Freesurfer

freesurfer@nmr.mgh.harvard.edu

11 participants
30080 discussions

Tkregister2 not opening GUI
by Isabelle Deschamps 04 Apr '22

04 Apr '22

External Email - Use Caution Good afternoon, I am trying to verify the registration and for some reason the GUI is not opening. I am using a Macbook Pro running macOS Montery with a 2.4 Gz Quad-Core Intel Core i5 I have Freesurfer version: maOS-7.2.0 I do not get an error when I run TKregister2 or TKregister_cmld This is the output that I get without the GUI opening No target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume (null) reg file (null) LoadVol 0 ZeroCRAS 1 7.2.0 Diagnostic Level -1 % % % % % % % % avi2talxfm talairach.xfm --------------------- 1.00857 0.02020 -0.00990 -0.12365; -0.01789 1.03251 0.24795 -28.10577; 0.02556 -0.30660 1.20913 3.54973; 0.00000 0.00000 0.00000 1.00000; INFO: loading target /Volumes/RestingState/fMRI/fMRI/Freesurfer/S0010_FS/mri/orig.mgz Zeroing CRAS of target new xfm ----------------- 1.00857 0.02020 -0.00990 1.93629; -0.01789 1.03251 0.24795 -11.46406; 0.02556 -0.30660 1.20913 -50.28331; 0.00000 0.00000 0.00000 1.00000; --------------------- Ttarg: -------------------- -1.00000 0.00000 0.00000 128.00000; -0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; INFO: loading movable /Applications/freesurfer/7.2.0/average/mni305.cor.mgz Tmov: -------------------- -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; mkheaderreg = 0, float2int = 0 ---- Input registration matrix -------- 1.00857 0.02020 -0.00990 1.93629; -0.01789 1.03251 0.24795 -11.46406; 0.02556 -0.30660 1.20913 -50.28331; 0.00000 0.00000 0.00000 1.00000; Determinant 1.33659 subject = S0010_FS RegMat --------------------------- 1.00857 0.02020 -0.00990 1.93629; -0.01789 1.03251 0.24795 -11.46406; 0.02556 -0.30660 1.20913 -50.28331; 0.00000 0.00000 0.00000 1.00000; UnZeroing CRAS for fstal output xfm Any help would be greatly appreciated. Isabelle

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slice timing for multiband fMRI
by Laura Doll 04 Apr '22

04 Apr '22

External Email - Use Caution Hi everyone, We are currently piloting an fMRI measurement with multiband sequence on a 3T Siemens scanner to increase resolution, but I don't know how to do the slice timing correction: I assume, that I have to use a slicedelay file instead of the usual up/down/even/odd/siemens flags? But how do I know which slices were excited simultaneously? Our multiband acceleration factor is 2, if I got our MRI physicist correctly, GRAPPA acceleration is also 2, and we are using a TR of 2s. More details of the sequence are in the attached pdf (which is unfortunately in German). Looking forward to any suggestions. Best, Laura

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Questions regarding ROI creation for SPM based on FreeSurfer parcellation
by Falko Mecklenbrauck 04 Apr '22

04 Apr '22

External Email - Use Caution Dear FreeSurfer-Experts, I’m in need of your experience to help me with a decision in my current project: I want to use certain areas, that were identified by structural graph theoretical analyses based on the FreeSurfer parcellation and DTI data, as Regions of interest in SPM. We already have a script that helps with the transfer and creation of ROIs however it is still unclear what’s the best way to create the ROIs. Here are a few of my ideas and pros and cons regarding these: 1. Parcel the MNI T1 standard brain used in SPM with FreeSurfer and create the ROIs from the identified regions from that PRO: direct use of the standard space, that is later used in SPM’s group level analysis CON: SPM tends to be peculiar in giving information about their standard template, so I am unsure if the one I found in the spm12-folder is the correct one to use 2. Extract the ROIs of each participant individually and then use SPM to normalize and averaging/summing these PRO: Ending up in same space as the SPM analysis CON: identified regions are (at the moment) not individually identified, although they could be; normalization is difficult with just ROIs ALTERNATIVE: use FreeSurfer not on individual “raw” T1 images but on already normalized T1 images and then do the ROIs individually per participant. Probably, I am also forgetting another possibility. I am looking forward to hearing your ideas and comments. Thank you very much in advance, Best wishes, Falko

