Freesurfer March 2022

freesurfer@nmr.mgh.harvard.edu

86 participants
124 discussions

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

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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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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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WM error near the right putamen
by Gabor Perlaki 01 Apr '22

01 Apr '22

External Email - Use Caution Dear all, fswiki suggests that " There are regions where the surfaces are not intended to be accurate that you should be aware of: Areas around the hippocampus and amygdala. " I also found inaccuracy of the WM surface near the putamen and accumbens regions. WM surface goes into the putamen (please see the attached picture). Do I need to fix this error or is it normal? Are the thickness of ctx-rh-medialorbitofrontal and the volume of right putamen valid in this case? Thank you in advance, Gabor

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Re: [Freesurfer] illegal instruction 4 Mac M1
by fsbuild 31 Mar '22

31 Mar '22

External Email - Use Caution Hello Miriam, I can reproduce your error running mri_sclimbic_seg on an M1 Mac running MacOS BigSur with the latest freesurfer development build.  We will look into this and see what can be done. - R. On Mar 31, 2022, at 16:14, Miriam Taza <miriam.taza(a)mail.mcgill.ca> wrote:        External Email - Use Caution        Hello,I am trying to run mri_sclimbic_seg command using dev version of freesurfer on my macbook pro m1 max (monterey version 12.2.1) and I keep getting illegal instruction: 4 (here is the output)/Applications/freesurfer/python/scripts/mri_sclimbic_seg --i Desktop/doc/corlab/sub-121123/anat/sub-121123_T1w.nii.gz --o Desktop/doc/derivatives/MT/corlab/sclimbic_output/sub-121123/anat/rois/sub-121123_atlas-sclimbic_dseg.niiExcluding seg [853]Using CPUIllegal instruction: 4I am very new to coding and first time using freesurfer. Unfortunately, my lab mates have not had a similar problem as they all have intel-based macs. Thanks!_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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illegal instruction 4 Mac M1
by Miriam Taza 31 Mar '22

31 Mar '22

External Email - Use Caution Hello, I am trying to run mri_sclimbic_seg command using dev version of freesurfer on my macbook pro m1 max (monterey version 12.2.1) and I keep getting illegal instruction: 4 (here is the output) /Applications/freesurfer/python/scripts/mri_sclimbic_seg --i Desktop/doc/corlab/sub-121123/anat/sub-121123_T1w.nii.gz --o Desktop/doc/derivatives/MT/corlab/sclimbic_output/sub-121123/anat/rois/sub-121123_atlas-sclimbic_dseg.nii Excluding seg [853] Using CPU Illegal instruction: 4 I am very new to coding and first time using freesurfer. Unfortunately, my lab mates have not had a similar problem as they all have intel-based macs. Thanks!

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Tracula fsl commands fail in Freesurfer docker
by Clément Nicolas Graffard 31 Mar '22

31 Mar '22

External Email - Use Caution Hi, I am trying to use tracula within the freesurfer docker (freesurfer:7.2.0) but some commands related to fsl fail because the fsl script is not found. For example, within the trac-preproc command, the subcommand bet /input/inputData/sub-010017/dmri/lowb.nii.gz /input/inputData/sub-010017/dmri/lowb_brain.nii.gz -m -f 0.3 is launched but this script is named bet.fsl instead of just bet in the folder /usr/local/freesurfer/bin inside the docker. This causes the command to fail. Have I missed some initialization steps ? Many thanks, Clément Nicolas--Graffard

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bedpostx error inside trac-all
by Mirro, Amy 31 Mar '22

31 Mar '22

External Email - Use Caution Hello, I am trying to run trac-all -bedp and I am running into the following error: /opt/freesurfer/bin/bedpostx_mgh: 128: /opt/freesurfer/bin/bedpostx_mgh: Syntax error: "(" unexpected Others have encountered this error previously, and you had advised running bedpostx locally (as oppsoed to bedpostx_mgh). I was wondering, however, if there is a way to still run bedpostx inside trac-all. I was looking at the source code for trac-all in your github (branch 7.2), and I noticed that line 611 calls bedpostx_mgh despite being within the "if (! $onpbs)" conditional. Would changing line 611 from: set cmd = (bedpostx_mgh -n $nstick -model 1 $dtdir/dmri) to set cmd = (bedpostx -n $nstick -model 1 $dtdir/dmri) fix the problem? If it's helpful: I am running on centos7 and my build stamp is: freesurfer-linux-centos7_x86_64-7.2.0-20210720-aa8f76b Thanks, Amy ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

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Freesurfer March 2022