Freesurfer

freesurfer@nmr.mgh.harvard.edu

16 participants
30065 discussions

Freeview in FreeSurfer 6.0
by Wu Jianxiao (Jadecci) 21 Aug '17

21 Aug '17

Dear FreeSurfer team, I was viewing MNI152 template from FSL in freeview using FreeSurfer 6.0, and somehow there was a shift between 1mm and 2mm template. The problem does not show in FreeSurfer 5.3. Is there an error with freeview in FS6 or did the command change? The command I used is as follow: freeview $FSL_DIR/data/standard/MNI152_?mm_brain.nii.gz Thank you! Wu Jianxiao Department of Physiology & Department of Electrical and Computer Engineering National University of Singapore

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Custom intensities in aparc+aseg
by Martin Kavec 20 Aug '17

20 Aug '17

Dear all, I ran my subjects through recon-all successfully. I am in a need to have custom intensities for segmentation and parcellation in aparc+aseg. Say, 10 - ventricles, 20 - amygdala, 30 - putamen, ... I would appreciate advice on how I could achieve that. Thanks in advance, Martin

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Freesurfer manual edit problems
by Chethana Kishore 19 Aug '17

19 Aug '17

sir/maam, i request your help in solving in a query of mine. while the manual edit is being done , and we use the "save the main volume" button to save the progress. but subsequently on opening the image to further our edits it appears as a very brightly intense image and difficulty in differentiating the grey/white matter leading it to be unuseable. can u please suggest how to solve this problem? Thanks and regards Chethana K

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pet surfer
by John Anderson 18 Aug '17

18 Aug '17

Hi Dr Greve, I followed the steps in WIKI to do SUV-surface based analyses + PVC. I have the following questions and I highly appreciate your input: 1. Why the dimension of the images (mgx.gm, mgx.ctx.gm and mgx.ctx.subgm) is not like the original SUV image that has been fed to the pipeline. i.e. I start with image-dimensions 128X128X128 : 2X2X2 and end up with 79X113X102 : 2X2X2 Also FOV is different as well between the original SUV image /256/ and the output mgx images /158/. How this happen? I am I doing something wrong? 2. Some voxels in the mgx images has negative signal intensity. is this normal? Thank you for any clarification. John

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Solution found for: recon_all error on MacOS 10.12.13 Sierra
by Alissa Stafford 18 Aug '17

18 Aug '17

Hi, I was having the same problem as described here: https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2017-March/050544.ht… when I was trying to run selxavg3-sess. I realize that this error was mentioned in the release notes and that the potential fix was sourcing freesurfer and then typing "sudo -E fs_update” into terminal. fs_update seemed to run without any problems, but did not fix the lazy symbol binding error. I did end up fixing the problem after many hours. My fix: I went to http://hpc.sourceforge.net/, downloaded gcc-7.1-bin.tar.gz and followed the instructions on the webpage. I found this error and solution described for another software package here: https://www.ncl.ucar.edu/Download/macosx.shtml#InstallCompilers. I wish I understood compilers enough to figure out exactly what is going on, but I only know that this fixed my error. I subscribe to the freesurfer emails, but don’t think I am able to add to an old thread or anything so wanted to contact you two directly. I am hoping you could add this to the original thread or the release notes so that others can use this if fs_update does not work for them either. Best, Alissa

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Curvature in FreeSurfer
by Kasper Jessen 18 Aug '17

18 Aug '17

Dear FreeSurfer, We have been discussing the mean curvature provided by FreeSurfer software. As i understand the mean curvature is measured as 1/r and has a unit of 1/mm. But a) What is the curvature an expression of? Is it the degree of folding of the brain and is it the white matter surface or pial surface? b) An increased value of mean curvature - does that mean an increase in folding of the brain? c) What is the expected association between the mean curvature; and cortical thickness and surface area? Any suggestions of litterature? I have read through two webpages below, but unfortunately the confusion still exist :-) http://mathworld.wolfram.com/MeanCurvature.html http://mathworld.wolfram.com/GaussianCurvature.html I am aware that this may be a simple question but the different measures of curvature (fx. gaussian vs mean curvature) made us discuss the differences and what it is an expression of. Best regards, Kasper

