Freesurfer

freesurfer@nmr.mgh.harvard.edu

14 participants
30063 discussions

Re: [Freesurfer] Tracula - QA for Forceps Minor
by Yendiki, Anastasia 06 Oct '17

06 Oct '17

Hi Abby - You can try first reinitializing without increasing the number of control points, and if that doesn’t work then increase them. Increasing the number of control points increases the degrees of freedom in the shape of the path, which can be good, e.g., for the corpus callosum of subjects with enlarged ventricles, but otherwise may make things noisier. Best, a.y From: <freesurfer-bounces(a)nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu>> on behalf of Abigail Waters <awaters2(a)su.suffolk.edu<mailto:awaters2@su.suffolk.edu>> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Date: Friday, August 25, 2017 at 1:32 PM To: "freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>" <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Subject: [Freesurfer] Tracula - QA for Forceps Minor Hello - We've processed approximately 500 DTI scans using Tracula and are in the process of visually inspecting the forceps minor for errors. For subjects with dramatic errors (see image 1) we will be redoing the -path step of Tracula with control points set to 7 and reinit = 1. Is this an appropriate solution? In order to generate the fminor_PP_avg33_mni_bbr_cpts_7 files, would we need to redo the whole pipeline, or just parts of it? We would also like to know if any of the following issues described below are errors or normal variation in white matter tracts: 1. Spread of white matter at the ends of the curve (see image 2) 2. Overlapping of the white matter across hemispheres in the prefrontal region (see image 3) 3. Non-smooth surfaces with small protrusions along the length of the forceps minor (see image 4_1 and 4_2) 4. Slightly larger single protrusions of white matter (see image 5) And if so, would increasing the number of control points to 7 increase the quality of the reconstruction? Please let me know if you need any additional information. Best Abby

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TMI(total motion index) of diffusion MRI
by 이 정환 06 Oct '17

06 Oct '17

Hello I’m attempting to analysis diffusion MRI using TRACULA. As mentioned on article "Spurious group differences due to head motion in a diffusion MRI study", I tried to calculate TMI(total motion index) first. The problem is that, upper and lower quartile of Percent Bad Slices are both 0. Upper and lower quartile of avg dropout score are both 1. Calculating TMI on some subjects using those values figured out at questionable results because difference of upper and lower quartile values is used as denominator in formula. I those cases, should I exclude Percent Bad slices and avg dropout score calculating TMI? Does anyone have any thoughts on it? Thanks in advance.

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Re: [Freesurfer] Error with TRACULA using dcm and nii
by Yendiki, Anastasia 06 Oct '17

