Freesurfer

freesurfer@nmr.mgh.harvard.edu

5 participants
30076 discussions

FSL View in the virtual box version?
by Jeffrey Crawford 11 Nov '16

11 Nov '16

Hello there! I currently use the virtualbox version of freesurfer on my windows and the CentOS 4 (32b) version on a linux computer. I noticed today that the Virtual box version does not seem to have fsl view. I found this link to a blog where this person has a virtual box that contained fslview, but I think his methods and version are different from the typical installation procedures. http://kylemathewson.com/cnl-virtualbox-setup/ I was just wondering if it is possible to use fslview on the virtual box version or not and how I might go about obtaining that capability?

2 1

Large Ventricles
by Tamara Tavares 11 Nov '16

11 Nov '16

Hello, I have a participant who has very large ventricles and as a result, there are substantial errors in the aseg output. Looking at the mailing list, I see that the newest version of Freesurfer is suppose to be better at handling large ventricles; however, I want to be consistent with the Freesurfer version I have been using (version 5.1). Are there any other recommendations with dealing with large ventricles? Thank you in advance for your help, Tamara

2 1

ERROR: make_roi_paths did not complete successfully!
by Hari Guragain 11 Nov '16

11 Nov '16

Hi Freesurfer experts, I was working on to conduct the local gyrification index analysis. I am getting the following error message when I used the option -localGI in recon-all. -------------------------------------------------------------------- Improper assignment with rectangular empty matrix. Error in dsearchn (line 79) [d(i),t(i)] = min(sum((x-yi).^2,2)); Error in mesh_vertex_nearest (line 29) nearestIndex = dsearchn(vertices,points); Error in reorganize_verticeslist (line 28) [nextindex,nextvalue]=mesh_vertex_nearest(mesh_total.vertices(remaininglist,:),mesh_total.vertices(verticeslist(start_vertex),:)); Error in make_roi_paths (line 93) reorglist = reorganize_verticeslist (mesh_total, A, mesh_outer, perim, verticeslist, step); ERROR: make_roi_paths did not complete successfully! -------------------------------------------------------------------- I have seen people have similar problem long time ago ( https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg33701.html) I also tried to check the SearchProjectionOnPial.m file and it looks same as what was attached in the email. Can anyone help on this? I will really appreciate. Thank you, Hari

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Re: [Freesurfer] QDEC and LGI {Disarmed}
by Caverzasi, Eduardo 11 Nov '16

11 Nov '16

Hi, I am using the QDEC tool to compare two groups looking at differences in thickness and local gyration index. Once I finish running an analysis (design) and displayed the results through the gui, it is possible to find cluster and visualize the distribution of values within each cluster. Is it possible to extract the values for each cluster? The legend of the threshold is not clear, and I want to make sure to interpret correctly the results (red cord for increased in Ctrl vs Dys and blue cord for decreased in ctrl vs Dys. Best regards, Edu

1 0

computing ICC with LME
by Tanmay Nath 10 Nov '16

10 Nov '16

Hi, I am trying to compute the between state ICC (using LME MATLAB toolbox) for my data but the lme_fit fails to converge in most of the voxels and thus gives me ICC = 0. Increasing the number of iterations have not helped me and it still does not converge Any suggestions? Am I missing anything? Thanks Warm Regards, Tanmay Nath

1 0

reusing mri_surf2surf transformation
by Chris Filo Gorgolewski 10 Nov '16

10 Nov '16

Hi, I need to convert a big number of scalar surface maps from fsaverage to one particular subject space. This means running mri_surf2surf command many times. For each execution the same transformation is calculated and then applied. Since estimating the transformation take a substantial amount of time I was wondering if I could calculate the transformation once and just apply it (which is a common thing in volumetric registration). I perused the website and the command line options, but I could not find anything. Is it possible to save and reuse surface transformations? Best, Chris

2 8

Optseq2 - Repeating Stimuli and Contrasting the Repetitions
by Ruthie Shaffer 10 Nov '16

10 Nov '16

Hi all, I’m posting to ask for advice on setting up certain parameters in optseq2: Specifically, in optseq2, how can one set up parameters to best optimize a task where there are say 20 items presented 3 times, where the relevant contrasts are between the first, second, and third presentations of the same items? Meaning the second presentation must come sometime after the first and the third presentation must come sometime after the second? Thank you so much for any help on this! Best wishes, Ruth

2 1

aparcstats2table
by Martin Juneja 10 Nov '16

10 Nov '16

Hi everyone, I am trying to use following command to save stats from a set of subjects in a table format: aparcstats2table --qdec qdec.dat --hemi lh --meas thickness -t zzz.txt But after I run this, I get following error: Traceback (most recent call last): File "/usr/local/freesurfer/bin/aparcstats2table", line 353, in <module> subj_listoftuples = assemble_inputs(options) File "/usr/local/freesurfer/bin/aparcstats2table", line 228, in assemble_inputs fsid=row['fsid'].strip() KeyError: 'fsid' My qdec.dat file looks like below: fsid HC003_1 HC004_1 HC006_1 HC015_1 This command works fine if I use subject IDs individually here e.g. aparcstats2table --subjects HC_Example HC003_1 HC004_1 HC006_1 HC015_1 --hemi lh --meas thickness -t zzz.txt Another question I have here is: How can I average these thickness stats and display it on standard fsaverage? Any help would be really appreciated.

3 5

mri_average vs mri_concat
by Trisanna Sprung-Much 10 Nov '16

10 Nov '16

Hi Doug I spoke with you at the Freesurfer tutorial last week about using mri_average to average my sulcal labels and get a probability map on fsaverage. You had suggested using "mri_concat" instead, which is a newer command. So, I performed the following command: *mri_concat all files --o output.mgz --mean --keep-datatype* I had to put --keep-datatype or else it tried to create an annot file. This worked just fine. My question then is concerning *the min and max values *when this average is overlayed in Freeview. See the snapshot attached. The values seem to be based on 256 instead of percentage and this is what happens when I used "mri_average" without specifying the "-p". Is there a way to illustrate the values in percentage in a similar way with mri_concat? Many thanks! Trisanna -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology

4 23

Vertex-labeling
by Foteini Protopapa 10 Nov '16

10 Nov '16

Dear FS experts, I have a volume with specific clusters and I project it to a surface using mri_vol2surf. How can I determine the edges of my clusters now? By getting the surface I get a vector, but I don't know the "labels" of this vector. To which point (in mm) each value corresponds? Thanks in advance, Foteini.

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