Freesurfer

freesurfer@nmr.mgh.harvard.edu

30132 discussions

create high resolution ribbon
by Rouhollah Abdollahi 13 Dec '12

13 Dec '12

Dear Freesurfer experts, I tried to create high resolution ribbon from pial and white surfaces. Actually I found this question in mailing list but the answer was not clear. I have a register.dat file and white and pial surfaces. My aim is to create a high resolution ribbon from those by using register.dat. What is the stream line or commands to do that? -- Best Regards Rouhollah Abdollahi

2 1

Re: [Freesurfer] WM-hypointensities
by Gabriel Gonzalez Escamilla 12 Dec '12

12 Dec '12

2 1

WM-hypointensities
by Gabriel Gonzalez Escamilla 12 Dec '12

12 Dec '12

2 3

Per-vertex regressors
by Lars M. Rimol 12 Dec '12

12 Dec '12

Hi all, I want to use the --prv (per vertex regressors) option in mri_glmfit, but there is very little information in the Wiki and I couldn't find any relevant info in the mailing list. I have two .mgz files, one contains the dependent variable, the other is the source of my pvr. I tried loading one column from the second file and appending it to the design matrix in Matlab for each vertex (in a loop), but it's too time consuming to be feasible. Someone tipped me about the pvr option in mri_glmfit but from the Wiki (see below) it seems I would have to load the regressors individually here as well..? What is pvr1, pvr2 etc. in the example below? Text files? That's either going to be one very long command line or I have to use a loop here too (probably in Matlab). Is there any way to tell mri_glmfit. "for each vertex in the dependent variable file, take the corresponding vector from the pvr-file and append it to the design matrix"? [from the WIki:] --pvr pvr1 <--prv pvr2 ...> Per-voxel (or vertex) regressors (PVR). Normally, the design matrix is 'global', ie, the same matrix is used at each voxel. This option allows the user to specify voxel-specific regressors to append to the design matrix. Note: the contrast matrices must include columns for these components. Thank you! -- yours, Lars M. Rimol, PhD Division of Mental Health and Addiction Institute of Clinical Medicine University of Oslo P.O. Box 85 Vinderen, 0319 Oslo, Norway

2 1

clarifications about running bedpost instead of tracl-all step 2
by s0675204 12 Dec '12

