Freesurfer November 2017

freesurfer@nmr.mgh.harvard.edu

110 participants
198 discussions

Merging two groups
by Ramesh Babu 01 Dec '17

01 Dec '17

Hi, I have done recon-all -all processing for 2 groups in separate subjects directories. I want to put all subjects in one dkirectory. Should I copy paste all subject’s folders in one directory or is there any others steps to merge? Thanks in advance RB

2 5

GPU compile cuda8/centos7
by Meij, Henk 30 Nov '17

30 Nov '17

Just wanted to report back a success. I had to do some fixes so hope this helps anybody. My gpus are GTX1080Ti and the CPU involved is E5-2620 dual 10 core on this server. The vanilla cpu recon-all finished in 7 hours, the gpu run finished in 4.3 hours. Q: I seem to not have any errors or indications why mri_glmfit or mri_robust_register cuda binaries did not compile. Any ideas? -Henk In configure file (from previous post) comment out the with_cuda="" line https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2016-June/046236.html CUDA_DIR="" with_cuda="" In utils/mrifilter.c uncomment line defining 'int width, weight, height' above the test if (width <=1 || height <=1 || depth <=1) on line 3005 then find Makefiles with incorrect gpu arch for the gpu packages change architecture from sm_?? to sm_61 (multiple times per file) which nvcc export PATH=/usr/local/cuda/bin:$PATH locate libcuda.so export LD_LIBRARY_PATH=/usr/lib64:/usr/local/cuda/lib64:$LD_LIBRARY_PATH ./configure --disable-Werror --with-pkgs-dir=/usr/local/centos6-x86_64-packages --prefix=/usr/local/freesurfer-6.0.0 --with-cuda=/usr/local/cuda make clean make -j 4 make install yields ./bin/mris_flatten_cuda ./bin/mris_sphere_cuda ./bin/mris_fix_topology_cuda ./bin/mri_segstats_cuda ./bin/mri_em_register_cuda ./bin/mri_vol2vol_cuda ./bin/mris_inflate_cuda ./bin/mri_ca_register_cuda

3 6

error hipp subfields
by John Papatriantafyllou 30 Nov '17

30 Nov '17

dear Fs experts i have the whole process to get the hipp subfields. But after some mr's that are processed well i get an error (attachment) I have to do the whole process from the beggining And so on Is there an answer? John <https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campai…> Virus-free. www.avast.com <https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campai…> <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>

3 5

[Re] medial wall label in Freesurfer 6
by M del Mar Velasco 30 Nov '17

30 Nov '17

Hi, I have installed the patch and it doesn't fix the label files problem. We have tried make_average_subject with the other 56 subjects and Medial_wall.label contains about 300 vertexs. It is very different from the other 60 subjects. Nevertheless, we have also repeated the test with Freesurfer 5.3 and there is not any problem, all 116 subjects works fine. Best, M del Mar

2 1

Trouble building 6.0.0 on centos7
by Sol Jerome 30 Nov '17

30 Nov '17

Hi, I'm trying to build freesurfer on centos7 and I'm pretty sure that this failure is due to a missing build dependency. Can someone please help me determine what I'm missing? Making all in lta_convert make[2]: Entering directory `/builddir/build/BUILD/freesurfer-6.0.0/lta_convert' make[2]: Leaving directory `/builddir/build/BUILD/freesurfer-6.0.0/lta_convert' make[2]: *** No rule to make target `lta_convert.help.xml.h', needed by `all'. Stop. make[1]: *** [all-recursive] Error 1 make[1]: Leaving directory `/builddir/build/BUILD/freesurfer-6.0.0' make: *** [all] Error 2 Thanks, Sol

