Freesurfer

freesurfer@nmr.mgh.harvard.edu

17 participants
30066 discussions

Clarification for aseg edits in longitudinal phase
by Tamara Tavares 26 Jul '17

26 Jul '17

Hello, I have made edits to aseg files in the longitudinal outputs (participantID.long.participantID-temp). I am beginning the reconstruction phase and as suggested by a response to an earlier post I am running: recon-all -long tpN1 template ID -autorecon2-noaseg -autorecon3, where tpN1 is cross-sectional output and template ID is the template of the participant. My questions are: 1) Does the script essentially take the edits I made in the aseg longitudinal outputs and reconstructs the longitudinal files using the cross and template files? 2) Does this script begin running recon-all during recon-all2, after the aseg files are suppose to be created? Thank you, Tamara

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Segmentation Violation problem in surface files
by Yagmur Ozdemir 19 25 Jul '17

25 Jul '17

Hello freesurfer experts, I am trying to use an occipital lobe template adapted to my data as several surface and volume files, and there seems to be a problem with the surface files. Whenever I try to open a surface overlay (in .mgz format) in freeview this error comes up; freadFloat: fread failed freadFloat: fread failed ... [0]PETSC ERROR: ------------------------------------------------------------------------ [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range ... When I try to convert this file to nifti format a seemingly similar error comes up; (...) mri_convert rh.template_areas.mgz AU_areas_template_rh.nii.gz mri_convert.bin rh.template_areas.mgz AU_areas_template_rh.nii.gz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from rh.template_areas.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (1, 0, 0) j_ras = (0, 1, 0) k_ras = (0, 0, 1) writing to AU_areas_template_rh.nii.gz... NIFTI FORMAT ERROR: nslices 117239 in volume exceeds 32768 I have tried to debug but failed so far. Has anyone come across a similar problem and do you have an opinion onto what might be causing this? The same adapted template's volume files work just fine. --I am using Ubuntu 16.04& freesurfer v.6 Thank you so much! Idil

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How to create mask for Total Graymatter and White matter Volume
by M Janani 25 Jul '17

25 Jul '17

Hi Team, I would like to create mask for Total Gray matter and white matter volume. I was able to get the total white matter volume using the below mentioned command mri_binarize -i aparc+aseg.mgz --wm --o wm.mgz But I couldn't find any option to create the mask for Total Gray matter. Any help would be really grateful. Regards, Janani ::DISCLAIMER:: ---------------------------------------------------------------------------------------------------------------------------------------------------- The contents of this e-mail and any attachment(s) are confidential and intended for the named recipient(s) only. E-mail transmission is not guaranteed to be secure or error-free as information could be intercepted, corrupted, lost, destroyed, arrive late or incomplete, or may contain viruses in transmission. The e mail and its contents (with or without referred errors) shall therefore not attach any liability on the originator or HCL or its affiliates. Views or opinions, if any, presented in this email are solely those of the author and may not necessarily reflect the views or opinions of HCL or its affiliates. Any form of reproduction, dissemination, copying, disclosure, modification, distribution and / or publication of this message without the prior written consent of authorized representative of HCL is strictly prohibited. If you have received this email in error please delete it and notify the sender immediately. Before opening any email and/or attachments, please check them for viruses and other defects. ----------------------------------------------------------------------------------------------------------------------------------------------------

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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

2 1

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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