Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30090 discussions

bbregister + mri_vol2vol different results
by Paul Glad Mihai 18 Jul '17

18 Jul '17

Hello, I'm getting two different results from the coregistration step. When I run bbregister on the mean epi it coregisters properly and writes out _bbreg.nii. The next step involves registering the realigned epi time series to the T1 image using the same transform matrix calculated from the mean image. But the results fail miserably. I've attached some sample images. I came across the same result after transforming the matrix it to ITK space and applying the transform using ANTs' applyTransform, which tells me that the ITK conversion works, but this registration goes wrong. Or I may not really understand what I'm doing, lol. Here are the commands: bbregister --t2 --epi-mask --init-header --fslmat /data/pt_nmc002/TDMGB_FMRI_coreg/tmp/preproc/_subject_id_sub-01/bbreg/mapflow/_bbreg0/meanusub-01_task-spespk_run-01_bold_bbreg_sub-01.mat --reg /data/pt_nmc002/TDMGB_FMRI_coreg/tmp/preproc/_subject_id_sub-01/bbreg/mapflow/_bbreg0/meanusub-01_task-spespk_run-01_bold_bbreg_sub-01.dat --o /data/pt_nmc002/TDMGB_FMRI_coreg/tmp/preproc/_subject_id_sub-01/bbreg/mapflow/_bbreg0/meanusub-01_task-spespk_run-01_bold_bbreg.nii --mov /data/pt_nmc002/TDMGB_FMRI_coreg/tmp/preproc/_subject_id_sub-01/bbreg/mapflow/_bbreg0/meanusub-01_task-spespk_run-01_bold.nii --s sub-01 mri_vol2vol --fsl /data/pt_nmc002/TDMGB_FMRI_coreg/tmp/preproc/_subject_id_sub-01/bbreg/mapflow/_bbreg0/meanusub-01_task-spespk_run-01_bold_bbreg_sub-01.mat --mov /data/pt_nmc002/TDMGB_FMRI_coreg/tmp/preproc/_subject_id_sub-01/coreg_func/mapflow/_coreg_func0/usub-01_task-spespk_run-01_bold.nii --targ /data/pt_nmc002/TDMGB_FMRI_coreg/tmp/preproc/_subject_id_sub-01/brainextract/sub-01_acq-T1w_brain.nii.gz --o /data/pt_nmc002/TDMGB_FMRI_coreg/tmp/preproc/_subject_id_sub-01/coreg_func/mapflow/_coreg_func0/usub-01_task-spespk_run-01_bold_warped.nii Regards, Glad -- Paul Glad Mihai, PhD Independent Research Group "Neural Mechanisms of Human Communication" Max Planck Institute for Human Cognitive and Brain Sciences Stephanstraße 1A, 04103 Leipzig, Germany Phone: +49 (0) 341-9940-2478 E-mail: mihai(a)cbs.mpg.de

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how to extract data that are removed effects of covariates
by hiroki.sato＠med.tohoku.ac.jp 18 Jul '17

18 Jul '17

Dear experts, I’m new to analysis with use of the Freesurfer. I compared grey matter thickness between two groups using Qdec with several covariates (i.e. nuisance factors) such as age, gender and intracranial volume (ICV). I found regions that significantly differed between the two groups. I would like to ask about how to extract data in these regions in each subject related with the effect of groups after effects of covariates were removed. On the discussion forum, I found the solutions to extract raw data in the ROIs. But in the communication, they did not discuss about how to remove covariate’s effects. I would appreciate if you could let me know about how to extract values related with the effect of group or how to remove covariate’s effects from raw data. Thank you for your guidance! Best, Hiroki

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RBV PVC: Saving output file before upsampling
by SudEEpti 18 Jul '17

18 Jul '17

Hello, Is there a way to save the PVC (RBV) output in native PET resolution, before upsampling? Would you also be able to share the command that is used for upsampling? I would like to play with a different type of interpolation. Thank you very much. Su

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t1 mri_convert fails
by clemens.schroeder＠uzh.ch 18 Jul '17

18 Jul '17

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 nicks(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 [clschr@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

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vertex coordinates and thickness in mgh file
by Giuliano Giari 18 Jul '17