06 Oct '17

Hi Christopher – If you have not resolved this, please send along the bvals and gradient table files. It seems to expect a 35th volume in your nifti file, which has 34 volumes. Best, a.y From: <freesurfer-bounces(a)nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu>> on behalf of "Ferrier, Christopher Q." <cferri(a)lsuhsc.edu<mailto:cferri@lsuhsc.edu>> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Date: Tuesday, September 5, 2017 at 5:50 PM To: "freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>" <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Subject: [Freesurfer] Error with TRACULA using dcm and nii Hi Freesurfer Team!. We are trying to use TRACULA to analyze the structural connectivity of PD patients scanned on a 3 tesla Philips Ingenia. We have run the tutorial data without any problems but encounter errors when using our own data. We ran recon-all on all of our subjects without any problem and follow the exact steps that worked for the tutorial data but encounter different errors when using the dcm or nii version of the DTI scans. Our nii files go from scanner to CD to Osirix to DICOM to dcm2nii which gives us the nii files and the bvals and bvecs. Here is the error for the nii DTI scans (included bvals and gradients in the config file for the nii files). [Christinas-iMac:Freesurfer_temp/PD800/diffusion_recons] christina% trac-all -prep -c/Volumes/CFERRIER/Freesurfer_temp/PD800/dmrirc.tutorial ERROR: flag -c/Volumes/CFERRIER/Freesurfer_temp/PD800/dmrirc.tutorial unrecognized -prep -c/Volumes/CFERRIER/Freesurfer_temp/PD800/dmrirc.tutorial [Christinas-iMac:Freesurfer_temp/PD800/diffusion_recons] christina% trac-all -prep -c /Volumes/CFERRIER/Freesurfer_temp/PD800/dmrirc.tutorial INFO: SUBJECTS_DIR is /Volumes/CFERRIER/Freesurfer_temp/PD800/diffusion_recons INFO: Diffusion root is /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT Actual FREESURFER_HOME /Applications/Freesurfer trac-preproc -c /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/scripts/dmrirc.local -log /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/scripts/trac-all.log -cmd /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/scripts/trac-all.cmd #------------------------------------- /Applications/Freesurfer/bin/trac-preproc #------------------------------------- #@# Image corrections Thu Aug 31 14:45:46 CDT 2017 mri_convert --bvec-voxel /Volumes/CFERRIER/Freesurfer_temp/PD800/orig_nii/PD800_DTI_combined.nii /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi_orig.nii.gz mri_convert.bin --bvec-voxel /Volumes/CFERRIER/Freesurfer_temp/PD800/orig_nii/PD800_DTI_combined.nii /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi_orig.nii.gz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /Volumes/CFERRIER/Freesurfer_temp/PD800/orig_nii/PD800_DTI_combined.nii... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.999339, -0.0363145, -0.00163044) j_ras = (-0.0363101, 0.99508, 0.0921851) k_ras = (0.00172524, -0.0921834, 0.995741) writing to /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi_orig.nii.gz... cp /Volumes/CFERRIER/Freesurfer_temp/PD800/bvecs/PD800_bvecs.txt /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi_orig.bvecs cp /Volumes/CFERRIER/Freesurfer_temp/PD800/bvals/PD800_bvals.txt /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi_orig.bvals mv -f /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/bvecs.tmp /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi_orig.bvecs mv -f /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/bvals.tmp /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi_orig.bvals orientLAS /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi_orig.nii.gz /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi_orig_las.nii.gz INFO: input image orientation is LAS INFO: input image determinant is -9.1875 mri_convert -oni 128 -onj 128 -onk 50 -oid -0.999339 -0.0363145 -0.00163044 -ojd -0.0363101 0.99508 0.0921851 -okd 0.00172524 -0.0921834 0.995741 -oc 7.38609 19.7949 1.17333 -rt nearest /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi_orig.nii.gz /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi_orig_las.nii.gz mri_convert.bin -oni 128 -onj 128 -onk 50 -oid -0.999339 -0.0363145 -0.00163044 -ojd -0.0363101 0.99508 0.0921851 -okd 0.00172524 -0.0921834 0.995741 -oc 7.38609 19.7949 1.17333 -rt nearest /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi_orig.nii.gz /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi_orig_las.nii.gz normalizing out_i_direction: (-0.999339, -0.0363145, -0.00163044) -> (-0.999339, -0.0363145, -0.00163044) normalizing out_j_direction: (-0.0363101, 0.99508, 0.0921851) -> (-0.0363101, 0.99508, 0.0921851) normalizing out_k_direction: (0.00172524, -0.0921834, 0.995741) -> (0.00172524, -0.0921834, 0.995741) $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi_orig.nii.gz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.999339, -0.0363145, -0.00163044) j_ras = (-0.0363101, 0.99508, 0.0921851) k_ras = (0.00172524, -0.0921834, 0.995741) Reslicing using nearest writing to /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi_orig_las.nii.gz... INFO: found /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi_orig.bvals, copying INFO: found /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi_orig.bvecs, converting to LAS mv -f /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi_orig_las.bvecs /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/bvecs mv -f /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi_orig_las.bvals /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/bvals eddy_correct /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi_orig_las.nii.gz /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi.nii.gz 0 processing /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi_tmp0000 processing /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi_tmp0001 processing /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi_tmp0002 processing /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi_tmp0003 processing /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi_tmp0004 processing /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi_tmp0005 processing /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi_tmp0006 processing /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi_tmp0007 processing /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi_tmp0008 processing /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi_tmp0009 processing /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi_tmp0010 processing /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi_tmp0011 processing /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi_tmp0012 processing /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi_tmp0013 processing /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi_tmp0014 processing /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi_tmp0015 processing /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi_tmp0016 processing /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi_tmp0017 processing /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi_tmp0018 processing /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi_tmp0019 processing /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi_tmp0020 processing /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi_tmp0021 processing /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi_tmp0022 processing /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi_tmp0023 processing /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi_tmp0024 processing /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi_tmp0025 processing /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi_tmp0026 processing /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi_tmp0027 processing /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi_tmp0028 processing /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi_tmp0029 processing /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi_tmp0030 processing /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi_tmp0031 processing /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi_tmp0032 processing /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi_tmp0033 mv -f /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/bvecs /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/bvecs.norot xfmrot /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi.ecclog /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/bvecs.norot /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/bvecs R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. ln -sf /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi.nii.gz /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/data.nii.gz mri_convert --frame 34 /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi.nii.gz /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/lowb.nii.gz mri_convert.bin --frame 34 /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi.nii.gz /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/lowb.nii.gz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi.nii.gz... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.999339, -0.0363145, -0.00163044) j_ras = (-0.0363101, 0.99508, 0.0921851) k_ras = (0.00172524, -0.0921834, 0.995741) keeping frame 34 ERROR: valid frame numbers are between 0 and 33 Darwin Christinas-iMac.local 14.5.0 Darwin Kernel Version 14.5.0: Thu Apr 21 20:40:54 PDT 2016; root:xnu-2782.50.3~1/RELEASE_X86_64 x86_64 trac-preproc exited with ERRORS at Thu Aug 31 14:54:59 CDT 2017 Here is the error I encounter when running the original dicom files through tracula [Christinas-iMac:Freesurfer_temp/PD800/diffusion_recons] christina% trac-all -prep -c /Volumes/CFERRIER/Freesurfer_temp/PD800/dmrirc.tutorial INFO: SUBJECTS_DIR is /Volumes/CFERRIER/Freesurfer_temp/PD800/diffusion_recons INFO: Diffusion root is /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT Actual FREESURFER_HOME /Applications/Freesurfer trac-preproc -c /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/scripts/dmrirc.local -log /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/scripts/trac-all.log -cmd /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/scripts/trac-all.cmd #------------------------------------- /Applications/Freesurfer/bin/trac-preproc #------------------------------------- #@# Image corrections Thu Aug 31 15:31:12 CDT 2017 mri_convert --bvec-voxel /Volumes/CFERRIER/Freesurfer_temp/PD800/orig_nii/PD800_DTI.dcm /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi_orig.nii.gz mri_convert.bin --bvec-voxel /Volumes/CFERRIER/Freesurfer_temp/PD800/orig_nii/PD800_DTI.dcm /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi_orig.nii.gz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /Volumes/CFERRIER/Freesurfer_temp/PD800/orig_nii/PD800_DTI.dcm... Starting DICOMRead2() dcmfile = /Volumes/CFERRIER/Freesurfer_temp/PD800/orig_nii/PD800_DTI.dcm dcmdir = /Volumes/CFERRIER/Freesurfer_temp/PD800/orig_nii WARNING: tag image orientation not found in /Volumes/CFERRIER/Freesurfer_temp/PD800/orig_nii/PD800_DTI.dcm ERROR: don't know how to get DWI parameters from --Philips -- ERROR: GetDICOMInfo(): dcmGetDWIParams() 1 DICOM File: /Volumes/CFERRIER/Freesurfer_temp/PD800/orig_nii/PD800_DTI.dcm break DICOMRead.c:5228 Ref Series No = 601 Found 5 files, checking for dicoms WARNING: tag image orientation not found in /Volumes/CFERRIER/Freesurfer_temp/PD800/orig_nii/PD800_DTI.dcm ERROR: don't know how to get DWI parameters from --Philips -- ERROR: GetDICOMInfo(): dcmGetDWIParams() 1 DICOM File: /Volumes/CFERRIER/Freesurfer_temp/PD800/orig_nii/PD800_DTI.dcm break DICOMRead.c:5228 WARNING: tag image orientation not found in /Volumes/CFERRIER/Freesurfer_temp/PD800/orig_nii/PD806_DTI.dcm ERROR: don't know how to get DWI parameters from --Philips Healthcare-- ERROR: GetDICOMInfo(): dcmGetDWIParams() 1 DICOM File: /Volumes/CFERRIER/Freesurfer_temp/PD800/orig_nii/PD806_DTI.dcm break DICOMRead.c:5228 WARNING: tag image orientation not found in /Volumes/CFERRIER/Freesurfer_temp/PD800/orig_nii/PD809_DTI.dcm ERROR: don't know how to get DWI parameters from --Philips Healthcare-- ERROR: GetDICOMInfo(): dcmGetDWIParams() 1 DICOM File: /Volumes/CFERRIER/Freesurfer_temp/PD800/orig_nii/PD809_DTI.dcm break DICOMRead.c:5228 Found 1 dicom files in series. WARNING: tag image orientation not found in /Volumes/CFERRIER/Freesurfer_temp/PD800/orig_nii/PD800_DTI.dcm ERROR: don't know how to get DWI parameters from --Philips -- ERROR: GetDICOMInfo(): dcmGetDWIParams() 1 DICOM File: /Volumes/CFERRIER/Freesurfer_temp/PD800/orig_nii/PD800_DTI.dcm break DICOMRead.c:5228 WARNING: tag image orientation not found in /Volumes/CFERRIER/Freesurfer_temp/PD800/orig_nii/PD806_DTI.dcm ERROR: don't know how to get DWI parameters from --Philips Healthcare-- ERROR: GetDICOMInfo(): dcmGetDWIParams() 1 DICOM File: /Volumes/CFERRIER/Freesurfer_temp/PD800/orig_nii/PD806_DTI.dcm break DICOMRead.c:5228 WARNING: tag image orientation not found in /Volumes/CFERRIER/Freesurfer_temp/PD800/orig_nii/PD809_DTI.dcm ERROR: don't know how to get DWI parameters from --Philips Healthcare-- ERROR: GetDICOMInfo(): dcmGetDWIParams() 1 DICOM File: /Volumes/CFERRIER/Freesurfer_temp/PD800/orig_nii/PD809_DTI.dcm break DICOMRead.c:5228 First Sorting Computing Slice Direction WARNING: it appears that the image position for all slices is the same. This is a problem with the DICOM file. Using direction cosines from col and row to compute slice direction, but the output may be misoriented. Vs: 0 0 0 Vs: nan nan nan Second Sorting IsDWI = 0, IsPhilipsDWI = 0 Counting frames nframes = 1 nslices = 1 ndcmfiles = 1 PE Dir = UNKNOWN (dicom read) Loading pixel data TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0, -0, 0) j_ras = (-0, -0, 0) k_ras = (nan, nan, nan) writing to /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi_orig.nii.gz... mri_probedicom --i /Volumes/CFERRIER/Freesurfer_temp/PD800/orig_nii/PD800_DTI.dcm > /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dcminfo.dat cp /Volumes/CFERRIER/Freesurfer_temp/PD800/bvecs/PD800_bvecs.txt /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi_orig.bvecs cp /Volumes/CFERRIER/Freesurfer_temp/PD800/bvals/PD800_bvals.txt /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi_orig.bvals mv -f /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/bvecs.tmp /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi_orig.bvecs mv -f /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/bvals.tmp /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi_orig.bvals orientLAS /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi_orig.nii.gz /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi_orig_las.nii.gz mat = NULL! MatrixFree: NULL mat POINTER! mat = NULL! MatrixFree: NULL mat POINTER! mat = NULL! MatrixFree: NULL mat POINTER! INFO: input image orientation is III INFO: input image determinant is nan order: Subscript out of range. Darwin Christinas-iMac.local 14.5.0 Darwin Kernel Version 14.5.0: Thu Apr 21 20:40:54 PDT 2016; root:xnu-2782.50.3~1/RELEASE_X86_64 x86_64 trac-preproc exited with ERRORS at Thu Aug 31 15:32:20 CDT 2017 Thanks for your help. We tried to go through everything but nothing seems to be working.