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mris_register vs surfreg
by Juergen Haenggi 18 Aug '17

18 Aug '17

Dear FS experts we constructed a customized template (using make_average_subject) to register the individual surfaces on that template instead of the fsaverage template. we recognized that there are, at least, two ways to do this either using mris_register or using surfreg. Is there any difference between the two tools and which tool is recommended? Thanks in advance Regards Jürgen ----------------------------------------------------------------------------------------------------- University of Zurich Dr. Jürgen Hänggi, Ph.D. Department of Psychology Division Neuropsychology Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi(a)psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) This email (and any attachment/s) contains confidential and/or privileged information. If you are not the intended recipient (or have received this email in error) please notify the sender immediately and destroy this email. Any unauthorised copying, disclosure or distribution of the material in this email is strictly forbidden. -----------------------------------------------------------------------------------------------------

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recon-all with multiple images with different voxel sizes
by Gustav Mårtensson 18 Aug '17

18 Aug '17

Hi! We are processing images using recon-all -all -3T -mprage -qcache -hippocampal-subfields-T1 -brainstem-structures We've encountered an issue when we're trying to use multiple inputs (acquired at the same timepoint and with comparable quality). The issue is due to the two images having slightly different voxel sizes: ERROR: MultiRegistration:: loadMovables: images have different voxel sizes. Currently not supported, maybe first make conform? Debug info: size(1) = 1, 1, 1.2 size(0) = 1.05469, 1.05469, 1.2 MultiRegistration::loadMovables: voxel size is different /tmp/adni/freesurfer/6.0.0/0a9cfea9-7668-4a2c-927c-378ff5109fe1/mri/orig/002.mgz. which we can see confirm from the DICOMs in the PixelSpacing tag. So, we have three questions: 1. In general, should using multiple images jointly for processing yield better results? 2. If so, what would you suggest for our case with images of two different protocols? Any flags that could help? Or perform coregistration pre-run? 3. Let's say we have a cohort where all subjects have two T1-images but where some subjects have two images acquired with slightly different protocols (e.g. different voxel sizes) and jointly processing can't be done. Do you think it is better to combine images in as many cases we can (and use only a single image for the remaining cases) or only use one image per case for all cases? In other words, we are wondering if it could bias our data set if the subset of that has been multi-image processed is "better" than those processed with only a single image. We're running on FS6 (freesurfer-Linux-centos6_x86_ 64-stable-pub-v6.0.0-2beb96c) and I've attached a log file from one of the failing cases. Thank you for your help! Best regards, -- Gustav Mårtensson | PhD student Division of Clinical Geriatrics Department of Neurobiology, Care Sciences and Society Karolinska Institutet ___________________________________ Karolinska Institutet – a medical university

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Fwd: Antwort: Re: t1 mri_convert fails
by Dino Digma 17 Aug '17

