Freesurfer

freesurfer@nmr.mgh.harvard.edu

15 participants
30096 discussions

Reproducibility of freesurfer analyses across different version of linux
by Knut J Bjuland 29 Aug '16

29 Aug '16

Dear FreeSurfer experts,I found this paper about named “Reproducibility of neuroimaging analyses across operating systems” (Glatard et al., 2015). There were differences in cortical morphometry like cortical thicknes between images proscced in the same version of freesurfer with different version of Linux or glibc for Freesurfer, and according to the paper, it was caused by how different version of glibc handles small single precssion floating numbers. I have therefore some questions. Are there plans for freesurfer to use double floating numbers in steps that may be affected by numerical stability? Or can this problem be solved by using staticall linking glibc into Freesurfer? Best regards Knut Jørgen BjulandPhD candidateNTNU

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Results different between mean-centered and raw covariates -- glm_fit
by Corinna Bauer 29 Aug '16

29 Aug '16

Hello all, I am wondering why results would change completely for between group volume analysis when using demeaned/mean-centered ICV compared to using ICV as a covariate in mri_glmfit? See the figures below. Does demeaning the covariate inherently change the results comapred to the raw covariate values? Thanks Corinna

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wm.mgz enclosed in pial/white surface
by Fire Tech 29 Aug '16

29 Aug '16

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How to transfer the VTK cortical surface to the diffusion space?
by Islem Rekik 29 Aug '16

29 Aug '16

Hi there! Since this is my first time using FreeSurfer, I found it quite challenging to get the handle on the different coordinate systems used. My goal is to generate vtk files where the vtk cortical surface and the vtk fiber tracts are in the same space (for one individual subject). Basically, I used recon-all to generate the cortical surfaces and trac-all to generate dtifit_FA.mgz and dtifit_V1.mgz for tractography in the original diffusion space. I used the transformation matrices generated in dmri/xmfs to transfer the cortical surface into the diffusion space, but not of them seem to work. What I find quite confusing is that when I visualize the surface lh.pial and the anatomical image brainmask.mgz using FreeView they nicely overlap; however, after I convert lh.pial to lh.pial.vtk and brainmask.mgz to brainmask.mha and visualize them using Paraview, they are in different spaces. To do so, I used the command line mri_surf2surf so the surface will overlay with brainmask.mha image when using Paraview, but none of the transformation matrices seems to warp the surface onto the anatomical (structural FreeSurfer) space. I also tried to warp it to the diffusion space and the anatomical original space, but it never overlapped with the images nested in these respective spaces. It is always floating somewhere else! I would like to know which transformation I need to: 1. apply to have the VTK surface overlap with the brainmask.mha image in the anatomical space and, 2. apply another transformation to transfer the VTK surface to the diffusion space where I perform tractography. Also, does TRACULA perfom whole brain tractography? I really appreciate your help! Kindly, Islem

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Hippo campal subfield segmentation
by Boris Marendic 27 Aug '16

27 Aug '16

Hello, I am new to using FreeSurfer, and need a little help. I have downloaded and installed FS 2 days ago (from https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall ). To verify the installation I proceeded with all steps on the first page, and everything worked fine. Then I decided to try the hippo campal segmentation, and I tried the scripts on the following page: https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldSegmentation?hi ghlight=%28hippo%29 . Running the first script recon-all -s bert -all -hippo-subfields resulted in a 20+ hour run of FS which completed successfully. Then I started the kvlQuantifyHippocampalSubfieldSegmentations.sh to analyze the bert results, and it died on me. I looked into the errors and into the script itself using an editor, and I found out that the script wants to descend (or "cd") into some folders named "left" and "right". However, running the "recon-all" script on the test subject bert (from above) did not generate "left" and "right" folders at all. I looked through the archived messages and did not find an answer to my issue. Can you help me out here? Is this a known bug and are there updated scripts that I should maybe download? The output of the kvlQuantifyHippocampalSubfieldSegmentations.sh script is provided below Thank you in advance Boris Marendic ---------------------------------------------------------------------------- ----------------------------- OUTPUT OF THE SCRIPT kvlQuantifyHippocampalSubfieldSegmentations.sh > kvlQuantifyHippocampalSubfieldSegmentations.sh /home/freesurfer/subjects resultsDirectory /home/freesurfer/subjects cd /home/freesurfer/subjects numberOfSubjects: 12 resultsDirectory /home/freesurfer/subjects startIndex: 1 endIndex: 12 Sides to evaluate: left right Current subject: bert/ cd bert/ Quantifying subject bert/ left Doing left side cd left /home/freesurfer/bin/kvlQuantifyHippocampalSubfieldSegmentations.sh: line 22: cd : left: No such file or directory failed to do cd left