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Re: [Freesurfer] mri_vol2vol anatomical to functional
by Manenti, Giorgio 04 Apr '22

04 Apr '22

External Email - Use Caution I'm not sure I understand what you are saying or what the problem is. Can you provide the actual command line you are using, all the terminal output, and a picture that shows what the problem is? Hi Douglas, thank you for your time; I am trying to get the ribbon at functional space resolution (I need it to extract the white matter from my ROIs) Here I am copying the 2 commands (one using .reg file, the second using .lta) I am using, and the terminal terminal outputs. Attached you will also find 3 screenshots from freeview with 1) original ribbon 2) ribbon transformed in functional space using the .reg file and 3) ribbon transformed using the .lta file. (Please Note: I am using Matlab to integrate this analysis in the general pipeline, so the command are started by the s=system() function;) %%%%%%REG s=system(['mri_vol2vol --reg ' regpath ' --mov ' inputvol ' --targ ' funcTemp ' --o ' outputvol ]); regio_read_register: loading lta Matrix from regfile: 0.99982 -0.01069 -0.01533 -0.11505; 0.01423 -0.09676 0.99521 -0.84297; 0.01212 0.99525 0.09659 -5.72961; 0.00000 0.00000 0.00000 1.00000; movvol Anatomy_Processed/hum_15477.long.long002/mri/lh.ribbon.mgz targvol FSfast_struc/all_sub/f02_Sess03/bold/ecc_lh/conjunction_pe/v1_trai_vol.nii outvol Anatomy_Processed/hum_15477.long.long002/mri/lh.ribbon_func.mgz regfile FSfast_struc/all_sub/f02_Sess03/bold/register.dof6.lta invert 0 tal 0 talres 2 regheader 0 noresample 0 interp trilinear (1) precision float (3) Gdiag_no -1 Synth 0 SynthSeed 1649422337 Final tkRAS-to-tkRAS Matrix is: 0.99982 -0.01069 -0.01533 -0.11505; 0.01423 -0.09676 0.99521 -0.84297; 0.01212 0.99525 0.09659 -5.72961; 0.00000 0.00000 0.00000 1.00000; Vox2Vox Matrix is: 2.01888 -0.03096 0.02351 23.93213; 0.02447 0.19504 -2.18955 197.85437; -0.02873 -2.00955 -0.21287 240.49161; 0.00000 0.00000 0.00000 1.00000; Resampling Output registration matrix is identity mri_vol2vol done %%%%%%LTA s=system(['mri_vol2vol --lta ' ltapath ' --mov ' inputvol ' --targ ' funcTemp ' --o ' outputvol ]); Matrix from LTA: 0.99983 -0.01069 -0.01533 -0.11505; 0.01423 -0.09676 0.99521 -0.84293; 0.01212 0.99525 0.09659 -5.72960; 0.00000 0.00000 0.00000 1.00000; Anatomy_Processed/hum_15477.long.long002/mri/lh.ribbon.mgz FSfast_struc/all_sub/f02_Sess03/bold/ecc_lh/conjunction_pe/v1_trai_vol.nii INFO: src volume info differs from the one stored in lta. gets modified now. volume geometry: extent : (256, 256, 256) voxel : ( 1.0000, 1.0000, 1.0000) x_(ras) : (-1.0000, -0.0000, -0.0000) y_(ras) : ( 0.0000, 0.0000, -1.0000) z_(ras) : (-0.0000, 1.0000, 0.0000) c_(ras) : ( 0.2540, 9.2232, 8.1562) file : Anatomy_Processed/hum_15477.long.long002/mri/lh.ribbon.mgz volume geometry: extent : (104, 104, 69) voxel : ( 2.0192, 2.0192, 2.2000) x_(ras) : (-0.9995, -0.0137, 0.0296) y_(ras) : ( 0.0126, -0.9991, -0.0397) z_(ras) : ( 0.0301, -0.0393, 0.9988) c_(ras) : ( 1.5530, 16.4346, 14.9788) file : bold/template.nii.gz INFO: dst volume info differs from the one stored in lta. gets modified now. volume geometry: extent : (104, 104, 69) voxel : ( 2.0192, 2.0192, 2.2000) x_(ras) : (-0.9995, -0.0137, 0.0296) y_(ras) : ( 0.0126, -0.9991, -0.0397) z_(ras) : ( 0.0301, -0.0393, 0.9988) c_(ras) : ( 1.5530, 16.4345, 14.9788) file : FSfast_struc/all_sub/f02_Sess03/bold/ecc_lh/conjunction_pe/v1_trai_vol.nii volume geometry: extent : (256, 256, 256) voxel : ( 1.0000, 1.0000, 1.0000) x_(ras) : (-1.0000, -0.0000, -0.0000) y_(ras) : ( 0.0000, 0.0000, -1.0000) z_(ras) : (-0.0000, 1.0000, 0.0000) c_(ras) : ( 0.2540, 9.2232, 8.1562) file : Anatomy_Processed/hum_15496.long.long002/mri/orig.mgz movvol Anatomy_Processed/hum_15477.long.long002/mri/lh.ribbon.mgz targvol FSfast_struc/all_sub/f02_Sess03/bold/ecc_lh/conjunction_pe/v1_trai_vol.nii outvol Anatomy_Processed/hum_15477.long.long002/mri/lh.ribbon_func.mgz regfile FSfast_struc/all_sub/f02_Sess03/bold/register.dof6.lta invert 0 tal 0 talres 2 regheader 0 noresample 0 interp trilinear (1) precision float (3) Gdiag_no -1 Synth 0 SynthSeed 1649445621 Final tkRAS-to-tkRAS Matrix is: 0.99828 0.04446 -0.03809 2.43217; 0.03729 0.01869 0.99913 9.13850; -0.04513 0.99884 -0.01700 12.13850; 0.00000 0.00000 0.00000 1.00000; Vox2Vox Matrix is: 2.01577 -0.07692 -0.09781 28.12225; -0.09113 -0.03433 -2.19744 198.19705; -0.07530 -2.01747 0.04112 244.54424; 0.00000 0.00000 0.00000 1.00000; Resampling Output registration matrix is identity mri_vol2vol done Many thanks again, Best Giorgio