17 Aug '17

Hi Bruce, I'm having very similar to this thread. How do I know the proper value to re-scale them by? Sorry if this is a basic question - I'm very new to FreeSurfer. Thanks! Best, Dino you need to scale them. WHy do you have negative values? I would scale them so that the min is 0 and the mean is around 100 or so. In matlab it would be something like: first copy 001.mgz to 001.orig.mgz thne in matlab do: [v,M,mr] = load_mgh('001.orig.mgz') ; v = (v - min(v(:))) * 100; save_mgh(v, '001.mgz', M,mr); I'm guessing about the 100. You could use hist to check where the peak of the distribution is and be more accurate if you want cheers Bruce On Tue, 18 Jul 2017, clemens.schroe...(a)uzh.ch wrote: The rawavg.mgz is not empty. Many values are around 0 but there are also values between 0.2 and 0.5 (and values between -0.4 and -0.5 in CSF). It really seems like orig.mgz is all 0. How low do the values need to be for the conversion to set them to 0? Is there anything I can do to use recon-all on my data? -----freesurfer-boun...(a)nmr.mgh.harvard.edu schrieb: -----An: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Von: Bruce Fischl Gesendet von: freesurfer-boun...(a)nmr.mgh.harvard.edu Datum: 18.07.2017 16:11 Betreff: Re: [Freesurfer] t1 mri_convert fails is the rawavg.mgz also empty? The TE=0 only means that nifti doesn't store the MR parameters - it shouldn't change anything. If the rawavg.mgz is not empty look at what the values are - maybe they (or the nifti) are too low and the conversion to uchar sets them to 0? On Tue, 18 Jul 2017,clemens.schroe...(a)uzh.ch wrote: > Hello Developers > > I am trying to run recon-all on a number of MP2RAGE T1 images but I fail. > > Using tkmedit, I noticed that orig/001.mgz looks fine but orig.mgz is all-0. > Also, mri_convert assumes TE=0, which is false. > > Do you have any advice for me? > > The recon-all.log is attached > > FreeSurfer freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c > My OS is OSX El Capitan 10.11.6 > uname -a: Darwin MAC15-0004.local 15.6.0 Darwin Kernel Version 15.6.0: Tue > Apr 11 16:00:51 PDT 2017; root:xnu-3248.60.11.5.3~1/RELEASE_X86_64 x86_64 > > > Here is the print from the command: > > MAC15-0004:t1 clschr$ recon-all -s example -i example.nii -all > -hippocampal-subfields-T1 > Subject Stamp: > Current Stamp: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c > INFO: SUBJECTS_DIR is /Users/clschr/Desktop/7T/t1 > Actual FREESURFER_HOME /Applications/freesurfer > Darwin vpn-89-206-117-41.uzh.ch 15.6.0 Darwin Kernel Version 15.6.0: Tue Apr > 11 16:00:51 PDT 2017; root:xnu-3248.60.11.5.3~1/RELEASE_X86_64 x86_64 > /Users/clschr/Desktop/7T/t1/example > \n mri_convert /Users/clschr/Desktop/7T/t1/example.nii > /Users/clschr/Desktop/7T/t1/example/mri/orig/001.mgz \n > mri_convert.bin /Users/clschr/Desktop/7T/t1/example.nii > /Users/clschr/Desktop/7T/t1/example/mri/orig/001.mgz > $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ > reading from /Users/clschr/Desktop/7T/t1/example.nii... > niiRead(): NIFTI_UNITS_UNKNOWN, assuming mm > TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 > i_ras = (-0.999967, 0.00331038, 0.00735774) > j_ras = (0.00506133, 0.967573, 0.252542) > k_ras = (0.00628314, -0.252571, 0.967558) > writing to /Users/clschr/Desktop/7T/t1/example/mri/orig/001.mgz... > #-------------------------------------------- > #@# MotionCor Tue Jul 18 09:20:32 CEST 2017 > Found 1 runs > /Users/clschr/Desktop/7T/t1/example/mri/orig/001.mgz > Checking for (invalid) multi-frame inputs... > WARNING: only one run found. This is OK, but motion > correction cannot be performed on one run, so I'll > copy the run to rawavg and continue. > \n cp /Users/clschr/Desktop/7T/t1/example/mri/orig/001.mgz > /Users/clschr/Desktop/7T/t1/example/mri/rawavg.mgz \n > /Users/clschr/Desktop/7T/t1/example > \n mri_convert /Users/clschr/Desktop/7T/t1/example/mri/rawavg.mgz > /Users/clschr/Desktop/7T/t1/example/mri/orig.mgz --conform \n > mri_convert.bin /Users/clschr/Desktop/7T/t1/example/mri/rawavg.mgz > /Users/clschr/Desktop/7T/t1/example/mri/orig.mgz --conform > $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ > reading from /Users/clschr/Desktop/7T/t1/example/mri/rawavg.mgz... > TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 > i_ras = (-0.999967, 0.00331038, 0.00735774) > j_ras = (0.00506133, 0.967573, 0.252542) > k_ras = (0.00628314, -0.252571, 0.967558) > changing data type from float to uchar (noscale = 0)... > MRIchangeType: Building histogram > Reslicing using trilinear interpolation > writing to /Users/clschr/Desktop/7T/t1/example/mri/orig.mgz... > \n mri_add_xform_to_header -c > /Users/clschr/Desktop/7T/t1/example/mri/transforms/talairach.xfm > /Users/clschr/Desktop/7T/t1/example/mri/orig.mgz > /Users/clschr/Desktop/7T/t1/example/mri/orig.mgz \n > INFO: extension is mgz > #-------------------------------------------- > #@# Talairach Tue Jul 18 09:20:41 CEST 2017 > /Users/clschr/Desktop/7T/t1/example/mri > \n mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 > --proto-iters 1000 --distance 50 \n > /Users/clschr/Desktop/7T/t1/example/mri > /Applications/freesurfer/bin/mri_nu_correct.mni > --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 > --distance 50 > nIters 1 > $Id: FreeSurferEnv.csh,v 1.89 2016/06/09 14:54:31 zkaufman Exp $ > Darwin vpn-89-206-117-41.uzh.ch 15.6.0 Darwin Kernel Version 15.6.0: Tue Apr > 11 16:00:51 PDT 2017; root:xnu-3248.60.11.5.3~1/RELEASE_X86_64 x86_64 > Tue Jul 18 09:20:41 CEST 2017 > Program nu_correct, built from: > Package MNI N3, version 1.12.0, compiled by ni...(a)gust.nmr.mgh.harvard.edu > (x86_64-apple-darwin11.4.2) on 2015-06-19 at 15:37:08 > /usr/bin/bc > tmpdir is ./tmp.mri_nu_correct.mni.37996 > /Users/clschr/Desktop/7T/t1/example/mri > mri_convert orig.mgz ./tmp.mri_nu_correct.mni.37996/nu0.mnc -odt float > mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.37996/nu0.mnc -odt float > $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ > reading from orig.mgz... > TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 > i_ras = (-1, -5.82077e-10, -4.65661e-10) > j_ras = (-4.65661e-10, 0, -1) > k_ras = (3.49246e-10, 1, 1.49012e-08) > changing data type from uchar to float (noscale = 0)... > writing to ./tmp.mri_nu_correct.mni.37996/nu0.mnc... > > -------------------------------------------------------- > Iteration 1 Tue Jul 18 09:20:45 CEST 2017 > nu_correct -clobber ./tmp.mri_nu_correct.mni.37996/nu0.mnc > ./tmp.mri_nu_correct.mni.37996/nu1.mnc -tmpdir > ./tmp.mri_nu_correct.mni.37996/0/ -iterations 1000 -distance 50 > [cls...@vpn-89-206-117-41.uzh.ch:/Users/clschr/Desktop/7T/t1/example/mri/] > [2017-07-18 09:20:45] running: > /Applications/freesurfer/mni/bin/nu_estimate_np_and_em -parzen -log > -sharpen 0.15 0.01 -iterations 1000 -stop 0.001 -shrink 4 -auto_mask > -nonotify -b_spline 1.0e-7 -distance 50 -quiet -execute -clobber -nokeeptmp > -tmpdir ./tmp.mri_nu_correct.mni.37996/0/ > ./tmp.mri_nu_correct.mni.37996/nu0.mnc > ./tmp.mri_nu_correct.mni.37996/nu1.imp > > Error: Composite mask volume is empty. Check for one of the following: > 1) the user supplied mask is empty (all zeros) > 2) the values within the region of interest are entirely less than one > 3) the user supplied background threshold is too high > 4) the intersection of the various masking options yields an empty mask > nu_correct: crashed while running nu_estimate_np_and_em (termination > status=65280) > ERROR: nu_correct > Darwin vpn-89-206-117-41.uzh.ch 15.6.0 Darwin Kernel Version 15.6.0: Tue Apr > 11 16:00:51 PDT 2017; root:xnu-3248.60.11.5.3~1/RELEASE_X86_64 x86_64 > > > Here is the header information of the image: > > % vpn-89-206-116-146:t1 clschr$ fslhd example.nii > filename example.nii > > sizeof_hdr 348 > data_type FLOAT32 > dim0 3 > dim1 180 > dim2 256 > dim3 256 > dim4 1 > dim5 1 > dim6 1 > dim7 1 > vox_units Unknown > time_units Unknown > datatype 16 > nbyper 4 > bitpix 32 > pixdim0 0.000000 > pixdim1 0.800000 > pixdim2 0.781000 > pixdim3 0.781000 > pixdim4 0.006900 > pixdim5 0.000000 > pixdim6 0.000000 > pixdim7 0.000000 > vox_offset 352 > cal_max 0.0000 > cal_min 0.0000 > scl_slope 0.000000 > scl_inter 0.000000 > phase_dim 0 > freq_dim 0 > slice_dim 0 > slice_name Unknown > slice_code 0 > slice_start 0 > slice_end 0 > slice_duration 0.000000 > time_offset 0.000000 > intent Unknown > intent_code 0 > intent_name T1TFE > intent_p1 0.000000 > intent_p2 0.000000 > intent_p3 0.000000 > qform_name Scanner Anat > qform_code 1 > qto_xyz:1 -0.799974 0.003954 0.004913 71.792442 > qto_xyz:2 0.002648 0.755674 -0.197258 -65.335892 > qto_xyz:3 0.005892 0.197235 0.755663 -137.084869 > qto_xyz:4 0.000000 0.000000 0.000000 1.000000 > qform_xorient Right-to-Left > qform_yorient Posterior-to-Anterior > qform_zorient Inferior-to-Superior > sform_name Scanner Anat > sform_code 1 > sto_xyz:1 -0.799974 0.003953 0.004907 71.792442 > sto_xyz:2 0.002648 0.755674 -0.197258 -65.335892 > sto_xyz:3 0.005886 0.197235 0.755663 -137.084869 > sto_xyz:4 0.000000 0.000000 0.000000 1.000000 > sform_xorient Right-to-Left > sform_yorient Posterior-to-Anterior > sform_zorient Inferior-to-Superior > file_type NIFTI-1+ > file_code 1 > descrip phase=-y;TE=2.5;time=20170201134952; > aux_file ;Philips;WIP MP2RAGE 0p > > _______________________________________________ Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine athttp://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. _______________________________________________ Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine athttp://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

