Freesurfer

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17 participants
30099 discussions

Qdec Help
by Abrishamchi, Aurash David 27 Aug '14

27 Aug '14

Hello, I am running Qdec analysis on about 100 subjects and correcting with FDR. Once I do this I click the "find clusters and go to max" button and Qdec gives me a plot of all the data as well as taking me to the max vertex in the #1 cluster. I want to extract the data from the table so that I can put it in excel and calculate some correlations however I cannot find a way to do so without hovering or clicking on each data point and manually entering the values into excel. As you can imagine this is very tedious when there are 100 subjects and 12 regions that we are looking at. Please let me know if there is an alternative way to export the data into excel or even to a word processing file so that the values can be copied and pasted into excel. Apologies for the long e-mail, Let me know if you need any clarification. Best, Aurash Abrishamchi Research Co Op - NCRI - Massachusetts General Hospital 165 Cambridge Street, Suite 600 Boston, MA 02214 P: 617-726-4284 AAbrishamchi(a)mgh.harvard.edu<mailto:AAbrishamchi@mgh.harvard.edu>

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Cortical gray matter surface area
by will brown 27 Aug '14

27 Aug '14

Hi all, I am a little unclear as to how to find the cortical grey matter volume in the stats output files. The ?.aparc.stats file shows: Measure Cortex, WhiteSurfArea, White Surface Total Area, XXXX, mm^2 What about grey? Thanks, Will

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Individual commands in preproc-sess
by Reza Rajimehr 26 Aug '14

26 Aug '14

Hi, I want to use FreeSurfer v5.3 and its FS-FAST for the functional analysis of monkey data. To have a better control on the parameters of the analysis, I prefer to run the individual commands of preproc-sess one-by-one and check the output of each stage before proceeding with the rest of preproc-sess. Specifically I may manually edit the functional-anatomical registration, so I want to check the registration before moving on to the next step in preproc-sess. Also I need to skip the human-specific aspects of the analysis (e.g. Talairaching) if there are such things in preproc-sess. So is there a list of individual commends, in an appropriate order, that are used in preproc-sess? If someone has a routine for monkey data analysis with FreeSurfer v5.3, I would be happy to know about that as well. Thanks, Reza

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White Matter and Pial Edit Question
by Thomas DeRamus 26 Aug '14

26 Aug '14

Dear Freesurfer Experts, I'm working on a younger population (around age 8), and I seem to have an issue with the pial and wm surfaces grabbing dura on the images. I've run gcut, -wsthresh at about 15, and even used the talairach_with_skull_2.lta registration file to no avail, and I'd rather not do manual edits if I don't have to. Now I made the mistake of using a skull-stripped version of my original T1 and feeding into the pipeline before, but those images came out significantly better looking than the raw T1 files. Problem is it thew off the TICV measures by close to 500k compared to the originals. So my question is, would it be feasible or kosher to put the brainmask and wm.mgz values from those skull-stripped images into the problem folders grabbing too much dura and re-running the subjects starting from autorecon2? Thank you. -- *Thomas DeRamus* UAB Department of Psychology, Behavioral Neuroscience Graduate Research Trainee Civitan International Research Center 1719 6th Ave S, Suite 235J, Birmingham, AL 35233 *Phone*: 205-934-0971 *Email:* tpderamus(a)gmail.com, faustus(a)uab.edu

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Color scale in tksurfer
by Katharina Zech 26 Aug '14

26 Aug '14

Dear all, I've got a question: is the color that I get for significant clusters in tksurfer depending on the contrast vector specified? For example: when I get a red cluster and my question of interest would be: "is there a difference between Males and Females regressing out the effect of age and handedness?", then the clusters would pop-up in red for Males being bigger then Woman. Is that correct? Thanks! Katharina

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ERROR: cannot find AFNI command 3dvolreg.afni
by Robby De Pauw 26 Aug '14

