Freesurfer

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30132 discussions

Mean FA values for major tracts all greater than 1
by Katherine Damme 05 Sep '18

05 Sep '18

External Email - Use Caution Hello Freesurfer Support group, I have run tracula on hundreds of subjects for a study and their primary tracts are all showing that MFA is greater than 1. Typically, I expected that MFA should be in the .3 to 1 range. Should I be suspicious that these MFA values are over the top of that range or is this common for major tracts like the forceps major? Thank you for your insights on this potential error. Kate

2 1

mris_compute_parc_overlap average minimum distance measurement
by Zimmerman, Jared 05 Sep '18

05 Sep '18

External Email - Use Caution Hi Freesurfers, I’m using mris_compute_parc_overlap to compare the similarity between two parcellations and I’m curious about how the average minimum distance measurement is calculated. The help text for the function says “… a table of mean minimum distances between corresponding labels.” My questions are 1) what set of measurements is being meaned here, and 2) what exactly is the measurement. My current interpretation is that for every vertex in annot1 the minimum distance to a vertex in annot2 with the same label is calculated such that overlapping regions have a distance of zero. The mean is then calculated over these distance measures for all vertices in a given label. If this is true, do you recommend doing any subject level corrections? Seems like subjects with larger cortical surface areas would be biased to have larger distances. Thanks, Jared

2 1

long_mris_slopes: error: cannot create a table with longitudinal pc1
by Shatil, Anwar Shahadat 05 Sep '18

05 Sep '18

External Email - Use Caution ?Dear Doug: I am trying to get a table containing pc1 values for each subject in a longitudinal study and failed to extract this. I use the code below: long_mris_slopes --qdec ./qdec/long.qdec.table.2.dat --meas thickness --hemi lh --do-avg --do-rate --do-pc1 --do-spc --do-stack --do-label --time years --qcache fsaverage --sd /Users/richardaviv/Desktop/Longitudinal_FS --out-pc1 out-pc1.dat It says long_mris_slopes: error: no such option: --out-pc1 However in the --help file it says: Within-Subject Output: Pass these to overwrite the default names: --out-avg=OUT_AVG filename to store temporal average in <template>/stats/<OUT_AVG> (default: long.<stats>.<meas>-avg.dat) --out-rate=OUT_RATE filename to store rate in <template>/stats/<OUT_RATE> (default: long.<stats>.<meas>-rate.dat) --out-pc1fit=OUT_PC1FIT filename to store pct. change (to tp1fit) in <template>/stats/<OUT_PC1FIT> (default: long.<stats>.<meas>-pc1fit.dat) --out-pc1=OUT_PC1 filename to store pct. change (to tp1) in <template>/stats/<OUT_PC1> (default: long.<stats>.<meas>-pc1.dat) --out-spc=OUT_SPC filename to store sym. pct. change in <template>/stats/<OUT_SPC> (default: long.<stats>.<meas>-spc.dat) --out-resid=OUT_RESID filename to store residual in <template>/stats/<OUT_RESID> (default: long.<stats>.<meas>-resid<resid>.dat), requires --resid <int> --out-stack=OUT_STACK filename to store stacked measure file <template>/stats/<OUT_STACK> (default: long.<stats>.<meas>-stack.dat) Stacked Tables: To output tables with results from all subjects --stack-avg=STACK_AVG full filename to stack temporal average tables (default no stacking) --stack-rate=STACK_RATE full filename to stack rate tables (default no stacking) --stack-pc1fit=STACK_PC1FIT full filename to stack pct. change to tp1fit tables (default no stacking) --stack-pc1=STACK_PC1 full filename to stack pct. change to tp1 tables (default no stacking) --stack-spc=STACK_SPC full filename to stack sym. pct. tables (default no stacking) --stack-resid=STACK_RESID full filename to stack residual tables (default no stacking)? Am I writing the code wrong?? I never got any long.<stats>.<meas>-pc1.dat file in <template>/stats/ folder except bunch of mgh files in <template>/surf/ folder. Thanks, Anwar -- Anwar S. Shatil Research Assistant Department of Medical Imaging Sunnybrook Health Sciences Centre Room AB204, 2075 Bayview Avenue Toronto, ON M4N 3M5 Tel: 416.480.6100 ext. 89617 Email: anwar.shatil(a)sunnybrook.ca This e-mail is intended only for the named recipient(s) and may contain confidential, personal and/or health information (information which may be subject to legal restrictions on use, retention and/or disclosure). No waiver of confidence is intended by virtue of communication via the internet. Any review or distribution by anyone other than the person(s) for whom it was originally intended is strictly prohibited. If you have received this e-mail in error, please contact the sender and destroy all copies.

2 4

Get corresponding vertex of another subject
by Michael . 05 Sep '18

05 Sep '18

External Email - Use Caution Hi, i want to create a lookup table for the vertex correspondence between the subjects A & B (pial files). e.g verticesA(100) corresponds to verticesB(122) Of course the number of vertices is different between the subjects, e.g one vertex of A can correspond to several vertices from B. Currently, I am reading in the pial files of subject A using 'read_surf' and create two label files (lh/rh) containing all vertices. In order to get the corresponding vertices of Subject B, i use "label2label". label file A: #!ascii label, from subject 142350 0 -7.814680 -88.725967 9.598738 1.000000 1 -8.505306 -88.835274 9.457685 2.000000 2 -9.234029 -89.900490 9.420641 3.000000 resulting label file: #!ascii label , from subject cvs_avg35_inMNI152/Segmentation vox2ras=TkReg 137427 888 -7.179 -84.047 -28.333 1.0000000000 642 -7.533 -84.272 -28.382 2.0000000000 637 -7.717 -84.612 -28.118 3.0000000000 But how can I interpret the result? Can I assume that verticesA(0) corresponds to verticesB(888)? Or verticesA(0) corresponds to verticesB(888)? Or is there another way to create such a lookup table? Thank you in advance!

1 0

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>*

2 2

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

1 0

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. ________________________________

3 5

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

3 2

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

3 2

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