Freesurfer November 2019

freesurfer@nmr.mgh.harvard.edu

87 participants
122 discussions

(no subject)
by Nader Razmara 19 Dec '19

19 Dec '19

External Email - Use Caution Hi experts I use freesurfer vm 5.3 on oracle vb 6 with 8 GB ram. When i use mri_cvs_register as: mri_cvs_register --mov subjid --mni or mri_cvs_register --mov subjid --template subjid in both cases it stops in step 2 by diffrent errors. I asked zollei this problem and she sujest that it is ram problem. My question is: If it is true. How many ram this command needs? Thanks Nader Phd student in medical engineering Alzheimer research project

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flat maps in native space
by Nasiriavanaki, Zahra 12 Dec '19

12 Dec '19

Hi Freesurfer experts I was trying to make flat maps for individual subjects, following instruction in https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferOccipitalFlattenedPatch. For some of my subjects, the flat maps are distorted (attached image). Please let me know what you think. Thanks Mona [cid:5edcb33b-2248-4b84-938f-3f5afa365555] Zahra (Mona) Nasiriavanaki Postdoctoral Research Fellow Martinos Center for Biomedical Imaging Massachusetts General Hospital 149 13th Street, 149-2615 Charlestown, MA, USA, 02129

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Using pre-segmented results
by Jordi Huguet 10 Dec '19

10 Dec '19

External Email - Use Caution Hi there, I wonder if its somehow possible to feed FreeSurfer's recon-all with pre-existing segmented maps (based on prior segmentation procedure e.g. SPM or ANTs) to "improve" FreeSurfer results. For some images I am working with the FreeSurfer's WM segmentation output is not optimal so I am looking for alternatives to improve the final results on such specific cases without requiring any manual intervention. Any comments, examples or shared reflections on this regard are kindly welcome. Thanks in advance, Jordi Huguet

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Converting labels drew by freeview to volume Error: coordinate mismatch
by zorothustra 04 Dec '19

04 Dec '19

External Email - Use Caution Hello Freesurfer Developers, I'm trying to get superior colliculus' ROI mannually by freeview. I load "orig.mgz" as volumes and set the "orig.mgz" as the ROI's template then draw the ROI and save it as a label file. After that I use "mri_label2vol --label sc.label --temp T1.nii --reg register.dat --o sc.nii", "T1.nii" is my initial structure image, "register.dat" got from the code:" tkregister2 --mov T1.nii --s SUB --regheader --noedit --reg register.dat", and it worked, but the coordinate mismatch, much different from the SC's position in the T1 space( Load T1.nii as volume and SC.label as ROI in freeview, and they are matched). Can anyone help me? Thank you! 1)FreeSurfer version: freesurfer-local-build-dev-20191104 2)platform: Ubuntu 18.04

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Re: [Freesurfer] freeview parallelized binary
by Hoopes, Andrew 04 Dec '19

04 Dec '19

Hi Dustin, The freeview binaries that we ship are the same binaries installed on the cluster. You should try specifying the number of threads available to openmp by setting the OMP_NUM_THREADS env variable to something like 4 or 8 on your local machine to see if this makes a difference. Best, Andrew From: <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of "Clark, Dustin Christopher" <clarkdc(a)bu.edu> Reply-To: FS Help <freesurfer(a)nmr.mgh.harvard.edu> Date: Tuesday, November 26, 2019 at 9:43 AM To: FS Help <freesurfer(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] freeview parallelized binary External Email - Use Caution Hello, We recently noticed freeview on the MGH cluster was using multiple cores when loading niftis, however, our local installation only uses one core when loading the same nifiti. Is it possible to get access to this freeview binary or the source code to build it for parallelization on our system? Thank you, Dustin Clark

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Map fMRI data onto surface
by An 03 Dec '19

03 Dec '19

External Email - Use Caution Hi there, I want to map the intensities of the fMRI 4D volumes onto its surface in order to get the functional values on each vertex in each frame. I have done the following steps for achieving this: 1. ran recon-all on its anatomical volume. 2. register the fMRI series with the anatomical volume by using bbregister. 3. assign values from volumes to each surface vertex through the command mri_vol2surf. I have got a result of mapping the 4D volumes intensities onto its surfaces but there are 35.5% vertices assigned 0 value in every time frame. I am wondering is the ratio reasonable and how could I improve the result? I guess resolution would be one of reasons causing the high 0 value ratio, my fMRI data is 2mm^3 and anatomical data is 1mm^3. Many thanks for your help. Best, An

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Question on GLM - correlation
by Barletta, Valeria 02 Dec '19