12 Dec '12

Hello, thank you for your help with the first steps of running Tracula. I was trying to run trac-all step 3 (paths), but was getting an error with the mergedph1samples file. I saw on the mailbase that you have suggested to run bedpost directly to fix this I have 3 questions about this: 1) do I need to delete any of the (temporary?) files or folders created by trac-all step 2 before running bedpost 2) should I run bedpost INSTEAD of trac-all step 2 for the remaining subjects? 3) you have suggested on the list to run bedpost as: bedpostx /usr/local/freesurfer/subjects/C001/dmri is this the same dmri folder as created by tracula step 1 (for each subject) Thank you so much for your help with this - I really appreciate it best wishes Prerona On 10 December 2012 19:54, Anastasia Yendiki <ayendiki(a)nmr.mgh.harvard.edu> wrote: > > I'm guessing that this shows up in the scripts/trac-all.log of a particular > subject? Then it applies to that subject. > > > On Mon, 10 Dec 2012, s0675204 wrote: > >> Hello >> >> My trac- preproc has completed. However, I am confused about the >> status message. It says: >> >> #------------------------------------- >> trac-preproc finished without error at Mon Dec 10 16:32:20 EST 2012 >> ERROR: cannot find /home/canlilab/SBU/data/recon_output/00387 >> >> Does this mean it was completed succesfully for everyone or everyone >> but that 00387 person? >> >> Is there any way I can verify this? >> >> thank you so much for your help >> >> best wishes, >> >> Prerona >> >> >> On 8 December 2012 13:38, Anastasia Yendiki >> <ayendiki(a)nmr.mgh.harvard.edu> wrote: >>> >>> >>> In your dmrirc, you define multiple subjects, but only one bvecfile and >>> one >>> bvalfile that are used for all subjects. >>> >>> >>> On Sat, 8 Dec 2012, s0675204 wrote: >>> >>>> the values are the same but each subject has an individual bvec & bval >>>> file. so it depends on how the script will read it? >>>> >>>> On 8 December 2012 00:03, Anastasia Yendiki >>>> <ayendiki(a)nmr.mgh.harvard.edu> wrote: >>>>> >>>>> >>>>> >>>>> Are the bvecs/bvals not the same for all subjects? >>>>> >>>>> >>>>> On Fri, 7 Dec 2012, s0675204 wrote: >>>>> >>>>>> oh! i thought this was how these were meant to be! i will do that. >>>>>> sadly i left the lab and came home for the day but i will try it as >>>>>> soon as i am back and let you know! >>>>>> thank you so much! do we have to do this for each subject or just one >>>>>> time? >>>>>> >>>>>> >>>>>> >>>>>> On 7 December 2012 23:51, Anastasia Yendiki >>>>>> <ayendiki(a)nmr.mgh.harvard.edu> wrote: >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> I see. Can you try formatting them in columns (1 column for the bvals >>>>>>> and >>>>>>> 3 >>>>>>> columns for the bvecs)? >>>>>>> >>>>>>> >>>>>>> On Fri, 7 Dec 2012, s0675204 wrote: >>>>>>> >>>>>>>> yes! these are the original files >>>>>>>> >>>>>>>> well these are the files i pointed to in my config file. and i think >>>>>>>> the script copies them over to the dmrirc folder? >>>>>>>> >>>>>>>> best wishes, >>>>>>>> >>>>>>>> Prerona >>>>>>>> >>>>>>>> >>>>>>>> On 7 December 2012 23:38, Anastasia Yendiki >>>>>>>> <ayendiki(a)nmr.mgh.harvard.edu> wrote: >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> Yes, I can see that each of the bvecs/bvals files is one long line. >>>>>>>>> Was >>>>>>>>> that >>>>>>>>> the case for the original files that you specified in the dmrirc? >>>>>>>>> >>>>>>>>> >>>>>>>>> On Fri, 7 Dec 2012, s0675204 wrote: >>>>>>>>> >>>>>>>>>> Hi Anastasia >>>>>>>>>> >>>>>>>>>> I had attached the files, but maybe they did not go through to the >>>>>>>>>> mailing list? So I am sending them to your email id. Hope this is >>>>>>>>>> okay >>>>>>>>>> >>>>>>>>>> best wishes, >>>>>>>>>> >>>>>>>>>> Prerona >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> ---------- Forwarded message ---------- >>>>>>>>>> From: s0675204 <s0675204(a)sms.ed.ac.uk> >>>>>>>>>> Date: 7 December 2012 19:44 >>>>>>>>>> Subject: Re: [Freesurfer] Running Tracula: trac-preproc exited >>>>>>>>>> with >>>>>>>>>> ERRORS >>>>>>>>>> To: freesurfer(a)nmr.mgh.harvard.edu >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> Hello >>>>>>>>>> >>>>>>>>>> I think I spoke to soon! >>>>>>>>>> >>>>>>>>>> It ended with errors again. >>>>>>>>>> >>>>>>>>>> I get the error message: "bvecs and bvals don't have the same >>>>>>>>>> number >>>>>>>>>> of >>>>>>>>>> entries" >>>>>>>>>> >>>>>>>>>> I saw on some older messages on the mail-base you said that we >>>>>>>>>> need >>>>>>>>>> to >>>>>>>>>> check that the number of entries in the bvals is same as and bvecs >>>>>>>>>> is >>>>>>>>>> 3 times as much as the number of