Freesurfer

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Freesurfer Digest, Vol 193, Issue 3
by Faith Gunning 02 Mar '20

02 Mar '20

External Email - Use Caution Thanks, Lauren. Faith ________________________________ From: freesurfer-bounces(a)nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of freesurfer-request(a)nmr.mgh.harvard.edu <freesurfer-request(a)nmr.mgh.harvard.edu> Sent: Monday, March 2, 2020 12:00 PM To: freesurfer(a)nmr.mgh.harvard.edu <freesurfer(a)nmr.mgh.harvard.edu> Subject: [EXTERNAL] Freesurfer Digest, Vol 193, Issue 3 Send Freesurfer mailing list submissions to freesurfer(a)nmr.mgh.harvard.edu To subscribe or unsubscribe via the World Wide Web, visit https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.e… or, via email, send a message with subject or body 'help' to freesurfer-request(a)nmr.mgh.harvard.edu You can reach the person managing the list at freesurfer-owner(a)nmr.mgh.harvard.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of Freesurfer digest..."

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Issue with make_average_subject
by imurrieta＠hsctmexico.com 02 Mar '20

02 Mar '20

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recon-all-failure with file links
by Ian 02 Mar '20

02 Mar '20

External Email - Use Caution Oops, looks like the files didn't attach. Here are links to the logs: https://obd-public.s3.eu-west-2.amazonaws.com/recon-all-standard_out_log.log https://obd-public.s3.eu-west-2.amazonaws.com/recon-all-status.log https://obd-public.s3.eu-west-2.amazonaws.com/recon-all.log Hi all. I have a T1 scan which I run through recon-all with: recon-all -all -parallel -subjid freesurfer (after mksubjdirs etc) On my office machine, recon-all completes successfully. On a cloud machine (16GB of ram), it fails after about 4 hours. I have attached the logs - the only immediate error I can see is "Cannot find rh.white.H". Any advice would be much appreciated, thank you. Ian -- *Ian Hardingham* Chief Technology Officer signature_873986710 ian.hardingham(a)oxfordbraindiagnostics.com <mailto:terry.pollard@oxfordbraindiagnostics.com> +44 (0)7789 770555 Oxford Centre for Innovation | New Road | Oxford | OX1 1BY Oxford Brain Diagnostics Ltd is a company registered in England and Wales | Company No. 11703979 | VAT No. 321 3026 62

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DPABI V4.3, DPABISurf V1.3 and DPARSF V5.0 were released!
by YAN Chao-Gan 02 Mar '20

02 Mar '20

External Email - Use Caution Dear colleagues, We are pleased to announce the release of DPABI V4.3, DPABISurf V1.3 and DPARSF V5.0. New features of DPABI_V4.3_200301 (download at http://rfmri.org/dpabi, please also update the docker file by: docker pull cgyan/dpabi): 1. Stability Analysis module was added. You can calculate volume-based and surface-based stability from DPABI->Dynamic & Stability Analyses. You can read our recent work for the details of stability measure: Li, L., Lu, B., Yan, C.G. (2019). Stability of dynamic functional architecture differs between brain networks and states. Neuroimage, 116230, doi:10.1016/j.neuroimage.2019.116230. 2. Field map correction was added, both for DPARSF and DPABISurf. If you want to perform field map Correction, you need to arrange each subject's field map DICOM files in one directory, and then put them in "FieldMap" directory under the working directory. i.e.:';... '{Working Directory}\FieldMap\PhaseDiffRaw\Subject001\xxxxx001.dcm';... '{Working Directory}\FieldMap\PhaseDiffRaw\Subject001\xxxxx002.dcm';... '...';... '{Working Directory}\FieldMap\PhaseDiffRaw\Subject002\xxxxx001.dcm';... '{Working Directory}\FieldMap\PhaseDiffRaw\Subject002\xxxxx002.dcm';... '...';... '{Working Directory}\FieldMap\Magnitude1Raw\Subject001\xxxxx001.dcm';... '{Working Directory}\FieldMap\Magnitude1Raw\Subject001\xxxxx002.dcm';... '...';... '{Working Directory}\FieldMap\Magnitude1Raw\Subject002\xxxxx001.dcm';... '{Working Directory}\FieldMap\Magnitude1Raw\Subject002\xxxxx002.dcm';... '...';... '...';... Then you can click the button of “FieldMap” button to set field map correction parameters. In most cases, you can use the default “0” value to let the program read the parameters (e.g., echo times) from the DICOM files. 3. Check data organization function added. For the new users of DPARSF and DPABISurf, most of the errors were caused by data organization! Please use DPABI->Utilities->Check Data Organization to check your data organization before running DPARSF or DPABISurf. This program will lead you to organize your data correctly with prompting messages! 4. Slice timing information read from DICOM files. If you are starting with DICOM files, you no longer need to set the slice timing correction parameters. Just leave it as default (slice number: 0), then DPARSF or DPABISurf will read the parameters from DICOM files. This new feature thanks to Dr. Chris Rorden's new dcm2niiX program (version v1.0.20190902). 5. DPARSF V5.0 now is compatible with BIDS format. You can start with BIDS format data by checking checkbox “BIDS to DPARSF” and setting “Starting Directory Name” to “BIDS”. 6. DPABISurf V1.3. Check and re-run fmriprep failed subjects. If for any reason, the program failed fmriprep running in DPABISurf, you just need to re-run starting with the step “Preprocessing with fmriprep” and set the “Starting Directory Name” to “BIDS” in DPABISurf_Pipeline. Alternatively, you can run a single checking step from DPABI->DPABISurf->Utilities->Re-Run fmriprep Failed Subjects. 7. DPABI->Utilities->DICOM Sorter. Now DICOM Sorter will remove illegal characters for file names in DICOM sorter. E.g., a subject id of “Wang’#$#’s” will no longer cause a problem in sorting DICOM files. 8. y_Call_DPABISurf_VIEW_FromVolume.m and y_Call_DPABISurf_VIEW.m were added. Now you can use script to call DPABISurf_VIEW to generate surface maps (with higher quality now) in batch. Remember to add “close all” in the for loop to prevent too many windows. Tips: 1) For Linux or Mac OS, please start matlab from terminal in order to reach docker in DPABI (e.g., Linux: matlab; Mac: open /Applications/MATLAB_R2018a.app/). 2) Before running DPABISurf_Pipeline, you can test the docker environment by running DPABI->DPABISurf->Utilities->Volume-Surface Projector. If the file can be successfully projected to surface, then the software is all set. Best, Chao-Gan -- Chao-Gan YAN, Ph.D. Professor, Principal Investigator Director, International Big-Data Center for Depression Research Deputy Director, Magnetic Resonance Imaging Research Center Institute of Psychology, Chinese Academy of Sciences 16 Lincui Road, Chaoyang District, Beijing 100101, China - Initiator <http://rfmri.org/DPARSF>DPABI <http://rfmri.org/DPABI> <http://rfmri.org/DPARSF>, <http://dpabi.org>DPARSF <http://rfmri.org/DPARSF>, PRN <http://rfmri.org/PRN> and The R-fMRI Network <http://rfmri.org> (RFMRI.ORG <http://rfmri.org/>) http://rfmri.org/yan http://scholar.google.com/citations?user=lJQ9B58AAAAJ

