Freesurfer November 2016

freesurfer@nmr.mgh.harvard.edu

120 participants
214 discussions

mri_info --tkr2scanner result for run with multiple input scans
by Krieger, Donald N. 11 Nov '16

11 Nov '16

If I run recon-all with both a T1 and a T2 scan and switch t2pial, does mri_info -tkr2scanner give me the transform to the T1 scanner frame of reference? And if I run recon-all with many T1's , what does mri_info -tkr2scanner give me then? Thanks - Don

2 5

Mean intensity with mri_segstats : different results with .annot or .label
by Matthieu Vanhoutte 11 Nov '16

11 Nov '16

Dear experts, I am in trouble with two ways of computing mean intensity with mri_segstats. First I have used on .annot files with three different labels inside (SegId 1 to 3) : *mri_segstats --annot fsaverage lh cache.th23.pos.sig.ocn.annot --i lh.PET.fsaverage.sm10.mgh --sum lh.pet.sum* which give me those results: # ColHeaders Index SegId NVertices Area_mm2 StructName Mean StdDev Min Max Range 1 1 27805 14182.6 cluster-001 8.8194 1.4351 6.2105 14.2947 8.0842 2 2 2321 1047.3 cluster-002 10.3661 1.0848 8.8375 12.9317 4.0942 3 3 552 313.1 cluster3 10.3365 0.4711 9.3719 11.8694 2.4975 Second I have created on .label files containing the three segmented labels (SegId 1 to 3) and used this label with mri_segstats: *mri_segstats --slabel fsaverage lh lh.th23.cluster.thresh1.3.label --i lh.PET.fsaverage.sm10.mgh --excludeid 0 --sum lh.pet.label.sum * which give me those results: *# ColHeaders Index SegId NVertices Area_mm2 StructName Mean StdDev Min Max Range * * 1 1 30678 15542.9 Seg0001 8.9637 1.4701 6.2105 14.2947 8.0842 * I verified if I obtained the same results with the two ways (.annot or .label) and everything is fine comparing NVertices, Area_mm2 but Mean in first way gives me (8.8194+10.3661+10.3365)/3 = 9.84066 and with .label file Mean = 8.9637. Did I have miss anything and how is computed mean intensity ? Many thanks in advance. Best regards, Matthieu

2 8

CVS repository
by Melvin Robinson 11 Nov '16

11 Nov '16

I am trying to checkout the development version of Freesurfer from the CVS repository. I need to build against VTK 7.1 instead of 5.6 for freeview and am using these instructions: https://surfer.nmr.mgh.harvard.edu/fswiki/ReadOnlyCVS Using this command: cvs -d :pserver:anonymous@fsvm.nmr.mgh.harvard.edu:/usr/fscvsroot checkout -P dev Results in the following error: cvs server: cannot find module `dev' - ignored Can you tell me the correct module name?

2 1

AAL atlas
by stella maris sanchez 11 Nov '16

11 Nov '16

Hi all! I'm very new using FS and I have some questions. I have been doing parcellations with the FreeSurferLUT on a few subjects, with the comand recon-all and it worked OK. Now I'd want to try with the AAL atlas, I mean, I want my subject's brain parcellated in the AAL atlas. I have the template corresponding to AAL parcellation in nifti format, so how can I obtain this parcellation in my subject space? what (and how) comands I have to use? Thanks in advanced! Cheers.- Stella

2 3

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

1 0

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

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Freesurfer November 2016