volumes. I have checked that this >>>>>>>>>> is >>>>>>>>>> the case >>>>>>>>>> >>>>>>>>>> I am wondering if it is some formatting problem? there are no >>>>>>>>>> spaces >>>>>>>>>> at the end of the file. and there are no end of line markers >>>>>>>>>> either. >>>>>>>>>> >>>>>>>>>> Please could you advise me? I have attached the files and also >>>>>>>>>> pasted >>>>>>>>>> the contents below >>>>>>>>>> >>>>>>>>>> My config file is still the same (as pasted below) except I tried >>>>>>>>>> changing >>>>>>>>>> nb0 to 2 >>>>>>>>>> >>>>>>>>>> (# Number of low-b images >>>>>>>>>> # Must be specified if inputs are not DICOM >>>>>>>>>> # Default: Read from DICOM header >>>>>>>>>> # >>>>>>>>>> set nb0 = 2) >>>>>>>>>> >>>>>>>>>> best wishes, >>>>>>>>>> >>>>>>>>>> Prerona >>>>>>>>>> >>>>>>>>>> ========================================================= >>>>>>>>>> bvals: >>>>>>>>>> >>>>>>>>>> 0 800 800 800 800 800 800 800 800 800 800 800 800 800 800 800 800 >>>>>>>>>> 800 >>>>>>>>>> 800 800 800 0 800 800 800 800 800 800 800 800 800 800 800 800 800 >>>>>>>>>> 800 >>>>>>>>>> 800 800 800 800 800 800 >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> bvecs: >>>>>>>>>> >>>>>>>>>> 0 0.99864840507507 0.01463935524225 0.01274211052805 >>>>>>>>>> 0.85177010297775 >>>>>>>>>> 0.86449736356735 0.85295587778091 0.83894062042236 0.7912425994873 >>>>>>>>>> 0.51641523838043 0.46147873997688 0.54209464788436 >>>>>>>>>> 0.44143822789192 >>>>>>>>>> 0.52723878622055 0.4250853061676 0.51590526103973 0.43744987249374 >>>>>>>>>> 0.50455766916275 0.05208261311054 0.06073396280407 >>>>>>>>>> 0.00979638285934 >>>>>>>>>> 0 >>>>>>>>>> 0.99864840507507 0.01463935524225 0.01274211052805 >>>>>>>>>> 0.85177010297775 >>>>>>>>>> 0.86449736356735 0.85295587778091 0.83894062042236 0.7912425994873 >>>>>>>>>> 0.51641523838043 0.46147873997688 0.54209464788436 >>>>>>>>>> 0.44143822789192 >>>>>>>>>> 0.52723878622055 0.4250853061676 0.51590526103973 0.43744987249374 >>>>>>>>>> 0.50455766916275 0.05208261311054 0.06073396280407 >>>>>>>>>> 0.00979638285934 >>>>>>>>>> 0 >>>>>>>>>> -0.00687454920262 0.96709138154983 0.62002921104431 >>>>>>>>>> 0.52092331647872 >>>>>>>>>> 0.18501849472522 -0.42448142170906 -0.44344407320022 >>>>>>>>>> 0.15539556741714 >>>>>>>>>> 0.60610836744308 0.88347893953323 0.71210372447967 >>>>>>>>>> 0.30400663614273 >>>>>>>>>> -0.23736105859279 -0.70398008823394 -0.85636389255523 >>>>>>>>>> -0.73376137018203 -0.22848516702652 -0.00803200621157 >>>>>>>>>> 0.51328992843627 >>>>>>>>>> 0.93218487501144 0 -0.00687454920262 0.96709138154983 >>>>>>>>>> 0.62002921104431 >>>>>>>>>> 0.52092331647872 0.18501849472522 -0.42448142170906 >>>>>>>>>> -0.44344407320022 >>>>>>>>>> 0.15539556741714 0.60610836744308 0.88347893953323 >>>>>>>>>> 0.71210372447967 >>>>>>>>>> 0.30400663614273 -0.23736105859279 -0.70398008823394 >>>>>>>>>> -0.85636389255523 >>>>>>>>>> -0.73376137018203 -0.22848516702652 -0.00803200621157 >>>>>>>>>> 0.51328992843627 >>>>>>>>>> 0.93218487501144 0 0.05151799321174 -0.2540076971054 >>>>>>>>>> -0.78447526693344 >>>>>>>>>> 0.05591572076082 -0.46734625101089 -0.3037790954113 >>>>>>>>>> 0.31549325585365 >>>>>>>>>> 0.5914282798767 0.60493636131286 0.08063688874244 >>>>>>>>>> -0.44614082574844 >>>>>>>>>> -0.84422290325164 -0.81589156389236 -0.56895911693573 >>>>>>>>>> -0.02196817658841 0.51983833312988 0.83259600400924 >>>>>>>>>> 0.99861049652099 >>>>>>>>>> 0.85606354475021 0.36184993386268 0 0.05151799321174 >>>>>>>>>> -0.2540076971054 >>>>>>>>>> -0.78447526693344 0.05591572076082 -0.46734625101089 >>>>>>>>>> -0.3037790954113 >>>>>>>>>> 0.31549325585365 0.5914282798767 0.60493636131286 0.08063688874244 >>>>>>>>>> -0.44614082574844 -0.84422290325164 -0.81589156389236 >>>>>>>>>> -0.56895911693573 -0.02196817658841 0.51983833312988 >>>>>>>>>> 0.83259600400924 >>>>>>>>>> 0.99861049652099 0.85606354475021 0.36184993386268 >>>>>>>>>> On 7 December 2012 14:08, Anastasia Yendiki >>>>>>>>>> <ayendiki(a)nmr.mgh.harvard.edu> wrote: >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> Great, I love easy problems :) >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> On Fri, 7 Dec 2012, s0675204 wrote: >>>>>>>>>>> >>>>>>>>>>>> Thank you! It's chugging away now >>>>>>>>>>>> >>>>>>>>>>>> best wishes, >>>>>>>>>>>> >>>>>>>>>>>> Prerona >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> On 7 December 2012 13:46, Anastasia Yendiki >>>>>>>>>>>> <ayendiki(a)nmr.mgh.harvard.edu> wrote: >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> Hi Prerona - You need to uncomment the bvecfile and bvalfile >>>>>>>>>>>>> definitions >>>>>>>>>>>>> in >>>>>>>>>>>>> your configuration file. >>>>>>>>>>>>> >>>>>>>>>>>>> Hope