2 7

TRACULA error "R: Subscript out of range"
by Anna Mynick 30 Nov '17

30 Nov '17

Hi all, I’m trying to run TRACULA on a single subject’s data, but trac-all -prep is exiting with the output below. Most notably, I think, is the section of the output that says "R: Subscript out of range.” repeatedly and then the section afterwards that says “keeping frames 0 1 2 3 4 5 6 7 8 9 / ERROR: valid frame numbers are between 0 and 0”. Does anyone have thoughts on what might be going on here? I’ve attached my bvecs and bvals too, in case there is trouble there too. Thanks very much for any help. Best, Anna —————————————————— INFO: SUBJECTS_DIR is /mindhive/nklab/u/amynick/Tracula/Tracula_trio/diffusion_recons INFO: Diffusion root is /mindhive/nklab/u/amynick/Tracula/Tracula_trio//diffusion_tutorial Actual FREESURFER_HOME /cm/shared/openmind/freesurfer/6.0.0 INFO: current FREESURFER_HOME does not match that of previous processing. Current: /cm/shared/openmind/freesurfer/6.0.0 Previous: /software/pkg/freesurfer/freesurfer-6.0.0 trac-preproc -c /mindhive/nklab/u/amynick/Tracula/Tracula_trio//diffusion_tutorial/kancon02/scripts/dmrirc.local -log /mindhive/nklab/u/amynick/Tracula/Tracula_trio//diffusion_tutorial/kancon02/scripts/trac-all.log -cmd /mindhive/nklab/u/amynick/Tracula/Tracula_trio//diffusion_tutorial/kancon02/scripts/trac-all.cmd #------------------------------------- /cm/shared/openmind/freesurfer/6.0.0/bin/trac-preproc #------------------------------------- #@# Image corrections Thu Nov 30 13:40:35 EST 2017 mri_convert --bvec-voxel /mindhive/nklab/u/amynick/Tracula/Tracula_trio//diffusion_tutorial/kancon02/orig/171000-1-1.dcm /mindhive/nklab/u/amynick/Tracula/Tracula_trio//diffusion_tutorial/kancon02/dmri/dwi_orig.nii.gz mri_convert.bin --bvec-voxel /mindhive/nklab/u/amynick/Tracula/Tracula_trio//diffusion_tutorial/kancon02/orig/171000-1-1.dcm /mindhive/nklab/u/amynick/Tracula/Tracula_trio//diffusion_tutorial/kancon02/dmri/dwi_orig.nii.gz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /mindhive/nklab/u/amynick/Tracula/Tracula_trio//diffusion_tutorial/kancon02/orig/171000-1-1.dcm... Getting Series No INFO: Found 4505 files in /mindhive/nklab/u/amynick/Tracula/Tracula_trio//diffusion_tutorial/kancon02/orig INFO: Scanning for Series Number 1 Scanning Directory INFO: found 128 files in series INFO: loading series header info. RunNo = 0 INFO: sorting. sdfiSameSlicePos() eps = 0.000001 INFO: (160 160 128), nframes = 1, ismosaic=0 sdfi->UseSliceScaleFactor 0 datatype = 4, short=4, float=3 PE Dir ROW ROW AutoAlign matrix detected AutoAlign Matrix --------------------- 1.00000 0.00000 0.00000 0.00000; 0.00000 1.00000 0.00000 0.00000; 0.00000 0.00000 1.