Freesurfer

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30090 discussions

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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Re: [Freesurfer] converting vertex numbers in .label files to R, A, S coordinates
by Florence Campana 27 Jul '17

27 Jul '17

Hi Doug, Thank you for your reply. I computed the tkRAS coordinates using the formula TkRAS = Torig*[C R S 1]’. It returns me coordinates such as: [113, -119,88], [105, -103, 96]. I wonder whether such tkRAS coordinates are normal since in label files obtained by saving ROI upon a certain threshold in tksurfer, the coordinates seem fairly different: non integers, and in different ranges e.g. [-36.806 -18.293 64.462], [-21.393 -61.263 8.910]) etc. However, when I create a label file (via write_label.m) with -1 in the first column and with the TkRAS coordinates that I computed in the columns 2,3,4 , and then via tksurfer load this label and then save the selected label, I obtain a new label with R A S coordinates as [34.198 -48.599 29.835], [35.364 -45.689 31.179], i.e. similar to the one that I have in my ROI label files. Could you please help me to figure out what my tkRAS values (e.g.[113, -119,88], [105, -103, 96) correspond to, versus the ones returned by tksurfer ([34.198 -48.599 29.835], [35.364 -45.689 31.179])? I hope that it makes sense. Thank you so much! Florence *From:* Douglas Greve <greve(a)nmr.mgh.harvard.edu> *Date:* July 24, 2017 at 4:06:25 PM EDT *To:* <freesurfer(a)nmr.mgh.harvard.edu> *Subject:* *Re: [Freesurfer] converting vertex numbers in .label files to R, A, S coordinates* *Reply-To:* Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Try using mri_label2label with the --paint option. I think the vertex numbers need to be -1 (not random numbers). You will also need to convert the RAS to "tkregisterRAS", one of our internal coordinate systems. See https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems, you'll need to do the inverse of case #1. On 7/19/17 12:28 PM, Li Guo wrote: *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*

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Extract coordinates from .mgh file
by Redwan Maatoug 27 Jul '17

27 Jul '17

Hi experts, I just want to know a way to extract the coordinates from a ROI mgh file. I know that I can load the file with tksurfer but I have 100 .mgh files so if I could run a command line to have the coordinates in a .txt file or in a .m it would be helpful. Thank you, Redwan

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