Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30088 discussions

Final result of CVS
by Antonella Kis 08 Dec '11

08 Dec '11

Dear Lilla, I was running the mri_cvs_register with the flag --noaseg and no argument for my target template so as I understood the registration was done on the cvs template as you can see below: mri_cvs_register--mov P01 --noaseg After registration I got 4 files: combined_tocvs_avg35_elreg_norm.m3z combined_tocvs_avg35_elreg_norm_aseg.mgz el_reg_tocvs_avg35.mgz nlalign-norm.m3z nlalign-norm.mgz Is the nlalign-norm.mgz the final result of my CVS and contains contributions from ALL registration steps? Also is the cvs atlas included in the file that you sent me some time ago called: cvs_avg35? Thank you very much for your time and help. Regards, Antonella

2 3

trac-all flag for doing all 3 processing steps?
by Scott Hayes 08 Dec '11

08 Dec '11

Hi, I'm new to tracula, but I'm wondering if I'm overlooking or misunderstanding the flags. It appears that one types in the trac-all command 3 times to process a subject (or group of subjects) >trac-all -prep -c ConfigFile >trac-all -bedp -c ConfigFile >trac-all -path -c ConfigFile Is there a way to specify all three steps w/ one command? That is, could I specify: >trac-all -all -C ConfigFile (I don't see it stated in the help, but maybe it's implicitly understood to work this way?) Thanks for your guidance. Best, Scott

2 1

Re: [Freesurfer] freeview: segmentation fault
by Ruopeng Wang 08 Dec '11

08 Dec '11

I have no problem loading this file in freeview, in both old and new versions. Have you used freeview before on the same system? Did it work? Ruopeng On 12/08/2011 02:33 PM, Xin Zheng wrote: > Hi Ruopeng, > > It seems to be with all files. Attached is one of them. > > Thanks! > Xin > > On Thu, Dec 8, 2011 at 2:22 PM, Ruopeng Wang<rpwang(a)nmr.mgh.harvard.edu> wrote: >> Does it happen with just that file or with other files as well? Would it >> be possible to send us that volume file? >> >> Ruopeng >> >> On 12/08/2011 02:03 PM, Xin Zheng wrote: >>> Hi, >>> >>> We are trying to open something using freeview (ie. freeview -v >>> SubjectID_template/mri/norm.mgz) and would get a segmentation fault. >>> When we tried to open it directly from the freeview GUI, it will load >>> to about 7% and segmentation fault would occur again. We're using >>> Freesurfer 5.1.0 on Fedora 11. Does anyone know what could be the >>> problem? >>> >>> Thanks, >>> Xin >>> _______________________________________________ >>> 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 2

freeview: segmentation fault
by Xin Zheng 08 Dec '11

08 Dec '11

Hi, We are trying to open something using freeview (ie. freeview -v SubjectID_template/mri/norm.mgz) and would get a segmentation fault. When we tried to open it directly from the freeview GUI, it will load to about 7% and segmentation fault would occur again. We're using Freesurfer 5.1.0 on Fedora 11. Does anyone know what could be the problem? Thanks, Xin

3 2

Re: [Freesurfer] Commands not installed w/ PPC Tiger distribution
by Iain DeWitt 08 Dec '11

08 Dec '11

Yes, this fixes it. Thanks Nick! > you can try downloading and installing this: > > > http://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.1.0/freesurfer-Darw… > > > to install, cp this file to /Applications, then type: > > sudo tar zxvf freesurfer-Darwin-tiger-ppc-stable-pub-v5.1.0.tar.gz > > n. > > > > On Wed, 2011-12-07 at 14:58 -0500, Iain DeWitt wrote: > > Following up on Ashley's post from 06 Jun 2011 (see below), I also find > > certain commands (see below) are not installed with the current (v5.1) PPC OS > > X Tiger distribution. I had to go back to v4.3 to get a complete set of > > commands. > > > > cheers > > Iain > > > > talairach_avi: Command not found. > > mri_watershed: Command not found. > > mri_segment: Command not found. > > mri_tessellate: Command not found. > > mri_concatenate_lta: Command not found. > > mri_normalize_tp2: Command not found. > > mris_smooth: Command not found. > > mris_inflate: Command not found. > > mris_curvature: Command not found. > > mris_sphere: Command not found. > > mris_fix_topology: Command not found. > > mris_topo_fixer: Command not found. > > mris_ca_label: Command not found. > > mris_euler_number: Command not found. > > mris_make_surfaces: Command not found. > > mris_register: Command not found. > > mris_volmask: Command not found. > > mris_anatomical_stats: Command not found. > > mrisp_paint: Command not found. > > mris_curvature_stats: Command not found. > > mris_calc: Command not found. > > mri_robust_register: Command not found. > > mri_robust_template: Command not found. > > mri_segstats: Command not found. > > > > > > Commands missing in freesurfer directory > > ANN40 > > Mon, 06 Jun 2011 06:22:06 -0700 > > > > Hi all, > > > > I recently downloaded and installed freesurfer for a Mac PowerPC. I tried > > running recon-all on my data and an error message came up saying command > > not found for talairach_avi and many other commands. I looked in my > > /Applications/freesurfer/bin directory and that file wasn't there. All > > the commands that had worked such as mri_convert were. Does anyone know > > what could be causing this problem? > > > > Thanks, > > Ashley > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > _______________________________________________ > 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. > >

1 0

tracula and corona radiata
by Cat Chong 08 Dec '11

08 Dec '11

Hello Experts, I would like to be able to get measurements of the anterior portion of the corona radiata using tracula. Is this a possibility? I did not see it as an "option" in paths to reconstruct. thank you very much for your help, catherine

2 1

trackvis, and a separate question about surface transforms
by Colin Reveley 08 Dec '11

08 Dec '11

Hello; first, regarding the information here: http://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferTrackVisTransforms This looks to me very much like snippets of code to help people write their own code to read and transform files, byte by byte, with the help of the trackvis .trk header/file spec. That's great. Thanks. But has anyone written a script or some C or something to actually do that. If not, and if I do that in the form probably of C source, does anyone want the code? second: I'm using freeesurfer for ex-vivo macaque data. It's been a struggle but I've got there. There is something I would like to do: as well as keeping what I have, I would like to tilt the volume's nose up a few degrees (I'd probably use the afni "nudge" plugin for that, or something) and then apply the same transform to my white and pial surfaces. The idea there being to use the surfaces as diagrams in the same cut plane as diagrams in an atlas (the pandya white matter atlas, the paxinos atlas), mark areas and then transform those areas off else where (into diffusion data as masks in fact). I hope that's clear. I just want to apply an arbitrary (actually, a rigid body) linear transform to the surfaces and volumes so that when viewed coronally in sequence in freeview they are in the same plane as diagrams in an atlas, and I can compare the two by eye. the pial and white surfaces together look line like diagrams, and this is very helpful actually. especially if they are in the same cut plane as the atlas diagrams. thanks, Colin

2 1

Re: [Freesurfer] tracula ERROR: must specify brain mask volume for output subject
by Priti Srinivasan 08 Dec '11