this helps, >>>>>>>>>>>>> a.y >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> On Fri, 7 Dec 2012, s0675204 wrote: >>>>>>>>>>>>> >>>>>>>>>>>>>> Hello >>>>>>>>>>>>>> >>>>>>>>>>>>>> I am trying to run Tracula on a set of dicoms files. I have >>>>>>>>>>>>>> run >>>>>>>>>>>>>> recon-all previously. >>>>>>>>>>>>>> I am getting a message trac-preproc exited with ERRORS >>>>>>>>>>>>>> >>>>>>>>>>>>>> Please can anyone advise me on this? >>>>>>>>>>>>>> I have listed all the details (command, error/output, config >>>>>>>>>>>>>> file) >>>>>>>>>>>>>> below >>>>>>>>>>>>>> >>>>>>>>>>>>>> Thank you so much for your help >>>>>>>>>>>>>> >>>>>>>>>>>>>> best wishes, >>>>>>>>>>>>>> >>>>>>>>>>>>>> Prerona >>>>>>>>>>>>>> >>>>>>>>>>>>>> DETAILS >>>>>>>>>>>>>> ========================================= >>>>>>>>>>>>>> command used: trac-all -prep -c >>>>>>>>>>>>>> ./scripts/dmrirc_single_subject >>>>>>>>>>>>>> >>>>>>>>>>>>>> ========================================= >>>>>>>>>>>>>> error message >>>>>>>>>>>>>> >>>>>>>>>>>>>> ========================================= >>>>>>>>>>>>>> canlilab@112-205:~/SBU/data/tracula$ trac-all -prep -c >>>>>>>>>>>>>> ./scripts/dmrirc_single_subject >>>>>>>>>>>>>> INFO: SUBJECTS_DIR is /home/canlilab/SBU/data/recon_output >>>>>>>>>>>>>> INFO: Diffusion root is /home/canlilab/SBU/data/tracula >>>>>>>>>>>>>> Actual FREESURFER_HOME /home/canlilab/freesurfer >>>>>>>>>>>>>> trac-preproc -c >>>>>>>>>>>>>> /home/canlilab/SBU/data/tracula/00075/scripts/dmrirc.local >>>>>>>>>>>>>> -log >>>>>>>>>>>>>> /home/canlilab/SBU/data/tracula/00075/scripts/trac-all.log >>>>>>>>>>>>>> -cmd >>>>>>>>>>>>>> /home/canlilab/SBU/data/tracula/00075/scripts/trac-all.cmd >>>>>>>>>>>>>> #------------------------------------- >>>>>>>>>>>>>> /home/canlilab/freesurfer/bin/trac-preproc >>>>>>>>>>>>>> #------------------------------------- >>>>>>>>>>>>>> #@# Image corrections Fri Dec 7 10:42:30 EST 2012 >>>>>>>>>>>>>> mri_convert >>>>>>>>>>>>>> /home/canlilab/SBU/data/dti_dicoms/00075/data_1.dcm >>>>>>>>>>>>>> /home/canlilab/SBU/data/tracula/00075/dmri/dwi_orig.nii.gz >>>>>>>>>>>>>> mri_convert >>>>>>>>>>>>>> /home/canlilab/SBU/data/dti_dicoms/00075/data_1.dcm >>>>>>>>>>>>>> /home/canlilab/SBU/data/tracula/00075/dmri/dwi_orig.nii.gz >>>>>>>>>>>>>> $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ >>>>>>>>>>>>>> reading from >>>>>>>>>>>>>> /home/canlilab/SBU/data/dti_dicoms/00075/data_1.dcm... >>>>>>>>>>>>>> Getting Series No >>>>>>>>>>>>>> INFO: Found 44 files in >>>>>>>>>>>>>> /home/canlilab/SBU/data/dti_dicoms/00075 >>>>>>>>>>>>>> INFO: Scanning for Series Number 7 >>>>>>>>>>>>>> Scanning Directory >>>>>>>>>>>>>> INFO: found 42 files in series >>>>>>>>>>>>>> INFO: loading series header info. >>>>>>>>>>>>>> >>>>>>>>>>>>>> RunNo = 6 >>>>>>>>>>>>>> WARNING: Run 1 appears to be truncated >>>>>>>>>>>>>> Files Found: 42, Files Expected (lRep+1): 2 >>>>>>>>>>>>>> FileName >>>>>>>>>>>>>> /home/canlilab/SBU/data/dti_dicoms/00075/data_1.dcm >>>>>>>>>>>>>> Identification >>>>>>>>>>>>>> NumarisVer syngo MR B17 >>>>>>>>>>>>>> ScannerModel TrioTim >>>>>>>>>>>>>> PatientName S790_P72_TC >>>>>>>>>>>>>> Date and time >>>>>>>>>>>>>> StudyDate 20120502 >>>>>>>>>>>>>> StudyTime 120741.390000 >>>>>>>>>>>>>> SeriesTime 125649.953000 >>>>>>>>>>>>>> AcqTime 125626.150000 >>>>>>>>>>>>>> Acquisition parameters >>>>>>>>>>>>>> PulseSeq ep_b0 >>>>>>>>>>>>>> Protocol DTI >>>>>>>>>>>>>> PhEncDir COL >>>>>>>>>>>>>> EchoNo 1 >>>>>>>>>>>>>> FlipAngle 90 >>>>>>>>>>>>>> EchoTime 93 >>>>>>>>>>>>>> InversionTime -1 >>>>>>>>>>>>>> RepetitionTime 5500 >>>>>>>>>>>>>> PhEncFOV 220 >>>>>>>>>>>>>> ReadoutFOV 220 >>>>>>>>>>>>>> Image information >>>>>>>>>>>>>> RunNo 6 >>>>>>>>>>>>>> SeriesNo 7 >>>>>>>>>>>>>> ImageNo 1 >>>>>>>>>>>>>> NImageRows 896 >>>>>>>>>>>>>> NImageCols 896 >>>>>>>>>>>>>> NFrames 42 >>>>>>>>>>>>>> SliceArraylSize 40 >>>>>>>>>>>>>> IsMosaic 1 >>>>>>>>>>>>>> ImgPos 772.3238 773.0634 185.5347 >>>>>>>>>>>>>> VolRes 1.7188 1.7188 3.0000 >>>>>>>>>>>>>> VolDim 128 128 40 >>>>>>>>>>>>>> Vc -0.9983 0.0151 -0.0555 >>>>>>>>>>>>>> Vr -0.0000 -0.9648 -0.2629 >>>>>>>>>>>>>> Vs -0.0575 -0.2625 0.9632 >>>>>>>>>>>>>> VolCenter 0.0000 0.0000 0.0000 >>>>>>>>>>>>>> TransferSyntaxUID 1.2.840.10008.1.2.1 >>>>>>>>>>>>>> INFO: sorting. >>>>>>>>>>>>>> INFO: (128 128 40), nframes = 42, ismosaic=1 >>>>>>>>>>>>>> Could not parse NUMARIS version string syngo MR B17 >>>>>>>>>>>>>> found in dicom tag 18,1020 (len = 3 != 6) >>>>>>>>>>>>>> Repetition Time = 5500, TR = 5500 ms >>>>>>>>>>>>>> PE Dir COL COL >>>>>>>>>>>>>> AutoAlign matrix detected >>>>>>>>>>>>>> AutoAlign Matrix --------------------- >>>>>>>>>>>>>> 1.000 0.000 0.000 