Freesurfer

freesurfer@nmr.mgh.harvard.edu

30088 discussions

Is voxel size resampled during recon-all? And different voxel size in longitudinal studies
by Daniel Ferreira 05 Sep '18

05 Sep '18

External Email - Use Caution Dear colleagues, I was wondering if resampling voxel size is done during recon-all. Also, I have data with voxel resolution of 1x1x1 mm at baseline and 1,2x1,2x1,2 at follow-up. I was wondering if recon-all does any computation by default (or can be performed by any way) that minimizes these differences in somehow. Thank you very much Dani -- *Daniel Ferreira, PhD, Assistant Professor* Division of Clinical Geriatrics; Department of Neurobiology, Care Sciences and Society Karolinska Institutet (Sweden) *Address: **Blickagången 16, 141 52 Huddinge | phone: +46 720128047 | email: daniel.ferreira.padilla(a)ki.se <daniel.ferreira.padilla(a)ki.se>*

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error in selxavg3-sess - mismatch TE
by stdp82＠virgilio.it 05 Sep '18

05 Sep '18

External Email - Use Caution Hi list, I have run the FS-FAST analysis in line with the standard procedures that I use routinely. With new data, selxavg3-sess produces an errror: there is a mis-matched between the TE in the analysis (=3) and the TE in the data (=0). I have cheched the data information by fslinfo as well as MELODIC and both the operations confirm the data have a TE=3 that matches with TE reported in mkanalysis-sess . How is it possible? Please, could you help me? Thanks Stefano

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SurfaceRAS to Vertex coordinate system
by Bruss, Joel E 04 Sep '18

04 Sep '18

External Email - Use Caution If I load, say, orig.mgz and lh.pial, in FreeView and lay my cursor on a point, I can see RAS (and surfaceRAS) as well as TKReg RAS (orig) coordinates. Following the steps laid out on the CoordinateSystems web page I can convert back and forth between those coordinate systems. However, I can't figure out what I need to do to calculate the Vertex coordinates. I can load lh.pial in matlab and see the (+1) vertex number and coordinates, but I'd like to figure out the best way to get from Vertex x/y/z to TkReg RAS or SurfaceRAS. Is there an easy formula to calculate this? Thanks in advance for any and all responses. -Joel ________________________________ Notice: This UI Health Care e-mail (including attachments) is covered by the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521 and is intended only for the use of the individual or entity to which it is addressed, and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If you are not the intended recipient, any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please notify the sender immediately and delete or destroy all copies of the original message and attachments thereto. Email sent to or from UI Health Care may be retained as required by law or regulation. Thank you. ________________________________

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Stats Error
by Song, Da-Yea 04 Sep '18