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PhD Position in Multilingualism/Psycholinguistics
by Narly Golestani 01 Mar '20

01 Mar '20

External Email - Use Caution With the launch of a new ‘NCCR Evolving Language’ (http://www.snf.ch/SiteCollectionDocuments/nfs/Faktenblatt_NCCR_evolvinglang…) which involves nearly 40 different research groups from a large variety of disciplines across Switzerland, we seek to fill a PhD position for a four-year project starting in May 2020, or at the selected candidate’s convenience. Our goal is to make progress in understanding language giftedness from cognitive, psychological and neural perspectives. To this end, we plan to carry out a set of studies involving both behavioral measures of cognitive and language-related abilities (e.g. auditory/perceptual abilities, phonemic perception and production, inductive learning, working memory etc) and brain imaging measures (fMRI and sMRI). The research group involves two PIs (Golestani, Geneva; and Berthele, Fribourg) and a postdoc. Data will be collected with Francophone (mono- and multilingual) subjects. Applicants should hold an MA degree in psychology, linguistics or a related field (e.g. psycholinguistics, applied linguistics, multillingualism), have a good command French and English and have strong quantitative research and statistics skills. Additional mastery of German and experience with neuroimaging techniques would be a strong advantage. The NCCR places great emphasis on gender diversity and we particularly encourage women to apply. Applicants may send a pdf file including a cover letter, a CV, names and contact information of 2-3 references as well as any other relevant documents to Narly.Golestani(a)unige.ch<mailto:Narly.Golestani@unige.ch> and Raphael.berthele(a)unifr.ch<mailto:Raphael.berthele@unifr.ch>. Deadline for application: March 31 2020 ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Brain and Language Lab Prof. Narly GOLESTANI Department of Psychology Campus Biotech 9 Chemin des Mines, 1202 Genève +41 22 379 53 52 <https://outlook.unige.ch/owa/redir.aspx?SURL=5WTo-p-J-W9FrDydU-0WU4PdMytUGs…>http://www.brainandlanguagelab.org https://twitter.com/brain_lang_lab ----------------------------------------------------------------------------------------------------------------------------------------------------------------- <https://outlook.unige.ch/owa/redir.aspx?SURL=5WTo-p-J-W9FrDydU-0WU4PdMytUGs…>

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Postdoc position available - computational modeling and real-time fMRI neurofeedback of language
by Narly Golestani 01 Mar '20

01 Mar '20

External Email - Use Caution With the launch of a new ‘NCCR Evolving Language’ (http://www.snf.ch/SiteCollectionDocuments/nfs/Faktenblatt_NCCR_evolvinglang…) which involves nearly 40 different research groups from a large variety of disciplines across Switzerland, we seek to fill a Postdoc position for a four-year project starting in May 2020, or at the selected candidate’s earliest convenience. Our goal is to make progress in understanding the importance of prosody in language processing. To this end, we plan to carry out a set of studies involving both computational modeling of fMRI data and real-time fMRI neurofeedback to understand the mechanisms whereby prosody and rhythm support linguistic processing per se. The computational modeling work will be an extension of our recent work on the neural encoding of acoustic information in speech sounds (https://www.ncbi.nlm.nih.gov/pubmed/31285622) The research will be done in the group of Narly Golestani (www.brainandlanguagelab.org<http://www.brainandlanguagelab.org>) in Geneva, in collaboration with researchers in Switzerland and abroad (Elia Formisano in Maastricht, and Frank Scharnowski in Vienna). Applicants should hold a degree in Biomedical Engineering, Computational Neuroscience, or a related field, and should have solid experience in human brain imaging, and ideally also in computational modelling (i.e. encoding / decoding) of fMRI data, real-time fMRI based neurofeedback, machine learning, statistics and programming. The NCCR places great emphasis on gender diversity and we particularly encourage women to apply. To apply, please send a cover letter, CV, names and contact information of 2-3 references as well as any other relevant documents to Narly.Golestani(a)unige.ch<mailto:Narly.Golestani@unige.ch>. Feel free to contact me should you have any questions. Deadline for application: March 15th 2020 ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Brain and Language Lab Prof. Narly GOLESTANI Department of Psychology Campus Biotech 9 Chemin des Mines, 1202 Genève +41 22 379 53 52 <https://outlook.unige.ch/owa/redir.aspx?SURL=5WTo-p-J-W9FrDydU-0WU4PdMytUGs…>http://www.brainandlanguagelab.org https://twitter.com/brain_lang_lab ----------------------------------------------------------------------------------------------------------------------------------------------------------------- <https://outlook.unige.ch/owa/redir.aspx?SURL=5WTo-p-J-W9FrDydU-0WU4PdMytUGs…>

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Want to display some region
by yyxqq 01 Mar '20

01 Mar '20

External Email - Use Caution Hello, FreeSurfer experts, I want to use freesurfer to draw a 3D brain image of a specific region like Right-fimbria and subiculum in a template space. I have look through some materials today, but not find any resolution. Can you do me a favor? Thank you very much! Best regards, Yang

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Re: [Freesurfer] Creating the pial surface of the cerebellum: how to let the mris_make_surfaces to push the pial surface to the boundary
by CiRong Liu 28 Feb '20