18 Jul '17

Dear Freesurfer users, i have to run vertex by vertex analysis of cortical thickness across subjects. As of now i have processed my data using the recon-all command and then the mris_preproc (separately for each hemisphere). I have now two .mgh file but i don’t know where to find the info that i need, namely the cortical thickness at each vertex and their coordinates. Thank you, Giuliano

2 1

TalAviQA and mris_jacobian
by Helfand, Alexander I 17 Jul '17

17 Jul '17

Hi FreeSurfer Team, I was hoping I might be able to get some information about TalAviQA. I have read that this number is a spatial correlation between the input image and the image transformed to the Talairach atlas. Is that correct? Can you tell me any more about how this correlation is calculated? I hope this isn't a silly question, but besides the Euler numbers and the mris_jacobian command, are there any other quantitative metrics of how much warping was necessary for a particular subject's recon-all? Also, are there multiple ways to run mris_jacobian such that you can get information beyond lh/rh.white.preaparc? Might you be able to offer any hints as to other files to feed the mris_jacobian command besides 'mris_jacobian ../surf/l(r)h.white.preaparc ../surf/l(r)h.sphere.reg ../surf/l(r)h.jacobian_white' Finally, is there a complete set of documentation somewhere for the QA Tools package of scripts? Are these scripts up to date and compatible with Freesurfer 6? https://surfer.nmr.mgh.harvard.edu/fswiki/QATools suggests that v1.1 came out in 2012 and the current release for download is v1.2... Thanks for your time, thanks for your efforts creating and maintaining Freesurfer! Alex

2 1

spmregister
by John Anderson 17 Jul '17

17 Jul '17

Dear Freesurfer experts, I want to derive registration matrix between pcasl image and the structural space in Freesurfer (i.e. orig.mgz) If I open orig.mgz and the pcasl image in Freesurefr I see overlap between the images (attached Figure1). When I use "spmregister" as follow: spmregister --mov perfusion_calib.nii.gz --s SUBJ --reg reg.dat --fsvol orig --o CBF_T1.nii Then visualize "CBF_T1" using freeview I see mis-registration (attached Figure2) Please what I am doing wrong? Thank you for any guidance Jon

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qcache ERROR on longitudinal image processing with FreeSurfer v6.0
by Lisa Delalande 17 Jul '17

17 Jul '17

Hello everyone, I'm using the new version of FreeSurfer processing with longitudinal image processing. And at the step -base after a recon-all processing i would like to make a qcache processing but it doesn't work... "cannot find [...]/template_1-01VALAL/surf/lh.w-g.pct.mgh" (See in attachment longitudinal image processing withFSv6.0 first and FSv5.3). Thanks in advance, Best regards, Lisa

2 1

Custom Annotation: 1st Annot Visible in TKSurfer but not Freeview
by Ursula Tooley 17 Jul '17

17 Jul '17

Hi FreeSurfer Experts, I’ve created a custom annotation file in MATLAB, using read_annotation.m and write_annotation.m, relabeling the Glasser parcellation regions. It seems to display as expected in tksurfer and tkmedit, but in freeview the first annotation is completely transparent (see images below), although if I hover my mouse over the area, it’s labeled with the correct struct_name. I’ve changed the alpha value in the annotation file and see no difference in freeview, and also given some previous listserv posts tried changing the RGB values for that first annotation in colortable.table. View in tksurfer: tksurfer fsaverage lh inflated -annotation my_annotation.annot View in freeview: freeview $SUBJECTS_DIR/fsaverage/surf/lh.inflated:annot=my_annotation.annot Any help would be greatly appreciated. I’m running FS 6.0, Freeview V2, this occurs both locally on my OSX El Capitan and on an HPC running Linux Centos. Thanks in advance, Ursula --- Ursula Tooley Ph.D. Student Neuroscience Graduate Group University of Pennsylvania utooley(a)gmail.com 202.413.5627

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Re: [Freesurfer] FS Version 6 Long Processing
by Allison Rainford 17 Jul '17

17 Jul '17

Hi FreeSurfer Team, My lab has recently begun editing longitudinal data in version 6 and have found that we cannot use the same flags for -autorecon2 as we did when running longs in version 5.1. Typically, after making any necessary edits to a long, we run -autorecon2-pial -autorecon3. This flag hasn't been successful in version 6, producing an error message that the flag is unrecognized. Because we still only require some brainmask edits on the longs, we would like to know how we can continue to run these to process only pial. All help is greatly appreciated! Allison

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