Freesurfer October 2017

freesurfer@nmr.mgh.harvard.edu

119 participants
179 discussions

mri_cvs_register error
by miracle ozzoude 21 Oct '17

21 Oct '17

Hello, I am trying to run mri_cvs_register on a subject and I got an error (please see attached log file). Below was the command I used. Thank you. mri_cvs_register --mov 01091p --mni --step1 --step2 --step3 --outdir /Users/MiracleOz/Documents/improvervsdeclinermri/01091p/cvs --asegfname aparc+aseg --openmp 1 Best, Paul

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Re: [Freesurfer] Recon-all for Allen Brain Institute T1 image
by Melanie Ganz 21 Oct '17

21 Oct '17

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seek help
by 辛雨萌 21 Oct '17

21 Oct '17

Dear FreeSurfer Experts, I'm a beginner in cognitive neuronscience and so new to the FreeSurfer. Recently I got some datas from AFNI, and in the documents I only found some surfaces that had been created by FreeSurfer. However, the documents only include some resting state volumes without the structural volumes. The format of the surfaces is ".asc", they can be opened by FreeSurfer. But turn to the cortical parcellation, there is only a file called "XXX.annot.niml.dset" and cannot be opened in the freeview or tktools. I'm wondering how can I get the cortical parcellation and stats about the cortical thickness from these files? Thank you!

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lta_convert does not produce ITK transforms that are correctly applied by antsApplyTransforms
by Christopher Markiewicz 20 Oct '17

20 Oct '17

Hi, I've used `bbregister` to generate a transform `bold2T1.lta` from `bold.nii` to `T1.mgz` (assume we have a `T1.nii` as well for the sake of ANTs). The following produces a well-aligned output: mri_convert --apply_transform bold2T1.lta bold.nii bold_space-T1.nii As does the following: lta_convert --inlta bold2T1.lta --outfsl bold2T1.mat c3d_affine_tool -ref T1.nii -src bold.nii bold2T1.mat -fsl2ras -oitk bold2T1.txt antsApplyTransforms -i bold.nii -r T1.nii -o bold_space-T1.nii -t bold2T1.txt However, if one skips the FSL step, the registration is quite far off: lta_convert --inlta bold2T1.lta --outitk bold2T1.txt antsApplyTransforms -i bold.nii -r T1.nii -o bold_space-T1.nii -t bold2T1.txt Comparing the ITK transform files: LTA-FSL-ITK #Insight Transform File V1.0 #Transform 0 Transform: MatrixOffsetTransformBase_double_3_3 Parameters: 0.9895096215486424 0.011126830936108464 -0.00042204653562094823 -0.01079971161879626 0.872329255299452 -0.42602926756857834 -0.004755964529051335 0.42420535065804454 0.8878552541301569 -1.3066136395454464 -45.60342165876236 -43.10584860730749 FixedParameters: 0 0 0 LTA-ITK #Insight Transform File V1.0 #Transform 0 Transform: AffineTransform_double_3_3 Parameters: 0.98950976133346558 0.011126830242574215 -0.00042204943019896746 -0.010799713432788849 0.87232941389083862 -0.42602935433387756 -0.0047559700906276703 0.42420542240142822 0.88785547018051147 -2.2848172187805176 -2.9065067768096924 11.744022369384766 FixedParameters: 0 0 0 To 5 significant digits, these are the same, except the last three (translation) parameters. And the `AffineTransform_double_3_3` is different from `MatrixOffsetTransformBase_double_3_3`, though I'm not sure whether this has any effect. Here is the original LTA: type = 1 # LINEAR_RAS_TO_RAS nxforms = 1 mean = 0.0000 0.0000 0.0000 sigma = 1.0000 1 4 4 1.010462999343872e+00 -1.063966564834118e-02 4.625014495104551e-03 -2.332115173339844e+00 1.228639855980873e-02 9.293417930603027e-01 -4.459420144557953e-01 2.507942199707031e+00 4.575361963361502e-04 4.440840482711792e-01 9.132194519042969e-01 -1.201664733886719e+01 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 9.999998807907104e-01 src volume info valid = 1 # volume info valid filename = /scratch/fmriprep_wf/single_subject_02_wf/func_preproc_task_short_wf/bold_reg_wf/bbreg_wf/bbregister/uni_masked_xform.nii.gz volume = 64 64 34 voxelsize = 3.125000000000000e+00 3.125000000000000e+00 4.000000000000000e+00 xras = -1.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 yras = 0.000000000000000e+00 1.000000000000000e+00 0.000000000000000e+00 zras = 0.000000000000000e+00 0.000000000000000e+00 1.000000000000000e+00 cras = -1.090248107910156e+00 -1.071614074707031e+01 1.619928741455078e+01 dst volume info valid = 1 # volume info valid filename = /scratch/fmriprep_wf/single_subject_02_wf/anat_preproc_wf/t1_merge/sub-02_T1w_template.nii.gz volume = 160 192 192 voxelsize = 1.000000000000000e+00 1.333333015441895e+00 1.333333015441895e+00 xras = 1.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 yras = 0.000000000000000e+00 1.000000000000000e+00 0.000000000000000e+00 zras = 0.000000000000000e+00 0.000000000000000e+00 1.000000000000000e+00 cras = -3.000000000000000e+00 2.999969482421875e+00 -8.000030517578125e+00 subject sub-02 fscale 0.100000 If it would be useful, I can provide any relevant images for testing. -- Chris Markiewicz Center for Reproducible Neuroscience Stanford University