28 Feb '20

External Email - Use Caution Hi, Douglas, Thank you for your reply. I tried adding -max XXX. If I set the "-max 5" as the default values, the mris_mask_surfaces would finish running. However, if I set the "-max" more than 5, the mris_mask_surfaces would crash during the running - *Segmentation fault (core dumped).* *This is my computer config:* *1) Freesurfer Version - * freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c 2) Platform: Linux Mint 19.2 3) uname -a: Linux 4.15.0-60-generic #67-Ubuntu SMP Thu Aug 22 16:55:30 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux *Here is the error msg (at the end)for example:* $mris_make_surfaces -max 10 -max_csf 0.1 -min_gray_at_csf_border 1 -orig_wm orig -noaseg -noaparc -T1 ceb_sm marmosetceb_v2 rh using max_thickness = 10.0 reading original vertex positions from orig not using aseg volume to prevent surfaces crossing the midline not using aparc to prevent surfaces crossing the midline using ceb_sm as T1 volume... $Id: mris_make_surfaces.c,v 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading volume /home/cirong/bin/freesurfer/subjects/marmosetceb_v2/mri/filled.mgz... reading volume /home/cirong/bin/freesurfer/subjects/marmosetceb_v2/mri/ceb_sm.mgz... resampling filled volume to be in voxel register with T1 reading volume /home/cirong/bin/freesurfer/subjects/marmosetceb_v2/mri/wm.mgz... changing type of input wm volume to UCHAR... resampling wm volume to be in voxel register with T1 0 bright wm thresholded. 0 bright non-wm voxels segmented. reading original surface position from /home/cirong/bin/freesurfer/subjects/marmosetceb_v2/surf/rh.orig... computing class statistics... border white: 170215 voxels (0.34%) border gray 211849 voxels (0.42%) WM (79.0): 80.8 +- 7.5 [70.0 --> 106.0] GM (71.0) : 71.9 +- 8.9 [30.0 --> 105.0] using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=70+-10.4, GM=69+-10.4 setting MIN_GRAY_AT_WHITE_BORDER to 60.1 (was 70) setting MAX_BORDER_WHITE to 77.5 (was 105) setting MIN_BORDER_WHITE to 69.0 (was 85) setting MAX_CSF to 8.0 (was 40) setting MAX_GRAY to 62.5 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 60.1 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 8.0 (was 40) mean inside = 74.8, mean outside = 73.4 smoothing surface for 5 iterations... repositioning cortical surface to gray/white boundary smoothing T1 volume with sigma = 2.000 vertex spacing 0.87 +- 0.21 (0.01-->1.75) (max @ vno 190205 --> 190741) face area 0.31 +- 0.12 (0.00-->0.93) mean border=73.1, 45600 (45600) missing vertices, mean dist 2.1 [3.9 (%15.7)->2.6 (%84.3))] %31 local maxima, %44 large gradients and % 2 min vals, 0 gradients ignored mean absolute distance = 2.85 +- 2.92 7642 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... tol=1.0e-04, sigma=2.0, host=unkno, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 1 randomSeed 0 000: dt: 0.0000, sse=2428827.0, rms=6.800 001: dt: 0.5000, sse=2228267.0, rms=6.217 (8.575%) 002: dt: 0.5000, sse=2028263.5, rms=5.645 (9.199%) 003: dt: 0.5000, sse=1886400.0, rms=5.096 (9.731%) 004: dt: 0.5000, sse=1814327.0, rms=4.583 (10.072%) 005: dt: 0.5000, sse=1721364.9, rms=4.121 (10.063%) 006: dt: 0.5000, sse=1625707.9, rms=3.724 (9.648%) 007: dt: 0.5000, sse=1655070.8, rms=3.394 (8.851%) 008: dt: 0.5000, sse=1652526.4, rms=3.136 (7.621%) 009: dt: 0.5000, sse=1610117.9, rms=2.940 (6.224%) 010: dt: 0.5000, sse=1561510.9, rms=2.795 (4.945%) 011: dt: 0.5000, sse=1554297.9, rms=2.681 (4.083%) 012: dt: 0.5000, sse=1584733.6, rms=2.592 (3.329%) 013: dt: 0.5000, sse=1583861.1, rms=2.517 (2.880%) 014: dt: 0.5000, sse=1546283.4, rms=2.452 (2.578%) 015: dt: 0.5000, sse=1573124.0, rms=2.396 (2.291%) 016: dt: 0.5000, sse=1560157.1, rms=2.343 (2.203%) rms = 2.30, time step reduction 1 of 3 to 0.250... 017: dt: 0.5000, sse=1584955.1, rms=2.296 (2.021%) rms = 2.27, time step reduction 2 of 3 to 0.125... 018: dt: 0.2500, sse=1413241.2, rms=2.266 (1.279%) rms = 2.25, time step reduction 3 of 3 to 0.062... 019: dt: 0.1250, sse=1348002.0, rms=2.251 (0.692%) positioning took 2.0 minutes smoothing T1 volume with sigma = 1.000 vertex spacing 0.81 +- 0.26 (0.02-->3.05) (max @ vno 1015 --> 1374) face area 0.31 +- 0.17 (0.00-->2.54) mean border=73.2, 37029 (33580) missing vertices, mean dist -0.4 [1.3 (%54.3)->0.9 (%45.7))] %45 local maxima, %34 large gradients and % 3 min vals, 0 gradients ignored mean absolute distance = 1.13 +- 2.38 7372 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... tol=1.0e-04, sigma=1.0, host=unkno, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 000: dt: 0.0000, sse=1247019.2, rms=2.658 020: dt: 0.5000, sse=1660886.4, rms=2.513 (5.452%) 021: dt: 0.5000, sse=1696660.5, rms=2.429 (3.370%) 022: dt: 0.5000, sse=1582424.1, rms=2.353 (3.102%) 023: dt: 0.5000, sse=1592837.6, rms=2.296 (2.425%) 024: dt: 0.5000, sse=1575169.2, rms=2.246 (2.202%) rms = 2.20, time step reduction 1 of 3 to 0.250... 025: dt: 0.5000, sse=1552572.5, rms=2.202 (1.924%) rms = 2.18, time step reduction 2 of 3 to 0.125... 026: dt: 0.2500, sse=1465932.9, rms=2.178 (1.103%) rms = 2.16, time step reduction 3 of 3 to 0.062... 027: dt: 0.1250, sse=1308048.4, rms=2.165 (0.619%) positioning took 0.9 minutes smoothing T1 volume with sigma = 0.500 vertex spacing 0.80 +- 0.27 (0.03-->3.21) (max @ vno 1015 --> 1374) face area 0.26 +- 0.15 (0.00-->2.57) mean border=73.1, 36657 (30198) missing vertices, mean dist -0.2 [1.2 (%53.9)->0.9 (%46.1))] %64 local maxima, %15 large gradients and % 2 min vals, 0 gradients ignored mean absolute distance = 1.05 +- 1.90 5676 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... tol=1.0e-04, sigma=0.5, host=unkno, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 000: dt: 0.0000, sse=1326640.1, rms=2.462 028: dt: 0.5000, sse=1621191.5, rms=2.312 (6.099%) 029: dt: 0.5000, sse=1624567.6, rms=2.238 (3.187%) 030: dt: 0.5000, sse=1600156.1, rms=2.183 (2.467%) rms = 2.14, time step reduction 1 of 3 to 0.250... 031: dt: 0.5000, sse=1617027.1, rms=2.144 (1.794%) rms = 2.12, time step reduction 2 of 3 to 0.125... 032: dt: 0.2500, sse=1457184.9, rms=2.121 (1.087%) rms = 2.11, time step reduction 3 of 3 to 0.062... 033: dt: 0.1250, sse=1341353.0, rms=2.109 (0.564%) positioning took 0.7 minutes smoothing T1 volume with sigma = 0.250 vertex spacing 0.79 +- 0.27 (0.03-->3.02) (max @ vno 166101 --> 167636) face area 0.25 +- 0.14 (0.00-->2.52) mean border=73.0, 36288 (28156) missing vertices, mean dist -0.2 [1.0 (%53.1)->0.8 (%46.9))] %73 local maxima, % 7 large gradients and % 2 min vals, 0 gradients ignored mean absolute distance = 0.93 +- 1.64 5026 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... tol=1.0e-04, sigma=0.2, host=unkno, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 000: dt: 0.0000, sse=1345812.6, rms=2.264 034: dt: 0.5000, sse=1665688.5, rms=2.172 (4.051%) rms = 2.13, time step reduction 1 of 3 to 0.250... 035: dt: 0.5000, sse=1612717.9, rms=2.133 (1.821%) rms = 2.11, time step reduction 2 of 3 to 0.125... 036: dt: 0.2500, sse=1435326.8, rms=2.109 (1.107%) rms = 2.10, time step reduction 3 of 3 to 0.062... 