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; FileName /mindhive/nklab/u/amynick/Tracula/Tracula_trio//diffusion_tutorial/kancon02/orig/171000-1-1.dcm Identification NumarisVer syngo MR B17 ScannerModel TrioTim PatientName KanCon02 Date and time StudyDate 20161216 StudyTime 163713.171000 SeriesTime 164740.250000 AcqTime 164708.722500 Acquisition parameters PulseSeq *fl3d1_ns Protocol AAHScout_32ch PhEncDir ROW EchoNo 1 FlipAngle 8 EchoTime 1.37 InversionTime -1 RepetitionTime 3.15 PhEncFOV 260 ReadoutFOV 260 Image information RunNo 0 SeriesNo 1 ImageNo 1 NImageRows 160 NImageCols 160 NFrames 1 SliceArraylSize 1 IsMosaic 0 ImgPos 101.6000 130.0000 130.0000 VolRes 1.6250 1.6250 1.6000 VolDim 160 160 128 Vc -0.0000 -1.0000 0.0000 Vr -0.0000 -0.0000 -1.0000 Vs -1.0000 -0.0000 0.0000 VolCenter -0.8000 0.0000 0.0000 TransferSyntaxUID unknown UseSliceScaleFactor 0 (slice 0: 1) IsDWI = 0 INFO: no Siemens slice order reversal detected (good!). TR=3.15, TE=1.37, TI=-1.00, flip angle=8.00 i_ras = (-0, -1, 0) j_ras = (-0, -0, -1) k_ras = (-1, -0, 0) writing to /mindhive/nklab/u/amynick/Tracula/Tracula_trio//diffusion_tutorial/kancon02/dmri/dwi_orig.nii.gz... mri_probedicom --i /mindhive/nklab/u/amynick/Tracula/Tracula_trio//diffusion_tutorial/kancon02/orig/171000-1-1.dcm > /mindhive/nklab/u/amynick/Tracula/Tracula_trio//diffusion_tutorial/kancon02/dmri/dcminfo.dat cp /mindhive/nklab/u/amynick/Tracula/Tracula_trio//diffusion_tutorial/kancon02/orig/gradients.txt /mindhive/nklab/u/amynick/Tracula/Tracula_trio//diffusion_tutorial/kancon02/dmri/dwi_orig.bvecs cp /mindhive/nklab/u/amynick/Tracula/Tracula_trio//diffusion_tutorial/kancon02/orig/bvalues.txt /mindhive/nklab/u/amynick/Tracula/Tracula_trio//diffusion_tutorial/kancon02/dmri/dwi_orig.bvals mv -f /mindhive/nklab/u/amynick/Tracula/Tracula_trio//diffusion_tutorial/kancon02/dmri/bvecs.tmp /mindhive/nklab/u/amynick/Tracula/Tracula_trio//diffusion_tutorial/kancon02/dmri/dwi_orig.bvecs mv -f /mindhive/nklab/u/amynick/Tracula/Tracula_trio//diffusion_tutorial/kancon02/dmri/bvals.tmp /mindhive/nklab/u/amynick/Tracula/Tracula_trio//diffusion_tutorial/kancon02/dmri/dwi_orig.bvals orientLAS /mindhive/nklab/u/amynick/Tracula/Tracula_trio//diffusion_tutorial/kancon02/dmri/dwi_orig.nii.gz /mindhive/nklab/u/amynick/Tracula/Tracula_trio//diffusion_tutorial/kancon02/dmri/dwi_orig_las.nii.gz INFO: input image orientation is PIL INFO: input image determinant is -4.225 mri_convert -oni 128 -onj 160 -onk 160 -oid -1 0 0 -ojd 0 1 0 -okd 0 0 1 -oc -0.812503 1.625 1.6125 -rt nearest /mindhive/nklab/u/amynick/Tracula/Tracula_trio//diffusion_tutorial/kancon02/dmri/dwi_orig.nii.gz /mindhive/nklab/u/amynick/Tracula/Tracula_trio//diffusion_tutorial/kancon02/dmri/dwi_orig_las.nii.gz mri_convert.bin -oni 128 -onj 160 -onk 160 -oid -1 0 0 -ojd 0 1 0 -okd 0 0 1 -oc -0.812503 1.625 1.6125 -rt nearest /mindhive/nklab/u/amynick/Tracula/Tracula_trio//diffusion_tutorial/kancon02/dmri/dwi_orig.nii.gz /mindhive/nklab/u/amynick/Tracula/Tracula_trio//diffusion_tutorial/kancon02/dmri/dwi_orig_las.nii.gz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /mindhive/nklab/u/amynick/Tracula/Tracula_trio//diffusion_tutorial/kancon02/dmri/dwi_orig.nii.gz... TR=3.15, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0, -1, 