Freesurfer

freesurfer@nmr.mgh.harvard.edu

30132 discussions

Intracranial Volume
by Tamara Tavares 01 Dec '17

01 Dec '17

Hello, Just a quick question regarding the computed intracranial volume. I have ran Freesurfer version 5.1 and I have been using the intracranial volume from the aseg.stats file to correct for head size. I just want to ensure this is where I get the intracranial volume from. Thank you in advance for your help. Best, Tamara

3 2

hippocampus subfields
by 郑凤莲 01 Dec '17

01 Dec '17

Hi professor, I am using Freesurfer for DTI data. When I run 'mri_segstats', I got the result that there was an obvious difference in left hippocampus, but no difference in right hippocampus. Then, I run segmentation of hippocampus subfields. The result showed there is no difference in total left or right hippocampus, and only in two right hippocampus subfields has significant difference. Why is there inconsistent result in two means? Thank you very much. Sincerely, Zheng

3 19

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

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