037: dt: 0.1250, sse=1305283.9, rms=2.097 (0.555%) positioning took 0.5 minutes writing white matter surface to /home/cirong/bin/freesurfer/subjects/marmosetceb_v2/surf/rh.white... writing smoothed curvature to rh.curv writing curvature file /home/cirong/bin/freesurfer/subjects/marmosetceb_v2/surf/rh.curv writing smoothed area to rh.area writing curvature file /home/cirong/bin/freesurfer/subjects/marmosetceb_v2/surf/rh.area vertex spacing 0.79 +- 0.27 (0.01-->3.24) (max @ vno 1015 --> 1374) face area 0.24 +- 0.14 (0.00-->2.12) smoothing surface for 5 iterations... repositioning cortical surface to gray/csf boundary. smoothing T1 volume with sigma = 2.000 mean border=46.6, 59907 (59907) missing vertices, mean dist 10.2 [0.0 (%0.0)->14.1 (%100.0))] %23 local maxima, % 7 large gradients and %41 min vals, 5938 gradients ignored averaging target values for 5 iterations... perforing initial smooth deformation to move away from white surface tol=1.0e-04, sigma=2.0, host=unkno, nav=16, nbrs=2, l_surf_repulse=1.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.05 000: dt: 0.0000, sse=22236570.0, rms=27.443 001: dt: 0.0500, sse=21651240.0, rms=27.069 (1.363%) 002: dt: 0.0500, sse=21290688.0, rms=26.835 (0.862%) 003: dt: 0.0500, sse=21029676.0, rms=26.665 (0.635%) 004: dt: 0.0500, sse=20819052.0, rms=26.527 (0.519%) 005: dt: 0.0500, sse=20636676.0, rms=26.406 (0.454%) 006: dt: 0.0500, sse=20471550.0, rms=26.296 (0.415%) 007: dt: 0.0500, sse=20317400.0, rms=26.194 (0.391%) 008: dt: 0.0500, sse=20170454.0, rms=26.095 (0.375%) 009: dt: 0.0500, sse=20028784.0, rms=26.000 (0.365%) 010: dt: 0.0500, sse=19890884.0, rms=25.907 (0.358%) positioning took 1.0 minutes mean border=46.4, 57828 (53089) missing vertices, mean dist 9.6 [0.2 (%0.0)->13.3 (%100.0))] %24 local maxima, % 7 large gradients and %40 min vals, 4827 gradients ignored tol=1.0e-04, sigma=2.0, host=unkno, nav=16, nbrs=2, l_surf_repulse=1.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.05 000: dt: 0.0000, sse=21510736.0, rms=26.320 011: dt: 0.0500, sse=21370844.0, rms=26.231 (0.338%) 012: dt: 0.0500, sse=21233808.0, rms=26.144 (0.333%) 013: dt: 0.0500, sse=21098910.0, rms=26.057 (0.331%) 014: dt: 0.0500, sse=20965742.0, rms=25.972 (0.329%) 015: dt: 0.0500, sse=20834178.0, rms=25.887 (0.327%) 016: dt: 0.0500, sse=20703918.0, rms=25.802 (0.326%) 017: dt: 0.0500, sse=20575078.0, rms=25.719 (0.324%) 018: dt: 0.0500, sse=20447296.0, rms=25.635 (0.324%) 019: dt: 0.0500, sse=20320634.0, rms=25.553 (0.323%) 020: dt: 0.0500, sse=20195002.0, rms=25.470 (0.323%) positioning took 1.1 minutes mean border=46.3, 57994 (51335) missing vertices, mean dist 9.3 [0.1 (%0.0)->12.8 (%100.0))] %24 local maxima, % 7 large gradients and %40 min vals, 4820 gradients ignored tol=1.0e-04, sigma=2.0, host=unkno, nav=16, nbrs=2, l_surf_repulse=1.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.05 000: dt: 0.0000, sse=20284860.0, rms=25.363 021: dt: 0.0500, sse=20159524.0, rms=25.281 (0.323%) 022: dt: 0.0500, sse=20035252.0, rms=25.199 (0.323%) 023: dt: 0.0500, sse=19911852.0, rms=25.118 (0.322%) 024: dt: 0.0500, sse=19789384.0, rms=25.037 (0.322%) 025: dt: 0.0500, sse=19667922.0, rms=24.957 (0.322%) 026: dt: 0.0500, sse=19547232.0, rms=24.877 (0.322%) 027: dt: 0.0500, sse=19427442.0, rms=24.797 (0.321%) 028: dt: 0.0500, sse=19308560.0, rms=24.717 (0.321%) 029: dt: 0.0500, sse=19190536.0, rms=24.638 (0.321%) 030: dt: 0.0500, sse=19073444.0, rms=24.559 (0.320%) positioning took 1.2 minutes mean border=46.3, 58182 (49681) missing vertices, mean dist 9.0 [0.1 (%0.1)->12.4 (%99.9))] %24 local maxima, % 7 large gradients and %40 min vals, 4842 gradients ignored tol=1.0e-04, sigma=2.0, host=unkno, nav=16, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 000: dt: 0.0000, sse=19160218.0, rms=24.467 031: dt: 0.5000, sse=18407090.0, rms=23.957 (2.084%) 032: dt: 0.5000, sse=17688926.0, rms=23.460 (2.077%) 033: dt: 0.5000, sse=17006668.0, rms=22.976 (2.063%) 034: dt: 0.5000, sse=16360864.0, rms=22.507 (2.040%) 035: dt: 0.5000, sse=15751547.0, rms=22.055 (2.009%) 036: dt: 0.5000, sse=15177610.0, rms=21.620 (1.973%) 037: dt: 0.5000, sse=14637857.0, rms=21.201 (1.936%) 038: dt: 0.5000, sse=14127666.0, rms=20.797 (1.904%) 039: dt: 0.5000, sse=13644749.0, rms=20.407 (1.877%) 040: dt: 0.5000, sse=13185130.0, rms=20.028 (1.856%) 041: dt: 0.5000, sse=12746617.0, rms=19.660 (1.838%) 042: dt: 0.5000, sse=12325521.0, rms=19.300 (1.832%) 043: dt: 0.5000, sse=11921329.0, rms=18.948 (1.825%) 044: dt: 0.5000, sse=11532627.0, rms=18.603 (1.819%) 045: dt: 0.5000, sse=11158549.0, rms=18.265 (1.816%) 046: dt: 0.5000, sse=10795637.0, rms=17.932 (1.826%) 047: dt: 0.5000, sse=10442737.0, rms=17.601 (1.845%) 048: dt: 0.5000, sse=10097535.0, rms=17.271 (1.871%) 049: dt: 0.5000, sse=9762229.0, rms=16.945 (1.887%) 050: dt: 0.5000, sse=9437930.0, rms=16.624 (1.896%) 051: dt: 0.5000, sse=9120953.0, rms=16.304 (1.927%) 052: dt: 0.5000, sse=8813598.0, rms=15.987 (1.940%) 053: dt: 0.5000, sse=8514504.0, rms=15.673 (1.965%) 054: dt: 0.5000, sse=8222812.0, rms=15.361 (1.991%) 055: dt: 0.5000, sse=7938257.0, rms=15.051 (2.021%) 056: dt: 0.5000, sse=7662795.0, rms=14.744 (2.040%) Segmentation fault (core dumped) Data were here: https://pitt.box.com/s/6269a9mnwbs6zi0azn08dn55u47yfa7i ------------------------ Douglas N. Greve <https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=from…> Mon, 24 Feb 2020 06:34:51 -0800 <https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=date…> Try setting -max XXX where XXX is the maximum allowable thickness. It is default to 5, so try something large On 2/21/2020 11:36 AM, CiRong Liu wrote: External Email - Use Caution Dear experts of the freesurfer, I was trying to create the white matter and pial surfaces of the cerebellum of the marmoset, based on ultra-high (80um) resolution ex-vivo images. I manually segment the cerebellum into the white matter and the gray matter and change the header information to 1mm. Based on the manual segmented files, I created white matter surfaces (rh.orig). I tried to use the mris_make_surfaces to expand the white matter to create the matched pial surface. However, the /mris_make_surfaces/ failed to push the surface enough. See the attached files and screenshots. I tried smoothing the segmentation, enhancing the contrasts, and tested different expert option (for example: -max_csf 0.1 -min_gray_at_csf_border 1) This was this best I got, but still cannot get an optimal result (not pushed enough): /mris_mask_surfaces -max_csf 0.1 -min_gray_at_csf_border 1 -orig_wm orig -orig_pial orig -noaseg -noaparc -T1 ceb_sm marmosetceb rh / Since I have already manually segmented the cerebellum, *is there a way to force the /mris_make_surfaces/ to expand to the boundary of the image?* The files can be download to replicate what I did:https://pitt.box.com/s/6269a9mnwbs6zi0azn08dn55u47yfa7i Thank you very much! Best Regards, CiRong Liu _______________________________________________ Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _____________________________________ Best Regards, CiRong Liu

