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30067 discussions

WM surface ignoring wm.mgz edits
by KALEY E ELLIS 07 Jul '17

07 Jul '17

Dear FreeSurfer Developers, We are attempting to make manual white matter edits to our subjects. The edits are saving; however, after running with recon-all, the WM surface does not appear to be taking into account our edits made to wm.mgz. Below is additional information, and I have attached our recon-all.log. We are only editing the cross because our dataset is comprised of single timepoints. We are using FreeSurfer v5.3 and our operating system is OS X El Capitan version 10.11.6. Command to open and edit WM: freeview -v mri/T1.mgz mri/brainmask.mgz mri/wm.mgz:opacity=0.5 -f surf/lh.white:edgecolor=yellow surf/lh.pial:edgecolor=red surf/rh.white:edgecolor=yellow surf/rh.pial:edgecolor=red Command to submit edits: recon-all -autorecon2-wm -autorecon3 -subjid Recon-all log (see attached) Thank you, Kaley Ellis Associate Research Specialist Center for Healthy Minds Waisman Center for Brain Imaging and Behavior University of Wisconsin-Madison

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wm.mgz in the internal structures
by Karla Rivera Figueroa 07 Jul '17

07 Jul '17

Hi all, Do you need to edit the wm mask where the internal structures shown in the aseg are? are the structures supposed to be covered entirely with the wm mask? Karla

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Matlab Problem LME
by Clara Kühn 07 Jul '17

07 Jul '17

Dear FreeSurfer experts, I am following the LME tutorial for the spatiotemporal mass-univariate model on Matlab 8.2. When I get to the point where the covariance estimates are segmented into homogeneous regions I run into a problem. Nothing really happens in Matlab anymore. This is my command: [lhRgs,lhRgMeans] = lme_mass_RgGrow (lhsphere, lhRe, lhTh0, lhcortex, 2, 95); And this is what the Matlab output looks like: connected to 12 workers. Starting region growing algorithm Computing seeds ... I've tried this already last week and nothing happened for a few days. When I terminate the command this is the Matlab output: Operation terminated by user during kron (after line 36) In lme_mass_RgGrow>homogenity (line 299) if (sum(sum(DistRgParams <= kron(ones(1,nv),thr),1) == np) >= prc*nv/100) &&... In lme_mass_RgGrow>merge (line 320) if homogenity(Re,Params,auxRgs,Rkn,nst,prc) In lme_mass_RgGrow>split (line 269) [Rgs,mrg] = merge(Rgs,Re,Params,mrgRgs(i),mrgRgs(j),nst,prc); In lme_mass_RgGrow>seeds (line 208) [Rgs,spltf(i),nnRgs] = split(Rgs,Re,Params,coord,splRgs(i),nst,prc); In lme_mass_RgGrow>vtxwGrowing (line 77) [Rgs1,Rgseed,Rgstd]= seeds(Re(:,maskvtx),Params(:,maskvtx),coord(:,maskvtx),nst,prc); In lme_mass_RgGrow (line 62) Regions = vtxwGrowing(Re,Theta,sphcoord,AdjM,maskvtx,nst,prc); I have then copied the function and added a few "fprintf" (see attachment) to get an idea as to where matlab has problems and the output looks like this: Starting region growing algorithm Computing seeds ... point5 point6 point7 point8 point7 point8 point7 point8 point7 point8 point7 point8 point7 point8 point7 point6 point7 point8 point7 point8 point7 point8 point7 point8 point7 point8 point7 [...] If I understand that correctly, matlab gets hung up on functions 'function tf = homogenity(Re,Params,Rgs,Rn,nst,prc)' and 'function [Rgs,tf] = merge(Rgs,Re,Params,Rn1,Rn2,nst,prc)'. Does anybody have an idea what that means and how it can be fixed? How long is this step supposed to take? I have 81 subjects with 1 - 3 time points. Any help or suggestions would be much appreciated! Cheers 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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bbregister vs spmregister vs mri_coreg
by John Anderson 06 Jul '17