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Clusters and significance maps
by Laura Willers de Souza 04 Apr '22

04 Apr '22

External Email - Use Caution Hello FreeSurfer Developers, I would like to know if there is any way to visualize the clusters that survive correction for multiple comparisons with a color gradient corresponding to the corrected significance level? As in this image below (article link https://secure-web.cisco.com/1qOoEvjPnK_m3u0z_SOdGWxN5T-4Pz-fU8mFBd-TCs-_nQ…) [cid:04a0dc7a-9b96-4922-ada8-1337d936f1b0] Thanks in advance! Laura Willers de Souza Master Student in Biochemistry Zimmer Lab - Federal University of Rio Grande do Sul - Porto Alegre/RS - Brazil

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lh.white surface co-registration
by Salar Dini, Elaheh 04 Apr '22

04 Apr '22

External Email - Use Caution Dear Freesurfer experts, Is there a way to move lh.white of a subject to a new coordinate? Something quite similar as volumetric co-registration but for surfaces. To be exact, I have moved a subject's brainmask.mgz, orig.mgz, aparc+aseg.mgz, and T1 mgz to a new coordinate using mri_coreg and subsequently vol2vol, but the surfaces are still in the original coordinate and doesn't match the volumes. Is there a way to move the surface files to the new coordinate? OS: Centos 7, Freesurfer version: 7.2.0 Thank you for your time and help. Kindly, Ela

