Freesurfer

freesurfer@nmr.mgh.harvard.edu

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Re: [Freesurfer] trac-all problem
by Anastasia Yendiki 12 Feb '13

12 Feb '13

Sorry, reading stuff from the dicom header will not work for all dicom versions. It should work for Siemens dicoms though. On Tue, 12 Feb 2013, Jon Wieser wrote: > according to the > http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula > > nb0 does not need to be specified when using original dicoms. , but i'll try defining the nb0 variable > thanks > Jon > > > ----- Original Message ----- > From: "Anastasia Yendiki" <ayendiki(a)nmr.mgh.harvard.edu> > To: "Jon Wieser" <wieser(a)uwm.edu> > Cc: "freesurfer" <freesurfer(a)nmr.mgh.harvard.edu> > Sent: Tuesday, February 12, 2013 10:49:18 AM > Subject: Re: [Freesurfer] trac-all problem > > > Hi Jon - My guess is you didn't define the nb0 variable in your > configuration file, see here: > http://www.freesurfer.net/fswiki/dmrirc > > The new version, which will come out in a few days, will be able to figure > it out without you having to specify it but with the current version you > have to. > > Hope this helps, > a.y > > On Tue, 12 Feb 2013, Jon Wieser wrote: > >> hello >> >> i am trying to process the dti data with trac-all. I am new to tracula >> my input images are 3300 dicoms, 60 slices and 55 dti diffusions >> i have attached my dmrirc_single_subject file >> >> >> i did the following command: >> >> trac-all -prep -c /Studies/MJMRI/DTI/dmrirc_single_subject >> >> and got the result: >> >> >> >> INFO: SUBJECTS_DIR is /Studies/MJMRI/MJ0012 >> INFO: Diffusion root is /Studies/MJMRI/MJ0012 >> Actual FREESURFER_HOME /Applications/freesurfer >> trac-preproc -c /Studies/MJMRI/MJ0012/freesurfer/scripts/dmrirc.local -log /Studies/MJMRI/MJ0012/freesurfer/scripts/trac-all.log -cmd /Studies/MJMRI/MJ0012/freesurfer/scripts/trac-all.cmd >> #------------------------------------- >> /Applications/freesurfer/bin/trac-preproc >> #------------------------------------- >> #@# Image corrections Mon Feb 11 12:41:04 CST 2013 >> mri_convert /Studies/MJMRI/MJ0012//s780/i1735678.MRDC.1 /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig.nii.gz >> mri_convert /Studies/MJMRI/MJ0012//s780/i1735678.MRDC.1 /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig.nii.gz >> $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ >> reading from /Studies/MJMRI/MJ0012//s780/i1735678.MRDC.1... >> Starting DICOMRead2() >> dcmfile = /Studies/MJMRI/MJ0012//s780/i1735678.MRDC.1 >> dcmdir = /Studies/MJMRI/MJ0012//s780 >> Ref Series No = 13 >> Found 3304 files, checking for dicoms >> Found 3300 dicom files in series. >> First Sorting >> Computing Slice Direction >> Vs: 0 0 2 >> Vs: 0 0 1 >> Second Sorting >> Counting frames >> nframes = 55 >> nslices = 60 >> ndcmfiles = 3300 >> PE Dir = COL (dicom read) >> TransferSyntaxUID: --1.2.840.10008.1.2.1-- >> jpegUID: --1.2.840.10008.1.2.4-- >> Loading pixel data >> TR=9300.00, TE=76.20, TI=0.00, flip angle=90.00 >> i_ras = (-1, 0, 0) >> j_ras = (0, -1, 0) >> k_ras = (-0, -0, 1) >> writing to /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig.nii.gz... >> mri_probedicom --i /Studies/MJMRI/MJ0012//s780/i1735678.MRDC.1 > /Studies/MJMRI/MJ0012/freesurfer/dmri/dcminfo.dat >> flip4fsl /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig.nii.gz /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig_flip.nii.gz >> INFO: input image orientation is LPS >> INFO: input image determinant is 2 >> fslswapdim /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig.nii.gz x -y z /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig_flip.nii.gz >> INFO: left-right orientation was flipped by fslswapdim >> fslorient -forceradiological /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig_flip.nii.gz >> INFO: found /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig.mghdti.bvals, converting to FSL format >> INFO: found /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig.mghdti.bvecs, converting to FSL format >> mv -f /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig_flip.mghdti.bvecs /Studies/MJMRI/MJ0012/freesurfer/dmri/bvecs >> mv -f /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig_flip.mghdti.bvals /Studies/MJMRI/MJ0012/freesurfer/dmri/bvals >> eddy_correct /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig_flip.nii.gz /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi.nii.gz 0 >> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0000 >> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0001 >> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0002 >> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0003 >> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0004 >> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0005 >> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0006 >> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0007 >> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0008 >> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0009 >> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0010 >> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0011 >> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0012 >> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0013 >> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0014 >> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0015 >> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0016 >> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0017 >> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0018 >> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0019 >> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0020 >> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0021 >> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0022 >> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0023 >> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0024 >> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0025 >> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0026 >> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0027 >> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0028 >> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0029 >> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0030 >> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0031 >> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0032 >> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0033 >> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0034 >> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0035 >> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0036 >> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0037 >> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0038 >> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0039 >> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0040 >> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0041 >> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0042 >> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0043 >> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0044 >> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0045 >> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0046 >> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0047 >> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0048 >> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0049 >> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0050 >> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0051 >> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0052 >> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0053 >> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0054 >> mv -f /Studies/MJMRI/MJ0012/freesurfer/dmri/bvecs /Studies/MJMRI/MJ0012/freesurfer/dmri/bvecs.norot >> xfmrot /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi.ecclog /Studies/MJMRI/MJ0012/freesurfer/dmri/bvecs.norot /Studies/MJMRI/MJ0012/freesurfer/dmri/bvecs >> fslroi /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi.nii.gz /Studies/MJMRI/MJ0012/freesurfer/dmri/lowb.nii.gz 0 >> >> Usage: fslroi <input> <output> <xmin> <xsize> <ymin> <ysize> <zmin> <zsize> >> fslroi <input> <output> <tmin> <tsize> >> >> fslroi <input> <output> <xmin> <xsize> <ymin> <ysize> <zmin> <zsize> <tmin> <tsize> >> Note: indexing (in both time and space) starts with 0 not 1! >> Darwin psy-cerebellum.uits.uwm.edu 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:32:41 PDT 2011; root:xnu-1504.15.3~1/RELEASE_X86_64 x86_64 >> >> trac-preproc exited with ERRORS at Mon Feb 11 13:25:16 CST 2013 >> >> >> can you tell me how to fix this? >> Thanks >> Jon Wieser >> UW-Milwaukee >> > > > 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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Troubleshooting the preproc
by Susan Kuo 12 Feb '13