06 Jul '17

Dear Freesurfer experts, I see that the tool "mri_coreg" has been implemented recently in Free Surfer 6 and I really wanted to know what are the differences between the registration tools "bbregister", " spmregister" and "mri_coreg"! Kindly: 1. Are these tools similar? if not what are the differences ? 2. Is there any preference of using a tool over the others for specific type of data. For example: A. If I want to register FA map to T1 image which tool is more robust? B. if I want to register FA map to MNI space which tool is more robust? I highly appreciate your input on this! John

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Raw Cortical thickness values
by Muhammad Naveed Iqbal Qureshi 06 Jul '17

06 Jul '17

Dear Community, I need to know how can I read the numeric cortical thickness values from freesurfer processed files. (as there are too many in the surf folder) Thank you. Best Regards Naveed

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Average myelination within ROI
by SHAHIN NASR 06 Jul '17

06 Jul '17

Hi Surfers, I want to measure the average amount of myelinations within my ROI(s), I have already generated my myelination maps on surfaces (e.g. lh.myelin_ProjFrac0p5.nii ). Then I used mri_segstats as below: mri_segstats --i lh.myelin_ProjFrac0p5.nii --slabel SBJ_001 lh lh.V1 --sum V1_Stats.txt --accumulate but the numbers don't make any sense. For instance: # ColHeaders Index SegId NVertices Area_mm2 StructName Mean StdDev Min Max Range 1 0 125261 82573.4 Seg0000 110280.4453 0.2922 -5.5000 51.0000 56.5000 2 1 1138 764.8 Seg0001 941.0988 0.1572 0.2675 1.4203 1.1527 How can mean=941.0988 when the max=1.4203 ??? Regards -- Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School

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Re: [Freesurfer] Still confused by group analysis..
by Douglas Greve 06 Jul '17

06 Jul '17

On 6/12/13 7:03 AM, Tudor Popescu wrote: > > Sorry Doug, wasn't sure whether you'd seen my last reply to this.. > > On 6 Jun 2013 21:37, "Tudor Popescu" <tudor3(a)gmail.com > <mailto:tudor3@gmail.com>> wrote: > > Thanks Doug, > > > > So if I want to use the study-specific "average" subject > surface with mri_surf2surf, rather than the generic > "fsaverage" one, how can this be done given that the > required ls.white file only exists in the latter but not > in the former? Can I just rename (or duplicate) ls.white > into ls.white_avg? > > You can copy it or create a symbolic link. > > So it is OK to copy the required lh.white file from the generic > average subject "fsaverage" and apply mri_surf2surf upon the > study-specific average subject ("average")? It still seems to me > that "average" should have its own (different) lh.white... > Yes it should. Did make_average_subject not create it? > > > > Shouldn't the input to mri_glmfit be the output of > mri_surf2surf? In the group tutorial, the former is > "lh.gender_age.thickness.10.mgh" while the latter is > "lh.gender_age.thickness.10B.mgh". Or should it just be > the unsmoothed output of mris_preproc? > > Yes, I can't remember why I put the "B" there, maybe to keep > people from overwriting lh.gender_age.thickness.10.mgh during > the tutorial and having to wait the 10min or so for it to get > recreated. > > But if all these commands transform the same file (output of > mris_preproc becomes input of mri_surf2surf, which then feeds into > mri_glmfit), then why is it still necessary to keep intact the > original lh.gender_age.thickness.10.mgh, when all you need for the > group analysis is the mri_surf2surf'd version? > Sorry, I'm lost here. What are the names of the files? > > > > Assuming the label files (corresponding to my ROI, and > extracted from the Destrieux atlas) are different for each > subject, and given mri_glmfit is called just once, for all > subjects, which label file (corresponding to what subject) > should I point it to? > > You need to create the label in the average subject. There is > a Destrieux atlas there. > > Again, by "average subject" do you mean here the generic one > (fsaverage) or the study-specific one (average)? Should the former > be used at any point of a group analysis, if the latter exists? > If you are doing your group analysis on a custom average, then do not use fsaverage at any point. doug

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content of "subjects_dir"
by Schumman Resonance 05 Jul '17

05 Jul '17

Dear free surfer community, Silly question here. I note the default "subjects_dir" in freesurfer contains a bunch of directories and files. If I set the environment so that my "subjects_dir" is not the default location, do I need to move any of the files in the original location to the new one? I hope this makes sense. Thanks, Kev

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Question mri_glmfit fwhm smoothing
by Van Der Deijl, Rosanne 05 Jul '17