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TRACULA trac-all prep error
by Fred Sampedro 06 Oct '17

06 Oct '17

Dear TRACULA users, I'm trying to preprocess a DTI subject in TRACULA which has an already reconed-all error-free T1. I followed the tutorial, but trac-all -prep exited with errors very fast. Please find attached the log and error files, and the dmrirc. Also bvals and bvecs (were obtained from dcm2nii). The raw dti.nii.gz has 16 volumes, the first being b0 and then 15 directions. Any ideas on what could be happening would be much appreciated, Thanks a lot in advance, Fred-

2 1

Problem with mris_anatomical_stats on .label which is threshold under negative value on FS-FAST, using tksurfer
by stdp82＠virgilio.it 06 Oct '17

06 Oct '17

Hi list, aftermri_label2label --srcsubject Subj01 --srclabel ROI.label --trgsubject Subj01 --trglabel Subj01/label/ROI.label --hemi lh --regmethod surfaceandmris_anatomical_stats -l Subj01/label/ROI.label -b Subj01 I have run mris_anatomical_stats -l Subj01/ROI_neg.label -b Subj01 lh the following error has been produced: Subj01/mri/wm.mgz...reading input surface Subj01/surf/lh.white...Using TH3 vertex volume calcTotal face volume 211969Total vertex volume 209028 (mask=0)reading input pial surface Subj01/surf/lh.pial...reading input white surface Subj01/surf/lh.white...No such file or directorymris_anatomical_stats: could not open label file Subj01/label/ROI_neg.labelNo such file or directorySubj01: could not read label file Subj01/label/ROI_neg.label This error did not occur for another label (Red_positive.label) which is threshold over positive value. Please take in account that the Blue_negative.label is obtain from FS-FAST map using tksurfer.Blue_negative.label expresses the difference for FC of group B < FC of group A.Conversely, Red_positive cluster shows difference for FC of group A > FC of group BPlease also note that clusters were thresholded before to save the .label with tksurfer +at 1.3 for defining Red_positive.label and at for defining - 1.3. I do not know if this step could induce an error in label properties. Thanks Stefano

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TRACULA qc: forceps minor and major
by Linnea Marie Dramdal Borg 06 Oct '17

06 Oct '17

Hi, We have run into some issues with our forceps major and forceps minor tractographies. I have attached examples: In "fminor_bro_139.png", there is a "bridge" in forceps minor in the space between the hemispheres. We've also come across other cases of bridging in forceps minor, with somewhat unusual voxel intensity distribution, such as in "fminor_onestripe_otherwOK.png" and" fminor_litenbro_OKornot_210.png". Also, "fmajor_132_toolateral.png", fmajor brances out in the left hemisphere (right in the picture). All of these cases seem pretty bad to us. Do you agree? In contrast, "fminor_allslicesOKbutone_158.png" looks fine, but there is one slice where it branches out to some extent. Are we correct in assuming this won't affect the results too much, or is there something we can/should do about this? Thank you, Linnea Marie

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Postdoc and PhD student positions, TU Dresden, Germany
by Katharina von Kriegstein 06 Oct '17

06 Oct '17

We are seeking a postdoc and two PhD students to work in the Neural Mechanisms of Human Communication Research Group led by Katharina von Kriegstein at the TU Dresden, Germany. Postdoc Position The main research goal of the position is to investigate behavioural and neuroscience principles of perceptual learning and their translation to evidence-based teaching and training programmes. For more information on the position and application instructions see: http://tinyurl.com/y9396qdd PhD positions The main research goal of the two positions is to investigate behavioural and neuroscience principles of voice and face perception (identity and speech) in neurotypical populations as well as in populations with developmental person recognition deficits (i.e. phonagnosia and prosopagnosia). For more information on the position and application instructions see: http://tinyurl.com/ybvodeqo The Human Communication Research Group is currently based at the Max Planck Institute for Human Cognitive and Brain Sciences in Leipzig (MPI-CBS; www.cbs.mpg.de/independent-research-groups/human-communication) and will be newly established at the TU Dresden. The TU Dresden offers an excellent, interdisciplinary scientific environment. Research will be carried out at the Department of Psychology of the TU Dresden, which houses a Neuroimaging Centre (http://www.nic-tud.de) The centre is equipped with a research-only 3-Tesla MRI machine, MRI-compatible eye tracking, EEG systems, and a neurostimulation unit including neuronavigaton, TMS and tDCS devices. All experimental facilities are supported by experienced physics and IT staff. For analyses with high computational demands, there is access to the TU Dresden high-performance computing clusters. There are also strong existing collaborations with the MPI-CBS in Leipzig involving 7 Tesla-MRI, Connectome scanner, and MEG data acquisitions. --- Prof. Dr. Katharina von Kriegstein Max Planck Institute for Human Cognitive and Brain Sciences Stephanstr. 1A, 04103 Leipzig, Germany Technische Universität Dresden Bamberger Str. 7, 01187 Dresden, Germany Phone +49 (0) 341-9940-2476 http://www.cbs.mpg.de/independent-research-groups/human-communication https://twitter.com/kvonkriegstein