2 1

beta testing FreeSurfer v7 beta: recon-all-status.log, samseg
by Antonin Skoch 28 Feb '20

28 Feb '20

External Email - Use Caution Dear experts, I began to test beta v7 version of FreeSurfer. I noticed that some entries in recon-all-status.log seem missing (i.e. white and pial surface placement - there is entry Cortical Parc while following entry is Refine Pial Surfs). Running samseg` --t1w $s/mri/T1.mgz --t2w $s/mri/T2.mgz --s $s --refmode t1w exits with error in samseg2recon since command set segvol = `find "$samsegdir" -iname "*crispSegmentation.nii" -print` results with empty string set to segvol variable. Antonin

2 1

Re: [Freesurfer] DOSS questions
by Ferraro, Pilar 28 Feb '20

28 Feb '20

External Email - Use Caution Thank you so much for all the help! Below you can find few remaining questions I have following your suggestions! Message: 6 Date: Mon, 24 Feb 2020 09:24:00 -0500 From: "Douglas N. Greve" <dgreve(a)mgh.harvard.edu<mailto:dgreve@mgh.harvard.edu>> Subject: Re: [Freesurfer] GLM DOSS questions To: <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Message-ID: <62cf0ae8-3d78-aa44-7a44-17cd603a8934(a)mgh.harvard.edu<mailto:62cf0ae8-3d78-aa44-7a44-17cd603a8934@mgh.harvard.edu>> Content-Type: text/plain; charset="utf-8" On 2/21/2020 4:01 AM, Ferraro, Pilar wrote: ????????External Email - Use Caution Dear Freesurfer experts, I?ve just completed a GLM analysis in Freesurfer and I?d like to be sure that all the steps I?ve performed are the right ones. My analysis is looking at age related changes in cortical thickness in one group of patients, after regressing out the effects of disease duration. I obviously assume an inverse relationship between age and cortical thickness so that older age would be associated with cortical thickness reductions in specific brain regions. To test this hypothesis with Freesurfer I?ve used a GLM DOSS design. I?ve generated a fsgd file with the first column being the list of patients, the second column the age of patients, and the third column the disease duration. Then I?ve run the mris_preproc command. Afterward,? I?ve generated 2 contrast matrices (one for the left and one for the right hemisphere) with the following structure: 0 -1 0. 1 question. Is the contrast matrices structure I?ve chosen the most appropriate one for the hypothesis I?d like to test? Yes, but if you are going to use -1, you need to keep track of that when you specify the sign (but you are using abs so it does not matter). Also, you don't need different fsgd and contrast files for each hemisphere. >> Thank you! Then, I?ve run the glm analysis using the mri_glmfit command. To visualize the results I?ve used the freeview -f command and set the overlay_threshold to 1,5 instead of 4, cause I was interested in looking at all results significant at p < 0.05. 2 question. Is the overlay_threshold I?ve used the correct one? for visualization, you can use whatever threshold you want. But if you are going to use monte carlo simulations, then you need p<.001. If you want to keep p<.05, then you have to do permutation. >> I totally understand your point on the need for p<.001 threshold for Monte Carlo Simulation. However, in this first step of results visualization as an exploratory starting point I was just interested in uncorrected results generated with the mri_glmfit command with threshold p<0.05. So, was the command I’ve reported above the correct one in this case? Lastly, I was interested in looking at my results after Montecarlo correction, so I?ve run the simulation using the mri_glmfit-sim command. However, here I?ve changed few options: mri_glmfit-sim \ ? --glmdir lh.dur.glmdir \ ? --cache 4 neg \ (here I?ve changed to 1,5 since I was interested again at a P value < 0,05 and not < 0.0001 and I?ve changed the neg option with abs since I was interested in absolute values identified through the previously run analysis) ? --cwp? 0.05\ ? --2spaces 3 question. Are the edits I made to the command correct? It is not perfectly clear to me which one should be the preferred sign for the analysis (neg, pos or abs?). abs is an unsigned test. If you have an aprior hypothesis, then you can set the sign to that. Eg, if you are expecting the age slope to be negative, then you could choose negative (or in your case positive since you flipped the sign in the contrast) >> Sounds good, thanks for the explanation! In the end, in order to visualize the Montecarlo corrected results I?ve used again the Freeview -f command and again I?ve sent the overlay threshold to 1,5 since I was interested in all significant clusters at P < 0,05. 4 question. Again, this threshold is the correct one for my purpose? It will show all the clusters that are at p<.05 corrected. >> Ok, so, if I’ve correctly understood, I need to change this step either: a) Running a permutation instead of Monte Carlo simulation if I want to keep the p value < 0.05, or b) keep the Monte Carlo Simulation but change the p value to < 0.001. Is that correct? Also, for the Permutation analysis should I follow your detailed steps explanation reported in here: MultipleComparisonsV6.0Perm<https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultipleComparisonsV6.…> ? I have one last question concerning the Montecarlo simulation. Are there any cases in which you would suggest to do not use it since it would not be an appropriate correction? I'm recommending that everyone use permutation at this point. MC can generate inlfated false positives >> Thanks for the helpful tip! I’m a little bit concerned cause I have a quite small sample size (26 patients and 37 healthy controls for the comparison, while the regression analysis is run only in the patients group). At this point I presume it would be better to firstly run the permutation with p< 0.05, and then, only in case of no results with this procedure, eventually look at results with Monte Carlo p<0.001. Would that be a good option? Thanks again for all your help! Sorry for the long email but I needed to report all the steps in order to get an answer. Many thanks for all the help you?ll be able to provide. Best, Pilar Ferraro _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20200224/0… ------------------------------ Message: 7 Date: Mon, 24 Feb 2020 09:25:38 -0500 From: "Douglas N. Greve" <dgreve(a)mgh.harvard.edu<mailto:dgreve@mgh.harvard.edu>> Subject: Re: [Freesurfer] surfreg function To: <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Message-ID: <6075b7ad-ad3a-c483-2208-ee6fd048f5d0(a)mgh.harvard.edu<mailto:6075b7ad-ad3a-c483-2208-ee6fd048f5d0@mgh.harvard.edu>> Content-Type: text/plain; charset="utf-8" it is ok to spec -surfreg, but is not necessary in this case mris_preproc will change the name when you spec a target subject (eventhough the says that the default is sphere.reg) On 2/21/2020 6:20 AM, Marina Fern?ndez wrote: ????????External Email - Use Caution Hi Doug, Thank you for your replay. I understood that if I did not specify "--surfreg my_avg_subject.sphere.reg" ?mri_preproc was going to use the original file (sphere.reg), because in the help of