0.000; >>>>>>>>>>>>>> 0.000 1.000 0.000 0.000; >>>>>>>>>>>>>> 0.000 0.000 1.000 0.000; >>>>>>>>>>>>>> 0.000 0.000 0.000 1.000; >>>>>>>>>>>>>> >>>>>>>>>>>>>> FileName >>>>>>>>>>>>>> /home/canlilab/SBU/data/dti_dicoms/00075/data_1.dcm >>>>>>>>>>>>>> Identification >>>>>>>>>>>>>> NumarisVer syngo MR B17 >>>>>>>>>>>>>> ScannerModel TrioTim >>>>>>>>>>>>>> PatientName S790_P72_TC >>>>>>>>>>>>>> Date and time >>>>>>>>>>>>>> StudyDate 20120502 >>>>>>>>>>>>>> StudyTime 120741.390000 >>>>>>>>>>>>>> SeriesTime 125649.953000 >>>>>>>>>>>>>> AcqTime 125626.150000 >>>>>>>>>>>>>> Acquisition parameters >>>>>>>>>>>>>> PulseSeq ep_b0 >>>>>>>>>>>>>> Protocol DTI >>>>>>>>>>>>>> PhEncDir COL >>>>>>>>>>>>>> EchoNo 1 >>>>>>>>>>>>>> FlipAngle 90 >>>>>>>>>>>>>> EchoTime 93 >>>>>>>>>>>>>> InversionTime -1 >>>>>>>>>>>>>> RepetitionTime 5500 >>>>>>>>>>>>>> PhEncFOV 220 >>>>>>>>>>>>>> ReadoutFOV 220 >>>>>>>>>>>>>> Image information >>>>>>>>>>>>>> RunNo 6 >>>>>>>>>>>>>> SeriesNo 7 >>>>>>>>>>>>>> ImageNo 1 >>>>>>>>>>>>>> NImageRows 896 >>>>>>>>>>>>>> NImageCols 896 >>>>>>>>>>>>>> NFrames 42 >>>>>>>>>>>>>> SliceArraylSize 40 >>>>>>>>>>>>>> IsMosaic 1 >>>>>>>>>>>>>> ImgPos 113.4156 146.2544 -24.5854 >>>>>>>>>>>>>> VolRes 1.7188 1.7188 3.0000 >>>>>>>>>>>>>> VolDim 128 128 40 >>>>>>>>>>>>>> Vc -0.9983 0.0151 -0.0555 >>>>>>>>>>>>>> Vr -0.0000 -0.9648 -0.2629 >>>>>>>>>>>>>> Vs -0.0575 -0.2625 0.9632 >>>>>>>>>>>>>> VolCenter 0.1478 26.0388 -1.8116 >>>>>>>>>>>>>> TransferSyntaxUID 1.2.840.10008.1.2.1 >>>>>>>>>>>>>> sagrev = 0, correv =0, trarev = 0 >>>>>>>>>>>>>> Vs = -0.0574949 -0.262456 0.963229 >>>>>>>>>>>>>> INFO: no Siemens slice order reversal detected (good!). >>>>>>>>>>>>>> TR=5500.00, TE=93.00, TI=-1.00, flip angle=90.00 >>>>>>>>>>>>>> i_ras = (-0.998346, 0.0151149, -0.0554726) >>>>>>>>>>>>>> j_ras = (-3.31902e-08, -0.964826, -0.262891) >>>>>>>>>>>>>> k_ras = (-0.0574949, -0.262456, 0.963229) >>>>>>>>>>>>>> writing to >>>>>>>>>>>>>> /home/canlilab/SBU/data/tracula/00075/dmri/dwi_orig.nii.gz... >>>>>>>>>>>>>> mri_probedicom --i >>>>>>>>>>>>>> /home/canlilab/SBU/data/dti_dicoms/00075/data_1.dcm >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> /home/canlilab/SBU/data/tracula/00075/dmri/dcminfo.dat >>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>> flip4fsl >>>>>>>>>>>>>> /home/canlilab/SBU/data/tracula/00075/dmri/dwi_orig.nii.gz >>>>>>>>>>>>>> >>>>>>>>>>>>>> /home/canlilab/SBU/data/tracula/00075/dmri/dwi_orig_flip.nii.gz >>>>>>>>>>>>>> INFO: input image orientation is LPS >>>>>>>>>>>>>> INFO: input image determinant is 8.86231 >>>>>>>>>>>>>> fslswapdim >>>>>>>>>>>>>> /home/canlilab/SBU/data/tracula/00075/dmri/dwi_orig.nii.gz >>>>>>>>>>>>>> x -y z >>>>>>>>>>>>>> >>>>>>>>>>>>>> /home/canlilab/SBU/data/tracula/00075/dmri/dwi_orig_flip.nii.gz >>>>>>>>>>>>>> INFO: left-right orientation was flipped by fslswapdim >>>>>>>>>>>>>> fslorient -forceradiological >>>>>>>>>>>>>> >>>>>>>>>>>>>> /home/canlilab/SBU/data/tracula/00075/dmri/dwi_orig_flip.nii.gz >>>>>>>>>>>>>> mv -f >>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>> /home/canlilab/SBU/data/tracula/00075/dmri/dwi_orig_flip.mghdti.bvecs >>>>>>>>>>>>>> /home/canlilab/SBU/data/tracula/00075/dmri/bvecs >>>>>>>>>>>>>> mv: cannot stat >>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>> `/home/canlilab/SBU/data/tracula/00075/dmri/dwi_orig_flip.mghdti.bvecs': >>>>>>>>>>>>>> No such file or directory >>>>>>>>>>>>>> Linux 112-205.psy.sunysb.edu 2.6.32-279.5.2.el6.x86_64 #1 SMP >>>>>>>>>>>>>> Fri >>>>>>>>>>>>>> Aug >>>>>>>>>>>>>> 24 01:07:11 UTC 2012 x86_64 x86_64 x86_64 GNU/Linux >>>>>>>>>>>>>> >>>>>>>>>>>>>> trac-preproc exited with ERRORS at Fri Dec 7 10:42:51 EST >>>>>>>>>>>>>> 2012 >>>>>>>>>>>>>> ============================================== >>>>>>>>>>>>>> >>>>>>>>>>>>>> config file: >>>>>>>>>>>>>> ============================================== >>>>>>>>>>>>>> # >>>>>>>>>>>>>> # dmrirc.example >>>>>>>>>>>>>> # >>>>>>>>>>>>>> # 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: 2011/05/24 06:47:12 $ >>>>>>>>>>>>>> # $Revision: 1.3.2.3 $ >>>>>>>>>>>>>> # >>>>>>>>>>>>>> # 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 /path/to/recons/of/ducks >>>>>>>>>>>>>> >>>>>>>>>>>>>> # Output directory where trac-all results will be saved >>>>>>>>>>>>>> # Default: Same as SUBJECTS_DIR >>>>>>>>>>>>>> # >>>>>>>>>>>>>> set dtroot = $pre_data/tracula >>>>>>>>>>>>>> >>>>>>>>>>>>>> # Subject IDs >>>>>>>>>>>>>> # >>>>>>>>>>>>>> set subjlist = (00075 00104 00122 00200 00308 00369 00387 >>>>>>>>>>>>>> 00400 >>>>>>>>>>>>>> 00422 >>>>>>>>>>>>>> 00452 00518 00568 00587 00624 00636 00686 00698 00727 00909 >>>>>>>>>>>>>> 00926 >>>>>>>>>>>>>> 00933 