0) j_ras = (-0, -0, -1) k_ras = (-1, -0, 0) Reslicing using nearest writing to /mindhive/nklab/u/amynick/Tracula/Tracula_trio//diffusion_tutorial/kancon02/dmri/dwi_orig_las.nii.gz... INFO: found /mindhive/nklab/u/amynick/Tracula/Tracula_trio//diffusion_tutorial/kancon02/dmri/dwi_orig.bvals, copying INFO: found /mindhive/nklab/u/amynick/Tracula/Tracula_trio//diffusion_tutorial/kancon02/dmri/dwi_orig.bvecs, converting to LAS mv -f /mindhive/nklab/u/amynick/Tracula/Tracula_trio//diffusion_tutorial/kancon02/dmri/dwi_orig_las.bvecs /mindhive/nklab/u/amynick/Tracula/Tracula_trio//diffusion_tutorial/kancon02/dmri/bvecs mv -f /mindhive/nklab/u/amynick/Tracula/Tracula_trio//diffusion_tutorial/kancon02/dmri/dwi_orig_las.bvals /mindhive/nklab/u/amynick/Tracula/Tracula_trio//diffusion_tutorial/kancon02/dmri/bvals eddy_correct /mindhive/nklab/u/amynick/Tracula/Tracula_trio//diffusion_tutorial/kancon02/dmri/dwi_orig_las.nii.gz /mindhive/nklab/u/amynick/Tracula/Tracula_trio//diffusion_tutorial/kancon02/dmri/dwi.nii.gz 0 processing /mindhive/nklab/u/amynick/Tracula/Tracula_trio//diffusion_tutorial/kancon02/dmri/dwi_tmp0000 mv -f /mindhive/nklab/u/amynick/Tracula/Tracula_trio//diffusion_tutorial/kancon02/dmri/bvecs /mindhive/nklab/u/amynick/Tracula/Tracula_trio//diffusion_tutorial/kancon02/dmri/bvecs.norot xfmrot /mindhive/nklab/u/amynick/Tracula/Tracula_trio//diffusion_tutorial/kancon02/dmri/dwi.ecclog /mindhive/nklab/u/amynick/Tracula/Tracula_trio//diffusion_tutorial/kancon02/dmri/bvecs.norot /mindhive/nklab/u/amynick/Tracula/Tracula_trio//diffusion_tutorial/kancon02/dmri/bvecs R: Subscript out of range. 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R: Subscript out of range. ln -sf /mindhive/nklab/u/amynick/Tracula/Tracula_trio//diffusion_tutorial/kancon02/dmri/dwi.nii.gz /mindhive/nklab/u/amynick/Tracula/Tracula_trio//diffusion_tutorial/kancon02/dmri/data.nii.gz mri_convert --frame 0 1 2 3 4 5 6 7 8 9 /mindhive/nklab/u/amynick/Tracula/Tracula_trio//diffusion_tutorial/kancon02/dmri/dwi.nii.gz /mindhive/nklab/u/amynick/Tracula/Tracula_trio//diffusion_tutorial/kancon02/dmri/lowb.nii.gz mri_convert.bin --frame 0 1 2 3 4 5 6 7 8 9 /mindhive/nklab/u/amynick/Tracula/Tracula_trio//diffusion_tutorial/kancon02/dmri/dwi.nii.gz /mindhive/nklab/u/amynick/Tracula/Tracula_trio//diffusion_tutorial/kancon02/dmri/lowb.nii.gz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /mindhive/nklab/u/amynick/Tracula/Tracula_trio//diffusion_tutorial/kancon02/dmri/dwi.nii.gz... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 1, 0) k_ras = (0, 0, 1) keeping frames 0 1 2 3 4 5 6 7 8 9 ERROR: valid frame numbers are between 0 and 0 Linux node044 3.10.0-514.26.2.el7.x86_64 #1 SMP Tue Jul 4 15:04:05 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux trac-preproc exited with ERRORS at Thu Nov 30 13:44:15 EST 2017