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FS-FAST outputs is X.mat used? {Disarmed}
by Kevin Aquino 17 Aug '17

17 Aug '17

Dear all, I have a question regarding the output from selxavg3-sess. I noticed that within an analysis there is a X.mat that looks like a design matrix -- however is this used at any stage of the analysis? The help message in selxavg3-sess reads: "This program will construct the design matrix for each run, fit the GLM, save regression coefficients, compute contrasts and significances of contrasts. The runs are combined together so the output is the average across runs (some would call this a "second-level" analysis)." so this looks like that x.mat is constructed and used for each run (and not saved by default). This then looks like X.mat is not used in the analysis -- it is just there for illustrative purposes? or have I misinterpreted the help message. If this is correct (i.e. X.mat in the output is not used) when making contrasts using mkcontrast-sess, is there a way to parametrically modulate each run? e.g. to model behavioural changes per run etc. Cheers, *Dr Kevin Aquino* Research fellow, Sir Peter Mansfield Magnetic Resonance Center, The University of Nottingham. Honorary Research Fellow School of Physics, Faculty of Science, University of Sydney *E* Kevin.aquino(a)nottingham.ac.uk, aquino(a)physics.usyd.edu.au | *W* https://kevinaquino.github.io <http://www.physics.usyd.edu.au/~aquino/> ---------------------------------------------- The brain is a wonderful organ. It starts working the moment you get up and does not stop until you get into the office. - Robert Frost CRICOS 00026A This email plus any attachments to it are confidential. Any unauthorised use is strictly prohibited. If you receive this email in error, please delete it and any attachments. Please think of our environment and only print this e-mail if necessary.

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