12 Feb '13

Hi FreeSurfer community, I am currently trying to troubleshoot my preprocessing part of TRACULA with the tutorial dataset (for *Diff001* as the subject, specifically), running *trac-all -corr -c <config dmrirc>*. I am running the commands in * subjectID/scripts/trac-all.cmd* one by one because I've had problems with some of the steps. Specifically, *flip4fsl* didn't work. I instead used *fslswapdim -x -y z* (*flip4fsl* uses *fslswapdim x -y z*, which doesn't generate the correct orientation for FSL in fact), followed by *fslorient -forceradiological*. I successfully ran *eddy_current *thereafter. Now I am stuck again, at FreeSurfer's *xfmrot, *which should look like: * * *xfmrot <transform file> <input vector file> [<output vector file>]* I specifically typed in: *xfmrot /j/dti7/Susie/freesurfer/subjects/diffusion_tutorial/Diff001/dmri/dwi.ecclog /j/dti7/Susie/freesurfer/subjects/diffusion_tutorial/Diff001/dmri/bvecs.norot /j/dti7/Susie/freesurfer/subjects/diffusion_tutorial/Diff001/dmri/bvecs* and received the following iterative errors: * avscale: Command not found. R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. * Can any of you help me? Thank you, Susie K

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trac-all problem
by Jon Wieser 12 Feb '13

12 Feb '13

hello i am trying to process the dti data with trac-all. I am new to tracula my input images are 3300 dicoms, 60 slices and 55 dti diffusions i have attached my dmrirc_single_subject file i did the following command: trac-all -prep -c /Studies/MJMRI/DTI/dmrirc_single_subject and got the result: INFO: SUBJECTS_DIR is /Studies/MJMRI/MJ0012 INFO: Diffusion root is /Studies/MJMRI/MJ0012 Actual FREESURFER_HOME /Applications/freesurfer trac-preproc -c /Studies/MJMRI/MJ0012/freesurfer/scripts/dmrirc.local -log /Studies/MJMRI/MJ0012/freesurfer/scripts/trac-all.log -cmd /Studies/MJMRI/MJ0012/freesurfer/scripts/trac-all.cmd #------------------------------------- /Applications/freesurfer/bin/trac-preproc #------------------------------------- #@# Image corrections Mon Feb 11 12:41:04 CST 2013 mri_convert /Studies/MJMRI/MJ0012//s780/i1735678.MRDC.1 /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig.nii.gz mri_convert /Studies/MJMRI/MJ0012//s780/i1735678.MRDC.1 /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig.nii.gz $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from /Studies/MJMRI/MJ0012//s780/i1735678.MRDC.1... Starting DICOMRead2() dcmfile = /Studies/MJMRI/MJ0012//s780/i1735678.MRDC.1 dcmdir = /Studies/MJMRI/MJ0012//s780 Ref Series No = 13 Found 3304 files, checking for dicoms Found 3300 dicom files in series. First Sorting Computing Slice Direction Vs: 0 0 2 Vs: 0 0 1 Second Sorting Counting frames nframes = 55 nslices = 60 ndcmfiles = 3300 PE Dir = COL (dicom read) TransferSyntaxUID: --1.2.840.10008.1.2.1-- jpegUID: --1.2.840.10008.1.2.4-- Loading pixel data TR=9300.00, TE=76.20, TI=0.00, flip angle=90.00 i_ras = (-1, 0, 0) j_ras = (0, -1, 0) k_ras = (-0, -0, 1) writing to /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig.nii.gz... mri_probedicom --i /Studies/MJMRI/MJ0012//s780/i1735678.MRDC.1 > /Studies/MJMRI/MJ0012/freesurfer/dmri/dcminfo.dat flip4fsl /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig.nii.gz /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig_flip.nii.gz INFO: input image orientation is LPS INFO: input image determinant is 2 fslswapdim /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig.nii.gz x -y z /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig_flip.nii.gz INFO: left-right orientation was flipped by fslswapdim fslorient -forceradiological /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig_flip.nii.gz INFO: found /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig.mghdti.bvals, converting to FSL format INFO: found /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig.mghdti.bvecs, converting to FSL format mv -f /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig_flip.mghdti.bvecs /Studies/MJMRI/MJ0012/freesurfer/dmri/bvecs mv -f /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig_flip.mghdti.bvals /Studies/MJMRI/MJ0012/freesurfer/dmri/bvals eddy_correct /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig_flip.nii.gz /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi.nii.gz 0 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0000 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0001 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0002 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0003 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0004 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0005 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0006 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0007 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0008 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0009 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0010 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0011 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0012 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0013 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0014 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0015 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0016 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0017 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0018 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0019 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0020 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0021 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0022 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0023 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0024 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0025 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0026 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0027 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0028 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0029 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0030 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0031 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0032 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0033 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0034 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0035 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0036 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0037 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0038 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0039 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0040 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0041 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0042 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0043 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0044 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0045 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0046 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0047 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0048 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0049 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0050 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0051 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0052 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0053 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0054 mv -f /Studies/MJMRI/MJ0012/freesurfer/dmri/bvecs /Studies/MJMRI/MJ0012/freesurfer/dmri/bvecs.norot xfmrot /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi.ecclog /Studies/MJMRI/MJ0012/freesurfer/dmri/bvecs.norot /Studies/MJMRI/MJ0012/freesurfer/dmri/bvecs fslroi /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi.nii.gz /Studies/MJMRI/MJ0012/freesurfer/dmri/lowb.nii.gz 0 Usage: fslroi <input> <output> <xmin> <xsize> <ymin> <ysize> <zmin> <zsize> fslroi <input> <output> <tmin> <tsize> fslroi <input> <output> <xmin> <xsize> <ymin> <ysize> <zmin> <zsize> <tmin> <tsize> Note: indexing (in both time and space) starts with 0 not 1! Darwin psy-cerebellum.uits.uwm.edu 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:32:41 PDT 2011; root:xnu-1504.15.3~1/RELEASE_X86_64 x86_64 trac-preproc exited with ERRORS at Mon Feb 11 13:25:16 CST 2013 can you tell me how to fix this? Thanks Jon Wieser UW-Milwaukee