mri_preproc it mentions this: --surfreg SurfReg : default is sphere.reg With this in mind,do you think it would not be necessary to specify it in mris_preproc? What is the difference between sphere.reg and my_avg_subject.sphere.reg? Best wishes, Marina _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20200224/8… ------------------------------ Message: 8 Date: Mon, 24 Feb 2020 09:26:14 -0500 From: "Douglas N. Greve" <dgreve(a)mgh.harvard.edu<mailto:dgreve@mgh.harvard.edu>> Subject: Re: [Freesurfer] how to convert the registered file (.lta) into NIfTI format in PETsurfer To: <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Message-ID: <362fe77d-51d2-2e69-1e5d-e273321b0dde(a)mgh.harvard.edu<mailto:362fe77d-51d2-2e69-1e5d-e273321b0dde@mgh.harvard.edu>> Content-Type: text/plain; charset="utf-8" Not sure what you are trying to do. An lta file is a matrix and nifti is a format for storing images. On 2/21/2020 7:52 AM, Kate Marvel wrote: ????????External Email - Use Caution Hi All, How do you convert the registered file (.lta) into NIfTI format in PETsurfer. Thanks, _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20200224/e… ------------------------------ Message: 9 Date: Mon, 24 Feb 2020 09:31:30 -0500 From: "Douglas N. Greve" <dgreve(a)mgh.harvard.edu<mailto:dgreve@mgh.harvard.edu>> Subject: Re: [Freesurfer] Optseq2 help needed To: <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Message-ID: <c4cecc27-ad82-b2bb-b174-0a6a9b20490e(a)mgh.harvard.edu<mailto:c4cecc27-ad82-b2bb-b174-0a6a9b20490e@mgh.harvard.edu>> Content-Type: text/plain; charset="utf-8" By default, optseq2 assumes that you want to perform an FIR analysis where you get an average for each post-stimulus time point so that you can create a waveform. This is in contrast to assuming the shape to the hemodyn respnse where you only estimate a single value (the amplitude). By default, the time between FIR waveform points is the TR, but you can perform sub-TR estimation by setting the dPSD to less than the TR. The problem is that every estimate you make reduces the efficienecy. So, assuming a shape is more efficient than an FIR because it only has one estimate. An FIR with dPDS=TR is more efficient than dPSD=TR/2 because there are half as many estimates. Probably when you go to analyze the data you will use an assumed shape, and then you will get the efficiency back. On 2/21/2020 9:43 AM, Gergely Darnai wrote: ????????External Email - Use Caution Dear Developers, I am planning to run PVT (psychomotor vigilance task) in fMRI using event related design. This is an extremely simple reaction time task: participant has to respond to the appeared geometric shape as quickly as possible. The key feature of this paradigm is that we will have fluctuating and quite rapid event presentation times (ranging between 300 and 500 msec). Another important information is that we will use FSL FEAT for the evaluation. We decided to use opseq2 to optimize the design with the following parameters: optseq2 --ntp 150 --tr 2 --psdwin 0 20 --ev evt1 1 45 --nkeep 3 --o exp --nsearch 10000 --tnullmin 3 --tnullmax 11 --repvar 10 Although with this design I get quite satisfying efficiency and VRF scores I do not understand that if I decrease dPSD why does it have significant negative effect on efficiency and VRF. Could you explain this? If I understand well, this is the only option to shift the onset of the event from the scanning points, and I would assume that if there is fluctuation in time between scanning points and stimuli presentation, it would help to "catch" the hemodynamic response easier (if the stimulus onset always goes together with the scans, we can always catch the same timepoints of the HRF). Did I misunderstand something? If I use FSL that is based on HRF estimation (and not on FIR), do these parameters (dPSD) and scores (efficiency & VRF) have meaning and function at all? My last question is related to event duration. Although I have fluctuating and short events, as you can see I chose 1 sec (because it has to be the integer multiple of the dPSD). Is it problematic? Thank you for your suggestions, Gergely ----------------------------------------- Gergely Darnai PhD Department of Behavioural Sciences Medical School, University of P?cs Phone: +36/72/536-256 Fax: +36/72/536-257 H-7624 Szigeti u. 12, P?cs, Hungary _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20200224/a… ------------------------------ Message: 10 Date: Mon, 24 Feb 2020 09:33:41 -0500 From: "Douglas N. Greve" <dgreve(a)mgh.harvard.edu<mailto:dgreve@mgh.harvard.edu>> Subject: Re: [Freesurfer] Creating the pial surface of the cerebellum: how to let the mris_make_surfaces to push the pial surface to the boundary To: <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Message-ID: <04884b22-53f5-2c7a-e07b-0aa0209532e6(a)mgh.harvard.edu<mailto:04884b22-53f5-2c7a-e07b-0aa0209532e6@mgh.harvard.edu>> Content-Type: text/plain; charset="utf-8" Try setting -max XXX where XXX is the maximum allowable thickness. It is default to 5, so try something large On 2/21/2020 11:36 AM, CiRong Liu wrote: ????????External Email - Use Caution Dear experts of the freesurfer, I was trying to create the white matter and pial surfaces of the?cerebellum of the marmoset, based on ultra-high (80um) resolution ex-vivo images. I manually segment the cerebellum into the white matter and the gray matter and change the header information to 1mm. Based on the manual?segmented files, I created white matter surfaces (rh.orig). I tried to use the mris_make_surfaces to expand the white matter to create the matched pial surface. However, the /mris_make_surfaces/ failed to push the surface enough. See the attached files and screenshots. I tried smoothing the segmentation, enhancing the contrasts, and tested different expert option (for example: -max_csf 0.1 -min_gray_at_csf_border 1) This was this best I got, but still cannot get an optimal result (not pushed enough): /mris_mask_surfaces -max_csf 0.1 -min_gray_at_csf_border 1 -orig_wm orig -orig_pial orig -noaseg -noaparc -T1 ceb_sm marmosetceb rh / Since I have already manually segmented the cerebellum, *is there a way to force the /mris_make_surfaces/ to expand to the boundary of the image?