04 Sep '18

External Email - Use Caution Hello, I'm extracting some stats from recon-all but noticed that it would stop running in the middle (error message: end: Not in while/foreach) . Any suggestions on how I could solve this problem would be greatly appreciated! Thank you so much in advance. Best regards, Da-Yea computing statistics for each annotation in rantaFL.annot. reading volume /g5/dcn/freesurfer_testing/subjects//3095_3T_011216_0/mri/wm.mgz... reading input surface /g5/dcn/freesurfer_testing/subjects//3095_3T_011216_0/surf/lh.white... Using TH3 vertex volume calc Total face volume 249500 Total vertex volume 245871 (mask=0) reading input pial surface /g5/dcn/freesurfer_testing/subjects//3095_3T_011216_0/surf/lh.pial... reading input white surface /g5/dcn/freesurfer_testing/subjects//3095_3T_011216_0/surf/lh.white... reading colortable from annotation file... colortable with 11 entries read (originally /freesurfer/FrontalLobeColorLUT.txt) atlas_icv (eTIV) = 1377325 mm^3 (det: 1.414413 ) lhCtxGM: 245607.578 244866.000 diff= 741.6 pctdiff= 0.302 rhCtxGM: 253269.330 252721.000 diff= 548.3 pctdiff= 0.217 lhCtxWM: 199421.968 199714.500 diff= -292.5 pctdiff=-0.147 rhCtxWM: 198426.788 199552.500 diff=-1125.7 pctdiff=-0.567 SubCortGMVol 53103.000 SupraTentVol 962619.664 (961451.000) diff=1168.664 pctdiff=0.121 SupraTentVolNotVent 951172.664 (950004.000) diff=1168.664 pctdiff=0.123 BrainSegVol 1091475.000 (1088903.000) diff=2572.000 pctdiff=0.236 BrainSegVolNotVent 1076628.000 (1076311.664) diff=316.336 pctdiff=0.029 BrainSegVolNotVent 1076628.000 CerebellumVol 126436.000 VentChorVol 11447.000 3rd4th5thCSF 3400.000 CSFVol 828.000, OptChiasmVol 188.000 MaskVol 1502516.000 structure is "anterior_cingulate" number of vertices = 3531 total surface area = 2414 mm^2 total gray matter volume = 6657 mm^3 average cortical thickness = 2.742 mm +- 0.824 mm average integrated rectified mean curvature = 0.116 average integrated rectified Gaussian curvature = 0.017 folding index = 37 intrinsic curvature index = 2.5 structure is "dlpfc" number of vertices = 10762 total surface area = 7059 mm^2 total gray matter volume = 20651 mm^3 average cortical thickness = 2.426 mm +- 0.665 mm average integrated rectified mean curvature = 0.125 average integrated rectified Gaussian curvature = 0.025 folding index = 150 intrinsic curvature index = 10.8 structure is "frontal_eye_field" number of vertices = 1371 total surface area = 927 mm^2 total gray matter volume = 2587 mm^3 average cortical thickness = 2.654 mm +- 0.526 mm average integrated rectified mean curvature = 0.111 average integrated rectified Gaussian curvature = 0.020 folding index = 12 intrinsic curvature index = 1.0 structure is "inferolateral_pfc" number of vertices = 4430 total surface area = 2928 mm^2 total gray matter volume = 9914 mm^3 average cortical thickness = 2.662 mm +- 0.654 mm average integrated rectified mean curvature = 0.124 average integrated rectified Gaussian curvature = 0.022 folding index = 64 intrinsic curvature index = 4.1 structure is "lateral_OFC" number of vertices = 5859 total surface area = 3926 mm^2 total gray matter volume = 11128 mm^3 average cortical thickness = 2.493 mm +- 0.732 mm average integrated rectified mean curvature = 0.128 average integrated rectified Gaussian curvature = 0.029 folding index = 74 intrinsic curvature index = 6.6 structure is "medial_OFC" number of vertices = 1871 total surface area = 1217 mm^2 total gray matter volume = 3722 mm^3 average cortical thickness = 2.641 mm +- 0.791 mm average integrated rectified mean curvature = 0.121 average integrated rectified Gaussian curvature = 0.036 folding index = 27 intrinsic curvature index = 2.9 structure is "mpfc" number of vertices = 6801 total surface area = 4531 mm^2 total gray matter volume = 15597 mm^3 average cortical thickness = 2.761 mm +- 0.652 mm average integrated rectified mean curvature = 0.127 average integrated rectified Gaussian curvature = 0.027 folding index = 86 intrinsic curvature index = 7.4 structure is "primary_motor" number of vertices = 6578 total surface area = 3910 mm^2 total gray matter volume = 12307 mm^3 average cortical thickness = 2.729 mm +- 0.549 mm average integrated rectified mean curvature = 0.094 average integrated rectified Gaussian curvature = 0.016 folding index = 52 intrinsic curvature index = 4.3 structure is "supplementary_motor_complex" number of vertices = 2427 total surface area = 1664 mm^2 total gray matter volume = 5088 mm^3 average cortical thickness = 2.595 mm +- 0.593 mm average integrated rectified mean curvature = 0.121 average integrated rectified Gaussian curvature = 0.023 folding index = 25 intrinsic curvature index = 2.2 structure is "lateral_premotor" number of vertices = 3941 total surface area = 2586 mm^2 total gray matter volume = 7468 mm^3 average cortical thickness = 2.642 mm +- 0.522 mm average integrated rectified mean curvature = 0.105 average integrated rectified Gaussian curvature = 0.023 folding index = 35 intrinsic curvature index = 4.1 computing statistics for each annotation in rantaFL.annot. reading volume /g5/dcn/freesurfer_testing/subjects//3095_3T_011216_0/mri/wm.mgz... reading input surface /g5/dcn/freesurfer_testing/subjects//3095_3T_011216_0/surf/rh.white... Using TH3 vertex volume calc Total face volume 257391 Total vertex volume 253779 (mask=0) reading input pial surface /g5/dcn/freesurfer_testing/subjects//3095_3T_011216_0/surf/rh.pial... reading input white surface /g5/dcn/freesurfer_testing/subjects//3095_3T_011216_0/surf/rh.white... reading colortable from annotation file... colortable with 11 entries read (originally /freesurfer/FrontalLobeColorLUT.txt) atlas_icv (eTIV) = 1377325 mm^3 (det: 1.414413 ) lhCtxGM: 245607.578 244866.000 diff= 741.6 pctdiff= 0.302 rhCtxGM: 253269.330 252721.000 diff= 548.3 pctdiff= 0.217 lhCtxWM: 199421.968 199714.500 diff= -292.5 pctdiff=-0.147 rhCtxWM: 198426.788 199552.500 diff=-1125.7 pctdiff=-0.567 SubCortGMVol 53103.000 SupraTentVol 962619.664 (961451.000) diff=1168.664 pctdiff=0.121 SupraTentVolNotVent 951172.664 (950004.000) diff=1168.664 pctdiff=0.123 BrainSegVol 1091475.000 (1088903.000) diff=2572.000 pctdiff=0.236 BrainSegVolNotVent 1076628.000 (1076311.664) diff=316.336 pctdiff=0.029 BrainSegVolNotVent 1076628.000 CerebellumVol 126436.000 VentChorVol 11447.000 3rd4th5thCSF 3400.000 CSFVol 828.000, OptChiasmVol 188.000 MaskVol 1502516.000 structure is "anterior_cingulate" number of vertices = 3332 total surface area = 2321 mm^2 total gray matter volume = 6663 mm^3 average cortical thickness = 2.866 mm +- 0.804 mm average integrated rectified mean curvature = 0.131 average integrated rectified Gaussian curvature = 0.020 folding index = 46 intrinsic curvature index = 2.4 structure is "dlpfc" number of vertices = 9975 total surface area = 6648 mm^2 total gray matter volume = 19598 mm^3 average cortical thickness = 2.528 mm +- 0.591 mm average integrated rectified mean curvature = 0.122 average integrated rectified Gaussian curvature = 0.024 folding index = 131 intrinsic curvature index = 9.7 structure is "frontal_eye_field" number of vertices = 1041 total surface area = 716 mm^2 total gray matter volume = 2230 mm^3 average cortical thickness = 2.746 mm +- 0.497 mm average integrated rectified mean curvature = 0.113 average integrated rectified Gaussian curvature = 0.019 folding index = 9 intrinsic curvature index = 0.8 structure is "inferolateral_pfc" number of vertices = 5727 total surface area = 3741 mm^2 total gray matter volume = 13361 mm^3 average cortical thickness = 2.918 mm +- 0.711 mm average integrated rectified mean curvature = 0.129 average integrated rectified Gaussian curvature = 0.027 folding index = 81 intrinsic curvature index = 6.0 structure is "lateral_OFC" number of vertices = 5282 total surface area = 3577 mm^2 total gray matter volume = 10853 mm^3 average cortical thickness = 2.722 mm +- 0.712 mm average integrated rectified mean curvature = 0.128 average integrated rectified Gaussian curvature = 0.031 folding index = 68 intrinsic curvature index = 6.3 structure is "medial_OFC" number of vertices = 2515 total surface area = 1658 mm^2 total gray matter volume = 4981 mm^3 average cortical thickness = 2.630 mm +- 0.880 mm average integrated rectified mean curvature = 0.137 average integrated rectified Gaussian curvature = 0.043 folding index = 41 intrinsic curvature index = 4.8 structure is "mpfc" number of vertices = 7124 total surface area = 4660 mm^2 total gray matter volume = 17198 mm^3 average cortical thickness = 3.001 mm +- 0.598 mm average integrated rectified mean curvature = 0.131 average integrated rectified Gaussian curvature = 0.030 folding index = 90 intrinsic curvature index = 8.8 structure is "primary_motor" number of vertices = 7001 total surface area = 4241 mm^2 total gray matter volume = 13708 mm^3 average cortical thickness = 2.789 mm +- 0.539 mm average integrated rectified mean curvature = 0.101 average integrated rectified Gaussian curvature = 0.016 folding index = 56 intrinsic curvature index = 4.7 structure is "supplementary_motor_complex" number of vertices = 2086 total surface area = 1420 mm^2 total gray matter volume = 4986 mm^3 average cortical thickness = 3.022 mm +- 0.623 mm average integrated rectified mean curvature = 0.108 average integrated rectified Gaussian curvature = 0.018 folding index = 19 intrinsic curvature index = 1.5 structure is "lateral_premotor" number of vertices = 3371 total surface area = 2278 mm^2 total gray matter volume = 7004 mm^3 average cortical thickness = 2.809 mm +- 0.586 mm average integrated rectified mean curvature = 0.101 average integrated rectified Gaussian curvature = 0.017 folding index = 29 intrinsic curvature index = 2.3 end: Not in while/foreach. ---------------------------------------------------------------------- Disclaimer: The materials in this e-mail are private and may contain Protected Information. 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1 0