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R: trac-all -path error
by stdp82＠virgilio.it 12 Feb '13

12 Feb '13

I'm attaching my trac-all file for check.Thanks, Stefano ----Messaggio originale---- Da: stdp82(a)virgilio.it Data: 11-feb-2013 14.42 A: <freesurfer(a)nmr.mgh.harvard.edu> Cc: <ayendiki(a)nmr.mgh.harvard.edu> Ogg: [Freesurfer] trac-all -path error Hi list, I'm running trac-all -path -c $FREESURFER/dmrirc_single_subject but I have this error: Loading mask from /Applications/freesurfer/subjects/subject_prova/Con02/dlabel/diff/aparc+aseg_mask.bbr.nii.gzLoading BEDPOST parameter samples from /Applications/freesurfer/subjects/subject_prova/Con02/dmri.bedpostXniiRead(): error opening file /Applications/freesurfer/subjects/subject_prova/Con02/dmri.bedpostX/merged_ph1samples.nii.gzERROR: Could not read /Applications/freesurfer/subjects/subject_prova/Con02/dmri.bedpostX/merged_ph1samples.nii.gz >From http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg22066.html I'm deducing that the error may be related trace-all upload. I have doing this upload but I visualize always the same error. I attached tract-all uploades file that live in /Applications/freesurfer/bin. Please, could you check it? I have also other question. May I run the second step of trac-all (bedpostx) using FSL on other pc? In this way, could I directly run in FSL dmri folder? Do you think that I should rename some files? Thanks, Stefano

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trac-all -path error
by stdp82＠virgilio.it 12 Feb '13

12 Feb '13

Hi list, I'm running trac-all -path -c $FREESURFER/dmrirc_single_subject but I have this error: Loading mask from /Applications/freesurfer/subjects/subject_prova/Con02/dlabel/diff/aparc+aseg_mask.bbr.nii.gzLoading BEDPOST parameter samples from /Applications/freesurfer/subjects/subject_prova/Con02/dmri.bedpostXniiRead(): error opening file /Applications/freesurfer/subjects/subject_prova/Con02/dmri.bedpostX/merged_ph1samples.nii.gzERROR: Could not read /Applications/freesurfer/subjects/subject_prova/Con02/dmri.bedpostX/merged_ph1samples.nii.gz >From http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg22066.html I'm deducing that the error may be related trace-all upload. I have doing this upload but I visualize always the same error. I attached tract-all uploades file that live in /Applications/freesurfer/bin. Please, could you check it? I have also other question. May I run the second step of trac-all (bedpostx) using FSL on other pc? In this way, could I directly run in FSL dmri folder? Do you think that I should rename some files? Thanks, Stefano

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Re: [Freesurfer] mean cortical thickness of significant clusters in qdec
by Douglas N Greve 12 Feb '13

