Freesurfer July 2017

freesurfer@nmr.mgh.harvard.edu

118 participants
198 discussions

Freesurfer commands
by Aziz Nanthaamornphong 25 Jul '17

25 Jul '17

Hi Freesurfer Experts, Currently, I am using these command excited in Matlab to extract the coordinates of volume. *mri = MRIread('aseg.mgz');pos = find(mri.vol == 17 | mri.vol == 53);* *[i,j,k] = ind2sub(mri.volsize,pos);* I would like to run these command in the Freesurfer itself rather than using Matlab. Can I do that? Which command are qual? Best Wishes, Aziz

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converting vertex numbers in .label files to R, A, S coordinates
by Li Guo 25 Jul '17

25 Jul '17

Dear Freesurfer experts, My question concerns the .label files and the correspondence between the vertex numbers (in the first column) and the R,A,S coordinates. I have the R,A,S coordinates of voxels that I want to display on the surface. For this purpose, I created a label file with the R,A,S coordinates (col 2,3,4) and random vertex ID in the col 1 (since I do not know what is the vertex ID for a given R,A,S coordinate). I displayed the content of the label file via tksurfer. However, tksurfer reads vertex ID, not R,A,S coordinates. I wonder whether anyone knows about a function computing the vertex ID based on the R,A,S coordinates, or an alternative solution to represent the vertices on the surface based on the voxel coordinates--and the registration file I assume? Thank you very much! Best Li Guo & Florence Campana Thanks a lot!

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How to capture atrophy in frontal and temporal lobes with pial surface
by Eric Mitchell 25 Jul '17

25 Jul '17

Hello developers, I'm attempting to get measurements from the temporal and frontal lobes of individuals with dementia, resulting in atrophy of these areas. The pial surface does not include many of the anterior portions of these lobes. I've read through a number of archived posts on how to include these missing grey matter areas, but there doesn't seem to be a consensus. Also the WM does not extend into these areas. I have attached example images. Any thoughts on how I should approach this? Thanks, Eric Running: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c This email is directed in confidence solely to the person named above and may contain confidential, privileged or personal health information. Please be aware that this email may also be released to members of the public under Ontario's Freedom of Information and Protection of Privacy Act if required. Review, distribution, or disclosure of this email by anyone other than the person(s) for whom it was originally intended is strictly prohibited. If you are not an intended recipient, please notify the sender immediately via a return email and destroy all copies of the original message. Thank you for your cooperation.

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Cerebral White Matter vs Cortical White Matter
by Dowling, Kevin Francis 24 Jul '17

24 Jul '17

Dear Freesurfer Experts, My apologies for what is admittedly a very simple question, however I have not been able to find an answer on the forum. We are running some analyses in an older version of Freesurfer (5.0) to compare the results to some earlier work. When I run asegstats2table for all of my subjects, the header is {lh/rh}CorticalWhiteMatterVol. However, when I visualize the aseg.mgz file using freeview (from Freesurfer 6.0) the right and left hemispheric cerebral white matter are labeled {Right/Left}-Cerebral-White-Matter. I am familiar with the morphemetry stats page of the wiki (for versions 5.2 and higher) and two prior postings discussing this question, though the latter posting suggests for earlier Freesurfer versions these terms may refer to different measures. However, I'm afraid that I am still a bit unclear as to whether there is a difference. (see : https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2014-March/036949.ht… & https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-May/018494.html ) Are these terms the same or are they calculated differently (perhaps {lr/rh}CorticalWhiteMatterVol = {Right/Left}-Cerebral-White-Matter + any white matter hypointensities)? Thank you very much in advance for your help! Best wishes, Kevin Kevin F. Dowling Clinical Research Coordinator Brain Genomics Laboratory Division of Psychiatric Neuroimaging Martinos Center for Biomedical Imaging Massachusetts General Hospital 149 13th Street Charlestown, MA, 02129 (p) 617.643.2479

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Monte-Carlo in LME
by Jordi Pegueroles 24 Jul '17

24 Jul '17

Dear FS experts, I was wondering if someone had performed multiple comparisons (ie monte-carlo) with the LME analyses. I have found a thread (https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg40195.html) where Doug recommends to run a GLM fit with the same data and then overwrite the sig.mgh file with the LME one. My question is if is not more accurate to estimate the residuals from the LME model, then compute the relative smooth of the data with the mris_fwhm command and pass it as an argument in the mri_surfcluster command (mri_surfcluster --in $direct1/sig.mgh --csd /Applications/freesurfer/average/mult-comp-cor/fsaverage/${hemi}/cortex/fwhm${rfwhm}/abs/th13/mc-z.csd --cwsig $direct1/mc.abs.th13.sig.cluster.mgh --vwsig $direct1/abs.th13.sig.vertex.mgh --cwpvalthresh 0.05 --surf white). Thanks in advance. -- Jordi.