26 Aug '14

Dear FreeSurfer As I am trying to preprocess my fMRI data through FsFast, I came across this error: ERROR: cannot find AFNI command 3dvolreg.afni I’m using a mac and bash-shell. I’ve also attached the log-file. This is the command I used: preproc-sess -s GEZ_004_HACO/ -surface fsaverage -mni305 -fwhm 5 -per-run -fsd bold -stc up Regards Robby Robby De Pauw, dra. Ghent University Department of Physiotherapy and Rehabilitation Sciences 3B3 De Pintelaan 185 B-9000 Ghent Robby.DePauw(a)Ugent.be

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labelled tissue segmentation mask back to native
by Alejandra Machado 26 Aug '14

26 Aug '14

Hello, I was wondering if FS has an output mask (labelled volume) for each tissue types (gm+wm+venctricular_csf) that I can then turn into each subject's native space. I understand I can use aseg.mgz or even aparc+aseg.mgz and then run mri_label2vol. But then how do I get correspondent labelling for each subject in it's own native space? Thanks, Alejandra

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Fwd: Re: success and failure of wm surfaces in (almost) identical structural image
by Melanie Ganz 26 Aug '14

26 Aug '14

Thanks to Eugenio, for the tip! We did look at (orig,nu,T1,brainmask,norm,nu,noneck, aseg, wm, filled).mgz. The only one showing a difference where our white matter error occurs is filled.mgz. In some of the other previous images are minor differences around that area, but not overlapping the area. This starts with the brainmask.mgz. The wm.mgz looks almost identical though and this is what is used in making filled.mgz, right? Cheers, Mel and Vincent P.S.: Here's a quick script to visualize all differences: recon1='/data1/vbeliveau/atlas/proc/MR/recon/v0013_good'; %change this recon2='/data1/vbeliveau/atlas/proc/MR/recon/v0013_bad'; %change this dest='/data1/vbeliveau/atlas/test'; %change this img1=MRIread([recon1 '/mri/orig/001.mgz']); img2=MRIread([recon2 '/mri/orig/001.mgz']); img1.vol=img1.vol-img2.vol; MRIwrite(img1,[dest '/diff_raw.mgz']); disp('raw'); sum(img1.vol(:)>10e-4) vol={'orig','nu','T1','brainmask','norm','nu_noneck','aseg','brain','wm','filled'}; for n=1:numel(vol) img1=MRIread([recon1 '/mri/' vol{n} '.mgz']); img2=MRIread([recon2 '/mri/' vol{n} '.mgz']); img1.vol=img1.vol-img2.vol; MRIwrite(img1,[dest '/diff_' vol{n} '.mgz']); disp(vol{n}); sum(img1.vol(:)>10e-4) end -------- Original Message -------- Subject: Re: [Freesurfer] success and failure of wm surfaces in (almost) identical structural image Date: Tue, 26 Aug 2014 14:05:19 +0200 (CEST) From: Eugenio Iglesias <e.iglesias(a)bcbl.eu> To: Melanie Ganz <Melanie.Ganz(a)nru.dk> It'd be really helpful if you looked at where the two pipelines start to diverge. It's apparent that the origs are the same, and that the surfaces are different, but where does the divergence begin? Are the nu.mgz's similar? How about the the brainmask.mgz's? Here's the recon table: https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllDevTable Best, /E Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer ----- Original Message ----- From: "Melanie Ganz" <Melanie.Ganz(a)nru.dk> To: freesurfer(a)nmr.mgh.harvard.edu Sent: Tuesday, August 26, 2014 7:50:23 AM Subject: [Freesurfer] success and failure of wm surfaces in (almost) identical structural image Dear Freesurfer community, We've encountered a strange situation where the pial and wm surface delineation is successful for one image but contains wm (and subsequent pial) errors for another, almost identical structural image (see attached image, red and yellow are for the successful surface and blue and green are for the failed one). We've tried to identify the source for this discrepancy but I'm at a loss. All voxels of the original input images are identical to the 4th decimal and when converted to orig.mgz only a few voxels appear to be different due to rounding, none of which overlap with the wm surface errors. Both images were processed on the same setup (hardware and software, Freesurfer stable 5.3). Unfortunately, this error is quite systematic in my dataset; about 10% of the images show this type of error. Any suggestions on how to investigate this? I've uploaded example of good and bad at recon ftp://surfer.nmr.mgh.harvard.edu/transfer/incoming/failed_wm_recon.tar.gz in case you'd like to have a closer look. Thanks for your help. Vincent and Melanie _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine 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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matrix is ill-conditioned or badly scaled
by Jürgen Hänggi 26 Aug '14