08 Dec '11

Hi Paula, The * at the end of dtifit_FA.nii.gz may have been a problem (since it gives an unkown extension error? Extension: 146 (Uknown extension)) tcsh source /software/Freesurfer/5.1.0/SetUpFreeSurfer.csh freeview -v /mindhive/gablab/users/cpdla/Documents/s1001/dmri/dtifit_FA.nii.gz can you try running the above commands in that order and tell us if you get the same error? Thanks, Priti > hi, > i am trying to visualize the output of my trac-all results. > here is what i did: > cpdla@ba3:/$ tcsh > ba3:/> source /software/Freesurfer/5.1.0/Set > SetUpFreeSurfer.csh* SetUpFreeSurfer.sh* > ba3:/> source /software/Freesurfer/5.1.0/SetUpFreeSurfer.csh > -------- freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 -------- > Setting up environment for FreeSurfer/FS-FAST (and FSL) > FREESURFER_HOME /software/Freesurfer/5.1.0/ > FSFAST_HOME /software/Freesurfer/5.1.0/fsfast > FSF_OUTPUT_FORMAT nii > SUBJECTS_DIR /software/Freesurfer/5.1.0/subjects > MNI_DIR /software/Freesurfer/5.1.0//mni > /usr/share/fsl/4.1/etc/fslconf/fslmachtype.sh: Command not found. > FSL_DIR /usr/share/fsl/4.1 > *ba3:/> freeview -v > /mindhive/gablab/users/cpdla/Documents/s1001/dmri/dtifit_FA.nii.gz* > X Error: BadValue (integer parameter out of range for operation) 2 > Extension: 146 (Uknown extension) > Minor opcode: 3 (Unknown request) > Resource id: 0x24 > Abort > *ba3:/> freeview -tv > /mindhive/gablab/users/cpdla/Documents/s1001/dmri/dtifit_FA.nii.gz* > X Error: BadValue (integer parameter out of range for operation) 2 > Extension: 146 (Uknown extension) > Minor opcode: 3 (Unknown request) > Resource id: 0x24 > Abort > ba3:/> > > > On Thu, Dec 8, 2011 at 10:54 AM, Priti Srinivasan < > rspriti(a)nmr.mgh.harvard.edu> wrote: > >> Hi Paula, >> >> which image are you trying to open? If you're trying to open the merged >> files in freeview, you should use the -tv flag for opening it. Did you >> source the freesurfer environment before opening freeview? Can you give >> us >> the exact commandline you used? >> >> Priti >> >> > hi, >> > i am trying to visualize my results with freeview, and i am running >> into >> > this error. i am using freesurfer 5.1.0. do you know what the problem >> is? >> > : >> > >> > cpdla@ba3:~/Documents/s1001/dmri$ freeview >> > X Error: BadValue (integer parameter out of range for operation) 2 >> > Extension: 146 (Uknown extension) >> > Minor opcode: 3 (Unknown request) >> > Resource id: 0x24 >> > Abort >> > >> > >> > On Wed, Dec 7, 2011 at 12:52 PM, Priti Srinivasan < >> > rspriti(a)nmr.mgh.harvard.edu> wrote: >> > >> >> Hi Paula, >> >> >> >> Tracula uses anatomical labels/files from freesurfer cortical >> >> reconstruction to build the posterior distribution of the tracts. It >> >> looks >> >> like you may not have run freesurfer recon for your subject. >> >> >> >> To run freesurfer recon for your subject please refer to the >> following >> >> page: >> >> >> >> http://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferBeginnersGuide >> >> >> >> Especially, >> >> >> >> recon-all \ >> >> -i <one slice in the anatomical dicom series> \ >> >> -s <subject id that you make up> \ >> >> -sd <directory to put the subject folder in> \ >> >> -all >> >> >> >> Once this finishes processing you can re-run tracula to see if that >> >> solves >> >> the issue. >> >> >> >> Hope that is helpful, >> >> Priti >> >> >> >> >> >> >> >> > Hi. >> >> > >> >> > I am running into the following error: >> >> > ERROR: fio_pushd: >> >> /mindhive/gablab/users/cpdla/Documents//s1001/dlabel/mni >> >> > ERROR: must specify brain mask volume for output subject . >> >> > >> >> > I googled this error and it seems like you suggested this to >> someone >> >> else >> >> > : >> >> > "As for your error, it looks like maybe the freesurfer recon wasn't >> >> found, >> >> > so >> >> > it skipped some steps (diffusion-to-anatomical registration and >> mask >> >> > creation). >> >> > Does the freesurfer recon dir /home/ajfurst/Data/WRIISC/014/ exist? >> >> > >> >> > >> >> > a.y" >> >> > >> >> > What is the freesurfer recon dir supposed to look like? Any >> >> > suggestions on how to fix this error? Below is my output. >> >> > >> >> > Thanks, >> >> > C. Paula >> >> > >> >> > >> >> > >> >> > >> >> > ba3:~/Documents> trac-all -prep -c dmrirc_single_subject >> >> > set: Variable name must begin with a letter. >> >> > INFO: SUBJECTS_DIR is >> >> > /mindhive/gablab/users/cpdla/Documents/diffusion_recons >> >> > INFO: Diffusion root is /mindhive/gablab/users/cpdla/Documents/ >> >> > Actual FREESURFER_HOME /software/Freesurfer/5.1.0 >> >> > trac-preproc -c >> >> > /mindhive/gablab/users/cpdla/Documents//s1001/scripts/dmrirc.local >> >> -log >> >> > /mindhive/gablab/users/cpdla/Documents//s1001/scripts/trac-all.log >> >> -cmd >> >> > /mindhive/gablab/users/cpdla/Documents//s1001/scripts/trac-all.cmd >> >> > #------------------------------------- >> >> > /software/Freesurfer/5.1.0//bin/trac-preproc >> >> > #------------------------------------- >> >> > #@# Image corrections Tue Dec 6 22:02:37 EST 2011 >> >> > mri_convert /data/memory/sourcemem//s1001/156000-20-1.dcm >> >> > /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_orig.nii.gz >> >> > mri_convert /data/memory/sourcemem//s1001/156000-20-1.dcm >> >> > /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_orig.nii.gz >> >> > $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ >> >> > reading from /data/memory/sourcemem//s1001/156000-20-1.dcm... >> >> > Getting Series No >> >> > INFO: Found 3207 files in /data/memory/sourcemem//s1001 >> >> > INFO: Scanning for Series Number 20 >> >> > Scanning Directory >> >> > INFO: found 35 files in series >> >> > INFO: loading series header info. >> >> > >> >> > RunNo = 19 >> >> > WARNING: Run 1 appears to be truncated >> >> > Files Found: 35, Files Expected (lRep+1): 60 >> >> > FileName /data/memory/sourcemem//s1001/156000-20-1.dcm >> >> > Identification >> >> > NumarisVer syngo MR B15 >> >> > ScannerModel TrioTim >> >> > PatientName Gab_source_s1001 >> >> > Date and time >> >> > StudyDate 20091119 >> >> > StudyTime 170216.156000 >> >> > SeriesTime 180621.328000 >> >> > AcqTime 180331.855000 >> >> > Acquisition parameters >> >> > PulseSeq ep_b0#1 >> >> > Protocol DIFFUSION_HighRes_Short >> >> > PhEncDir COL >> >> > EchoNo 1 >> >> > FlipAngle 90 >> >> > EchoTime 84 >> >> > InversionTime -1 >> >> > RepetitionTime 7980 >> >> > PhEncFOV 256 >> >> > ReadoutFOV 256 >> >> > Image information >> >> > RunNo 19 >> >> > SeriesNo 20 >> >> > ImageNo 1 >> >> > NImageRows 1024 >> >> > NImageCols 1024 >> >> > NFrames 35 >> >> > SliceArraylSize 64 >> >> > IsMosaic 1 >> >> > ImgPos 863.3041 1153.2142 -113.6526 >> >> > VolRes 2.0000 2.0000 2.0000 >> >> > VolDim 128 128 64 >> >> > Vc -0.9895 -0.1445 0.0066 >> >> > Vr 0.1446 -0.9873 0.0662 >> >> > Vs -0.0031 0.0664 0.9978 >> >> > VolCenter 0.0000 0.0000 0.0000 >> >> > TransferSyntaxUID unknown >> >> > INFO: sorting. >> >> > INFO: (128 128 64), nframes = 35, ismosaic=1 >> >> > Could not parse NUMARIS version string syngo MR B15 >> >> > found in dicom tag 18,1020 (len = 3 != 6) >> >> > Repetition Time = 7980, TR = 7980 ms >> >> > PE Dir COL COL >> >> > AutoAlign matrix detected >> >> > AutoAlign Matrix --------------------- >> >> > 0.989 -0.141 0.034 4.549; >> >> > 0.145 0.949 -0.279 4.841; >> >> > 0.007 0.281 0.960 24.557; >> >> > 0.000 0.000 0.000 1.000; >> >> > >> >> > This looks like an MGH DTI volume >> >> > MGH DTI SeqPack Info >> >> > 0 ep_b0#1 0.000000 1 >> >> > 1 ep_b0#2 0.000000 2 >> >> > 2 ep_b0#3 0.000000 3 >> >> > 3 ep_b0#4 0.000000 4 >> >> > 4 ep_b0#5 0.000000 5 >> >> > 5 ep_b700#1 700.000000 1 >> >> > 6 ep_b700#2 700.000000 2 >> >> > 7 ep_b700#3 700.000000 3 >> >> > 8 ep_b700#4 700.000000 4 >> >> > 9 ep_b700#5 700.000000 5 >> >> > 10 ep_b700#6 700.000000 6 >> >> > 11 ep_b700#7 700.000000 7 >> >> > 12 ep_b700#8 700.000000 8 >> >> > 13 ep_b700#9 700.000000 9 >> >> > 14 ep_b700#10 700.000000 10 >> >> > 15 ep_b700#11 700.000000 11 >> >> > 16 ep_b700#12 700.000000 12 >> >> > 17 ep_b700#13 700.000000 13 >> >> > 18 ep_b700#14 700.000000 14 >> >> > 19 ep_b700#15 700.000000 15 >> >> > 20 ep_b700#16 700.000000 16 >> >> > 21 ep_b700#17 700.000000 17 >> >> > 22 ep_b700#18 700.000000 18 >> >> > 23 ep_b700#19 700.000000 19 >> >> > 24 ep_b700#20 700.000000 20 >> >> > 25 ep_b700#21 700.000000 21 >> >> > 26 ep_b700#22 700.000000 22 >> >> > 27 ep_b700#23 700.000000 23 >> >> > 28 ep_b700#24 700.000000 24 >> >> > 29 ep_b700#25 700.000000 25 >> >> > 30 ep_b700#26 700.000000 26 >> >> > 31 ep_b700#27 700.000000 27 >> >> > 32 ep_b700#28 700.000000 28 >> >> > 33 ep_b700#29 700.000000 29 >> >> > 34 ep_b700#30 700.000000 30 >> >> > bValue = 700 >> >> > nB0 = 5 >> >> > nDir = 30 >> >> > GradFile >> >> > >> >> >> /software/Freesurfer/5.1.0//diffusion/mgh-dti-seqpack/gradient_mgh_dti30.gdt >> >> > FileName /data/memory/sourcemem//s1001/156000-20-35.dcm >> >> > Identification >> >> > NumarisVer syngo MR B15 >> >> > ScannerModel TrioTim >> >> > PatientName Gab_source_s1001 >> >> > Date and time >> >> > StudyDate 20091119 >> >> > StudyTime 170216.156000 >> >> > SeriesTime 180621.328000 >> >> > AcqTime 180804.265000 >> >> > Acquisition parameters >> >> > PulseSeq ep_b700#30 >> >> > Protocol DIFFUSION_HighRes_Short >> >> > PhEncDir COL >> >> > EchoNo 1 >> >> > FlipAngle 90 >> >> > EchoTime 84 >> >> > InversionTime -1 >> >> > RepetitionTime 7980 >> >> > PhEncFOV 256 >> >> > ReadoutFOV 256 >> >> > Image information >> >> > RunNo 19 >> >> > SeriesNo 20 >> >> > ImageNo 35 >> >> > NImageRows 1024 >> >> > NImageCols 1024 >> >> > NFrames 35 >> >> > SliceArraylSize 64 >> >> > IsMosaic 1 >> >> > ImgPos 863.3041 1153.2142 -113.6526 >> >> > VolRes 2.0000 2.0000 2.0000 >> >> > VolDim 128 128 64 >> >> > Vc -0.9895 -0.1445 0.0066 >> >> > Vr 0.1446 -0.9873 0.0662 >> >> > Vs -0.0031 0.0664 0.9978 >> >> > VolCenter 0.0000 0.0000 0.0000 >> >> > TransferSyntaxUID unknown >> >> > sagrev = 0, correv =0, trarev = 0 >> >> > Vs = -0.00309869 0.0664423 0.997786 >> >> > INFO: no Siemens slice order reversal detected (good!). >> >> > TR=7980.00, TE=84.00, TI=-1.00, flip angle=90.00 >> >> > i_ras = (-0.989479, -0.144529, 0.00655128) >> >> > j_ras = (0.144644, -0.987267, 0.0661911) >> >> > k_ras = (-0.00309869, 0.0664423, 0.997786) >> >> > writing to >> >> > /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_orig.nii.gz... >> >> > Saving bvals and bvecs >> >> > mri_probedicom --i /data/memory/sourcemem//s1001/156000-20-1.dcm > >> >> > /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dcminfo.dat >> >> > flip4fsl >> >> > /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_orig.nii.gz >> >> > >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_orig_flip.nii.gz >> >> > INFO: input image orientation is LPS >> >> > INFO: input image determinant is 8 >> >> > fslswapdim >> >> > /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_orig.nii.gz >> x >> >> -y z >> >> > >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_orig_flip.nii.gz >> >> > INFO: left-right orientation was flipped by fslswapdim >> >> > fslorient -forceradiological >> >> > >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_orig_flip.nii.gz >> >> > INFO: found >> >> > >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_orig.mghdti.bvals, >> >> > converting