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recon -all removes tumour areas
by Sanjeev Nara 22 Jul '17

22 Jul '17

Hi Freesurfer experts, I am using recon -all for parcellating the MRI dataset into different brain regions. But the freesurfer removes the area's having tumour and creates a blank hole there. Is it possible to retain the Tumour areas. My goal is to create a forward model using MRI data. I have attached picture of one subject and highlighted the missing areas. Any suggestion and solution should be highly appreciated. Best regards Sanjeev Sanjeev Nara Predoctoral Researcher BCBL www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer

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Postdoctoral Position in Cognitive and Clinical Neuroscience, Boston, MA {Disarmed}
by Dustin Clark 21 Jul '17

21 Jul '17

Postdoctoral Position in Cognitive and Clinical Neuroscience Boston Attention and Learning Lab, VA Boston Healthcare System, Boston, MA The BALLAB (www. <http://www.bu.edu/ballab/>bu.edu/ballab/) at VA Boston is looking for a neuroimaging post-doctoral fellow starting this coming fall, 2017. Broadly, the BALLAB uses a variety of cognitive neuroscience tools (fMRI, EEG, TMS, psychophysics, cognitive training) to study attention and visual cognition, as well as cognitive and brain dysfunction in Veterans with psychiatric disorders. This specific position is funded by a VA grant to use fMRI connectomicsto understand and predict cognitive, functional, and clinical dysfunction in Veterans. Opportunities to work on a wide range of projects and with collaborators at VA, Boston University, and Harvard are ample, and new project development is welcome. Ph.D. in experimental psychology, cognitive neuroscience, neuroscience, or related field, as well as experience with programming and fMRI required. Two years of funding are available. If interested, please contact Mike Esterman (esterman(a)bu.edu)

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tracula error message
by Marissa Pifer 21 Jul '17

21 Jul '17

Hi Freesurfers, Could you help me interpret this error message? I am attempting to run TRACULA using version 6 on a MacBook Pro OS X El Capitan Version 10.11.3 helpdesks-MacBook-Pro-2:R01_DTI crc$ trac-all -prep -c dmrirc.example1 INFO: SUBJECTS_DIR is /Users/crc/Documents/myprojects/R01_DTI INFO: Diffusion root is /Users/CRC/Documents/myprojects/R01_DTI/tracresults Actual FREESURFER_HOME /Applications/freesurfer trac-preproc -c /Users/CRC/Documents/myprojects/R01_DTI/tracresults/NAH001-1/scripts/dmrirc.local -log /Users/CRC/Documents/myprojects/R01_DTI/tracresults/NAH001-1/scripts/trac-all.log -cmd /Users/CRC/Documents/myprojects/R01_DTI/tracresults/NAH001-1/scripts/trac-all.cmd #------------------------------------- /Applications/freesurfer/bin/trac-preproc #------------------------------------- #@# Image corrections Fri Jul 21 09:28:12 EDT 2017 mri_convert --bvec-voxel /Users/CRC/Documents/myprojects/R01_DTI/NAH001-1/DTI/nifty.nii.gz /Users/CRC/Documents/myprojects/R01_DTI/tracresults/NAH001-1/dmri/dwi_orig.nii.gz mri_convert.bin --bvec-voxel /Users/CRC/Documents/myprojects/R01_DTI/NAH001-1/DTI/nifty.nii.gz /Users/CRC/Documents/myprojects/R01_DTI/tracresults/NAH001-1/dmri/dwi_orig.nii.gz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /Users/CRC/Documents/myprojects/R01_DTI/NAH001-1/DTI/nifty.nii.gz... TR=3222.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.997757, 0.0345085, 0.057362) j_ras = (0.0453079, 0.978915, 0.19918) k_ras = (0.0492791, -0.201332, 0.978283) writing to /Users/CRC/Documents/myprojects/R01_DTI/tracresults/NAH001-1/dmri/dwi_orig.nii.gz... cp /Users/CRC/Documents/myprojects/R01_DTI/NAH001-1/DTI/bvec /Users/CRC/Documents/myprojects/R01_DTI/tracresults/NAH001-1/dmri/dwi_orig.bvecs cp /Users/CRC/Documents/myprojects/R01_DTI/NAH001-1/DTI/bval /Users/CRC/Documents/myprojects/R01_DTI/tracresults/NAH001-1/dmri/dwi_orig.bvals mv -f /Users/CRC/Documents/myprojects/R01_DTI/tracresults/NAH001-1/dmri/bvecs.tmp /Users/CRC/Documents/myprojects/R01_DTI/tracresults/NAH001-1/dmri/dwi_orig.bvecs mv -f /Users/CRC/Documents/myprojects/R01_DTI/tracresults/NAH001-1/dmri/bvals.tmp /Users/CRC/Documents/myprojects/R01_DTI/tracresults/NAH001-1/dmri/dwi_orig.bvals orientLAS /Users/CRC/Documents/myprojects/R01_DTI/tracresults/NAH001-1/dmri/dwi_orig.nii.gz /Users/CRC/Documents/myprojects/R01_DTI/tracresults/NAH001-1/dmri/dwi_orig_las.nii.gz dyld: lazy symbol binding failed: Symbol not found: ___emutls_get_address Referenced from: /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib Expected in: /usr/lib/libSystem.B.dylib dyld: Symbol not found: ___emutls_get_address Referenced from: /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib Expected in: /usr/lib/libSystem.B.dylib Trace/BPT trap ERROR: input file must be in NIfTI format Darwin helpdesks-MacBook-Pro-2.local 15.3.0 Darwin Kernel Version 15.3.0: Thu Dec 10 18:40:58 PST 2015; root:xnu-3248.30.4~1/RELEASE_X86_64 x86_64 trac-preproc exited with ERRORS at Fri Jul 21 09:29:59 EDT 2017 helpdesks-MacBook-Pro-2:R01_DTI crc$ It says at the end that the input file needs to be in nifty format, but my input file is in nifty format. Do you guys have any idea what could be going on here. I attached my dmrirc.example file for your reference as well. Thank you, Marissa

