Freesurfer

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30132 discussions

extract values for significant cluster
by Clara Kühn 31 Jul '17

31 Jul '17

Dear FreeSurfer experts, in the longitudinal 2 stage model I find a difference in rate between my two groups in right intra parietal sulcus for surface area (survives MC correction). I would like to look at the cortical thickness in that same cluster. Is it possible to use any of the output files from the MC correction as a mask or something to get the rate of change values for thickness in that region? Even though this region does not show a significant difference between the groups I would like to look at the individual values for rate of change in that specific region (like the ones I received in the cache.th30.abs.y.ocn.dat file) Could you please tell me if this is possible and how? Thank you very much! Clara -- Clara Kühn, Phd Candidate Max-Planck-Institute for Human Cognitive and Brain Science Department of Neuropsychology Stephanstrasse 1A 04103 Leipzig, Germany Phone: +49 341 - 9940 2271 Fax: +49 341 - 9940 2260 Web: www.cbs.mpg.de E-Mail: ckuehn(a)cbs.mpg.de

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Re: [Freesurfer] How to create mask for Total Graymatter and White matter Volume
by M Janani 31 Jul '17

31 Jul '17

Thanks Douglas <https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=from…> ---------------------------------------------------------------------------------------------------------------------------------------------------- try --gm On 07/25/2017 08:33 AM, M Janani wrote: > > 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. > > ---------------------------------------------------------------------------------------------------------------------------------------------------- > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Hippocampal subfields - molecular layer labelling Freesurfer 6.0
by Roddy Darren William 29 Jul '17

29 Jul '17

Hi, I know this has been addressed a bit before, but I remain confused! Apologies. 1…. The dentate anatomically has 3 layers [molecular layer/granular layer/polymorphic layer]. What layers exactly do Freesurfer output “GC_ML_DG” or “CG_ML" correspond to? Granular layer only? Or Granular layer with polymorphic layer? Or Granular layer, polymorphic layer and molecular layer? It’s mentioned in the Eugenio Iglesias’ article that the molecular layer of the dentate is included in the CA4 region. Is this where is it, or is it in the GC_ML_DG? 2…. By “molecular_layer_HP” does Freesurfer mean the ‘molecular layer’ i.e. ‘outermost’ band of Subiculum, CA1, CA2/3? Or Subiculum, CA1, CA2/3 and molecular layer of dentate? I would appreciate some clarification.. Wonderful application by the way. A great step forward for hippocampal research Many thanks.. Dr Darren Roddy Trinity College Institute of Neuroscience Room 3.36, The Lloyd Institute Trinity College Dublin Dublin 2 +353 86 6087927

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Re: [Freesurfer] Brain editing for TRACULA?
by Yuwen Hung 29 Jul '17

29 Jul '17

Dear DTI Expert: I wonder I may get help with this quick question - Is the brain editing necessary (or critical) for TRACULA processing? Thank you! Yuwen

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mri_glmfit-sim --grf question
by Jiahe Zhang 28 Jul '17

28 Jul '17

Dear Freesurfer experts, I'm trying to run multiple comparisons correction using mri_glmfit-sim. Since I'm working with volume data, I used -grf instead of -cache. The resulting map has bigger clusters with higher significance values than the original sig.mgh map from mri_glmfit. Is this normal? Is there anything I should change in my command? Here is the command: mri_glmfit-sim --glmdir r_PCC_glm --grf 1.3 pos --cwp 0.05 --2spaces Thanks, Jiahe -- Jiahe Zhang Ph.D. Candidate Department of Psychology Northeastern University 617-373-4789

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resolution/size mismatch when extracting BOLD from subfields of hippocampus
by Ji Won Bang 28 Jul '17

28 Jul '17

Dear Freesurfer experts, I'd appreciate any of your comments a lot! I'm trying to extract BOLD signals from subfields of hippocampus but somehow I find resolution/size mismatch such that the assigned voxel number of subfield hippocampus is greater than voxel numbers of whole brain BOLD data. I initially processed data using freesurfer version 5.3.0. but then recently created subfields of hippocampus using version 6.0 due to reviewer's request for additional analysis for hippocampus. Below are the steps that I tried. (1) creating subfields of hippocampus recon-all -s subjectID -hippocampal-subfileds-T1 mri_extract_label lh.hippoSfLabels-T1.v10.FSvoxelSpace.mgz 206 leftCA1.mgz mri_extract_label rh.hippoSfLabels-T1.v10.FSvoxelSpace.mgz 206 rightCA1.mgz mris_calc -o CA1.mgz leftCA1.mgz add rightCA1.mgz mri_convert CA1.mgz CA1.nii.gz mri_convert CA1.nii.gz $DATA_DIR/$SUBJECT/roimask/CA1.nii (2) extracting BOLD from subfield ROI using matlab code % get roi mask roi = MRIread([homeDir epiDir subject '/' roiDir rois{ROI} '.nii']); roimask = find(fast_vol2mat(roi)>0); Nvoxel = length(roimask); % loading BOLD data from run data = []; for RUN = 1 % read data from motion-corrected data f = MRIread([homeDir spider subject '/' boldDir dirs(RUN).name '/' boldFile '.nii']); fmat = fast_vol2mat(f); [numTR numVoxelAll] = size(fmat); data(:,:,:,RUN) = fmat(:,roimask)'; end Below is the error: Nvoxel(length of roimask) for CA1 is 1385 and for example, roimask(1) is 7576977 meaning that its voxel number is assigned to 7576977. Then size(fmat) = 150 175232. So fmat(:, roimask(1)) which is again fmat(:, 7576977) gives me an error that index exceeds matrix dimensions.... Why does it happen? Please help me extract the BOLD signals from subfields of hippocampus! Thanks for your help in advance. Best, Ji Won

