Freesurfer October 2017

freesurfer@nmr.mgh.harvard.edu

119 participants
179 discussions

License files with FreeSurfer 5.2.0
by Mike Schmidt 09 Oct '17

09 Oct '17

I am re-running some old scans on current hardware to do comparisons with 5.2.0 output from old hardware, 5.2.0 output from current hardware, and current 6.0.0 output, all of the same input image. I am aware that FreeSurfer 5.2.0 is deprecated and don't intend to use its output, per se. My problem is that I have copied a .license file (from February 2017) that works successfully with version 6.0.0 (known-good) into FreeSurfer 5.2.0's FREESURFER_HOME and FreeSurfer 5.2.0 finds the file, but says it is invalid. Renaming the .license file to license.txt resulted in it not being found at all. I've even retrieved an old license file (from prior to April 2015) from backup that I used to use (email address no longer exists), thinking I had used it with 5.2.0 in the past, but it is also reported as invalid. I've read in this forum that 6.0.0 uses a different license file format due to libcrypt changes. But I can't seem to get new or old licenses to work. Is it possible to register for a replacement old-style license? Or is there another way to get 5.2.0 to work? I have not applied for a new license as I have one that already works with 6.0.0 and have assumed another new one will work the same. Thank you for any assistance, Mike Schmidt

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Re: [Freesurfer] qdec.table_ref
by Martin Reuter 09 Oct '17

09 Oct '17

Hi Amy, please send your questions to the freesurfer email list . Try replacing ID with fsid , also you may need to fix the white spaces (replace multiple spaces with a single space or tab). Best, Martin > On 9. Oct 2017, at 03:09, 田阿敏 <237416567(a)qq.com> wrote: > > > Hi~ > > I am Amy from Zhejiang University in China. When I run QDEC to load the file qdec.table.dat, I always get this info: > > Loading data table /Applications/freesurfer/subjects/qdec/qdec.table.dat... > ERROR: QdecDataTable::Load did not find a column named 'fsid', 'ID', or 'Subject' in the first column of /Applications/freesurfer/subjects/qdec/qdec.table.dat! > Error loading the data table. > > > Attached are the files that I made to load the subjects information. > What's wrong? > ------------------ > 田阿敏 Tian Amin > 13071892606 > amintian(a)zju.edu.cn, 237416567(a)qq.com <mailto:237416567@qq.com> > Master Degree Candidate, > Zhejiang University Interdisciplinary Institute of Neuroscience and Technology, ZIINT. > Huajiachi Campus, No. 268 Kaixuan Road, Jianggan District, Hangzhou, Zhejiang Province, China, 310029. > > > <qdec.table_ref.dat><qdec.table_ref2.dat><qdec.table.dat>

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qdec.table_ref
by 田阿敏 08 Oct '17

08 Oct '17

Hi~ I am Amy from Zhejiang University in China. When I run QDEC to load the file qdec.table.dat, I always get this info: Loading data table /Applications/freesurfer/subjects/qdec/qdec.table.dat... ERROR: QdecDataTable::Load did not find a column named 'fsid', 'ID', or 'Subject' in the first column of /Applications/freesurfer/subjects/qdec/qdec.table.dat! Error loading the data table. Attached are the files that I made to load the subjects information. What's wrong? ------------------ 田阿敏 Tian Amin 13071892606 amintian(a)zju.edu.cn, 237416567(a)qq.com Master Degree Candidate, Zhejiang University Interdisciplinary Institute of Neuroscience and Technology, ZIINT. Huajiachi Campus, No. 268 Kaixuan Road, Jianggan District, Hangzhou, Zhejiang Province, China, 310029.

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recon-all exits with errors
by Ali Radaideh 07 Oct '17

07 Oct '17

Dear FreeSurfer Experts, I have just launched a new project and collected new T1 weighted images (as my previous ones) and started processing them using FreeSurfer. Unfortunaely non of them works with FreeSurfer. When I run recon-all -autorecon-all -s subjecname, I get the following error: #@# Talairach Fri Oct 6 09:20:02 EEST 2017 /home/ali/processing/Farah_hospital/MR.BASHEER_IGIAM/mcropped_noor/mri mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz Linux ali-XPS-L501X 4.8.0-54-generic #57-Ubuntu SMP Wed May 24 10:21:44 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux recon-all -s mcropped_noor exited with ERRORS at Fri Oct 6 09:20:05 EEST 2017 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting I have checked my images and they look fine and they are similar to the ones I have processed a year ago. I have searched for a solution to this error but unfortunately I did not find any. Could you please help me on this? Thanks alot in advance, Ali -- *Ali M. Al-Radaideh. PhDDepartment of Medical ImagingFaculty of Allied Health SciencesThe Hashemite University, Zarqa, JordanW.phone +962 5 3903333 ext.5422, 5355, 5364Email: ali.radaideh(a)hu.edu.jo <ali.radaideh(a)hu.edu.jo>* *webpage: http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM= <http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=>*

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Fw: Re: 1 mistake in FreeSurfer
by 田阿敏 07 Oct '17

07 Oct '17

------------------ 田阿敏 Tian Amin 13071892606 amintian(a)zju.edu.cn, 237416567(a)qq.com Master Degree Candidate, Zhejiang University Interdisciplinary Institute of Neuroscience and Technology, ZIINT. Huajiachi Campus, No. 268 Kaixuan Road, Jianggan District, Hangzhou, Zhejiang Province, China, 310029. ------------------ Original ------------------ From: "ltirrell";<ltirrell(a)nmr.mgh.harvard.edu>; Date: Sat, Oct 7, 2017 07:26 AM To: "田阿敏"<237416567(a)qq.com>; Subject: Re: 1 mistake in FreeSurfer Hello, This seems to be a problem with the version of python you're using. If you can use python 2.7, the issue should go away. If you continue to run into any issues, you should contact the freesurfer mailing list (freesurfer(a)nmr.mgh.harvard.edu) and they may be able to help. Best, Lee On Fri, 6 Oct 2017, ?????? wrote: > > Hi~ > > > Here is error report when I run aparcstats2table. Maybe adding the missing parentheses could solve the > problem. Thanks~ > > > > tianamindeMacBook-Pro:subjects amytian$ aparcstats2table -s subj1 --hemi lh > > File "/Applications/freesurfer/bin/aparcstats2table", line 156 > > print 'ERROR: atleast 1 subject must be provided' > > ^ > > SyntaxError: Missing parentheses in call to 'print' > > > > > ------------------ > ?????? Tian Amin > 13071892606 > amintian(a)zju.edu.cn, 237416567(a)qq.com > Master Degree Candidate, > Zhejiang University Interdisciplinary Institute of Neuroscience and Technology, ZIINT. > Huajiachi Campus, No. 268 Kaixuan Road, Jianggan District, Hangzhou, Zhejiang Province, China, 310029. > > > > 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 at http://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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Descriptions of regions in Yeo 2011 Network atlases
by Mehta, Chintan 06 Oct '17

06 Oct '17

Dear Freesurfer users, I am examining the Yeo 2011 17 Network atlases in Freesurfer 6.0. The regions are labeled 1 through 17. Is there a reference table mapping these numbers with the names of cognitive networks described by Yeo, et al. (2011) (<https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3174820/>https://www.ncbi.nlm.nih.gov/pubmed/21653723)? For example, would network 1 correspond to visual networks? I cannot find descriptions in the readme files except the color look-up table. Thank you. Best, Chintan

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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.

1 0

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-

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Freesurfer October 2017