to FSL format >> >> > INFO: found >> >> > >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_orig.mghdti.bvecs, >> >> > converting to FSL format >> >> > mv -f >> >> > >> >> >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_orig_flip.mghdti.bvecs >> >> > /mindhive/gablab/users/cpdla/Documents//s1001/dmri/bvecs >> >> > mv -f >> >> > >> >> >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_orig_flip.mghdti.bvals >> >> > /mindhive/gablab/users/cpdla/Documents//s1001/dmri/bvals >> >> > eddy_correct >> >> > >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_orig_flip.nii.gz >> >> > /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi.nii.gz 0 >> >> > processing >> >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0000 >> >> > processing >> >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0001 >> >> > processing >> >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0002 >> >> > processing >> >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0003 >> >> > processing >> >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0004 >> >> > processing >> >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0005 >> >> > processing >> >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0006 >> >> > processing >> >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0007 >> >> > processing >> >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0008 >> >> > processing >> >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0009 >> >> > processing >> >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0010 >> >> > processing >> >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0011 >> >> > processing >> >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0012 >> >> > processing >> >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0013 >> >> > processing >> >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0014 >> >> > processing >> >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0015 >> >> > processing >> >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0016 >> >> > processing >> >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0017 >> >> > processing >> >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0018 >> >> > processing >> >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0019 >> >> > processing >> >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0020 >> >> > processing >> >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0021 >> >> > processing >> >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0022 >> >> > processing >> >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0023 >> >> > processing >> >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0024 >> >> > processing >> >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0025 >> >> > processing >> >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0026 >> >> > processing >> >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0027 >> >> > processing >> >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0028 >> >> > processing >> >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0029 >> >> > processing >> >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0030 >> >> > processing >> >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0031 >> >> > processing >> >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0032 >> >> > processing >> >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0033 >> >> > processing >> >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0034 >> >> > mv -f /mindhive/gablab/users/cpdla/Documents//s1001/dmri/bvecs >> >> > /mindhive/gablab/users/cpdla/Documents//s1001/dmri/bvecs.norot >> >> > xfmrot >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi.ecclog >> >> > /mindhive/gablab/users/cpdla/Documents//s1001/dmri/bvecs.norot >> >> > /mindhive/gablab/users/cpdla/Documents//s1001/dmri/bvecs >> >> > fslroi >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi.nii.gz >> >> > /mindhive/gablab/users/cpdla/Documents//s1001/dmri/lowb.nii.gz 0 5 >> >> > fslmaths >> >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/lowb.nii.gz >> >> > -Tmean >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/lowb.nii.gz >> >> > bet /mindhive/gablab/users/cpdla/Documents//s1001/dmri/lowb.nii.gz >> >> > /mindhive/gablab/users/cpdla/Documents//s1001/dmri/lowb_brain.nii.gz >> >> -m >> >> -f >> >> > 0.3 >> >> > mv -f >> >> > >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/lowb_brain_mask.nii.gz >> >> > /mindhive/gablab/users/cpdla/Documents//s1001/dlabel/diff >> >> > #------------------------------------- >> >> > #@# Inter-subject registration Tue Dec 6 22:15:05 EST 2011 >> >> > flirt -in >> >> > /mindhive/gablab/users/cpdla/Documents//s1001/dmri/lowb_brain.nii.gz >> >> -ref >> >> > /usr/share/fsl/4.1/data/standard/MNI152_T1_1mm_brain.nii.gz -out >> >> > >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/lowb_brain_mni.nii.gz >> >> > -omat >> >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/xfms/diff2mni.mat >> >> > -cost mutualinfo >> >> > convert_xfm -omat >> >> > /mindhive/gablab/users/cpdla/Documents//s1001/dmri/xfms/mni2diff.mat >> >> > -inverse >> >> > /mindhive/gablab/users/cpdla/Documents//s1001/dmri/xfms/diff2mni.mat >> >> > #------------------------------------- >> >> > #@# Masks Tue Dec 6 22:15:47 EST 2011 >> >> > #------------------------------------- >> >> > #@# Tensor fit Tue Dec 6 22:15:47 EST 2011 >> >> > dtifit -k >> >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi.nii.gz >> >> -m >> >> > >> >> >> /mindhive/gablab/users/cpdla/Documents//s1001/dlabel/diff/lowb_brain_mask.nii.gz >> >> > -r /mindhive/gablab/users/cpdla/Documents//s1001/dmri/bvecs -b >> >> > /mindhive/gablab/users/cpdla/Documents//s1001/dmri/bvals -o >> >> > /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dtifit >> >> > 0 128 0 128 0 64 >> >> > 0 slices processed >> >> > 1 slices processed >> >> > 2 slices processed >> >> > 3 slices processed >> >> > 4 slices processed >> >> > 5 slices processed >> >> > 6 slices processed >> >> > 7 slices processed >> >> > 8 slices processed >> >> > 9 slices processed >> >> > 10 slices processed >> >> > 11 slices processed >> >> > 12 slices processed >> >> > 13 slices processed >> >> > 14 slices processed >> >> > 15 slices processed >> >> > 16 slices processed >> >> > 17 slices processed >> >> > 18 slices processed >> >> > 19 slices processed >> >> > 20 slices processed >> >> > 21 slices processed >> >> > 22 slices processed >> >> > 23 slices processed >> >> > 24 slices processed >> >> > 25 slices processed >> >> > 26 slices processed >> >> > 27 slices processed >> >> > 28 slices processed >> >> > 29 slices processed >> >> > 30 slices processed >> >> > 31 slices processed >> >> > 32 slices processed >> >> > 33 slices processed >> >> > 34 slices processed >> >> > 35 slices processed >> >> > 36 slices processed >> >> > 37 slices processed >> >> > 38 slices processed >> >> > 39 slices processed >> >> > 40 slices processed >> >> > 41 slices processed >> >> > 42 slices processed >> >> > 43 slices processed >> >> > 44 slices processed >> >> > 45 slices processed >> >> > 46 slices processed >> >> > 47 slices processed >> >> > 48 slices processed >> >> > 49 slices processed >> >> > 50 slices processed >> >> > 51 slices processed >> >> > 52 slices processed >> >> > 53 slices processed >> >> > 54 slices processed >> >> > 55 slices processed >> >> > 56 slices processed >> >> > 57 slices processed >> >> > 58 slices processed >> >> > 59 slices processed >> >> > 60 slices processed >> >> > 61 slices processed >> >> > 62 slices processed >> >> > 63 slices processed >> >> > #------------------------------------- >> >> > #@# Priors Tue Dec 6 22:15:54 EST 2011 >> >> > /software/Freesurfer/5.1.0//bin/dmri_train --outdir >> >> > /mindhive/gablab/users/cpdla/Documents//s1001/dlabel/mni --out >> >> > lh.cst_AS_avg33_mni_flt rh.cst_AS_avg33_mni_flt >> >> lh.ilf_AS_avg33_mni_flt >> >> > rh.ilf_AS_avg33_mni_flt lh.unc_AS_avg33_mni_flt >> >> rh.unc_AS_avg33_mni_flt >> >> > fmajor_PP_avg33_mni_flt fminor_PP_avg33_mni_flt >> >> lh.atr_PP_avg33_mni_flt >> >> > rh.atr_PP_avg33_mni_flt lh.ccg_PP_avg33_mni_flt >> >> rh.ccg_PP_avg33_mni_flt >> >> > lh.cab_PP_avg33_mni_flt rh.cab_PP_avg33_mni_flt >> >> lh.slfp_PP_avg33_mni_flt >> >> > rh.slfp_PP_avg33_mni_flt lh.slft_PP_avg33_mni_flt >> >> rh.slft_PP_avg33_mni_flt >> >> > --slist /tmp/subj33.s1001.8627.txt --trk >> dlabel/mni/lh.cst_AS.flt.trk >> >> > dlabel/mni/rh.cst_AS.flt.trk dlabel/mni/lh.ilf_AS.flt.trk >> >> > dlabel/mni/rh.ilf_AS.flt.trk dlabel/mni/lh.unc_AS.flt.trk >> >> > dlabel/mni/rh.unc_AS.flt.trk dlabel/mni/fmajor_PP.flt.trk >> >> > dlabel/mni/fminor_PP.flt.trk dlabel/mni/lh.atr_PP.flt.trk >> >> > dlabel/mni/rh.atr_PP.flt.trk dlabel/mni/lh.ccg_PP.flt.trk >> >> > dlabel/mni/rh.ccg_PP.flt.trk dlabel/mni/lh.cab_PP.flt.trk >> >> > dlabel/mni/rh.cab_PP.flt.trk dlabel/mni/lh.slfp_PP.flt.trk >> >> > dlabel/mni/rh.slfp_PP.flt.trk dlabel/mni/lh.slft_PP.flt.trk >> >> > dlabel/mni/rh.slft_PP.flt.trk --seg dlabel/mni/aparc+aseg.nii.gz >> >> --cmask >> >> > dlabel/mni/cortex+2mm.nii.gz --lmask 16 16 0 0 0 0 0 0 10 49 0 0 0 >> 0 0 >> >> 0 >> >> 0 >> >> > 0 --rois dlabel/mni/lh.cst_AS_roi1.flt.nii.gz >> >> > dlabel/mni/lh.cst_AS_roi2.flt.nii.gz >> >> dlabel/mni/rh.cst_AS_roi1.flt.nii.gz >> >> > dlabel/mni/rh.cst_AS_roi2.flt.nii.gz >> >> dlabel/mni/lh.ilf_AS_roi1.flt.nii.gz >> >> > dlabel/mni/lh.ilf_AS_roi2.flt.nii.gz >> >> dlabel/mni/rh.ilf_AS_roi1.flt.nii.gz >> >> > dlabel/mni/rh.ilf_AS_roi2.flt.nii.gz >> >> dlabel/mni/lh.unc_AS_roi1.flt.nii.gz >> >> > dlabel/mni/lh.unc_AS_roi2.flt.nii.gz >> >> dlabel/mni/rh.unc_AS_roi1.flt.nii.gz >> >> > dlabel/mni/rh.unc_AS_roi2.flt.nii.gz >> >> dlabel/mni/fmajor_PP_roi1.flt.nii.gz >> >> > dlabel/mni/fmajor_PP_roi2.flt.nii.gz >> >> dlabel/mni/fminor_PP_roi1.flt.nii.gz >> >> > dlabel/mni/fminor_PP_roi2.flt.nii.gz >> >> dlabel/mni/lh.atr_PP_roi1.flt.nii.gz >> >> > dlabel/mni/lh.atr_PP_roi2.flt.nii.gz >> >> dlabel/mni/rh.atr_PP_roi1.flt.nii.gz >> >> > dlabel/mni/rh.atr_PP_roi2.flt.nii.gz >> >> dlabel/mni/lh.ccg_PP_roi1.flt.nii.gz >> >> > dlabel/mni/lh.ccg_PP_roi2.flt.nii.gz >> >> dlabel/mni/rh.ccg_PP_roi1.flt.nii.gz >> >> > dlabel/mni/rh.ccg_PP_roi2.flt.nii.gz >> >> dlabel/mni/lh.cab_PP_roi1.flt.nii.gz >> >> > dlabel/mni/lh.cab_PP_roi2.flt.nii.gz >> >> dlabel/mni/rh.cab_PP_roi1.flt.nii.gz >> >> > dlabel/mni/rh.cab_PP_roi2.flt.nii.gz >> >> dlabel/mni/lh.slfp_PP_roi1.flt.nii.gz >> >> > dlabel/mni/lh.slfp_PP_roi2.flt.nii.gz >> >> > dlabel/mni/rh.slfp_PP_roi1.flt.nii.gz >> >> > dlabel/mni/rh.slfp_PP_roi2.flt.nii.gz >> >> > dlabel/mni/lh.slft_PP_roi1.flt.nii.gz >> >> > dlabel/mni/lh.slft_PP_roi2.flt.nii.gz >> >> > dlabel/mni/rh.slft_PP_roi1.flt.nii.gz >> >> > dlabel/mni/rh.slft_PP_roi2.flt.nii.gz --bmask >> >> > >> >> >> /mindhive/gablab/users/cpdla/Documents//s1001/dlabel/mni/lowb_brain_mask.flt.nii.gz >> >> > --fa >> >> > >> >> >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/mni/dtifit_FA.flt.nii.gz >> >> > --ncpts 5 --debug >> >> > ERROR: fio_pushd: >> >> /mindhive/gablab/users/cpdla/Documents//s1001/dlabel/mni >> >> > ERROR: must specify brain mask volume for output subject >> >> > _______________________________________________ >> >> > 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

