Freesurfer

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30132 discussions

Extract specific LGI and Volume values
by Tien Pham 06 Mar '20

06 Mar '20

External Email - Use Caution Dear FreeSurfer Experts, I am Tien Pham, I am stucked at this situation. I calculated longitudinal LGI changes in my data set with two time points using longitudinal pipeline. Now I would like to extract the regional LGI and gray matter volume in my longitudinal results using QDEC to draw the ROIs which is showed significant differences, label it and map to all subjects. Then I get the LGI value of the ROI I saved before using the command below: cd $SUBJECTS_DIR mris_anatomical_stats -l lh.untitled.label \ -t lh.pial_lgi \ -b \ -f subject_id/stats/lh.untitled.stats subject_id lh And this is the result: [toyama-no-iMac:/applications/freesurfer/subjects] toyama% mris_anatomical_stats -l lh.frontoinsula.label \ ? -t lh.pial_lgi \ ? -b \ ? -f VC019_1/stats/lh.frontoinsula.stats VC019_1 lh limiting computations to label lh.frontoinsula.label. using thickness file lh.pial_lgi. reading volume /applications/freesurfer/subjects/VC019_1/mri/wm.mgz... reading input surface /applications/freesurfer/subjects/VC019_1/surf/lh.white... reading input pial surface /applications/freesurfer/subjects/VC019_1/surf/lh.pial... reading input white surface /applications/freesurfer/subjects/VC019_1/surf/lh.white... table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name 6595 4368 15935 3.311 0.895 0.158 0.077 135 19.7 lh.frontoinsula.label As I saw there was no columns showing the LGI value, I did similar with gray matter volume, the result displayed the different in some values of the columns. Could you please help me to explain about this? Thank you very much. Best regards, Tien Pham

3 22

2 surface mri_glmfit as independent variables
by Adam Martersteck 06 Mar '20

06 Mar '20

External Email - Use Caution Hi FreeSurfer team, I have a question about running mri_glmfit with 2 different surface modalities as the independent variable and a single value per participant as the dependent variable. I'm trying to examine the unique and shared contribution of the 2 surfaces to predict a cognitive measure. E.g. Cognition ~ ?h.thickness + ?h.PET I tried mri_glmfit with the "--table" option, giving it a column of scores per participant (in the aseg2stats table format), and then using "--pvr lh.thickness-stack.fsaverage.mgh" and a second "--pvr lh.PET-stack.fsaverage.mgh", using contrasts matrices as [0 0 1], [0 1 0], and [0 1 1]. *When I run mri_glmfit it returns:* ERROR: mri_reshape: number of elements cannot change nv1 = 163842, nv1 = 1 It continues to run, but all surface maps are full of zeroes. Any suggestions? Is there a better way to do this? Thanks, Adam

2 1

Registration of DIR (Double Inversion Recovery) series
by Xiaojiang Yang 06 Mar '20

06 Mar '20

External Email - Use Caution Hi all, I want to register DIR (Double Inversion Recovery) series to T1 series using Freesurfer. I used the command line similar to that used for FLAIR registration: bbregister --s subject001 --mov dicom/subject001/20141003_MR/3_Sag_Space_DIR/2.25.97015757385982906453797720915266163627.dcm --lta subjects/subject001/mri/transforms/DirTest.auto.lta --init-coreg --T2 where the option --T2 is still used. Since in DIR series, gray matter is brighter than white matter, I use --T2 as the contrast argument. I wan's able to check how precise the results are. I will take some time to do check that. But anyone can tell me: Did I do it correctly? what is the better way or correct way to do the above-mentioned registration? Thank you! Xiaojiang

2 1

petsurfer
by Laboratorio de Neurociencia Funcional 06 Mar '20

06 Mar '20

External Email - Use Caution Dear Freesurfer experts, I have compared the PVC uptake values of gtm.stats with the values of gtm.nii.gz with the function load_nii in matlab. I noted that values in matlab are reversed, i. e., the first value in gtm.stats matches with the last value in gtm.nii.gz and so on. Could you confirm me that nopvc.nii.gz values are also reversed when loaded with load_nii in matlab? I have no way to check this. Thank you in advance. Best, Marina