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Re: [Freesurfer] Recon-all for Allen Brain Institute T1 image
by Sean Froudist Walsh 20 Oct '17

20 Oct '17

That would be great Melanie, thank you very much. And thanks to Bruce and Satra for the quick responses. How will I be able to find the processed files? Will it be announced somehow? Best wishes, Sean

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asking for literature
by Jiook Cha 20 Oct '17

20 Oct '17

Hello, Could anybody please point me to a paper/asbtract showing meaningful improvement of pial surface segmentation using additional T2 or Flair images in the recon-all procedure? Thanks, Jiook ᐧ

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FreeSurfer connection with another modality
by Josh Abusnaineh 20 Oct '17

20 Oct '17

Hello FreeSurfer Developers, The Installation and test part is complete! I was just wondering if FreeSurfer has a way to send/retrieve images from another station using AE_Title/port and IP. Please let me know. Thank you. Sincerely, Josh Snaineh TechCare Computers, Inc 1-310-202-0922<tel:1-310-202-0922> 1-866-FIX-PC4U<tel:18663497248> 1-866-349-7248<tel:18663497248> 2805 S. Robertson Blvd Los Angeles, CA 90034 Josh(a)mytechcare.com<mailto:Josh@mytechcare.com> http://www.mytechcare.com/ Your Total Computer Solution

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subcortical analysis in native space
by Jiahe Zhang 20 Oct '17

20 Oct '17

Hi Freesurfer experts, I would like to do a resting state analysis not in mni305, but in subject's native subcortical space. Here is the command I wrote: mkanalysis-sess -analysis seed.native -native -fwhm 0 -notask -taskreg seed.dat 1 -nuisreg vcsf.dat 5 -nuisreg wm.dat 5 -nuisreg mcprextreg 2 -polyfit 5 -nskip 4 -fsd rest -TR 2.34 -per-run -lpf .08 -hpf .01 The output is a whole brain map with noisy dots everywhere but no clusters (not even autocorrelation within seed location). Am I specifying everything correctly? I know my seed.dat is not the issue because I tested it using mkanalysis-sess -surface $subjectname and the output is as expected. Thanks, Jiahe -- Jiahe Zhang Ph.D. Candidate Department of Psychology Northeastern University 617-373-2649

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Re: [Freesurfer] Recon-all for Allen Brain Institute T1 image
by Melanie Ganz 20 Oct '17

20 Oct '17

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Yeo atlas FreeSurfer
by Martin Juneja 19 Oct '17

19 Oct '17

Hi experts, I am using Yeo atlas (7 networks) in my analysis. Where can I find name of all the regions involved in each of these 7 networks in Yeo atlas? Thanks.

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Freesurfer October 2017