26 Aug '14

Dear FS experts We run mri_glmfit and encountered the following error: INFO: gd2mtx_method is doss Saving design matrix to LTHV_Thickness_LH_correlation_memory2.glmdir/Xg.dat Normalized matrix condition is 1e+08 Design matrix ------------------ -------------------------------- ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08 The command line is as follow: mri_glmfit --y LTHV_lh_thickness.15.mgh --fsgd LTHV_fsgd_correlation_memory2.txt doss --glmdir LTHV_Thickness_LH_correlation_memory2.glmdir --surf average_LTHV_TP1 lh --C LTHV_Design_corr.mat cortex The FSGD and Design files are attached We did not find the problem. Thanks in advance for your help. Regards Jürgen Hänggi ---------------------------------------------------------------------------- Jürgen Hänggi, Ph.D. Division Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi[at]psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) This e-mail (and any attachment/s) contains confidential and/or privileged information. If you are not the intended recipient (or have received this e-mail in error) please notify the sender immediately and destroy this e-mail. Any unauthorised copying, disclosure or distribution of the material in this e-mail is strictly forbidden. ----------------------------------------------------------------------------

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trac-all bvec (nifti & many subjects)
by Barbara Kreilkamp 26 Aug '14

26 Aug '14

Dear Freesurfers, I am trying to run trac-all with many subjects through a configuration file. The first subject gets processed without error, but after that I keep getting errors, that the dwi_orig_flip.mghdti.bvecs file cannot be found. This is my command with the output (below configuration file and the log file) trac-all -prep -c dmrirc_bonn_running2only.txt -no-isrunning INFO: SUBJECTS_DIR is /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients INFO: Diffusion root is /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients Actual FREESURFER_HOME /Applications/freesurfer trac-preproc -c /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/4099/scripts/dmrirc.local -log /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/4099/scripts/trac-all.log -cmd /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/4099/scripts/trac-all.cmd -no-isrunning #------------------------------------- /Applications/freesurfer/bin/trac-preproc #------------------------------------- #@# Image corrections Tue 26 Aug 2014 10:34:54 BST mri_convert /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/4099/data.nii.gz /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/4099/dmri/dwi_orig.nii.gz mri_convert /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/4099/data.nii.gz /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/4099/dmri/dwi_orig.nii.gz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/4099/data.nii.gz... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.999333, -0.0350092, 0.0104045) j_ras = (-0.0349891, 0.999385, 0.00210945) k_ras = (0.010472, -0.001744, 0.999944) writing to /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/4099/dmri/dwi_orig.nii.gz... flip4fsl /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/4099/dmri/dwi_orig.nii.gz /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/4099/dmri/dwi_orig_flip.nii.gz INFO: input image orientation is LAS INFO: input image determinant is -5.02198 fslswapdim /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/4099/dmri/dwi_orig.nii.gz x y z /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/4099/dmri/dwi_orig_flip.nii.gz fslorient -forceradiological /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/4099/dmri/dwi_orig_flip.nii.gz mv -f /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/4099/dmri/dwi_orig_flip.mghdti.bvecs /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/4099/dmri/bvecs mv: rename /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/4099/dmri/dwi_orig_flip.mghdti.bvecs to /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/4099/dmri/bvecs: No such file or directory Darwin NEURO-220.local 13.1.0 Darwin Kernel Version 13.1.0: Wed Apr 2 23:52:02 PDT 2014; root:xnu-2422.92.1~2/RELEASE_X86_64 x86_64 Thanks in advance for all your help! All the best, Barbara My configuration file looks like this: # # This file contains commands that will be run by trac-all before an analysis. # It is used to set all parameters needed for the analysis. # # Remove a parameter from your dmrirc file if you want use the default value. # Parameters that don't have default values must be specified. # # Any other commands that you might want to run before an analysis can be added # to this file. # # Original Author: Anastasia Yendiki # CVS Revision Info: # $Author: ayendiki $ # $Date: 2013/02/16 22:49:06 $ # $Revision: 1.3.2.4 $ # # Copyright © 2011 The General Hospital Corporation (Boston, MA) "MGH" # # Terms and conditions for use, reproduction, distribution and contribution # are found in the 'FreeSurfer Software License Agreement' contained # in the file 'LICENSE' found in the FreeSurfer distribution, and here: # # https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferSoftwareLicense # # Reporting: freesurfer(a)nmr.mgh.harvard.edu # # # FreeSurfer SUBJECTS_DIR # T1 images and FreeSurfer segmentations are expected to be found here # setenv SUBJECTS_DIR /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients # Output directory where trac-all results will be saved # Default: Same as SUBJECTS_DIR # set dtroot = /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients # Subject IDs # set subjlist = ( 3258 3734^20100714^5 3790^20071127^6 3854 4099 4130^20081031^8 4279^20080519^8 4335^20080607^5 449^20070514^4 4585 4594^20081017^4 4597^20081110^5 4695 4928^20090226^12 4969 5018 5040 5125 5141 5236^20100706^12 5239 5346 5351 5377^20100615^14 5658 5948 5968 6091 6116 6189 6369 6541 6671 6770 7064 7174^20110828^5 7220 7231 7241 923^20080410^5 c0039 c0056 c0067 c0132 c0136 c0137 c0187 c0306 c0324 c0337 c0349 c0359 c0389 c0442 c0443 c0474 c0542 c0627 c0660 c0688 c0773 c1088 c3422 c3667 c3728 c3768 c3789 c3826 c4932 c5279 c5511 L4974 L4995 L5041 L5222 L5242 L5302 L5303 L5309 L5416 L5424 L5433 L5436 L5438 L5447 L5480 L5777 L6017 L6023 L6077 L6078 L6126 L6178 L6300 