02 Dec '19

Dear Freesurfers, I am running glmfit to assess for correlation between y and another continue variable across the cortex (ficvf), correcting for the effect of age, using the command: mri_glmfit \ --y {surfname_cme}.mgh \ --fsgd {contrast}.fsgd \ --C {contrast}.mat \ --pvr ${hemi}.ficvf.mgh" \ --surf fsaverage $hemi \ --glmdir ${glm_dir}/${hemi}_contrast-${contrast}_${surfname_cme} \ --no-prune This is my matrix: 1 0 0 And my fsgd file: Title CME Class MS Variable age Input MS069_R01_01 MS 29 Input MS070_R01_02_R1year MS 44 Input MS072_R01_04 MS 38 Input MS073_R01_05 MS 47 Input MS075_R01_07_R1year MS 34 Input MS076_R01_08 MS 25 Input MS077_R01_09 MS 30 Input MS078_R01_10 MS 22 Input MS080_R01_12 MS 52 Input MS081_R01_13 MS 31 Input MS082_R01_14 MS 37 Input MS084_R01_16 MS 42 Input MS086_R01_18 MS 28 Input MS087_R01_19_R1year MS 39 Input MS088_R01_20 MS 44 Input MS089_R01_29 MS 44 Input MS090_R01_21 MS 32 Input MS091_R01_22 MS 32 Input MS092_R01_23 MS 36 Input MS094_R01_25 MS 47 Input MS104_R01_36 MS 52 This is the result: [cid:8310494e-35a4-4aba-b586-ab908982ab21][cid:a9e74150-3e3a-4e1c-ac08-07bfe4e40dba] Am I proceeding correctly? Thank you, Valeria

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LGI issue?
by Miguel Ángel Rivas Fernández 02 Dec '19

02 Dec '19

External Email - Use Caution Dear Freesurfer experts, I ran the LGI in several subjects and all of them have finished without errors. However when I opened the [lr]h.pial_lgi surfaces in tksurfer I noticed that some part of the brain are not overlayed. What could be the reason? Do you recommend to do some specific quality control on the LGI output? I send to you a screenshot in attachment. Best regards, [image: Screen Shot 2019-11-27 at 16.46.14.png] [image: Screen Shot 2019-11-27 at 16.45.25.png] -- *Miguel Ángel Rivas Fernández*

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about mri_vol2surf and mri_surf2surf
by 于倩倩 02 Dec '19

02 Dec '19

External Email - Use Caution Hello, I have some questions about the command of mri_vol2surf and mri_surf2surf 1. For fMRI data, I find previous paper reported that they used standard SPM8 preprocessing routines, no normalize to standard MNI152 template. The T-map images were translated to the individual cortical surface by using mri_vol2surf function, and then by using mri_sur2surf, all images were translated to the fsaverage space for intersubject comparison. But for me, I use the FsFAST to analysis our fMRI data and get each individual P-value result about sig.nii.gz. How do I use mri_surf2surf function, for translating to fsaverage space? Would I use the preprocessing with fsaverage directly? 2. For quantitative T1 and MTV data, the pervious paper reported that they used similar method (mri_vol2surf and mri_surf2surf). Where can I get the register.dat, when I use the mri_vol2surf function? May I understand it estimates the the relation fMRI and T1? Would I use the mri_vol2surf function and obtain an individual's surf data in fsaverage space directly? 3. For labels, can I make a mask about the BA44 area in which structure is simile with the file sig.nii.gz? How? Best wished! Qianqian Yu

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Problems about registration and tksurfer
by 朱青 02 Dec '19

02 Dec '19

External Email - Use Caution Dear madam or sir, I'm a student in China who use the Freesurfer to analyse my fMRI data and overlay some results on the surface. I met some problems about registration when I map my retinotopic results on the surface. I analysed the retinotopy by the analysePRF toolbox of Kendrick Kay, and the sulutions are matrix, the rows are voxels and the column is polar angle or eccentricity. So I replaced the BOLD values by the solutions in a volume image, for example, the polar angle solution, and I used it as overlay volume image, meanwhile I used the original volume image which is same but BOLD value didn't been changed as the template image to register, but whichever methods listed in the multimodal registration I used, the overlay volume image couldn't been overlaid in correct position on the inflated surface by freeview, just like the pic1.png in the attachment, at the same time the overlay volume image could been overlaid on the orig surface in correct position like the pic2.png in the attachment, so my first problem is why the inflated surface couldn't be overlaid correctly but the orig surface could be with the same registration data and what can I do to make the overlay volume image overlay on the inflated surface in correct position by freeview? Moreover I also used tksurfer to overlay, fortunately the overlay volume image could overlay on the inflated surface in correct position. But the overlay color scale couldn't be color wheel like the red-green-blue. Furthermore, the display in the tksurfer is upside down just like the pic3.png in the attachment. So my second problem is if there are some ways to make the tksurfer color scale like the freeview and how to make the tksurfer display correctly? Best regards, Qing Zhu

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Freesurfer November 2019