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Hippocampal Subfields for T2-FLAIR images
by Hari Guragain 27 Aug '16

27 Aug '16

Dear Freesurfer community, I am trying to get the segmentation of hippocampal subfields by using the development version of the freesurfer. I have few normals with T2-FLAIR images along with T1 whose subfield volume needs to be calculated. I am wondering if the algorithm that calculate the hippocampal subfields can handle the T2-FLAIR? According to the wiki ( https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfields) it can handle the T2 but didn't say anything about the T2-FLAIR. It would be great if someone clarify this. Thank you, Hari Guragain

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Re: [Freesurfer] Visualising path.mean.txt in MNI space after trac-all -stat
by Elijah Mak 26 Aug '16

26 Aug '16

Hi Anastasia, Yes indeed. I am using a dev version of freeview. I could give it another go with the freeview that came with v5.3. But does this mean that I shoudl also I re-run the tracula -stat on a v5.3? Thanks! Best Wishes, Elijah

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Visualising path.mean.txt in MNI space after trac-all -stat
by Elijah Mak 26 Aug '16

26 Aug '16

Hi Anastasia and others, I am trying to visualise the *.path.mean.txt on MNI template after running trac-all -stat. I used this command: freeview -v $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz -w stats/*.path.mean.txt However, it looks like something has gone wrong with the labelling and position of the tracts (note the CST highlighted in green). https://www.dropbox.com/s/ndpkfgbrfgvt5q1/Screen%20Shot%202016-08-22%20at%2… Everything was fine and correctly labelled when I checked the merged tracks. Thanks again for your help! Best Wishes, Elijah P.S. On another note, the reinit=1 trick works very well and I was able to reconstruct the tracts in almost all cases. Thanks!

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Re: [Freesurfer] PET surface sampling
by Jonathan DuBois 26 Aug '16

26 Aug '16

Hi Doug, Thank you. I ran sampled the data and ran mri_glmfit as you suggested, although the resulting bp file seems to only have binary clusters (in the attached image the red cluster all have a value of 1 and everywhere else is 0). Is this the normal output? I expected a more varying map. Thanks Jonathan

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sig.sum files shows more clusters than sig.mgh image
by Oana Georgiana Rus 26 Aug '16

26 Aug '16

Dear Freesurfer experts, I have run an analysis on GM Volume in Freesurfer. The interested contrast was patients vs. controls. (/command mri_glimfit/) I then ran /mri_surfcluster/ command to get a text file with the significant clusters FDRcorrected and their peak coordinatesn- resulting in a *sig.mgh image* and a *sig.sum file*. *After looking at the sig.mgh image with tksurfer and searching for the significant clusters in the sig.sum files, I realized that one cluster which is pretty big is missing in the sig.mgh image but is present in the sig.sum file.* *Do you know why this could happen?Why is the image incomplete?* *Anybody encounterd something similar?* Because in the next step I want to extract the values of the significant clusters and correlate them with clinical scores, it would be good if thenumber of clusters in the result image and the result file coincide. Thanks in advance for your help. Best, Georgiana -- Oana Georgiana Rus PhD Student Neuroimaging Center TUM-NIC Klinikum rechts der Isar Technische Universität München Einsteinstr.1 81675 München Raum 5.8 Tel. 089 4140 7971

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