05 Jul '17

Hi, I have a question about mri_glmfit. As an input, you give e.g. the stacked thickness data from all subjects, smoothed with a certain fwhm. But then as an output file, it gives an fwhm.dat file, which, at least in my case, contains another smoothing level. I noticed this because I ran mri_glmfit-sim forclusterwise multiple comparison correction, which gives me the error: ERROR: cannot find /usr/local/freesurfer/stable6/average/mult-comp-cor/fsaverage/rh/cortex/fwhm33/abs/th13/mc-z.csd As input I gave data smoothed to 25fwhm, and not fwhm33, as it seems to think. But indeed, in the fwhm.dat file it gives fwhm = 32.940499. I read in the tutorial that the fwhm.dat file contains the average FWHM of the residual. But still my questions are: - what this means - why mri_glmfit-sim would need this number, and whether/how I can run the mult. comparison correction on the 25fwhm-smoothed data. Thank you in advance! - Rose Commands: mri_glmfit: mri_glmfit --fsgd $CALMGREY/CALM_FSGD.txt dods --C CALMlong_contrast1.mat --C CALMlong_contrast2.mat --C CALMlong_contrast3.mat --C CALMlong_contrast4.mat --glmdir rh.CALMlong.thickness-spc.fwhm25 --y rh.CALMlong.thickness-spc.stack.fwhm25.mgh --cortex --surf fsaverage rh mri_glmfit-sim: mri_glmfit-sim --glmdir rh.CALMlong.thickness-spc.fwhm0 --cache 1.3 neg --cwp --2spaces

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mri_glmfit error (mri_reshape number of elements)
by Mcnorgan, Christopher 05 Jul '17

05 Jul '17

Hi, I’m running a group-level analysis and have encountered an error that results in a core dump. The first-level analyses were run using the fsaverage surfaces, rather than self surfaces. I’ve already inspected the individual contrasts, loading the fsaverage surface in tksurfer and rendering each subject’s contrast as an overlay, and would now like to compute the group-level results. I first ran isxconcat-sess, and saw no errors indicated in the program output. mri_glmfit was then called as followed, and produced the following output (same result for the rh): $ mri_glmfit --y ces.nii.gz --wls cesvar.nii.gz --osgm --surf fsaverage lh --glmdir glm.wls --nii.gz Reading source surface /home/chris/LDT/fsaverage/surf/lh.white Number of vertices 163842 Number of faces 327680 Total area 65416.648438 AvgVtxArea 0.399267 AvgVtxDist 0.721953 StdVtxDist 0.195470 $Id: mri_glmfit.c,v 1.196.2.8 2012/11/01 18:51:41 greve Exp $ cwd /home/chris/LDT/RFX/LDT_fsaverage.sm4.rh/hi-v-lo cmdline mri_glmfit --y ces.nii.gz --wls cesvar.nii.gz --osgm --surf fsaverage lh --glmdir glm.wls --nii.gz sysname Linux hostname brocasarea machine x86_64 user chris FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 1 y /home/chris/LDT/RFX/LDT_fsaverage.sm4.rh/hi-v-lo/ces.nii.gz logyflag 0 usedti 0 labelmask /home/chris/LDT/fsaverage/label/lh.cortex.label maskinv 0 glmdir glm.wls IllCondOK 0 ReScaleX 1 DoFFx 0 wFile cesvar.nii.gz weightinv 1 weightsqrt 1 Creating output directory glm.wls Loading y from /home/chris/LDT/RFX/LDT_fsaverage.sm4.rh/hi-v-lo/ces.nii.gz Saving design matrix to glm.wls/Xg.dat Normalized matrix condition is 1 Matrix condition is 1 Found 149955 points in label. ERROR: mri_reshape: number of elements cannot change nv1 = 163842, nv1 = 537168 Pruning voxels by thr: 0.000000 Segmentation fault (core dumped) This seems to have its root in a mismatch between the vertices in the fsaverage lh.cortex label and those in the contrast data. However, I carried out subject-level analyses in the fsaverage surface space specifically to facilitate a group-level analysis in fsaverage surface space, so I can’t see where I went wrong. The only other post I could find that was similar was related to an attempt to carry out a group analysis in native surface space, which is not the case here. Thanks for your time

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