12 Feb '13

Anyone know how to reset the LOCAL? Even if temporarily to see if this is the problem? doug On 02/12/2013 08:23 AM, Richter, Julia wrote: > It says the same even if I put 1.3 in quotes. :( Any other possibility to get access to the data? > > > -----Ursprüngliche Nachricht----- > Von: Douglas N Greve [mailto:greve@nmr.mgh.harvard.edu] > Gesendet: Montag, 11. Februar 2013 19:04 > An: Richter, Julia; Freesurfer(a)nmr.mgh.harvard.edu > Betreff: Re: AW: AW: AW: [Freesurfer] mean cortical thickness of significant clusters in qdec > > > It may be a German operating system replacing 1.3 with 1,3. Maybe put it in quotes, ie, "1.3" > > On 02/11/2013 04:17 AM, Richter, Julia wrote: >> Dear Doug, >> >> this is what appears when I type my command in the command window: >> >> mri_glmfit-sim --cache 1.3 abs --cwpvalthresh .99 >> ERROR: thresh 1,3, must be 1.3, 2.0, 3.0, 3.3, 4.0 >> >> That's it...Any ideas why this is happening? >> >> Many thanks in advance! >> >> Best, Julia >> >> -----Ursprüngliche Nachricht----- >> Von: Douglas N Greve [mailto:greve@nmr.mgh.harvard.edu] >> Gesendet: Donnerstag, 7. Februar 2013 17:32 >> An: Richter, Julia; Freesurfer(a)nmr.mgh.harvard.edu >> Betreff: Re: AW: AW: [Freesurfer] mean cortical thickness of >> significant clusters in qdec >> >> it does not look like you changed the command line. Also, please cut and paste the info into the email instead of taking a snapshot. >> thanks >> doug >> >> On 02/04/2013 07:26 AM, Richter, Julia wrote: >>> This doesn't work either (see attachment) :( >>> >>> -----Ursprüngliche Nachricht----- >>> Von: Douglas N Greve [mailto:greve@nmr.mgh.harvard.edu] >>> Gesendet: Donnerstag, 31. Januar 2013 20:29 >>> An: Richter, Julia; Freesurfer(a)nmr.mgh.harvard.edu >>> Betreff: Re: AW: [Freesurfer] mean cortical thickness of significant >>> clusters in qdec >>> >>> The threshold must be in the form of -log10(pthreshold). So, if you >>> want pthreshold=.05, then use 1.3 doug >>> >>> >>> >>> On 01/31/2013 07:37 AM, Richter, Julia wrote: >>>> Dear Doug, >>>> >>>> thanks for your reply. I tried the command you suggested, but I always get an error message that there is something wrong with my threshold. I took a screenshot of the command window and attached it to this mail. I will be very happy if you have a look at it. >>>> >>>> Looking forward to your answer, >>>> >>>> Best, Julia >>>> >>>> -----Ursprüngliche Nachricht----- >>>> Von: freesurfer-bounces(a)nmr.mgh.harvard.edu >>>> [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] Im Auftrag von >>>> Douglas Greve >>>> Gesendet: Mittwoch, 30. Januar 2013 17:16 >>>> An: Richter, Julia; free surfer >>>> Betreff: Re: [Freesurfer] mean cortical thickness of significant >>>> clusters in qdec >>>> >>>> Oh, sorry, I thought you said you were using mri_glmfit-sim (which >>>> does not have an FDR option). Are you using the FDR in QDEC? If so, >>>> it will display the voxel-wise threshold that realizes the FDR >>>> threshold. You can then run mri_glmfit-sim --cache threshold sign >>>> --cwpvalthresh .99 where threshold is the voxelwise threshold from >>>> FDR and sign is either abs (absolute), pos, or neg. Setting >>>> cwpvalthresh=.99 tell it to report all clusters >>>> >>>> doug >>>> >>>> On 1/30/13 8:09 AM, Richter, Julia wrote: >>>>> No it is not...or I just do not find it. >>>>> >>>>> Might it be that I only get the xxx.y.ocn.dat if I correct for multiple comparisons with Monte Carlo? If yes, is there any possibility that I get this xxx.y.ocn.dat when correcting with FDR? >>>>> >>>>> Many thanks, Julia >>>>> >>>>> -----Ursprüngliche Nachricht----- >>>>> Von: freesurfer-bounces(a)nmr.mgh.harvard.edu >>>>> [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] Im Auftrag von >>>>> Douglas N Greve >>>>> Gesendet: Dienstag, 29. Januar 2013 18:46 >>>>> An: freesurfer(a)nmr.mgh.harvard.edu >>>>> Betreff: Re: [Freesurfer] mean cortical thickness of significant >>>>> clusters in qdec >>>>> >>>>> Hi Julia, it should just be created when mri_glmfit-sim runs. Is it not? >>>>> doug >>>>> >>>>> >>>>> On 01/29/2013 11:03 AM, Richter, Julia wrote: >>>>>> Dear FreeSurfer experts, >>>>>> >>>>>> I did a group analysis in qdec, found several significant clusters >>>>>> and would now like to extract the mean cortical thickness of each >>>>>> significant cluster. I know that I have to run mri_glmfit-sim to >>>>>> do this, but I do not understand which commands I need to get the >>>>>> xxx.y.ocn.dat as output by running mri_glmfit-sim. >>>>>> >>>>>> Any ideas? Any help is appreciated. J >>>>>> >>>>>> Best wishes, Julia >>>>>> >>>>>> >>>>>> >>>>>> _______________________________________________ >>>>>> Freesurfer mailing list >>>>>> Freesurfer(a)nmr.mgh.harvard.edu >>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>> -- >>>>> Douglas N. Greve, Ph.D. >>>>> MGH-NMR Center >>>>> greve(a)nmr.mgh.harvard.edu >>>>> Phone Number: 617-724-2358 >>>>> Fax: 617-726-7422 >>>>> >>>>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>>>> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>>>> Outgoing: >>>>> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >>>>> >>>>> _______________________________________________ >>>>> 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. >>>>> >>>>> >>>>> >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer(a)nmr.mgh.harvard.edu >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> -- >> Douglas N. Greve, Ph.D. >> MGH-NMR Center >> greve(a)nmr.mgh.harvard.edu >> Phone Number: 617-724-2358 >> Fax: 617-726-7422 >> >> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html >> Outgoing: >> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >> >> >> > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