2 1

Issue with BBR and Applying CVS Warps to Diffusion Data
by Austin Patrick 06 Mar '20

06 Mar '20

External Email - Use Caution Dear All, I have used CVS to align around 180 scans to a single, representative subject. I have then used BBR to align the mean b0 image to register the diffusion data to the native space T1 and then apply CVS warps; however, the resulting aligned images for calculated maps from the DWIs are very poor with a great deal of heterogeneity, especially at the boundary but also within white matter. The coefficient of variation of the mean b0 BB registered to the T1 is around 30% globally (excluding the edges of the brain) and 40% or greater for FA. I have reviewed the initial rigid registration of the b0s to the T1s for gross misalignment and found that FLIRT performed pretty well and didn’t fail for any of my subjects and didn’t require manual adjustment; however, the result of after applying the CVS warps is quite poor. The data T1s are 1mm (MPnRAGE) and the b0s are at 2mm. The DWIs were corrected for eddy currents, Gibbs’ ringing, rician noise, and B0 distortions and look pretty great. The DWIs are 70x180x180 at 2mm isotropic and the T1s are 256x256x256 at 1mm isotropic. Are there any suggestions for this issue? I have tried re-aligning the DTI parameter maps to the b0s before applying the CVS warps (although they should be in the same space) and I have tried using both the –t2 and –dti, as well as with/out the –fsl-init flag. Is bbregister shifting the origin for the images at all? Any help would be appreciated. Cheers, -Austin -- Austin M. Bazydlo, MS PhD Candidate Dept. of Medical Physics University of Wisconsin-Madison

2 5

registrations
by Octavian Lie 06 Mar '20

06 Mar '20

External Email - Use Caution Dear All, I need to register: 1. T1.mgz to a T1 postresection volume (no contrast), with large resection. Which one should I use, mri_robust_register, or bbregister, if the latter, which is the better initiator (nmi, spm, fsl)? 2. T1.mgz to a 3D FLAIR SPACE sequence (outside of the flair space recon-all flag), which FS registration tool should I use? 3. I then need to mask the coregistered T1 postresection with a T1.mgz mask. I would appreciate commands (either names, or full command lines), please advise. Thank you, Octavian

3 5

group analysis for same group in 2 conditions
by Marco Ninghetto 06 Mar '20

06 Mar '20

External Email - Use Caution Dear experts, I'm performing a study on visual pathways, in which each participant undergoes to 2 different conditions. One in normal sight (NG, i.e.: No Goggles) and second in narrowed sight using special goggles (YG, i.e.: Yes Goggles). I'd like to compare the results between these two conditions (basically, subject A, B, C in cond1 versus subject A, B, C in cond2). I created the FSGD file (attached as "RetinotopyStudy" file) and the contrast matrices, organised as: 1 -1 , named "YG-NG.mtx" > -1 1, named "NG-YG.mtx" In this FSGD sample file, I reported only subjects from 7 to 12. My folders are organised as follows: main >> recon_output >> sub-yy (X folders for X subjects) > >> Contrasts (with contrast files) > >> FSGD (with FSGD files) > >> fsaverage (subjects template > created during recon-all -qcache) > >> pRF_function >> analNG (inside, there are the functionals for > each subject in NG condition) > >> analYG (inside, there are the > functionals for each subject in YG condition) Once I used the pipeline for the retinotopy analysis <http://freesurfer.net/fswiki/FsFastIndividualRetinotopyAnalysis>and I have results for each participant, and now I'd like to make 2nd lev analysis. So the idea would be, as you probably already got it, condition Yes Goggles versus condition No Goggles. I use the command: mris_preproc --fsgd RetinotopyStudy --target fsaverage --hemi ?h --out > outputname.mgh But I'm not sure it would calculate in the right way. The question is: how would I organise the FSGD file or folders in such a way that FREESURFER would know that it has to compare results from the same subjects but from two different folders (analNG vs analYG)? Hoping that's clear, I really look forward to hear from you soon. Thank you for your time, Marco -- --------------------------------------------------- Marco Ninghetto, PhD candidate Laboratory of Neuroplasticity Nencki Institute of Experimental Biology Polish Academy of Sciences 3 Pasteur Street, 02-093 Warsaw, Poland