Freesurfer download issue
by Mengxue Kang 04 Sep '18

04 Sep '18

External Email - Use Caution Hello, I am trying to download FreeSurfer from " http://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall" and I can't open the download page. It keeps returning an error message below: This site can’t be reached The webpage at ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0/freesurfer-Darwi… might be temporarily down or it may have moved permanently to a new web address. ERR_FTP_FAILED Is there any other way to download the software? Thank you very much. Regards, Mengxue

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Re: [Freesurfer] fsaverage for a Left vs Right hemisphere Longitudinal
by Wang, Xiaoyu 04 Sep '18

04 Sep '18

External Email - Use Caution Thanks Martin, Yes, I did mean to have the right hemisphere added to the left hemisphere as a new time point. Can you explain on what you mean by run every subject only once? Do you mean to run xhemi for all of the subjects and then run a paired analysis? Xiaoyu

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NIFTI to pial.vtk space
by M. Jordan 04 Sep '18

04 Sep '18

External Email - Use Caution Hello, I have a CT NIFTI coregistered to the MRI NIFTI used for reconAll. When I export the .pial files to .vtk using mris_convert, they are shifted with respect to the MRI. Is there a way to process the CT NIFTI in such a way that it will match the .vtk pial files? Thank you!

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MNI to native space using mri_cvs_register and applyMorph
by Ehsan Tadayon 04 Sep '18

04 Sep '18

External Email - Use Caution Hi, I'm tyring to transform a bunch of MNI coordinates to subject's space using mri_cvs_register and applyMorph. I have run the mri_cvs_register but could'nt find detailed description of applyMorph. I appreciate any input on what command should be run to transform an MNI152 coordinate back to subject's space. thanks Ehsan.

1 0

Tools for FreeSurfer QC based on quality metrics?
by ts+ml＠rcmd.org 04 Sep '18

04 Sep '18

External Email - Use Caution Dear FreeSurfer experts, Which tools would you recommend to compute quality metrics for FreeSurfer 6 output? I would like to complement visual QC of the FreeSurfer segmentation output for structural images with automated metrics, e.g., outlier detection for the volume or CNR of certain subcortical structures or surface-based measures. Are there any tools for this? I guess I'm looking for something similar to the QATools for FreeSurfer 5 but for the latest FreeSurfer version. All the best, -- Tim Schäfer

1 0

error using -taskreg
by Addison Wu 03 Sep '18

03 Sep '18

External Email - Use Caution Dear List, I'm trying to use an external regressor to analyze fs-fast tutorial data. I understand a paradigm file would be the sane way to do it, but I'm just trying to understand how external regressors work. I first created a Extreg.dat file for each run of sess01, which contains a 142*5 matrix, saved it in the "00x" run folder. Then I ran mkanalysis-sess command: mkanalysis-sess \ -fsd bold -stc up -surface fsaverage rh \ -fwhm 5 -notask -TR 2 -taskreg Extreg.dat 1 \ -nskip 4 -analysis test.rh -force -per-run And a selxavg3-sess command: selxavg3-sess -s sess01 -analysis test.rh But I got an error report of this: Extension format = nii.gz INFO: key nSliceGroups unrecognized, line 11, skipping Error using basename Too many input arguments. Error in fast_ldanaflac (line 437) taskregevname = basename(taskreg,'dat'); % remove .dat Error in fast_selxavg3b (line 107) flac0 = fast_ldanaflac(analysis); 437 taskregevname = basename(taskreg,'dat'); % remove .dat K>> ------------------------------------------ ERROR: fast_selxavg3() failed\n I've tried a bunch of things, including removing the ".dat" manually for the file, or in the command lines, or changing the "taskreg" to -1 or 5, but none of them worked. Is there anyway I can solve the problem and use external regressors for the tutorial data? Thank you! Addison

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