Freesurfer August 2017

freesurfer@nmr.mgh.harvard.edu

145 participants
233 discussions

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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dat to lta
by John Anderson 17 Aug '17

17 Aug '17

Hi FS experts, Is there any way to convert the registration matrix reg.dat to reg.lta? Thank you John

3 4

mask alignment problem/mri_mask
by Yagmur Ozdemir 19 17 Aug '17

17 Aug '17

Hello freesurfer experts, A volume file I want to save as a mask(the orange/red shaded areas in the picture) on top of my volume file does not align as seen in the picture. I have used mri_vol2vol to align the mask to my native volume but apparently it did not work out. I am trying to correct this by using mri_mask now; I tried to use the option -xform %s which apparently applies the LTA transform to align mask to input volume, but now I get this error; >>lab@lab-ThinkStation-E31:~/Desktop/freesurfer/subjects/sub-01_MW/mri$ mri_mask -xform %s MW_IIHC_aTAL.nii native.areas_MW_aTAL.nii MW_aTAl_masked.nii transform file name is %s WARNING: hdr.dim[4] = 0 (nframes), setting to 1 niiRead(): NIFTI_UNITS_UNKNOWN, assuming mm DoAbs = 0 Apply the given LTA xfrom to the mask volume Reading transform ... ltaReadFile(%s): can't open file No such file or directory mri_mask.bin: could not read transform file %s No such file or directory I would deeply appreciate if someone could help me sort out this mess. Thank you all! Best, Idil

3 14

Using own parcellation atlas
by Julie Hall 17 Aug '17

17 Aug '17

Hi experts, I would like to use a different atlas other than the 'default' Freesurfer atlases, namely the Gordon Parcellation (surface based parcellation of 333 ROIs of the cortex) to segment my T1 datasets. So I can go on to use these segmentations for DTI connectome analysis using MRTrix (or MatLab). I have two questions: - I have this atlas as a nifti file. Do I need to transform this atlas into a different file for it to run in freesurfer? - Can I run this step in autorecon3 (step 28)? Or should I rerun recon-all all together? If so, could you help me with what commands I need to run (mris_ca_train?)” Thank you, Julie

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-nuiterations and -norm3diters under FreeSurfer 6.0
by Antonio Algaze Beato 17 Aug '17

17 Aug '17

Hi, I have a question regarding -nuiterations and -norm3diters. I would like to get a feel for the options available for fine-tuning the intensity normalization in FreeSurfer 6.0. I've seen mention of -nuiterations on some posts. Is this still an option in FreeSurfer 6.0? The reason I ask is because under the "Expert Preferences" section of recon-all -help there's only mention of "-norm3diters". However, further down, under the second "Expert Preferences" section, there's a description of -nuiterations as well as -norm3diters. Thanks!

2 1

Skullstriping problems
by MATEUS ROZALEM ARANHA 17 Aug '17

17 Aug '17

Hi, I had problems with skullstriping. I ran recon-all and part of the skull is being considered as cortex in the segmentation. I tried to fix this using: *recon-all -skullstrip -wsthresh 50 -clean-bm -subjid <subject name>* and than *recon-all -autorecon-pial -subjid <subject name>* But nothing changed. Do I need to run recon-all all over? Thanks, Mateus

2 4

Re: [Freesurfer] Response to Freesurfer list email
by Bruce Fischl 17 Aug '17

17 Aug '17

Hi Rose, you should post to the list as you will get better and faster answers (although this time I know it didn't work so well for you). I believe Martin published these numbers Bruce On Thu, 17 Aug 2017, Van Der Deijl, Rosanne wrote: > Dear Bruce, > > I think my message might have gotten lost in the Freesurfer mailing list > stream, so that's why I'm sending it to you again. Thank you in advance for > your help! > > Date: Mon, 14 Aug 2017 14:08:24 +0000 > From: "Van Der Deijl, Rosanne" <RVANDERDEIJL(a)mgh.harvard.edu> > Subject: Re: [Freesurfer] test-retest variability small subcortical > regions > To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: > <1D58C89E05A85B4E9512CDEA158803141CB99976(a)PHSX10MB5.partners.org> > Content-Type: text/plain; charset="iso-8859-1" > > Hi Bruce, > > I mean for the longitudinal analysis. > Forgot to mention this, sorry! > > Kind regards, > > Rose > > Date: Fri, 11 Aug 2017 12:39:58 -0400 (EDT) > From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] Test-retest reliability small subcortical > regions > To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: > <alpine.LRH.2.20.1708111239430.24300(a)door.nmr.mgh.harvard.edu> > Content-Type: text/plain; charset=US-ASCII; format=flowed > > Hi Rose > > do you mean cross-sectional or longitudinal analysis? > > cheers > Bruce > > On Fri, 11 Aug 2017, > Van Der Deijl, Rosanne wrote: > > > Dear Freesurfer team, > > > > I was wondering what the test-retest reliability is of comparing small > > regions in the subcortical volume, e.g. the amygdala. Has this improved > with > > the 6.0 version? > > > > Thank you! > > > > Kind regards, > > > > Rose > > >

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Freesurfer August 2017