* The files can be download to replicate what I did: https://pitt.box.com/s/6269a9mnwbs6zi0azn08dn55u47yfa7i Thank you very much! Best Regards, CiRong Liu _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20200224/b… ------------------------------ Message: 11 Date: Mon, 24 Feb 2020 09:36:58 -0500 From: "Douglas N. Greve" <dgreve(a)mgh.harvard.edu<mailto:dgreve@mgh.harvard.edu>> Subject: Re: [Freesurfer] Version Beta 7.0 To: <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Message-ID: <51a3e156-250a-4679-07e4-c2deaebbb7be(a)mgh.harvard.edu<mailto:51a3e156-250a-4679-07e4-c2deaebbb7be@mgh.harvard.edu>> Content-Type: text/plain; charset="utf-8" We have not released stable 7 yet. Technically we have not released 7beta yet but only because I need to make the announcement and write up some docs. On 2/24/2020 2:46 AM, Victor Montal Blancafort wrote: ????????External Email - Use Caution Freesurfer developers, I have seen from the download webpage, that there is already a v7.0 beta version. Since we were planing to re-run a lot of individuals 1000+ with Freesurfer6, I was wondering if you could provide timings regarding the release of stabe 7.0. Also, could you briefly explain the main changes in this version? We are mainly interested on cortical thickness analysis, so... there will be big differences in the recon-all pipeline? Thank you in advance! V. _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20200224/9… ------------------------------ Message: 12 Date: Mon, 24 Feb 2020 09:41:09 -0500 From: "Douglas N. Greve" <dgreve(a)mgh.harvard.edu<mailto:dgreve@mgh.harvard.edu>> Subject: Re: [Freesurfer] cluster size threshold To: <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Message-ID: <b66960f1-e9c7-4ccf-86db-4c6444bfbca2(a)mgh.harvard.edu<mailto:b66960f1-e9c7-4ccf-86db-4c6444bfbca2@mgh.harvard.edu>> Content-Type: text/plain; charset="utf-8" You need to find the correct CDF file, eg, if the final FWHM is 12, it would be in $FREESURFER_HOME/average/mult-comp-cor/fsaverage/lh/cortex/fwhm12/abs/th30/mc-z.cdf To get the FWHM look in glmdir/fwhm.dat and round down in the mc-z.cdf file, find the row where the MaxClustCDF drops below .05/2=.025, then look at the MaxClustBin for the critical cluster size On 2/24/2020 6:49 AM, Elisa Castaldi wrote: ????????External Email - Use Caution Dear experts, To perform a Monte Carlo based cluster correction, I have run the following line: mri_glmfit-sim --glmdir glmdir --mczsim 3 abs --cwp 0.05 --2spaces --a2009s I need to figure out which is the minimum number of voxels required for a cluster to be considered significant. In other words, which is the cluster _size_ threshold in this case? Where can I find this information? Thanks Elisa _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20200224/d… ------------------------------ Message: 13 Date: Mon, 24 Feb 2020 08:47:49 -0600 From: Kate Marvel <kmarvel54(a)gmail.com<mailto:kmarvel54@gmail.com>> Subject: Re: [Freesurfer] how to convert the registered file (.lta) into NIfTI format in PETsurfer To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Message-ID: <CAG9yhu5o0ehKA-2oLLovmUFC2M1SrPowGioDiesR2Dsbna4N3A(a)mail.gmail.com<mailto:CAG9yhu5o0ehKA-2oLLovmUFC2M1SrPowGioDiesR2Dsbna4N3A@mail.gmail.com>> Content-Type: text/plain; charset="utf-8" External Email - Use Caution Hi Douglas, Is there a way to save the registered PET image in NIfTi format instead of .lta? Kate On Mon, Feb 24, 2020 at 8:26 AM Douglas N. Greve <dgreve(a)mgh.harvard.edu<mailto:dgreve@mgh.harvard.edu>> wrote: Not sure what you are trying to do. An lta file is a matrix and nifti is a format for storing images. On 2/21/2020 7:52 AM, Kate Marvel wrote: External Email - Use Caution Hi All, How do you convert the registered file (.lta) into NIfTI format in PETsurfer. Thanks, _______________________________________________ Freesurfer mailing listFreesurfer(a)nmr.mgh.harvard.eduhttps<mailto:listFreesurfer@nmr.mgh.harvard.eduhttps>://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- kate -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20200224/f… ------------------------------ Message: 14 Date: Mon, 24 Feb 2020 09:50:25 -0500 (EST) From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu<mailto:fischl@nmr.mgh.harvard.edu>> Subject: Re: [Freesurfer] how to convert the registered file (.lta) into NIfTI format in PETsurfer To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Message-ID: <alpine.LRH.2.21.2002240949160.22762(a)door.nmr.mgh.harvard.edu<mailto:alpine.LRH.2.21.2002240949160.22762@door.nmr.mgh.harvard.edu>> Content-Type: text/plain; charset="utf-8" Hi Kate the .lta format is for a linear registration (in ascii). YOu can just cat it to see the contents - it is not a PET image (which will be stored in .mgz or .nii). mri_convert or mri_vol2vol can be used to apply the registration and/or change the output format (if you specify file.nii or file.nii.gz it will write in Nifti) cheers Bruce On Mon, 24 Feb 2020, Kate Marvel wrote: ????????External Email - Use Caution???????? Hi Douglas, Is there a way to save the registered PET image in NIfTi format instead of .lta? Kate On Mon, Feb 24, 2020 at 8:26 AM Douglas N. Greve <dgreve(a)mgh.harvard.edu<mailto:dgreve@mgh.harvard.edu>> wrote: Not sure what you are trying to do. An lta file is a matrix and nifti is a format for storing images. On 2/21/2020 7:52 AM, Kate Marvel wrote: ????????External Email - Use Caution???????? Hi All, How do you convert the registered file (.lta) into NIfTI format in PETsurfer. Thanks, _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- kate ------------------------------ Message: 15 Date: Mon, 24 Feb 2020 14:50:05 +0000 From: Adam Rytina <adam.rytina(a)outlook.cz<mailto:adam.rytina@outlook.cz>> Subject: Re: [Freesurfer] Apply transformation To: "Greve, Douglas N.,Ph.D." <DGREVE(a)mgh.harvard.edu<mailto:DGREVE@mgh.harvard.edu>>, "freesurfer-bounces(a)nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu>" <freesurfer-bounces(a)nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu>>, "freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>" <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Message-ID: <AM0PR0602MB3377640CAED11562C48DB7349AEC0(a)AM0PR0602MB3377.eurprd06.prod.outlook.com<mailto:AM0PR0602MB3377640CAED11562C48DB7349AEC0@AM0PR0602MB3377.eurprd06.prod.outlook.com>> Content-Type: text/plain; charset="iso-8859-2" External Email - Use Caution Hello all, is it possible to transform a binary mask (a transformation matrix 4x4 acquired by registration of an anatomical and a diffusion image) and change a final FOV by specifying a diffusion reference image? Or the transform can be applied only on structural image? I am still struggling with the transformation of my binary mask as explained below. Thanks a lot Regards Adam ________________________________ Od: Adam Rytina <adam.rytina(a)outlook.cz<mailto:adam.rytina@outlook.cz>> Odesl?no: st?eda 19. ?nora 2020 8:11 Komu: Greve, Douglas N.,Ph.D. <DGREVE(a)mgh.harvard.edu<mailto:DGREVE@mgh.harvard.edu>> P?edm?t: Fw: [Freesurfer] Apply transformation Hello, please, could you help me with this case? What am I doing wrong? Thanks a lot ________________________________ Od: freesurfer-bounces(a)nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu> <freesurfer-bounces(a)nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu>> za u?ivatele Adam Rytina <adam.rytina(a)outlook.cz<mailto:adam.rytina@outlook.cz>> Odesl?no: sobota 15. ?nora 2020 19:52 Komu: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> P?edm?t: Re: [Freesurfer] Apply transformation External Email - Use Caution Thanks, unfortunately, I am making some mistake but I don?t know where. First of all I run autorecon1 on my anatomical T1 data (the orig.mgz image is saved in /usr/local/freesurfer/subjects/anatomical). Then in the /usr/local/freesurfer/data I run mri_robust register command of the T1 and diffusion DWI data. The registration.lta file is saved here. Now