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Fwd: Microstructure imaging - finding a postdoc (fwd)
by Lilla Zollei 28 Jul '17

28 Jul '17

---------- Forwarded message ---------- > De: Cyril Poupon <cyril.poupon(a)gmail.com> > Dear All, > > please transfer this post-doc proposal to your post-docs or PhD students who could be interested to apply for a post-doc in Tim Dyrby's lab in Denmark to develop methods to probe brain tissue cytoarchitecture using diffusion MRI and to apply them in preclinical studies focused on brain plasticity. > Best, > > Cyril > > Cyril Poupon, PhD > Unité d'Imagerie RMN et de Spectroscopie (UNIRS) > CEA DRF/ISVFJ/NeuroSpin, Bat 145 > ---------- Forwarded message ---------- > From: Tim Dyrby <timd(a)drcmr.dk <mailto:timd@drcmr.dk>> > > Hi Cyril, > > I have a position for a postdoc, and wondered if you know of a postdoc that would love to take on new challenges by coming to DRCMR and working on microstructure imaging with special focus on preclinical MRI combined with many other cool imaging modalities? > > > I have attached the job description and it would be a great help if you could send it around to relevant people. > > > Hygge, > > Tim > > -- > Tim B. Dyrby > Associate Professor > Microstructure and Plasticity (MaP) Group > Danish Research Centre for Magnetic Resonance (DRCMR), section 714 > Center for Functional and Diagnostic Imaging and Research > Copenhagen University Hospital Hvidovre > Kettegård Allé 30 > 2650 Hvidovre > Denmark > Office phone: +45 38626542 <tel:+45%2038%2062%2065%2042> Mobile:+45 40790282 <tel:+45%2040%2079%2002%2082> > web: www.drcmr.dk/map <http://www.drcmr.dk/map> and www.drcmr.dk <http://www.drcmr.dk/> > & > Image Analysis and Computer Graphics section > Department of Applied Mathematics and Computer Science > Technical University of Denmark > Richard Petersens Plads, Building 324 > 2800 Kongens Lyngby > Denmark > Office Phone: +45 45253424 <tel:+45%2045%2025%2034%2024>

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Pial surface missing GM
by Jake Rieke 28 Jul '17

28 Jul '17

Hello surfers, I'm attempting to extend white and pial surfaces to encompass an unrecognized gyrus. The wm.mgz seems include the WM tissue, but the white surface does not extend to the WM boundary. I thought this might be related to an intensity normalization error and tried using control points, but that did not make a big difference in the resulting surfaces. I've attached pictures to better illustrate the problem. Thanks in advance for your help! Best regards, Jake

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Is it possible to run a conjunction analysis on longitudinal sMRI data in Freesurfer?
by Jennifer Legault 27 Jul '17

27 Jul '17

Hi Freesurfer experts, I'm wondering if it's possible to do a conjunction analysis on sMRI data in Freesurfer. I would like to compare longitudinal results from 2 experimental training groups and 1 control, where I can examine: 1) which regions underwent structural changes in both of the experimental groups as compared to the control and 2) experimental condition-specific changes between the groups when accounting for the normal amount of change expected (the controls). Of course, if you know of a better analysis to run to examine these questions, any feedback would be greatly appreciated. I have previously preprocessed the data using Freesurfer's longitudinal pipeline and I've run univariate LMEs using Freesurfer to compare each of the experimental groups to the control group separately. Do you know if I can I use mri_concat with the --conjunct option using the .sig files from the LME analyses, given that these are structural MRI data? I've only ever seen these analyses being done with fMRI data. Thank you for taking the time to read this email. Best, Jennifer Legault -- Jennifer Legault Ph.D candidate, Neuroscience Brain, Language, and Computation Lab The Pennsylvania State University

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problem with bedpostx
by Lars M. Rimol 27 Jul '17

27 Jul '17

Hi, Running trac-all -bedp and getting an error message I've never seen before. I'm running it on a desktop, not a cluster, which it warns agains - but it should still run, shouldn't it? larsrim:~/lbkabel/tbi/morfometri_test$ trac-all -bedp -c DWI/jobscripts/d1_1001_local.dmrirc INFO: SUBJECTS_DIR is /home/larsrim/lbkabel/tbi/morfometri_test INFO: Diffusion root is /home/larsrim/lbkabel/tbi/morfometri_test/DWI/TRACULA/local Actual FREESURFER_HOME /usr/local/freesurfer WARN: Running bedbostx locally - this might take a while WARN: It is recommended to run this step on a cluster bedpostx_mgh -n 2 /home/larsrim/lbkabel/tbi/morfometri_test/DWI/TRACULA/local/1001_c1/dmri /usr/local/freesurfer/bin/bedpostx_mgh: 131: /usr/local/freesurfer/bin/bedpostx_mgh: Syntax error: "(" unexpected Sincerely yours, Lars M. Rimol, PhD Senior Researcher Norwegian Advisory Unit for Functional MRI Department of Radiology St. Olav's University Hospital 7006 Trondheim Norway

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