00943 00983 00992 01049 01121 01329 01450 01509 01531 >>>>>>>>>>>>>> 01678 >>>>>>>>>>>>>> 01735 01746 01809 01843 01917 10039 10056 10089 10165 10171 >>>>>>>>>>>>>> 10227 >>>>>>>>>>>>>> 10238 10263 10314 10320 10326 10349 10407 10431 10435 10458 >>>>>>>>>>>>>> 10477 >>>>>>>>>>>>>> 10499 10500 10636 10750 11209 12210 12357 12472 12645 13493 >>>>>>>>>>>>>> 13958 >>>>>>>>>>>>>> 14302 14481 14530 15329 15345 15864 16654 17267 17478 18337 >>>>>>>>>>>>>> 18422 >>>>>>>>>>>>>> 18530 19259 19377 19725 20071 20383 21413 23846 24115 24531 >>>>>>>>>>>>>> 24781 >>>>>>>>>>>>>> 25962 26314 26475 28822 30510 30571 30927 31034 31049 31237 >>>>>>>>>>>>>> 31437 >>>>>>>>>>>>>> 31471 31531 32131 32162 32222) >>>>>>>>>>>>>> >>>>>>>>>>>>>> # In case you want to analyze only Huey and Louie >>>>>>>>>>>>>> # Default: Run analysis on all subjects >>>>>>>>>>>>>> # >>>>>>>>>>>>>> set runlist = (1 2 3 4 5 6 >>>>>>>>>>>>>> 7 >>>>>>>>>>>>>> 8 9 10 11 12 13 14 15 >>>>>>>>>>>>>> 16 >>>>>>>>>>>>>> 17 18 19 20 21 22 23 24 >>>>>>>>>>>>>> 25 >>>>>>>>>>>>>> 26 27 28 29 30 31 32 33 >>>>>>>>>>>>>> 34 >>>>>>>>>>>>>> 35 36 37 38 39 40 41 42 >>>>>>>>>>>>>> 43 >>>>>>>>>>>>>> 44 45 46 47 48 49 50 51 >>>>>>>>>>>>>> 52 >>>>>>>>>>>>>> 53 54 55 56 57 58 59 60 >>>>>>>>>>>>>> 61 62 63 64 65 66 67 68 >>>>>>>>>>>>>> 69 >>>>>>>>>>>>>> 70 71 72 73 74 75 76 77 >>>>>>>>>>>>>> 78 >>>>>>>>>>>>>> 79 80 81 82 83 84 85 86 >>>>>>>>>>>>>> 87 >>>>>>>>>>>>>> 88 89 90 91 92 93 94 95 >>>>>>>>>>>>>> 96 >>>>>>>>>>>>>> 97 98 99 100 101 102) >>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>> # 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 dcmroot = $pre_data/dti_dicoms >>>>>>>>>>>>>> set dcmlist = (00075/data_1.dcm \ >>>>>>>>>>>>>> 00104/data_1.dcm \ >>>>>>>>>>>>>> 00122/data_1.dcm \ >>>>>>>>>>>>>> 00200/data_1.dcm \ >>>>>>>>>>>>>> 00308/data_1.dcm \ >>>>>>>>>>>>>> 00369/data_1.dcm \ >>>>>>>>>>>>>> 00387/data_1.dcm \ >>>>>>>>>>>>>> 00400/data_1.dcm \ >>>>>>>>>>>>>> 00422/data_1.dcm \ >>>>>>>>>>>>>> 00452/data_1.dcm \ >>>>>>>>>>>>>> 00518/data_1.dcm \ >>>>>>>>>>>>>> 00568/data_1.dcm \ >>>>>>>>>>>>>> 00587/data_1.dcm \ >>>>>>>>>>>>>> 00624/data_1.dcm \ >>>>>>>>>>>>>> 00636/data_1.dcm \ >>>>>>>>>>>>>> 00686/data_1.dcm \ >>>>>>>>>>>>>> 00698/data_1.dcm \ >>>>>>>>>>>>>> 00727/data_1.dcm \ >>>>>>>>>>>>>> 00909/data_1.dcm \ >>>>>>>>>>>>>> 00926/data_1.dcm \ >>>>>>>>>>>>>> 00933/data_1.dcm \ >>>>>>>>>>>>>> 00943/data_1.dcm \ >>>>>>>>>>>>>> 00983/data_1.dcm \ >>>>>>>>>>>>>> 00992/data_1.dcm \ >>>>>>>>>>>>>> 01049/data_1.dcm \ >>>>>>>>>>>>>> 01121/data_1.dcm \ >>>>>>>>>>>>>> 01329/data_1.dcm \ >>>>>>>>>>>>>> 01450/data_1.dcm \ >>>>>>>>>>>>>> 01509/data_1.dcm \ >>>>>>>>>>>>>> 01531/data_1.dcm \ >>>>>>>>>>>>>> 01678/data_1.dcm \ >>>>>>>>>>>>>> 01735/data_1.dcm \ >>>>>>>>>>>>>> 01746/data_1.dcm \ >>>>>>>>>>>>>> 01809/data_1.dcm \ >>>>>>>>>>>>>> 01843/data_1.dcm \ >>>>>>>>>>>>>> 01917/data_1.dcm \ >>>>>>>>>>>>>> 10039/data_1.dcm \ >>>>>>>>>>>>>> 10056/data_1.dcm \ >>>>>>>>>>>>>> 10089/data_1.dcm \ >>>>>>>>>>>>>> 10165/data_1.dcm \ >>>>>>>>>>>>>> 10171/data_1.dcm \ >>>>>>>>>>>>>> 10227/data_1.dcm \ >>>>>>>>>>>>>> 10238/data_1.dcm \ >>>>>>>>>>>>>> 10263/data_1.dcm \ >>>>>>>>>>>>>> 10314/data_1.dcm \ >>>>>>>>>>>>>> 10320/data_1.dcm \ >>>>>>>>>>>>>> 10326/data_1.dcm \ >>>>>>>>>>>>>> 10349/data_1.dcm \ >>>>>>>>>>>>>> 10407/data_1.dcm \ >>>>>>>>>>>>>> 10431/data_1.dcm \ >>>>>>>>>>>>>> 10435/data_1.dcm \ >>>>>>>>>>>>>> 10458/data_1.dcm \ >>>>>>>>>>>>>> 10477/data_1.dcm \ >>>>>>>>>>>>>> 10499/data_1.dcm \ >>>>>>>>>>>>>> 10500/data_1.dcm \ >>>>>>>>>>>>>> 10636/data_1.dcm \ >>>>>>>>>>>>>> 10750/data_1.dcm \ >>>>>>>>>>>>>> 11209/data_1.dcm \ >>>>>>>>>>>>>> 12210/data_1.dcm \ >>>>>>>>>>>>>> 12357/data_1.dcm \ >>>>>>>>>>>>>> 12472/data_1.dcm \ >>>>>>>>>>>>>> 12645/data_1.dcm \ >>>>>>>>>>>>>> 13493/data_1.dcm \ >>>>>>>>>>>>>> 13958/data_1.dcm \ >>>>>>>>>>>>>> 14302/data_1.dcm \ >>>>>>>>>>>>>> 14481/data_1.dcm \ >>>>>>>>>>>>>> 14530/data_1.dcm \ >>>>>>>>>>>>>> 15329/data_1.dcm \ >>>>>>>>>>>>>> 15345/data_1.dcm \ >>>>>>>>>>>>>> 15864/data_1.dcm \ >>>>>>>>>>>>>> 16654/data_1.dcm \ >>>>>>>>>>>>>> 17267/data_1.dcm \ >>>>>>>>>>>>>> 17478/data_1.dcm \ >>>>>>>>>>>>>> 18337/data_1.dcm \ >>>>>>>>>>>>>> 18422/data_1.dcm \ >>>>>>>>>>>>>> 18530/data_1.dcm \ >>>>>>>>>>>>>> 19259/data_1.dcm \ >>>>>>>>>>>>>> 19377/data_1.dcm \ >>>>>>>>>>>>>> 19725/data_1.dcm \ >>>>>>>>>>>>>> 20071/data_1.dcm \ >>>>>>>>>>>>>> 20383/data_1.dcm \ >>>>>>>>>>>>>> 21413/data_1.dcm \ >>>>>>>>>>>>>> 23846/data_1.dcm \ >>>>>>>>>>>>>> 24115/data_1.dcm \ >>>>>>>>>>>>>> 24531/data_1.dcm \ >>>>>>>>>>>>>> 24781/data_1.dcm \ >>>>>>>>>>>>>> 25962/data_1.dcm \ >>>>>>>>>>>>>> 26314/data_1.dcm \ >>>>>>>>>>>>>> 26475/data_1.dcm \ >>>>>>>>>>>>>> 28822/data_1.dcm \ >>>>>>>>>>>>>> 30510/data_1.dcm \ >>>>>>>>>>>>>> 30571/data_1.dcm \ >>>>>>>>>>>>>> 30927/data_1.dcm \ >>>>>>>>>>>>>> 31034/data_1.dcm \ >>>>>>>>>>>>>> 31049/data_1.dcm \ >>>>>>>>>>>>>> 31237/data_1.dcm \ >>>>>>>>>>>>>> 31437/data_1.dcm \ >>>>>>>>>>>>>> 31471/data_1.dcm \ >>>>>>>>>>>>>> 31531/data_1.dcm \ >>>>>>>>>>>>>> 32131/data_1.dcm \ >>>>>>>>>>>>>> 32162/data_1.dcm \ >>>>>>>>>>>>>> 32222/data_1.dcm) >>>>>>>>>>>>>> >>>>>>>>>>>>>> # 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 bvecfile = $pre_data/DTI_Analysis/00075/bvecs.txt >>>>>>>>>>>>>> >>>>>>>>>>>>>> # Diffusion b-value table >>>>>>>>>>>>>> # Must be specified if inputs are not MGH DICOMs >>>>>>>>>>>>>> # Single-column format one value for each volume in the >>>>>>>>>>>>>> diffusion >>>>>>>>>>>>>> data >>>>>>>>>>>>>> set >>>>>>>>>>>>>> # Default: Read from DICOM header >>>>>>>>>>>>>> # >>>>>>>>>>>>>> #set bvalfile = $pre_data/DTI_Analysis/00075/bvals.txt >>>>>>>>>>>>>> >>>>>>>>>>>>>> # Number of low-b images >>>>>>>>>>>>>> # Must be specified if inputs are not DICOM >>>>>>>>>>>>>> # Default: Read from DICOM header >>>>>>>>>>>>>> # >>>>>>>>>>>>>> set nb0 = 1 >>>>>>>>>>>>>> >>>>>>>>>>>>>> # Perform registration-based B0-inhomogeneity compensation? >>>>>>>>>>>>>> # Default: 0 (no) >>>>>>>>>>>>>> # >>>>>>>>>>>>>> set dob0 = 0 >>>>>>>>>>>>>> >>>>>>>>>>>>>> # Input B0 field map magnitude DICOMs (file names relative to >>>>>>>>>>>>>> dcmroot) >>>>>>>>>>>>>> # Only used if dob0 = 1 >>>>>>>>>>>>>> # Default: None >>>>>>>>>>>>>> # >>>>>>>>>>>>>> #set b0mlist = (huey/fmag/XXX-1.dcm dewey/fmag/XXX-1.dcm >>>>>>>>>>>>>> louie/fmag/XXX-1.dcm) >>>>>>>>>>>>>> >>>>>>>>>>>>>> # Input B0 field map phase DICOMs (file names relative to >>>>>>>>>>>>>> dcmroot) >>>>>>>>>>>>>> # Only used if dob0 = 1 >>>>>>>>>>>>>> # Default: None >>>>>>>>>>>>>> # >>>>>>>>>>>>>> #set b0plist = (huey/fphas/XXX-1.dcm dewey/fphas/XXX-1.dcm >>>>>>>>>>>>>> louie/fphas/XXX-1.dcm) >>>>>>>>>>>>>> >>>>>>>>>>>>>> # Echo spacing for field mapping sequence (from sequence >>>>>>>>>>>>>> printout) >>>>>>>>>>>>>> # Only used if dob0 = 1 >>>>>>>>>>>>>> # Default: None >>>>>>>>>>>>>> # >>>>>>>>>>>>>> #set echospacing = 0.7 >>>>>>>>>>>>>> >>>>>>>>>>>>>> # 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 = 0.5 >>>>>>>>>>>>>> >>>>>>>>>>>>>> # Perform diffusion-to-T1 registration by flirt? >>>>>>>>>>>>>> # Default: 1 (yes) >>>>>>>>>>>>>> # >>>>>>>>>>>>>> set doregflt = 1 >>>>>>>>>>>>>> >>>>>>>>>>>>>> # Perform diffusion-to-T1 registration by bbregister? >>>>>>>>>>>>>> # Default: 0 (no) >>>>>>>>>>>>>> # >>>>>>>>>>>>>> set doregbbr = 0 >>>>>>>>>>>>>> >>>>>>>>>>>>>> # MNI template (the only option for inter-subject registration >>>>>>>>>>>>>> in >>>>>>>>>>>>>> this >>>>>>>>>>>>>> version) >>>>>>>>>>>>>> # Default: $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz >>>>>>>>>>>>>> # >>>>>>>>>>>>>> set mnitemp = $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz >>>>>>>>>>>>>> >>>>>>>>>>>>>> # 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 >>>>>>>>>>>>>> # >>>>>>>>>>>>>> set pathlist = ( lh.cst_AS rh.cst_AS \ >>>>>>>>>>>>>> lh.unc_AS rh.unc_AS \ >>>>>>>>>>>>>> lh.ilf_AS rh.ilf_AS \ >>>>>>>>>>>>>> fmajor_PP fminor_PP \ >>>>>>>>>>>>>> lh.atr_PP rh.atr_PP \ >>>>>>>>>>>>>> lh.ccg_PP rh.ccg_PP \ >>>>>>>>>>>>>> lh.cab_PP rh.cab_PP \ >>>>>>>>>>>>>> lh.slfp_PP rh.slfp_PP \ >>>>>>>>>>>>>> lh.slft_PP rh.slft_PP ) >>>>>>>>>>>>>> >>>>>>>>>>>>>> # Number of path control points >>>>>>>>>>>>>> # Default: 5 >>>>>>>>>>>>>> # >>>>>>>>>>>>>> set ncpts = 5 >>>>>>>>>>>>>> >>>>>>>>>>>>>> # 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 >>>>>>>>>>>>>> >>>>>>>>>>>>>> # Use long (more descriptive) directory hierarchy for saving >>>>>>>>>>>>>> path >>>>>>>>>>>>>> distributions? >>>>>>>>>>>>>> # By default paths distributions are saved directly under >>>>>>>>>>>>>> $subjectname/dpath >>>>>>>>>>>>>> # Default: 0 (no) >>>>>>>>>>>>>> # >>>>>>>>>>>>>> set dopathsubdirs = 0 >>>>>>>>>>>>>> >>>>>>>>>>>>>> # 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 = 5000 >>>>>>>>>>>>>> >>>>>>>>>>>>>> # Frequency with which MCMC path samples are retained for path >>>>>>>>>>>>>> distribution >>>>>>>>>>>>>> # Default: 5 (keep every 5th sample) >>>>>>>>>>>>>> # >>>>>>>>>>>>>> set nkeep = 5 >>>>>>>>>>>>>> ============================================== >>>>>>>>>>>>>> >>>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>>> 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. >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>> >>>>>>>>> >>>>>>>> >>>>>>>> >>>>>>> >>>>>> >>>>>> >>>>> >>>> >>>> >>> >> >> >