2 3

repeated measures ANOVA 2x2 covariate
by Agurne Sampedro Calvete 04 Apr '22

04 Apr '22

External Email - Use Caution Dear FreeSurfer experts, I am doing a repeated measures ANOVA 2x2 (2 groups and 2 time points) and I would like to include in the analysis a covariate that is constant over the 2 times (e.g., baseline medication). I would like to see a "group x time x covariate" interaction. What should the design look like? I know that without covariate the design is as follows: GroupDescriptorFile 1 Class Subject1 Class Subject2 Variables Tp1vsTp2.Group1 Tp1vsTp2.Grroup2 Input Subject1_time1 Subject1 1 0 Input Subject1_time2 Subject1 -1 0 Input Subject2_time1 Subject2 0 1 Input Subject2_time2 Subject02 0 -1 Design matrix: 1 0 1 0 1 0 -1 0 0 1 0 1 0 1 0 -1 Contrasts (.mtx files): Tp1vsTp2.Group1 0 0 1 0 Tp1vsTp2.Group2 0 0 0 -1 Interaction (timexgroup) 0 0 1 -1 However, I do not know how I could include the interaction with that covariate. Thank you very much in advance. Kind regards, Agurne

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password request for file FS_7_2_0_Ubuntu_18_04_06.ova.7z
by Anouck Matthijs 04 Apr '22

04 Apr '22

External Email - Use Caution Hello, I hope this email finds you well. I would like to request for the password to FS_7_2_0_Ubuntu_18_04_06.ova.7z<https://secure-web.cisco.com/1uT35qjETx2PBJuQg2agRxnXoPV7XDxnsMIStfOfoxzdC5…> file to be able to expand it. Thank you for your time. Anouck Matthijs PhD student Movement control & Neuroplasticity Research Group KU Leuven University Leuven, Belgium

1 0

Beta values
by Laura Willers de Souza 03 Apr '22

03 Apr '22

External Email - Use Caution Hello FreeSurfer Developers, I'm extracting beta values from some analyzes and I would like to know if I'm extracting and interpreting these values correctly. To extract the beta values I used this command: mri_segstats --seg lh.cortisol_CSF.glmdir/cortisol_CSF_slope/perm.th20.neg.sig.ocn.mgh --i lh.cortisol_CSF.glmdir/beta.mgh --excludeid 0 --avgwf lh.cortisol_CSF.beta.clusters.dat The model consists of 1 group and 1 covariate. I used the contrasts for intercept and slope. The beta values extraction file contains 2 lines (image below). [cid:c5a3c332-10fc-4726-b15e-672b02ded1fa] * Would the first line be the beta value for the intercept and the second line for the slope? * Thus the glm equation for the 1st cluster would be: cortical thickness = 2.57 - 0.12X + n Is this correct? Thanks in advance! Laura Willers de Souza Master Student in Biochemistry Zimmer Lab - Federal University of Rio Grande do Sul - Porto Alegre/RS - Brazil

2 1

transitioning from tkmedit to freeview
by Zeng, Victor (BIDMC - Keshavan - Psychiatry) 03 Apr '22

03 Apr '22

External Email - Use Caution Hi, My lab has been using tkmedit, although it is deprecated, for pial edits. We resist transitioning towards freeview due to changed functionality, which I understand because freeview is used for more than just pial edits but - Are there any tools that can I am not aware of that makes freeview similar to tkmedit? 1. the main thing is the removal of keyboard shortcuts. Being able to press ctrl-G to turn on/off segmentation rapidly, and ctrl-1/2 to turn on/off the T1.mgz rapidly makes quality checking a lot faster rather than having to manually click on the volume you want to turn off. 2. likewise, being able to press x/y/z to easily switch between views (sagittal, axial etc) 3. tkmedit in my lab was configured so that right click replaced voxel intensity to zero, and wheel click replaced voxel intensity to voxel intensity of the T1.mgz (essentially restoring the original voxel intensity). Can you configure the options so that it readily does that (I understand that instead of right click it would probably be left click now) Victor Zeng Beth Israel Deaconess Medical Center Keshavan Lab --

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