1 0

two sample t-test of paired differences
by Jörg Pfannmöller 12 Feb '13

12 Feb '13

Hello, I have two different results from a paired difference analysis lets call it A and B. How can I do a two sample t-test with those results (A-B)? Somehow I am stuck in using isxconcat-sess on the group results A and B. Help is highly appreciated. Cheers Joerg

2 1

average subject
by Linn Mittlestein 12 Feb '13

12 Feb '13

Dear freesurfer experts, i have a question regarding making my own average. I received this message Tue Feb 12 10:54:34 GMT 2013 make_average_volume done However, the stats file in the average subject is empty, and the tmp folder, but the other folders are not empty. Is this "normal"? Does the above message indicate that the make_subject is done, or should it say "finished without error etc". Thank you for your help, Kind Regards Linn

3 3

Fwd: error when using stats import in qdec
by Catherine Bois 12 Feb '13

12 Feb '13

Dear all, I have a question; I am trying to load data into qdec; the data table is loaded fine (although it lists age as continuous for some region, rather than discreet). However, When i try to generate the stats table, this error comes up. Does this mean I somehow have to manually set the subjects directory to where my subjects are (rather than the default that seems to be used), using the "generate stats table" option? If so, how is this done? Or is it a preprocessing step I have missed out? mkdir: cannot create directory `/usr/local2/freesurfer510/subjects/qdec': Permission denied ERROR: In /usr/pubsw/packages/KWWidgets/CVS-vtk560/KWWidgets/vtkKWTkUtilities.cxx, line 230 vtkKWQdecApp (0x30732c58): Script: vtkTemp2 GenerateStatsDataTables Returned Error on line 1: Uncaught exception: command failed: mkdir -p /usr/local2/freesurfer510/subjects/qdec/stats_tables/ Stack trace: Uncaught exception: command failed: mkdir -p /usr/local2/freesurfer510/subjects/qdec/stats_tables/ while executing "vtkTemp2 GenerateStatsDataTables" Grateful for your help Regards Catherine -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. ----- End forwarded message ----- -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

2 3

error when using stats import in qdec
by Catherine Bois 12 Feb '13

12 Feb '13

1 0

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