2 1

Truncate positive values in tksurfer
by Jürgen Hänggi 12 Dec '12

12 Dec '12

Dear FS experts How can I force tksurfer to truncate the positive values and not the negative ones? Thanks in advance Best regards Jürgen ---------------------------------------------------------------------------- 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. ----------------------------------------------------------------------------

3 2

left/right WM vols
by Gabriel Gonzalez Escamilla 12 Dec '12

12 Dec '12

1 0

Perirhinal Cortex ....how?
by Joshua Lee 11 Dec '12

11 Dec '12

Can I get thickness values for the perirhinal (posterior parahipp too maybe???) I came across http://surfer.nmr.mgh.harvard.edu/fswiki/PerirhinalArea35Labels but the labels download link isn't existent. I tried running the commands on that page anyway but of course it can't find the label... Thanks for any info you may share - Josh

2 2

unpacking error
by Staples, Lindsay Katharine 11 Dec '12

11 Dec '12

Hi- I don't know much about freesurfer other than the very basics. Can anyone tell me why I would be getting the following error when I run the second unpacking command? while executing "close $flfid" ("foreach" body line 149) invoked from within "foreach runcfg $unpackcfg { set RunNo [lindex $runcfg 0]; set SubDir [lindex $runcfg 1]; set Fmt [lindex $runcfg 2]; set Name [lindex $r..." (file "/usr/local/freesurfer/stable5_1_0/bin/unpacksdcmdir.tcl" line 1197) Thanks! Lindsay

2 3

func2roi-sess no bold/register.dat
by Keith Yoder 11 Dec '12

11 Dec '12

Hi all, I'm using FS 5.1.0, and trying to do an ROI analysis. I have completed an FS-FAST pipeline, and am now trying to use func2roi-sess with accumbens masks. I have run isxconcat-sess, mri_glmfit and mri_glmfit-sim for the contrast MMA_CUE-v-CAPO_CUE and the results make sense. I extracted left and right accumbens masks from individual subject aseg.mgz using mri_cor2label, and moved the accumbens.label files into the FS-FAST subdirectory for each subject (e.g. sub_name/labels/). The command I'm using is: func2roi-sess -roidef left_accumbens-avf-pos-2 -analysis both.sm05.mni305 -sesslabel left_accubmens -maskcontrast MMA_CUE-v-CAPO_CUE -maskthresh 2 -masktail pos -maskmap minsig -sf sessid_clean The command generates an error (s03 is the first subject listed in the sessid_clean file) ERROR (s03): cannot find source reg bold/register.dat Is there a registration step that didn't run during preproc-sess? There are registrations within each of the run directories within the subject's bold directory. For instance, within s03/bold there are four directories (001, 002, 003, 004), each with a register.d0f6.dat file, but the error message from func2roi-sess seems to want a single registration across all of the runs. Thanks, Keith -- Keith Yoder PhD Student, Integrative Neuroscience Social Cognitive Neuroscience Laboratory The University of Chicago 5846 S. University Avenue, Kelly 312 Chicago, IL 60637 Phone: 574-215-9678 kjyoder(a)uchicago.edu

2 1

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