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3D printing brains - advice for a faster method?
by Lisa Marie Cox 21 Jul '17

21 Jul '17

Hi all, I'm very much a beginner with Freesurfer and I have a little bit of an odd request. I'm currently 3D printing models of participants' brains as a thank-you for participating in our study. All the data has already been processed through recon-all. Our current process is simple - use mris_convert to get from ?h.pial to ?h.stl. (We don't print any of the subcortical structures just for simplicity's sake.) This gives us great models that we can print at a variety of resolutions, and from what I can tell it's the most popular/only method. The issue is that the models (which are about 3x3x2 in) take 12 to 20 hours each to print and we sometimes print ~7/week According to our 3D printing specialist, it takes so long essentially because they're not hollow and all the interior matter takes a long time. We'd like to be able to print them faster so we're not taking up all the 3D printer time at our library. Looking at the image below, it seems like the pial surface file (red outline) has a filled interior, at least when converted to .stl. I'm very unfamiliar with programs like MeshLab but our specialist says he's not able to hollow out the interior using any of his 3D printing programs. So what I need is either a 'hollow' version of the pial surface (or the cortical surface), or perhaps a file that is just the gray matter that can be converted to a .stl file. The ?h.ribbon.mgz files look like they might be a better option but from what I can tell, the mgz files won't convert to stl. (Again, I'm very new to Freesurfer, so any advice on this would be helpful!) I'm also open to ways to solve this in MeshLab if it just won't work in Freesurfer. Thanks, Lisa [image: Inline image 1] Faculty Research Assistant Neurocognitive Development Lab University of Maryland, College Park College Park, MD 20742 <mdclark(a)umd.edu>

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FW: reducing a matrix
by Linda Eva Heidinger 20 Jul '17

20 Jul '17

From: Linda Eva Heidinger Sent: Wednesday, July 19, 2017 1:31 PM To: Greve(a)nmr.mgh.harvard.edu Subject: reducing a matrix Hello Douglas, Thank you for your comments. However, I am wondering since it says that --gcam is an unknown option when I run it with mri_vol2vol, where I can find this option in the literature and if the command needs more -flags or not. I really appreciate your help but I need your command to run. Below is my command. mri_vol2vol --gcam run_003regraijNIFTI.nii boldregister003.dat $SUBJECTS_DIR/$subject/cvs/final_CVSmorph_tocvs_avg35_inMNI152.m3z $FREESURFER_HOME/subjects/cvs_avg35_inMNI152/mri.2mm/register.lta 0 subject003matrix.nii.gz Thanks, -Linda

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Freesurfer July 2017