements)

Hi, I’m running a group-level analysis and have encountered an error that results in a core dump. The first-level analyses were run using the fsaverage surfaces, rather than self surfaces. I’ve already inspected the individual contrasts, loading the fsaverage surface in tksurfer and rendering ea

[Freesurfer] individual mri_segstats waveforms for vertices or face in label

Though one workaround might be to subdivide a label many, many times using mris_divide_parcellation, I was wondering if it is possible to obtain a per-vertex (or even per-face) fMRI waveform for a label. In other words, rather than compute the average waveform across all vertices, as with mri_se

[Freesurfer] recon-all on previously segmented volumes

Hi, I’m having some issues generating surfaces for an individual and was hoping that a combination of tools might help. In this particular individual, the skull stripping went fine, but a fairly large proportion of the anterior temporal cortex (primarily inferior) volume is excluded from the dat

Re: [Freesurfer] selxavg3-sess problem: SVD input matrix contains NaN

An epiphany lead me to the solution to the problem, which I shall post here since I am apparently due to experience it again in 2019. The NAN values in the GLM matrices were the result of there being a condition that did not appear in any of the .par files across all of the runs. Once these file

[Freesurfer] Regressing out conditions of non-interest with selxavg3-sess

Hi, I have some BOLD data from a fast event-related experiment with 3 experimental conditions, 1, 2 and 3. A reviewer wants me to isolate the signal for condition 1. Under the assumptions of the GLM, the signal is a linear combination of A1+B2+C3+Error, so it seems that I need to construct a d

Re: [Freesurfer] Regressing out conditions of non-interest with selxavg3-sess

Hi Doug, Thanks for the prompt reply to what was essentially a 2-part question. Data were processed in both fsaverage and native space for different reasons, which is why I suggested the possibility of surface space incongruency on at the end, which your reply seemed to make more likely. It tur

[Freesurfer] Identifying labels overlapping with overlay volume

External Email - Use Caution I’ve got a custom .annot file covering the entire cortical surface in fsaverage space, and I wish to see which labels overlap with an overlay statistical contrast volume generated by mri_glmfit. I extracted the vertex indices from my custom .annot fil

Re: [Freesurfer] Desikan Atlas in volume space (ece ulug)

External Email - Use Caution Hi Ece, I believe you will find a walkthrough of the steps to do exactly what you want done on my lab wiki: http://ccnlab.psy.buffalo.edu/wiki/index.php/Annotation_Coordinates Hope this helps, Chris /** *

[Freesurfer] The mystery of the missing mcprextreg file

External Email - Use Caution Hello, I’ve been trying to get to the bottom of why selxavg3-sess is failing for lack of a mcprextreg motion correction parameters file for one or more of the functional runs. I have 6 runs of BOLD data, and following the last failed attempt, we clear

[Freesurfer] Followup on the mystery of the missing mcprextreg file

External Email - Use Caution Hi Doug, For some reason I’m having a problem replying to this list with my reply to your reply. To recap: some of my functional runs are missing the mcprextreg file, and so the GLM with the motion correction parameters is failing. You had asked whe

Re: [Freesurfer] Followup on the mystery of the missing mcprextreg file

the transfer completing successfully, I have also uploaded the file to my google drive where I’ll let it remain for the next few days if you want to get it from there instead: https://drive.google.com/open?id=1urPlFg3NU56RxtZslgLzk-pXef3Csye1 Thanks, Chris From: "Mcnorgan, Christ

Re: [Freesurfer] Followup on the mystery of the missing mcprextreg file

External Email - Use Caution Thanks for looking into the matter Doug, and I now have gotten to the bottom of the problem based on your suggestion about dropping volumes. For context, I have been collecting functional runs from a Phillips scanner using a self-paced task, and termi

[Freesurfer] mri_glmfit residualized data after motion correction

Hello FreeSurfers, I have an existing pipeline that computes the residualized time series after removing any linear trends using mri_glmfit: mri_glmfit --y ${source_dir}/${r}/${filepat}.${surf}.${hemi}.nii.gz \ --glmdir ${source_dir}/${r}/${hemi}.detrend \

[Freesurfer] Systematically Navigating .sphere vertices

External Email - Use Caution I’m interested in working with data mapped to the .sphere icosohedrons. I understand from a response from Doug back in 2017 that: waveforms = fast_vol2mat(MRIread('waveform.nii.gz')); will give me a v x time matrix of values from my functional val

[Freesurfer] Using mri_glmfit to regress out wm and ventricle signal

External Email - Use Caution I’ve been using mri_glmfit to regress out motion correction parameters and linear trends and saving residuals in surface space by first generating a QA matrix for the volume: mri_glmfit --y ${source_dir}/${r}/${filepat}.${surf}.${hemi}.nii.gz \

[Freesurfer] Are my slice-time corrected files being used in selxavg3-sess?

External Email - Use Caution Hi all, There was some ambiguity in communication from a previous MR technician regarding the slice ordering in our BOLD data. preproc-sess was applied to our data: preproc-sess -sf SUBJECTS -surface fsaverage lhrh -per-run -fsd bold -sliceorder up -f

[Freesurfer] discontiguous regions assigned to same label by mris_divide_parcellation

External Email - Use Caution I’ve been using the .annot files generated by group-level GLM results for functional masks for task-related functional connectivity studies. Depending on threshold and contrast, the clusters can be quite large, and I would prefer to use the mris_divid

[Freesurfer] Account password on Virtualbox VDI

External Email - Use Caution Hi, I have a couple students who are windows users who I am training remotely. They’ll be using the VDI found at: https://surfer.nmr.mgh.harvard.edu/fswiki/VM_67 I’ve never tried this and can give no guidance, as I have no Windows computers at my disp

[Freesurfer] tk applications failing to launch on VM (Windows)

External Email - Use Caution Hi, I run Freesurfer remotely on Ubuntu, and locally on my Mac, so I’ve not had this problem personally. Two students are working remotely with PCs and are using the VM installation you folks provided (https://surfer.nmr.mgh.harvard.edu/fswiki/rel7do