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Volume Version of ?h.sphere.reg and method to read it
by Daniel van de Velden 06 Oct '17

06 Oct '17

Dear Freesurfer Team, I am using your reconstruction pipeline for my study. Since I need to morph all my subjects to an average subject (using mne-python for this) for upcoming a Volume Source Analysis I deeply looked into the whole source-code of both software packages. Narowing down the problem, I think I will need a volume version of the ?h-sphere.reg files, which are created during the whole reconstruction process. Mne-python reads the subject specific 'sphere_tris' from this file. I can use the talairach.m3z, which is a nonlinear atlas warp. Or I can run CVS, which extends the surface warp into the volume. But how is it possible to read the warp map I got, e.g. CVS-based warp map, and use its information ? Yours sincerely, Daniel van de Velden .

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LGI error
by Nillo, Ryan Michael R 05 Oct '17

05 Oct '17

Hello FS users, I am using FreeSurfer version 5.3 to calculate local verification index and processing stopped at make_roi_paths. Here, I was given the error below. I searched in the archives and found a solution to the problem was to edit a few lines on SearchProjectionOnPial.m. The new script is included below the error. Any advice on how to fix this would be greatly appreciated. Make_roi_paths error ================= make_roi_paths('lh.pial','lh.pial-outer-smoothed',25,100,'/data/sugrue2/NF1_qdec/P0007/surf/tmp-mris_compute_lgi-lh.pial','/tmp/mrp_20907_.m'); exit ================= < M A T L A B (R) > Copyright 1984-2015 The MathWorks, Inc. R2015b (8.6.0.267246) 64-bit (glnxa64) August 20, 2015 For online documentation, see http://www.mathworks.com/support For product information, visit www.mathworks.com<http://www.mathworks.com>. modified_matlab = /working/sdl_analysis/software/freesufer_5.3_matlab Academic License >> loading datas ... FREESURFER_READ_SURF [v 1.2 ] ...reading surface file: lh.pial ...reading triangle file ...adding 1 to face indices for matlab compatibility. ...done ( 0.07 sec) FREESURFER_READ_SURF [v 1.2 ] ...reading surface file: lh.pial-outer-smoothed ...reading triangle file ...adding 1 to face indices for matlab compatibility. ...done ( 0.02 sec) preparing outer mesh structure ... face 5000 / 132292 face 10000 / 132292 face 15000 / 132292 face 20000 / 132292 face 25000 / 132292 face 30000 / 132292 face 35000 / 132292 face 40000 / 132292 face 45000 / 132292 face 50000 / 132292 face 55000 / 132292 face 60000 / 132292 face 65000 / 132292 face 70000 / 132292 face 75000 / 132292 face 80000 / 132292 face 85000 / 132292 face 90000 / 132292 face 95000 / 132292 face 100000 / 132292 face 105000 / 132292 face 110000 / 132292 face 115000 / 132292 face 120000 / 132292 face 125000 / 132292 face 130000 / 132292 mesh_outer = vertices: [66148x3 double] faces: [132292x3 double] facesOfVertex: [66148x1 struct] preparing pial mesh structure ... ...searching for mesh edges...done (140.10 sec). ... creating path file for vertex 1 / 66148 area file for outer ROIs saved at 1 In an assignment A(:) = B, the number of elements in A and B must be the same. Error in dsearchn (line 79) [d(i),t(i)] = min(sum((x-yi).^2,2)); Error in mesh_vertex_nearest (line 29) nearestIndex = dsearchn(vertices,points); Error in reorganize_verticeslist (line 28) [nextindex,nextvalue]=mesh_vertex_nearest(mesh_total.vertices(remaininglist,:),mesh_total.vertices(verticeslist(start_vertex),:)); Error in make_roi_paths (line 93) reorglist = reorganize_verticeslist (mesh_total, A, mesh_outer, perim, verticeslist, step); SearchProjectionOnPial.m Script function [verticeslist]=SearchProjectionOnPial(mesh_total,mesh_outer,perim, step) % step is typically set between 5 and 10. Default is 7, increasing it will % limit redundancies in the resulting path file. verticeslist=[]; si=max(size(perim)); for t=1:step:si [nearestIndexMT,nearestValuesMT]=mesh_vertex_nearest(mesh_total.vertices,mesh_outer.vertices(perim(t),:)); verticeslist= [verticeslist nearestIndexMT]; end verticeslist=unique(verticeslist); Sincerely, Ryan Nillo UCSF Center for Radiology and Biomedical Imaging Staff Research Associate