Re: [Freesurfer] tracula ERROR: must specify brain mask volume for output subject
by Priti Srinivasan 08 Dec '11

08 Dec '11

Hi Paula, which image are you trying to open? If you're trying to open the merged files in freeview, you should use the -tv flag for opening it. Did you source the freesurfer environment before opening freeview? Can you give us the exact commandline you used? Priti > hi, > i am trying to visualize my results with freeview, and i am running into > this error. i am using freesurfer 5.1.0. do you know what the problem is? > : > > cpdla@ba3:~/Documents/s1001/dmri$ freeview > X Error: BadValue (integer parameter out of range for operation) 2 > Extension: 146 (Uknown extension) > Minor opcode: 3 (Unknown request) > Resource id: 0x24 > Abort > > > On Wed, Dec 7, 2011 at 12:52 PM, Priti Srinivasan < > rspriti(a)nmr.mgh.harvard.edu> wrote: > >> Hi Paula, >> >> Tracula uses anatomical labels/files from freesurfer cortical >> reconstruction to build the posterior distribution of the tracts. It >> looks >> like you may not have run freesurfer recon for your subject. >> >> To run freesurfer recon for your subject please refer to the following >> page: >> >> http://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferBeginnersGuide >> >> Especially, >> >> recon-all \ >> -i <one slice in the anatomical dicom series> \ >> -s <subject id that you make up> \ >> -sd <directory to put the subject folder in> \ >> -all >> >> Once this finishes processing you can re-run tracula to see if that >> solves >> the issue. >> >> Hope that is helpful, >> Priti >> >> >> >> > Hi. >> > >> > I am running into the following error: >> > ERROR: fio_pushd: >> /mindhive/gablab/users/cpdla/Documents//s1001/dlabel/mni >> > ERROR: must specify brain mask volume for output subject . >> > >> > I googled this error and it seems like you suggested this to someone >> else >> > : >> > "As for your error, it looks like maybe the freesurfer recon wasn't >> found, >> > so >> > it skipped some steps (diffusion-to-anatomical registration and mask >> > creation). >> > Does the freesurfer recon dir /home/ajfurst/Data/WRIISC/014/ exist? >> > >> > >> > a.y" >> > >> > What is the freesurfer recon dir supposed to look like? Any >> > suggestions on how to fix this error? Below is my output. >> > >> > Thanks, >> > C. Paula >> > >> > >> > >> > >> > ba3:~/Documents> trac-all -prep -c dmrirc_single_subject >> > set: Variable name must begin with a letter. >> > INFO: SUBJECTS_DIR is >> > /mindhive/gablab/users/cpdla/Documents/diffusion_recons >> > INFO: Diffusion root is /mindhive/gablab/users/cpdla/Documents/ >> > Actual FREESURFER_HOME /software/Freesurfer/5.1.0 >> > trac-preproc -c >> > /mindhive/gablab/users/cpdla/Documents//s1001/scripts/dmrirc.local >> -log >> > /mindhive/gablab/users/cpdla/Documents//s1001/scripts/trac-all.log >> -cmd >> > /mindhive/gablab/users/cpdla/Documents//s1001/scripts/trac-all.cmd >> > #------------------------------------- >> > /software/Freesurfer/5.1.0//bin/trac-preproc >> > #------------------------------------- >> > #@# Image corrections Tue Dec 6 22:02:37 EST 2011 >> > mri_convert /data/memory/sourcemem//s1001/156000-20-1.dcm >> > /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_orig.nii.gz >> > mri_convert /data/memory/sourcemem//s1001/156000-20-1.dcm >> > /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_orig.nii.gz >> > $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ >> > reading from /data/memory/sourcemem//s1001/156000-20-1.dcm... >> > Getting Series No >> > INFO: Found 3207 files in /data/memory/sourcemem//s1001 >> > INFO: Scanning for Series Number 20 >> > Scanning Directory >> > INFO: found 35 files in series >> > INFO: loading series header info. >> > >> > RunNo = 19 >> > WARNING: Run 1 appears to be truncated >> > Files Found: 35, Files Expected (lRep+1): 60 >> > FileName /data/memory/sourcemem//s1001/156000-20-1.dcm >> > Identification >> > NumarisVer syngo MR B15 >> > ScannerModel TrioTim >> > PatientName Gab_source_s1001 >> > Date and time >> > StudyDate 20091119 >> > StudyTime 170216.156000 >> > SeriesTime 180621.328000 >> > AcqTime 180331.855000 >> > Acquisition parameters >> > PulseSeq ep_b0#1 >> > Protocol DIFFUSION_HighRes_Short >> > PhEncDir COL >> > EchoNo 1 >> > FlipAngle 90 >> > EchoTime 84 >> > InversionTime -1 >> > RepetitionTime 7980 >> > PhEncFOV 256 >> > ReadoutFOV 256 >> > Image information >> > RunNo 19 >> > SeriesNo 20 >> > ImageNo 1 >> > NImageRows 1024 >> > NImageCols 1024 >> > NFrames 35 >> > SliceArraylSize 64 >> > IsMosaic 1 >> > ImgPos 863.3041 1153.2142 -113.6526 >> > VolRes 2.0000 2.0000 2.0000 >> > VolDim 128 128 64 >> > Vc -0.9895 -0.1445 0.0066 >> > Vr 0.1446 -0.9873 0.0662 >> > Vs -0.0031 0.0664 0.9978 >> > VolCenter 0.0000 0.0000 0.0000 >> > TransferSyntaxUID unknown >> > INFO: sorting. >> > INFO: (128 128 64), nframes = 35, ismosaic=1 >> > Could not parse NUMARIS version string syngo MR B15 >> > found in dicom tag 18,1020 (len = 3 != 6) >> > Repetition Time = 7980, TR = 7980 ms >> > PE Dir COL COL >> > AutoAlign matrix detected >> > AutoAlign Matrix --------------------- >> > 0.989 -0.141 0.034 4.549; >> > 0.145 0.949 -0.279 4.841; >> > 0.007 0.281 0.960 24.557; >> > 0.000 0.000 0.000 1.000; >> > >> > This looks like an MGH DTI volume >> > MGH DTI SeqPack Info >> > 0 ep_b0#1 0.000000 1 >> > 1 ep_b0#2 0.000000 2 >> > 2 ep_b0#3 0.000000 3 >> > 3 ep_b0#4 0.000000 4 >> > 4 ep_b0#5 0.000000 5 >> > 5 ep_b700#1 700.000000 1 >> > 6 ep_b700#2 700.000000 2 >> > 7 ep_b700#3 700.000000 3 >> > 8 ep_b700#4 700.000000 4 >> > 9 ep_b700#5 700.000000 5 >> > 10 ep_b700#6 700.000000 6 >> > 11 ep_b700#7 700.000000 7 >> > 12 ep_b700#8 700.000000 8 >> > 13 ep_b700#9 700.000000 9 >> > 14 ep_b700#10 700.000000 10 >> > 15 ep_b700#11 700.000000 11 >> > 16 ep_b700#12 700.000000 12 >> > 17 ep_b700#13 700.000000 13 >> > 18 ep_b700#14 700.000000 14 >> > 19 ep_b700#15 700.000000 15 >> > 20 ep_b700#16 700.000000 16 >> > 21 ep_b700#17 700.000000 17 >> > 22 ep_b700#18 700.000000 18 >> > 23 ep_b700#19 700.000000 19 >> > 24 ep_b700#20 700.000000 20 >> > 25 ep_b700#21 700.000000 21 >> > 26 ep_b700#22 700.000000 22 >> > 27 ep_b700#23 700.000000 23 >> > 28 ep_b700#24 700.000000 24 >> > 29 ep_b700#25 700.000000 25 >> > 30 ep_b700#26 700.000000 26 >> > 31 ep_b700#27 700.000000 27 >> > 32 ep_b700#28 700.000000 28 >> > 33 ep_b700#29 700.000000 29 >> > 34 ep_b700#30 700.000000 30 >> > bValue = 700 >> > nB0 = 5 >> > nDir = 30 >> > GradFile >> > >> /software/Freesurfer/5.1.0//diffusion/mgh-dti-seqpack/gradient_mgh_dti30.gdt >> > FileName /data/memory/sourcemem//s1001/156000-20-35.dcm >> > Identification >> > NumarisVer syngo MR B15 >> > ScannerModel TrioTim >> > PatientName Gab_source_s1001 >> > Date and time >> > StudyDate 20091119 >> > StudyTime 170216.156000 >> > SeriesTime 180621.328000 >> > AcqTime 180804.265000 >> > Acquisition parameters >> > PulseSeq ep_b700#30 >> > Protocol DIFFUSION_HighRes_Short >> > PhEncDir COL >> > EchoNo 1 >> > FlipAngle 90 >> > EchoTime 84 >> > InversionTime -1 >> > RepetitionTime 7980 >> > PhEncFOV 256 >> > ReadoutFOV 256 >> > Image information >> > RunNo 19 >> > SeriesNo 20 >> > ImageNo 35 >> > NImageRows 1024 >> > NImageCols 1024 >> > NFrames 35 >> > SliceArraylSize 64 >> > IsMosaic 1 >> > ImgPos 863.3041 1153.2142 -113.6526 >> > VolRes 2.0000 2.0000 2.0000 >> > VolDim 128 128 64 >> > Vc -0.9895 -0.1445 0.0066 >> > Vr 0.1446 -0.9873 0.0662 >> > Vs -0.0031 0.0664 0.9978 >> > VolCenter 0.0000 0.0000 0.0000 >> > TransferSyntaxUID unknown >> > sagrev = 0, correv =0, trarev = 0 >> > Vs = -0.00309869 0.0664423 0.997786 >> > INFO: no Siemens slice order reversal detected (good!). >> > TR=7980.00, TE=84.00, TI=-1.00, flip angle=90.00 >> > i_ras = (-0.989479, -0.144529, 0.00655128) >> > j_ras = (0.144644, -0.987267, 0.0661911) >> > k_ras = (-0.00309869, 0.0664423, 0.997786) >> > writing to >> > /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_orig.nii.gz... >> > Saving bvals and bvecs >> > mri_probedicom --i /data/memory/sourcemem//s1001/156000-20-1.dcm > >> > /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dcminfo.dat >> > flip4fsl >> > /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_orig.nii.gz >> > /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_orig_flip.nii.gz >> > INFO: input image orientation is LPS >> > INFO: input image determinant is 8 >> > fslswapdim >> > /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_orig.nii.gz x >> -y z >> > /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_orig_flip.nii.gz >> > INFO: left-right orientation was flipped by fslswapdim >> > fslorient -forceradiological >> > /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_orig_flip.nii.gz >> > INFO: found >> > /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_orig.mghdti.bvals, >> > converting to FSL format >> > INFO: found >> > /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_orig.mghdti.bvecs, >> > converting to FSL format >> > mv -f >> > >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_orig_flip.mghdti.bvecs >> > /mindhive/gablab/users/cpdla/Documents//s1001/dmri/bvecs >> > mv -f >> > >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_orig_flip.mghdti.bvals >> > /mindhive/gablab/users/cpdla/Documents//s1001/dmri/bvals >> > eddy_correct >> > /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_orig_flip.nii.gz >> > /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi.nii.gz 0 >> > processing >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0000 >> > processing >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0001 >> > processing >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0002 >> > processing >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0003 >> > processing >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0004 >> > processing >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0005 >> > processing >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0006 >> > processing >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0007 >> > processing >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0008 >> > processing >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0009 >> > processing >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0010 >> > processing >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0011 >> > processing >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0012 >> > processing >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0013 >> > processing >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0014 >> > processing >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0015 >> > processing >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0016 >> > processing >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0017 >> > processing >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0018 >> > processing >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0019 >> > processing >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0020 >> > processing >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0021 >> > processing >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0022 >> > processing >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0023 >> > processing >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0024 >> > processing >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0025 >> > processing >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0026 >> > processing >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0027 >> > processing >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0028 >> > processing >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0029 >> > processing >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0030 >> > processing >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0031 >> > processing >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0032 >> > processing >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0033 >> > processing >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0034 >> > mv -f /mindhive/gablab/users/cpdla/Documents//s1001/dmri/bvecs >> > /mindhive/gablab/users/cpdla/Documents//s1001/dmri/bvecs.norot >> > xfmrot /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi.ecclog >> > /mindhive/gablab/users/cpdla/Documents//s1001/dmri/bvecs.norot >> > /mindhive/gablab/users/cpdla/Documents//s1001/dmri/bvecs >> > fslroi /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi.nii.gz >> > /mindhive/gablab/users/cpdla/Documents//s1001/dmri/lowb.nii.gz 0 5 >> > fslmaths >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/lowb.nii.gz >> > -Tmean /mindhive/gablab/users/cpdla/Documents//s1001/dmri/lowb.nii.gz >> > bet /mindhive/gablab/users/cpdla/Documents//s1001/dmri/lowb.nii.gz >> > /mindhive/gablab/users/cpdla/Documents//s1001/dmri/lowb_brain.nii.gz >> -m >> -f >> > 0.3 >> > mv -f >> > /mindhive/gablab/users/cpdla/Documents//s1001/dmri/lowb_brain_mask.nii.gz >> > /mindhive/gablab/users/cpdla/Documents//s1001/dlabel/diff >> > #------------------------------------- >> > #@# Inter-subject registration Tue Dec 6 22:15:05 EST 2011 >> > flirt -in >> > /mindhive/gablab/users/cpdla/Documents//s1001/dmri/lowb_brain.nii.gz >> -ref >> > /usr/share/fsl/4.1/data/standard/MNI152_T1_1mm_brain.nii.gz -out >> > /mindhive/gablab/users/cpdla/Documents//s1001/dmri/lowb_brain_mni.nii.gz >> > -omat >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/xfms/diff2mni.mat >> > -cost mutualinfo >> > convert_xfm -omat >> > /mindhive/gablab/users/cpdla/Documents//s1001/dmri/xfms/mni2diff.mat >> > -inverse >> > /mindhive/gablab/users/cpdla/Documents//s1001/dmri/xfms/diff2mni.mat >> > #------------------------------------- >> > #@# Masks Tue Dec 6 22:15:47 EST 2011 >> > #------------------------------------- >> > #@# Tensor fit Tue Dec 6 22:15:47 EST 2011 >> > dtifit -k >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi.nii.gz >> -m >> > >> /mindhive/gablab/users/cpdla/Documents//s1001/dlabel/diff/lowb_brain_mask.nii.gz >> > -r /mindhive/gablab/users/cpdla/Documents//s1001/dmri/bvecs -b >> > /mindhive/gablab/users/cpdla/Documents//s1001/dmri/bvals -o >> > /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dtifit >> > 0 128 0 128 0 64 >> > 0 slices processed >> > 1 slices processed >> > 2 slices processed >> > 3 slices processed >> > 4 slices processed >> > 5 slices processed >> > 6 slices processed >> > 7 slices processed >> > 8 slices processed >> > 9 slices processed >> > 10 slices processed >> > 11 slices processed >> > 12 slices processed >> > 13 slices processed >> > 14 slices processed >> > 15 slices processed >> > 16 slices processed >> > 17 slices processed >> > 18 slices processed >> > 19 slices processed >> > 20 slices processed >> > 21 slices processed >> > 22 slices processed >> > 23 slices processed >> > 24 slices processed >> > 25 slices processed >> > 26 slices processed >> > 27 slices processed >> > 28 slices processed >> > 29 slices processed >> > 30 slices processed >> > 31 slices processed >> > 32 slices processed >> > 33 slices processed >> > 34 slices processed >> > 35 slices processed >> > 36 slices processed >> > 37 slices processed >> > 38 slices processed >> > 39 slices processed >> > 40 slices processed >> > 41 slices processed >> > 42 slices processed >> > 43 slices processed >> > 44 slices processed >> > 45 slices processed >> > 46 slices processed >> > 47 slices processed >> > 48 slices processed >> > 49 slices processed >> > 50 slices processed >> > 51 slices processed >> > 52 slices processed >> > 53 slices processed >> > 54 slices processed >> > 55 slices processed >> > 56 slices processed >> > 57 slices processed >> > 58 slices processed >> > 59 slices processed >> > 60 slices processed >> > 61 slices processed >> > 62 slices processed >> > 63 slices processed >> > #------------------------------------- >> > #@# Priors Tue Dec 6 22:15:54 EST 2011 >> > /software/Freesurfer/5.1.0//bin/dmri_train --outdir >> > /mindhive/gablab/users/cpdla/Documents//s1001/dlabel/mni --out >> > lh.cst_AS_avg33_mni_flt rh.cst_AS_avg33_mni_flt >> lh.ilf_AS_avg33_mni_flt >> > rh.ilf_AS_avg33_mni_flt lh.unc_AS_avg33_mni_flt >> rh.unc_AS_avg33_mni_flt >> > fmajor_PP_avg33_mni_flt fminor_PP_avg33_mni_flt >> lh.atr_PP_avg33_mni_flt >> > rh.atr_PP_avg33_mni_flt lh.ccg_PP_avg33_mni_flt >> rh.ccg_PP_avg33_mni_flt >> > lh.cab_PP_avg33_mni_flt rh.cab_PP_avg33_mni_flt >> lh.slfp_PP_avg33_mni_flt >> > rh.slfp_PP_avg33_mni_flt lh.slft_PP_avg33_mni_flt >> rh.slft_PP_avg33_mni_flt >> > --slist /tmp/subj33.s1001.8627.txt --trk dlabel/mni/lh.cst_AS.flt.trk >> > dlabel/mni/rh.cst_AS.flt.trk dlabel/mni/lh.ilf_AS.flt.trk >> > dlabel/mni/rh.ilf_AS.flt.trk dlabel/mni/lh.unc_AS.flt.trk >> > dlabel/mni/rh.unc_AS.flt.trk dlabel/mni/fmajor_PP.flt.trk >> > dlabel/mni/fminor_PP.flt.trk dlabel/mni/lh.atr_PP.flt.trk >> > dlabel/mni/rh.atr_PP.flt.trk dlabel/mni/lh.ccg_PP.flt.trk >> > dlabel/mni/rh.ccg_PP.flt.trk dlabel/mni/lh.cab_PP.flt.trk >> > dlabel/mni/rh.cab_PP.flt.trk dlabel/mni/lh.slfp_PP.flt.trk >> > dlabel/mni/rh.slfp_PP.flt.trk dlabel/mni/lh.slft_PP.flt.trk >> > dlabel/mni/rh.slft_PP.flt.trk --seg dlabel/mni/aparc+aseg.nii.gz >> --cmask >> > dlabel/mni/cortex+2mm.nii.gz --lmask 16 16 0 0 0 0 0 0 10 49 0 0 0 0 0 >> 0 >> 0 >> > 0 --rois dlabel/mni/lh.cst_AS_roi1.flt.nii.gz >> > dlabel/mni/lh.cst_AS_roi2.flt.nii.gz >> dlabel/mni/rh.cst_AS_roi1.flt.nii.gz >> > dlabel/mni/rh.cst_AS_roi2.flt.nii.gz >> dlabel/mni/lh.ilf_AS_roi1.flt.nii.gz >> > dlabel/mni/lh.ilf_AS_roi2.flt.nii.gz >> dlabel/mni/rh.ilf_AS_roi1.flt.nii.gz >> > dlabel/mni/rh.ilf_AS_roi2.flt.nii.gz >> dlabel/mni/lh.unc_AS_roi1.flt.nii.gz >> > dlabel/mni/lh.unc_AS_roi2.flt.nii.gz >> dlabel/mni/rh.unc_AS_roi1.flt.nii.gz >> > dlabel/mni/rh.unc_AS_roi2.flt.nii.gz >> dlabel/mni/fmajor_PP_roi1.flt.nii.gz >> > dlabel/mni/fmajor_PP_roi2.flt.nii.gz >> dlabel/mni/fminor_PP_roi1.flt.nii.gz >> > dlabel/mni/fminor_PP_roi2.flt.nii.gz >> dlabel/mni/lh.atr_PP_roi1.flt.nii.gz >> > dlabel/mni/lh.atr_PP_roi2.flt.nii.gz >> dlabel/mni/rh.atr_PP_roi1.flt.nii.gz >> > dlabel/mni/rh.atr_PP_roi2.flt.nii.gz >> dlabel/mni/lh.ccg_PP_roi1.flt.nii.gz >> > dlabel/mni/lh.ccg_PP_roi2.flt.nii.gz >> dlabel/mni/rh.ccg_PP_roi1.flt.nii.gz >> > dlabel/mni/rh.ccg_PP_roi2.flt.nii.gz >> dlabel/mni/lh.cab_PP_roi1.flt.nii.gz >> > dlabel/mni/lh.cab_PP_roi2.flt.nii.gz >> dlabel/mni/rh.cab_PP_roi1.flt.nii.gz >> > dlabel/mni/rh.cab_PP_roi2.flt.nii.gz >> dlabel/mni/lh.slfp_PP_roi1.flt.nii.gz >> > dlabel/mni/lh.slfp_PP_roi2.flt.nii.gz >> > dlabel/mni/rh.slfp_PP_roi1.flt.nii.gz >> > dlabel/mni/rh.slfp_PP_roi2.flt.nii.gz >> > dlabel/mni/lh.slft_PP_roi1.flt.nii.gz >> > dlabel/mni/lh.slft_PP_roi2.flt.nii.gz >> > dlabel/mni/rh.slft_PP_roi1.flt.nii.gz >> > dlabel/mni/rh.slft_PP_roi2.flt.nii.gz --bmask >> > >> /mindhive/gablab/users/cpdla/Documents//s1001/dlabel/mni/lowb_brain_mask.flt.nii.gz >> > --fa >> > >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/mni/dtifit_FA.flt.nii.gz >> > --ncpts 5 --debug >> > ERROR: fio_pushd: >> /mindhive/gablab/users/cpdla/Documents//s1001/dlabel/mni >> > ERROR: must specify brain mask volume for output subject >> > _______________________________________________ >> > 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. >> >> >

1 0

overlapping of the surfaces from one hemisphere to another
by Eunjin Yoon 08 Dec '11

08 Dec '11

Dear, Freesurfer users I am processing 1.5T MR images, and found some overlapping of the surfaces from one hemisphere to another. I attached captured images of that subject. you can find the error center of the brain image. How can I fix that?? Thank you in advance. Best Regards, Eunjin

3 3

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