L6522 L6549 L6794 R1087 R4523 R4700 R4858 R5208 R5219 R5412 R5844 R5973 R5974 R6058 R6081 R6297 R6596 R6774 R7192 ) # In case you want to analyze only Huey and Louie # Default: Run analysis on all subjects set runlist = (5) # Input diffusion DICOMs (file names relative to dcmroot) # If original DICOMs don't exist, these can be in other image format # but then bvecfile, bvalfile, and nb0 must be specified (see below) set dcmlist = ( /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/3258/data.nii.gz /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/3734^20100714^5/data.nii.gz /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/3790^20071127^6/data.nii.gz /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/3854/data.nii.gz /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/4099/data.nii.gz /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/4130^20081031^8/data.nii.gz /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/4279^20080519^8/data.nii.gz /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/4335^20080607^5/data.nii.gz /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/449^20070514^4/data.nii.gz /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/4585/data.nii.gz /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/4594^20081017^4/data.nii.gz /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/4597^20081110^5/data.nii.gz /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/4695/data.nii.gz /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/4928^20090226^12/data.nii.gz /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/4969/data.nii.gz /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/5018/data.nii.gz /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/5040/data.nii.gz 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/Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/5948/data.nii.gz /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/5968/data.nii.gz /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/6091/data.nii.gz /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/6116/data.nii.gz /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/6189/data.nii.gz /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/6369/data.nii.gz /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/6541/data.nii.gz /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/6671/data.nii.gz /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/6770/data.nii.gz /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/7064/data.nii.gz /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/7174^20110828^5/data.nii.gz /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/7220/data.nii.gz /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/7231/data.nii.gz /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/7241/data.nii.gz /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/923^20080410^5/data.nii.gz /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/c0039/data.nii.gz /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/c0056/data.nii.gz /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/c0067/data.nii.gz /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/c0132/data.nii.gz /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/c0136/data.nii.gz /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/c0137/data.nii.gz /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/c0187/data.nii.gz /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/c0306/data.nii.gz /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/c0324/data.nii.gz /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/c0337/data.nii.gz /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/c0349/data.nii.gz /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/c0359/data.nii.gz /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/c0389/data.nii.gz /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/c0442/data.nii.gz /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/c0443/data.nii.gz /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/c0474/data.nii.gz /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/c0542/data.nii.gz /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/c0627/data.nii.gz /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/c0660/data.nii.gz /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/c0688/data.nii.gz /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/c0773/data.nii.gz /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/c1088/data.nii.gz /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/c3422/data.nii.gz /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/c3667/data.nii.gz /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/c3728/data.nii.gz /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/c3768/data.nii.gz /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/c3789/data.nii.gz /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/c3826/data.nii.gz /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/c4932/data.nii.gz /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/c5279/data.nii.gz /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/c5511/data.nii.gz /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/L4974/data.nii.gz /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/L4995/data.nii.gz /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/L5041/data.nii.gz /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/L5222/data.nii.gz /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/L5242/data.nii.gz /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/L5302/data.nii.gz /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/L5303/data.nii.gz /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/L5309/data.nii.gz /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/L5416/data.nii.gz /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/L5424/data.nii.gz /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/L5433/data.nii.gz /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/L5436/data.nii.gz /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/L5438/data.nii.gz /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/L5447/data.nii.gz /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/L5480/data.nii.gz /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/L5777/data.nii.gz /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/L6017/data.nii.gz /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/L6023/data.nii.gz /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/L6077/data.nii.gz /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/L6078/data.nii.gz /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/L6126/data.nii.gz /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/L6178/data.nii.gz /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/L6300/data.nii.gz /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/L6522/data.nii.gz /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/L6549/data.nii.gz /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/L6794/data.nii.gz /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/R1087/data.nii.gz /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/R4523/data.nii.gz /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/R4700/data.nii.gz /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/R4858/data.nii.gz /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/R5208/data.nii.gz /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/R5219/data.nii.gz /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/R5412/data.nii.gz /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/R5844/data.nii.gz /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/R5973/data.nii.gz /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/R5974/data.nii.gz /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/R6058/data.nii.gz /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/R6081/data.nii.gz /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/R6297/data.nii.gz /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/R6596/data.nii.gz /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/R6774/data.nii.gz /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/R7192/data.nii.gz ) # Diffusion gradient table # Must be specified if inputs are not MGH DICOMs # Three-column format, one row for each volume in the diffusion data set # Default: Read from DICOM header # set bveclist = ( /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/3258/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/3734^20100714^5/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/3790^20071127^6/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/3854/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/4099/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/4130^20081031^8/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/4279^20080519^8/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/4335^20080607^5/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/449^20070514^4/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/4585/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/4594^20081017^4/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/4597^20081110^5/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/4695/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/4928^20090226^12/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/4969/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/5018/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/5040/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/5125/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/5141/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/5236^20100706^12/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/5239/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/5346/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/5351/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/5377^20100615^14/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/5658/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/5948/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/5968/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/6091/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/6116/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/6189/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/6369/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/6541/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/6671/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/6770/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/7064/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/7174^20110828^5/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/7220/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/7231/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/7241/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/923^20080410^5/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/c0039/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/c0056/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/c0067/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/c0132/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/c0136/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/c0137/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/c0187/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/c0306/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/c0324/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/c0337/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/c0349/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/c0359/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/c0389/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/c0442/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/c0443/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/c0474/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/c0542/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/c0627/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/c0660/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/c0688/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/c0773/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/c1088/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/c3422/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/c3667/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/c3728/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/c3768/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/c3789/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/c3826/