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mri_aparc2aseg creates black file
by Sara Nolin 05 Oct '17

05 Oct '17

Freesurfer people, *I have a label file that I want to make into a volume file only in the white matter to use in diffusion tractography.* *I was told to use mri_aparc2aseg to put the labels onto the WM surface and make them into a volume. I made the label files into annotation files using the following commands:* mris_label2annot --ctab clut.2lhV1.ctab --s 100206 --h lh --l /data/user/snolin/subjects_reconall/100206/label/2_LH_V1.label --a 2V1 mris_label2annot --ctab clut.2rhV1.ctab --s 100206 --h rh --l /data/user/snolin/subjects_reconall/100206/label/2_RH_V1.label --a 2V1 *These ran with no errors and made annotation files. Then I ran mri_aparc2aseg using the following command:* mri_aparc2aseg --s 100206 --annot 2V1 --new-ribbon *This is my log file:* SUBJECTS_DIR /data/user/snolin/subjects_reconall subject 100206 outvol /data/user/snolin/subjects_reconall/100206/mri/2V1+aseg.mgz useribbon 0 baseoffset 0 RipUnknown 0 Reading lh white surface /data/user/snolin/subjects_reconall/100206/surf/lh.white Reading lh pial surface /data/user/snolin/subjects_reconall/100206/surf/lh.pial Loading lh annotations from /data/user/snolin/subjects_reconall/100206/label/lh.2V1.annot reading colortable from annotation file... colortable with 2 entries read (originally clut.2lhV1.ctab) Reading rh white surface /data/user/snolin/subjects_reconall/100206/surf/rh.white Reading rh pial surface /data/user/snolin/subjects_reconall/100206/surf/rh.pial Loading rh annotations from /data/user/snolin/subjects_reconall/100206/label/rh.2V1.annot reading colortable from annotation file... colortable with 2 entries read (originally clut.2rhV1.ctab) Have color table for lh white annotation Have color table for rh white annotation Loading ribbon segmentation from /data/user/snolin/subjects_reconall/100206/mri/ribbon.mgz Building hash of lh white Building hash of lh pial Building hash of rh white Building hash of rh pial Loading aseg from /data/user/snolin/subjects_reconall/100206/mri/aseg.mgz ASeg Vox2RAS: ----------- -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; ------------------------- Labeling Slice 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = 1764 Used brute-force search on 0 voxels Writing output aseg to /data/user/snolin/subjects_reconall/100206/mri/2V1+aseg.mgz *It creates the 2V1+aseg.mgz file and I tried opening it in freeview with the color lookup table that I used when I made it into an annotation file and there is nothing there. The file is 401KB, but its all black. * *Clicking around it comes up 41, 0, or 2000, but I can’t visually see anything. What have I done wrong here?* *As I mentioned before, I just want to use these label file for diffusion tractography, so if I am heading down the wrong path, I would appreciate advice.* Freesurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c Platform: linux based cluster Thank you! Sara Sims

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