I add an anatomical mask "3D_T1_brain_mask.nii" to the same folder /usr/local/freesurfer/data that I want to transform to the anatomical T1 space. In the same /usr/local/freesurfer/data I run : "mri_vol2vol --lta registration.lta --mov 3D_T1_brain_mask.nii --o f-in-anat3.nii --s anatomical --fstarg" To sum up, I am aiming to apply a transformation matrix on the T1 anatomical brain mask and transform it to the T1 space defined by 3D T1 image. The problem is this command transforms orig.mgz file (a skull stripped T1 image) instead of 3D_T1_brain_mask.nii. Please, do you know where I make mistake? Thanks a lot ________________________________ Od: freesurfer-bounces(a)nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu> <freesurfer-bounces(a)nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu>> za u?ivatele Douglas Greve <dgreve(a)mgh.harvard.edu<mailto:dgreve@mgh.harvard.edu>> Odesl?no: sobota 15. ?nora 2020 17:15 Komu: freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> P?edm?t: Re: [Freesurfer] Apply transformation Yes, mri_vol2vol On 2/15/20 11:07 AM, Adam Rytina wrote: External Email - Use Caution Hello all, I want to apply the saved transformation (a transformation matrix 4x4 acquired by registration of an anatomical and a diffusion image) on my input anatomical mask and change a final FOV by specifying a diffusion reference image (its voxels size). It means to apply the same command as the command ApplyXFM in FSL FLIRT. Does this option exist also in Freesurfer? Thanks a lot Regards Adam _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu><mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20200224/7… ------------------------------ Message: 16 Date: Mon, 24 Feb 2020 15:54:49 +0100 From: Marina Fern?ndez <marina.fdez.alvarez(a)gmail.com> Subject: [Freesurfer] skull stripping problem To: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <CAALjZmedHxapja0jycg2bF=JC81kOCqHytmcnM2ziwrX2T_gUA(a)mail.gmail.com> Content-Type: text/plain; charset="utf-8" External Email - Use Caution Dear Freesurfeer experts, After running the recon-all, a part of the temporal lobe of one subject was removed. I used the watershed algorithm to be less agressive in the skull stripping step: recon-all -skullstrip -wsthresh 35 -clean-bm -no-wsgcaatlas -subjid sub_001 And the problem was solved in the brainmask.mgz volume because I can see the temporal lobe completely, but the surfaces are still displaced. In order to correct the surfaces I used the white matter edit tool but there is no change after correcting WM and running the recon-all -autorecon2-wm -autorecon3. I also used control points and but the following error was shown in the terminal when I run the recon-all -autorecon2-cp -autorecon3: recon-all -s sub_001 existed with errors I detected that there are very high values in the white matter of this part of the temporal lobe (even 132), maybe it has something to do. What can I do to solve the problem with this subject? Thank you very much in advance. Best regards, Marina. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20200224/a… ------------------------------ Message: 17 Date: Mon, 24 Feb 2020 09:04:52 -0600 From: Kate Marvel <kmarvel54(a)gmail.com> Subject: Re: [Freesurfer] how to convert the registered file (.lta) into NIfTI format in PETsurfer To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <CAG9yhu7rcBLfPeMo-L9p7iaN7O54Gjm2PB9tJjMtDvSH-Q4kqw(a)mail.gmail.com> Content-Type: text/plain; charset="utf-8" External Email - Use Caution Hi Bruce, Thank you very much Bruce. Kate On Mon, Feb 24, 2020 at 8:50 AM Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> wrote: Hi Kate the .lta format is for a linear registration (in ascii). YOu can just cat it to see the contents - it is not a PET image (which will be stored in .mgz or .nii). mri_convert or mri_vol2vol can be used to apply the registration and/or change the output format (if you specify file.nii or file.nii.gz it will write in Nifti) cheers Bruce On Mon, 24 Feb 2020, Kate Marvel wrote: External Email - Use Caution Hi Douglas, Is there a way to save the registered PET image in NIfTi format instead of .lta? Kate On Mon, Feb 24, 2020 at 8:26 AM Douglas N. Greve <dgreve(a)mgh.harvard.edu wrote: Not sure what you are trying to do. An lta file is a matrix and nifti is a format for storing images. On 2/21/2020 7:52 AM, Kate Marvel wrote: External Email - Use Caution Hi All, How do you convert the registered file (.lta) into NIfTI format in PETsurfer. Thanks, _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- kate _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- kate -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20200224/8… ------------------------------ Message: 18 Date: Mon, 24 Feb 2020 15:50:26 +0000 From: "Russo, Andrew William" <AWRUSSO(a)mgh.harvard.edu> Subject: [Freesurfer] samseg permissions error To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <BL0PR04MB4593810C0E71B357FAEF1011E8120(a)BL0PR04MB4593.namprd04.prod.outlook.com> Content-Type: text/plain; charset="iso-8859-1" Hello Freesurfer Developers, I am trying to use the "samseg" function in /usr/local/freesurfer/dev but do not have permission to access the directory /usr/local/freesurfer/dev/subjects/fsaverage. Is this a restricted directory? ValueError: file /usr/local/freesurfer/dev/subjects/fsaverage/mri/orig.mgz does not exist ERROR: fs_time run_samseg I did not find any related issues with samseg on the archive and I have had it work in the past. Before running samseg I sourced the freesurfer environment: export FREESURFER_HOME=/usr/local/freesurfer/dev source $FREESURFER_HOME/SetUpFreeSurfer.sh (Using Freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0) Thank you in advance, Andrew ____________ Andrew Russo Clinical Research Coordinator Multiple Sclerosis Imaging Lab Massachusetts General Hospital 149 13th Street | Boston, MA 02129 617-726-7531 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20200224/9… ------------------------------ Message: 19 Date: Mon, 24 Feb 2020 16:15:20 +0000 From: "Harrigan, Timothy P." <Timothy.Harrigan(a)jhuapl.edu> Subject: [Freesurfer] Registration error To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <1fb1864f806f4eb89ba47f72b3d2a4be(a)aplex11.dom1.jhuapl.edu> Content-Type: text/plain; charset="us-ascii" External Email - Use Caution Hi, I'm trying to learn to use Freesurfer to see if I can use it for some academic work on TBI. I downloaded it to a spare laptop at home, and filled out the registration form, and I got a message that stated "Registration Error: Spammer. Go Away." How could I address this? Thanks Tim Timothy P. Harrigan ScD Research and Exploratory Development Division Johns Hopkins University Applied Physics Laboratory Phone: 240-228-5943 Cell/Text: 240-280-9444 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20200224/c… ------------------------------ _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer End of Freesurfer Digest, Vol 192, Issue 32 *******************************************

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