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/c4932/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/c5279/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/c5511/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/L4974/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/L4995/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/L5041/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/L5222/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/L5242/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/L5302/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/L5303/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/L5309/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/L5416/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/L5424/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/L5433/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/L5436/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/L5438/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/L5447/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/L5480/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/L5777/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/L6017/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/L6023/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/L6077/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/L6078/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/L6126/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/L6178/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/L6300/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/L6522/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/L6549/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/L6794/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/R1087/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/R4523/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/R4700/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/R4858/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/R5208/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/R5219/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/R5412/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/R5844/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/R5973/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/R5974/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/R6058/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/R6081/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/R6297/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/R6596/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/R6774/data.bvec /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/R7192/data.bvec ) # set bvallist = ( /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/3258/data.bval /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/3734^20100714^5/data.bval /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/3790^20071127^6/data.bval /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/3854/data.bval /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/4099/data.bval /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/4130^20081031^8/data.bval /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/4279^20080519^8/data.bval /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/4335^20080607^5/data.bval /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/449^20070514^4/data.bval /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/4585/data.bval /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/4594^20081017^4/data.bval /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/4597^20081110^5/data.bval /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/4695/data.bval /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/4928^20090226^12/data.bval /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/4969/data.bval /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/5018/data.bval /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/5040/data.bval /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/5125/data.bval /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/5141/data.bval /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/5236^20100706^12/data.bval /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/5239/data.bval /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/5346/data.bval /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/5351/data.bval /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/5377^20100615^14/data.bval /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/5658/data.bval /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/5948/data.bval /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/5968/data.bval /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/6091/data.bval /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/6116/data.bval /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/6189/data.bval /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/6369/data.bval /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/6541/data.bval /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/6671/data.bval /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/6770/data.bval /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/7064/data.bval /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/7174^20110828^5/data.bval /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/7220/data.bval /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/7231/data.bval /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/7241/data.bval /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/923^20080410^5/data.bval /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/c0039/data.bval /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/c0056/data.bval /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/c0067/data.bval /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/c0132/data.bval /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/c0136/data.bval /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/c0137/data.bval /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/c0187/data.bval /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/c0306/data.bval /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/c0324/data.bval /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/c0337/data.bval /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/c0349/data.bval /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/c0359/data.bval /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/c0389/data.bval /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/c0442/data.bval /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/c0443/data.bval /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/c0474/data.bval /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/c0542/data.bval /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/c0627/data.bval /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/c0660/data.bval /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/c0688/data.bval /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/c0773/data.bval /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/c1088/data.bval /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/c3422/data.bval /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/c3667/data.bval /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/c3728/data.bval /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/c3768/data.bval /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/c3789/data.bval /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/c3826/data.bval /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/c4932/data.bval /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/c5279/data.bval /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/c5511/data.bval /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/L4974/data.bval /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/L4995/data.bval /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/L5041/data.bval /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/L5222/data.bval /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/L5242/data.bval /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/L5302/data.bval /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/L5303/data.bval /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/L5309/data.bval /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/L5416/data.bval /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/L5424/data.bval /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/L5433/data.bval /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/L5436/data.bval /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/L5438/data.bval /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/L5447/data.bval /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/L5480/data.bval /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/L5777/data.bval /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/L6017/data.bval /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/L6023/data.bval /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/L6077/data.bval /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/L6078/data.bval /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/L6126/data.bval /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/L6178/data.bval /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/L6300/data.bval /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/L6522/data.bval /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/L6549/data.bval /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/L6794/data.bval /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/R1087/data.bval /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/R4523/data.bval /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/R4700/data.bval /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/R4858/data.bval /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/R5208/data.bval /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/R5219/data.bval /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/R5412/data.bval /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/R5844/data.bval /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/R5973/data.bval /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/R5974/data.bval /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/R6058/data.bval /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/R6081/data.bval /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/R6297/data.bval /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/R6596/data.bval /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/R6774/data.bval /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/R7192/data.bval ) # Number of low-b images # Must be specified if inputs are not DICOM # Default: Read from DICOM header # set nb0 = 6 # Perform registration-based B0-inhomogeneity compensation? # Default: 0 (no) # # Input B0 field map magnitude DICOMs (file names relative to dcmroot) # Only used if dob0 = 1 # Default: None # # Input B0 field map phase DICOMs (file names relative to dcmroot) # Only used if dob0 = 1 # Default: None # # Echo spacing for field mapping sequence (from sequence printout) # Only used if dob0 = 1 # Default: None # # Perform registration-based eddy-current compensation? # Default: 1 (yes) # set doeddy = 1 # Rotate diffusion gradient vectors to match eddy-current compensation? # Only used if doeddy = 1 # Default: 1 (yes) # set dorotbvecs = 1 # Fractional intensity threshold for BET mask extraction from low-b images # This mask is used only if usemaskanat = 0 # Default: 0.3 set thrbet = 0.2 # Perform diffusion-to-T1 registration by flirt? # Default: 0 (no) # set doregflt = 0 # Perform diffusion-to-T1 registration by bbregister? # Default: 1 (yes) # set doregbbr = 1 # Perform registration of T1 to MNI template? # Default: 1 (yes) # set doregmni = 1 # MNI template # Only used if doregmni = 1 # Default: $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz # # Perform registration of T1 to CVS template? # Default: 0 (no) # set doregcvs = 0 # CVS template subject ID # Only used if doregcvs = 1 # Default: cvs_avg35 # # Parent directory of the CVS template subject # Only used if doregcvs = 1 # Default: $FREESURFER_HOME/subjects # # Use brain mask extracted from T1 image instead of low-b diffusion image? # Has no effect if there is no T1 data # Default: 1 (yes) # set usemaskanat = 1 # Paths to reconstruct # Default: All paths in the atlas # # Number of path control