2 4

Open lab manager position in Perception & Brain Dynamics Laboratory at NYU Medical Center
by Wu, Yuan hao 06 Mar '20

06 Mar '20

External Email - Use Caution Sorry for spamming. The contact email in the previous mail contains a typo The Perception & Brain Dynamics Laboratory (http://www.med.nyu.edu/helab/) at New York University School of Medicine is looking for a lab manager to start in spring/summer 2020. The Laboratory is within the Neuroscience Institute at NYU Langone Health(http://www.med.nyu.edu/neuroscience), affiliated with Departments of Neurology, Neuroscience and Physiology, and Radiology. Our research focus is on understanding the neural bases of perceptual awareness using multimodal imaging (fMRI, MEG, EEG, ECoG) and stimulation (tDCS, TMS) techniques in humans, combined with computational neuroscience approaches. We are looking for a bright and driven candidate with a Bachelor's or Master's degree who is dedicated to neuroscience research. A variety of backgrounds, including neuroscience, biology, psychology, and computer science is possible, and experience with programming is highly desirable. In addition, the ideal candidate has high responsibility and dependability, as well as excellent critical thinking, organizational and leadership skills. Performing independent research is an important aspect of the position, in addition to lab management duties. A minimal commitment of 2 years is required. Interested candidates please send a cover letter, a CV, undergraduate and/or graduate transcript, and names and contacts of two to three referees, to Prof. Biyu J. He at biyu.jade.he(a)gmail.com, with the subject line "Lab manager application 2020". The application is rolling, so please submit your materials as soon as possible.

1 0

Open lab manager position in Perception & Brain Dynamics Laboratory at NYU Medical Center
by Wu, Yuan hao 06 Mar '20

06 Mar '20

External Email - Use Caution The Perception & Brain Dynamics Laboratory (http://www.med.nyu.edu/helab/) at New York University School of Medicine is looking for a lab manager to start in spring/summer 2020. The Laboratory is within the Neuroscience Institute at NYU Langone Health(http://www.med.nyu.edu/neuroscience), affiliated with Departments of Neurology, Neuroscience and Physiology, and Radiology. Our research focus is on understanding the neural bases of perceptual awareness using multimodal imaging (fMRI, MEG, EEG, ECoG) and stimulation (tDCS, TMS) techniques in humans, combined with computational neuroscience approaches. We are looking for a bright and driven candidate with a Bachelor's or Master's degree who is dedicated to neuroscience research. A variety of backgrounds, including neuroscience, biology, psychology, and computer science is possible, and experience with programming is highly desirable. In addition, the ideal candidate has high responsibility and dependability, as well as excellent critical thinking, organizational and leadership skills. Performing independent research is an important aspect of the position, in addition to lab management duties. A minimal commitment of 2 years is required. Interested candidates please send a cover letter, a CV, undergraduate and/or graduate transcript, and names and contacts of two to three referees, to Prof. Biyu J. He at biyu.jade.he(a)gmail.com, with the subject line "Lab manager application 2020". The application is rolling, so please submit your materials as soon as possible.

1 0

Fwd: FreeSurfer Course @ Caltech information - FOLLOW UP
by Paul Wighton 06 Mar '20

06 Mar '20

External Email - Use Caution Hi FreeSurfer friends, Does anybody have experience getting FreeView to run on Windows 10? Any suggestions on how to resolve this issue below? Or, are there any other installation notes you could pass along? Thanks, -Paul I’ve installed FreeSurfer on a Windows 10 machine with a WSL (Ubuntu 18.04 LTS) and Xming for graphical display. It generally works. However, when testing the installation using the examples on the website it fails to display the output volumes from Example 4 (see screenshot below). Do you have any idea what the problem might be? Thank you! Tessa

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