1 0

license file error
by Ritobrato Datta 30 Nov '17

30 Nov '17

Hi All, I am using Mac OS X Sierra and I downloaded free surfer 6 and when running recon I am getting the following error reading from IM-0001-0001.dcm... -------------------------------------------------------------------------- ERROR: Invalid FreeSurfer license key found in license file /Applications/freesurfer6/.license If you are outside the NMR-Martinos Center, go to http://surfer.nmr.mgh.harvard.edu/registration.html to get a valid license file (it's free). If you are inside the NMR-Martinos Center, make sure to source the standard environment. -------------------------------------------------------------------------- The license.txt file is a valid license file and the permissions are set as follows -rwxrwxrwx 1 root wheel 136 Nov 29 12:48 license.txt Can you please suggest what seems to be the problem ? Thanks Ri

2 1

mri_vol2surf wrong hemisphere
by Defenderfer, Matthew K 30 Nov '17

30 Nov '17

Hi, I have a strange issue I can't figure out. I am currently trying to use the parcellation from Gordon et al. 2014 (download link here<http://www.nil.wustl.edu/labs/petersen/Resources.html>) to create ROIs for the frontoparietal network. They provided a volume of the parcellation in MNI152 space for public use. I took this volume and applied the mri_vol2surf command to it to create 2 overlays of the parcels, 1 for each hemisphere. The code was: mri_vol2surf --mov Parcels_MNI_111.nii --trgsubject fsaverage --mni152reg --o lh.Parcels_fsaverage_111.mgh --hemi lh mri_vol2surf --mov Parcels_MNI_111.nii --trgsubject fsaverage --mni152reg --o rh.Parcels_fsaverage_111.mgh --hemi rh The code ran, but the LH parcels in the volume were transferred to the RH on the surface and vice versa. This is a problem since the parcellation is not symmetric across hemispheres.This is not a problem with the volume either as I looked at it overlayed with the MNI152 brain in fslview and saw that the parcels were on the correct hemisphere. Another problem is that 1 of the frontoparietal parcels, number 24, was not found on the surface of either hemisphere after turning it to a surface. I don't know why this would be the case since there are all cortical parcels. I'm including my output ?h.Parcels_fsaverage_111.mgh in the email. A link to download the original parcellation is above. Any help would be greatly appreciated. Thank you! Best, Matthew Defenderfer Matthew K. Defenderfer B.S. | Graduate Research Assistant Graduate Biomedical Sciences | Neuroscience UAB | The University of Alabama at Birmingham Laboratory of Kristina Visscher, PhD Department of Neurobiology CIRC 111 | C: (865) 805-6389

1 0

[Re] medial wall label in Freesurfer 6
by M del Mar Velasco 30 Nov '17

30 Nov '17

Hi, We are not using the make_average_subject 6.0.0-patch. Do you think it would be a possible solution? Where can I find that patch? On the other hand, we've noticed that recon-all, which is a final make_average_subject step, fails. I send you the recon-all.log. However, maybe it is not related with previous issue becuase label files are generated before. All the best, M del Mar

2 1

Recon-all with masked face and ears
by Buimer, E.E.L. 30 Nov '17

30 Nov '17

Dear FreeSurfer experts, We want to implement a deface method to ensure anonymity of participants before making the data available to researchers. Because the raw data is stored on the imaging platform XNAT, we preferred the mask_face method implemented on the XNAT server rather than FreeSurfer’s defacing. However, we will be using FreeSurfer for processing and segmentations afterwards. I am currently investigating the effect of face and earmasks on brain measures. I used FreeSurfer v5.3 (freesurfer-x86_64-unknown-linux-gnu-stable5-20130513) and the mask_face function developed for XNAT (Milchienko & Marcus, 2013) with the default normalized filter. The masks were not invasive and did not overlap with brain tissue. I compared output of the recon-all between T1 scans with and without masked face for a small sample. I found high correlations between the output of the two scans (extracted values: cortical thickness, surface area, (sub)cortical volume, global values). Slight differences seem to occur from the start of the recon-all (talairach transform). Adding ear masks to the face-masked scans, made the differences smaller (i.e. higher correlations with raw scans). Also, the recon-all run time appears to be reduced. Could you explain how face and ear information is used in the recon-all and why adding ear masks to masked-face scans might reduce run-time and improve reliability? Could it be the case that skull stripping is easier without ears for example? Thank you in advance. Kind regards, Elizabeth -------------------------------------------------------- Elizabeth Buimer, Research Assistant Department of Psychiatry, UMC Utrecht Room: A.01.161 e.e.l.buimer(a)umcutrecht.nl ------------------------------------------------------------------------------ De informatie opgenomen in dit bericht kan vertrouwelijk zijn en is uitsluitend bestemd voor de geadresseerde. Indien u dit bericht onterecht ontvangt, wordt u verzocht de inhoud niet te gebruiken en de afzender direct te informeren door het bericht te retourneren. Het Universitair Medisch Centrum Utrecht is een publiekrechtelijke rechtspersoon in de zin van de W.H.W. (Wet Hoger Onderwijs en Wetenschappelijk Onderzoek) en staat geregistreerd bij de Kamer van Koophandel voor Midden-Nederland onder nr. 30244197. Denk s.v.p aan het milieu voor u deze e-mail afdrukt. ------------------------------------------------------------------------------ This message may contain confidential information and is intended exclusively for the addressee. If you receive this message unintentionally, please do not use the contents but notify the sender immediately by return e-mail. University Medical Center Utrecht is a legal person by public law and is registered at the Chamber of Commerce for Midden-Nederland under no. 30244197. Please consider the environment before printing this e-mail.

2 1

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2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

Freesurfer November 2017