points # It can be a single number for all paths or a different number for each of the # paths specified in pathlist # Default: 7 for the forceps major, 6 for the corticospinal tract, # 4 for the angular bundle, and 5 for all other paths # # List of training subjects # This text file lists the locations of training subject directories # Default: $FREESURFER_HOME/trctrain/trainlist.txt # set trainfile = $FREESURFER_HOME/trctrain/trainlist.txt # Number of "sticks" (anisotropic diffusion compartments) in the bedpostx # ball-and-stick model # Default: 2 # set nstick = 2 # Number of MCMC burn-in iterations # (Path samples drawn initially by MCMC algorithm and discarded) # Default: 200 # set nburnin = 200 # Number of MCMC iterations # (Path samples drawn by MCMC algorithm and used to estimate path distribution) # Default: 5000 # set nsample = 7500 # Frequency with which MCMC path samples are retained for path distribution # Default: 5 (keep every 5th sample) # set nkeep = 5 # Reinitialize path reconstruction? # This is an option of last resort, to be used only if one of the reconstructed # pathway distributions looks like a single curve. This is a sign that the # initial guess for the pathway was problematic, perhaps due to poor alignment # between the individual and the atlas. Setting the reinit parameter to 1 and # rerunning "trac-all -prior" and "trac-all -path", only for the specific # subjects and pathways that had this problem, will attempt to reconstruct them # with a different initial guess. # Default: 0 (do not reinitialize) # set reinit = 0 My trac-all log is this Tue 26 Aug 2014 10:34:51 BST /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients /Applications/freesurfer/bin/trac-all -prep -c dmrirc_bonn_running2only.txt -no-isrunning Subject 4099 SUBJECTS_DIR /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients FREESURFER_HOME /Applications/freesurfer Actual FREESURFER_HOME /Applications/freesurfer build-stamp.txt: freesurfer-Darwin-lion-stable-pub-v5.3.0 NEURO-220 NEURO-220.local Darwin NEURO-220.local 13.1.0 Darwin Kernel Version 13.1.0: Wed Apr 2 23:52:02 PDT 2014; root:xnu-2422.92.1~2/RELEASE_X86_64 x86_64 cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited descriptors 256 memorylocked unlimited maxproc 709 PhysMem: 16G used (3274M wired), 48G unused. ######################################## Program versions: $Id: trac-all,v 1.22.2.12 2013/02/23 02:01:02 ayendiki Exp $ mri_convert --all-info ProgramName: mri_convert ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/08/26-09:34:53-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ User: NEURO-220 Machine: NEURO-220.local Platform: Darwin PlatformVersion: 13.1.0 CompilerName: GCC CompilerVersion: 40200 FLIRT version 6.0 $Id: bbregister,v 1.49.2.3 2013/03/25 18:04:53 greve Exp $ $Id: mri_cvs_register,v 1.15.2.12 2013/02/09 00:37:37 nicks Exp $ ProgramName: dmri_train ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/08/26-09:34:53-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: User: NEURO-220 Machine: NEURO-220.local Platform: Darwin PlatformVersion: 13.1.0 CompilerName: GCC CompilerVersion: 40200 ProgramName: dmri_paths ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/08/26-09:34:53-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: User: NEURO-220 Machine: NEURO-220.local Platform: Darwin PlatformVersion: 13.1.0 CompilerName: GCC CompilerVersion: 40200 ProgramName: dmri_pathstats ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/08/26-09:34:53-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: User: NEURO-220 Machine: NEURO-220.local Platform: Darwin PlatformVersion: 13.1.0 CompilerName: GCC CompilerVersion: 40200 ProgramName: dmri_mergepaths ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/08/26-09:34:53-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: User: NEURO-220 Machine: NEURO-220.local Platform: Darwin PlatformVersion: 13.1.0 CompilerName: GCC CompilerVersion: 40200 New invocation of trac-preproc NEURO-220 NEURO-220.local Darwin NEURO-220.local 13.1.0 Darwin Kernel Version 13.1.0: Wed Apr 2 23:52:02 PDT 2014; root:xnu-2422.92.1~2/RELEASE_X86_64 x86_64 cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited descriptors 256 memorylocked unlimited maxproc 709 PhysMem: 16G used (3275M wired), 48G unused. #------------------------------------- /Applications/freesurfer/bin/trac-preproc #------------------------------------- #@# Image corrections Tue 26 Aug 2014 10:34:54 BST mri_convert /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/4099/data.nii.gz /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/4099/dmri/dwi_orig.nii.gz mri_convert /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/4099/data.nii.gz /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/4099/dmri/dwi_orig.nii.gz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/4099/data.nii.gz... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.999333, -0.0350092, 0.0104045) j_ras = (-0.0349891, 0.999385, 0.00210945) k_ras = (0.010472, -0.001744, 0.999944) writing to /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/4099/dmri/dwi_orig.nii.gz... flip4fsl /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/4099/dmri/dwi_orig.nii.gz /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/4099/dmri/dwi_orig_flip.nii.gz INFO: input image orientation is LAS INFO: input image determinant is -5.02198 fslswapdim /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/4099/dmri/dwi_orig.nii.gz x y z /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/4099/dmri/dwi_orig_flip.nii.gz fslorient -forceradiological /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/4099/dmri/dwi_orig_flip.nii.gz mv -f /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/4099/dmri/dwi_orig_flip.mghdti.bvecs /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/4099/dmri/bvecs mv: rename /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/4099/dmri/dwi_orig_flip.mghdti.bvecs to /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/4099/dmri/bvecs: No such file or directory Darwin NEURO-220.local 13.1.0 Darwin Kernel Version 13.1.0: Wed Apr 2 23:52:02 PDT 2014; root:xnu-2422.92.1~2/RELEASE_X86_64 x86_64 trac-preproc exited with ERRORS at Tue 26 Aug 2014 10:36:26 BST

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