Freesurfer February 2013

freesurfer@nmr.mgh.harvard.edu

136 participants
236 discussions

Re: [Freesurfer] cannot find eddy_correct
by Anastasia Yendiki 05 Feb '13

05 Feb '13

In general the FSLDIR variable needs to be set up for freesurfer scripts to find FSL executables. Others on the list will be more qualified than me to address the VM aspects of this. On Tue, 5 Feb 2013, Varghese Chikku wrote: > Hi Anastasia, > First of all,thanks for your mail and forgive my ignorance again. > I have now downloaded FSL on VMplayer I also have FS running on Oracle > VM.So my question is if I run dti_recon,will freesurfer automatically > detect FSL,which is running on a different VM.- > Many thanks for your help, > Chikku > > On 4 February 2013 16:39, Anastasia Yendiki <ayendiki(a)nmr.mgh.harvard.edu> > wrote: > > Yes. > > On Mon, 4 Feb 2013, Varghese Chikku wrote: > > Dear Team, > I tried to run dt_recon and the systems > says cannot find > eddy_correct,Make sure FSL is installed. So ,do I > need to install the > whole FSL package to run this. > In Thanks > Chikku > > > > > 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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R: Re: R: Re: tracula bvecs error
by stdp82＠virgilio.it 05 Feb '13

05 Feb '13

Hi Anastasia, my original folder Diff01 in /Applications/freesurfer/subjects/subject_prova/Diff01 now contains:data.nii.gz (DWI), MPRAGE.nii.gz, bvecs, bvals.I have runned recon-all -all -i $SUBJECTS_DIR/MPRAGE.nii.gz -subject $SUBJECTS_DIR/hpth_subj01 without error and after trac-all -prep -c $FREESURFER_HOME/dmrirc_single_subject but I still have this error: /Applications/freesurfer/bin/dmri_train --outdir /Applications/freesurfer/subjects/subject_prova/Diff01/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.cab_PP_avg33_mni_flt rh.cab_PP_avg33_mni_flt lh.ccg_PP_avg33_mni_flt rh.ccg_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.Diff01.21529.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.cab_PP.flt.trk dlabel/mni/rh.cab_PP.flt.trk dlabel/mni/lh.ccg_PP.flt.trk dlabel/mni/rh.ccg_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.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.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.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 /Applications/freesurfer/subjects/subject_prova/Diff01/dlabel/mni/lowb_brain_mask.flt.nii.gz --fa /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/mni/dtifit_FA.flt.nii.gz --ncpts 5 --debugERROR: fio_pushd: /Applications/freesurfer/subjects/subject_prova/Diff01/dlabel/mniERROR: must specify brain mask volume for output subjectDarwin iMac-di-Stefano.local 12.2.1 Darwin Kernel Version 12.2.1: Thu Oct 18 12:13:47 PDT 2012; root:xnu-2050.20.9~1/RELEASE_X86_64 x86_64 trac-preproc exited with ERRORS at Tue Feb 5 07:54:09 CET 2013 Why? Can it depends from the files in the original folder Diff01? Please, if yes, may you explain which is the better arrangement of the MPRAGE and DWI in the folders. Thank you very much, Stefano ----Messaggio originale---- Da: ayendiki(a)nmr.mgh.harvard.edu Data: 4-feb-2013 4.48 A: <stdp82(a)virgilio.it> Cc: <freesurfer(a)nmr.mgh.harvard.edu> Ogg: Re: [Freesurfer] R: Re: tracula bvecs error No, putting your T1 in a folder is not the same as running freesurfer on it. You need to run recon-all on your T1. This is a piece of software that will segment your T1 (among other things). Tracula will need that segmentation to reconstruct your tracts. On Sun, 3 Feb 2013, stdp82(a)virgilio.it wrote: > Hi Anastasia, > I have put T1 in /Applications/freesurfer/subjects/subject_prova/Diff01/ > together data.nii.gz, bvals and bvecs. > My $SUBJECTS_DIR=$FREESURFER_HOME/subjects/subject_prova > T1 was called as T1_01.nii.gz. > This is well done? > > Thanks, > > Stefano > > ----Messaggio originale---- > Da: ayendiki(a)nmr.mgh.harvard.edu > Data: 3-feb-2013 20.50 > A: <stdp82(a)virgilio.it> > Cc: <freesurfer(a)nmr.mgh.harvard.edu> > Ogg: Re: [Freesurfer] tracula bvecs error > > > Do you have a freesurfer recon of your subject's T1 in the $SUBJECTS_DIR? > > On Sun, 3 Feb 2013, stdp82(a)virgilio.it wrote: > > > I think that I have resolved the bvecs error by using sudo nano option but > > now in the next step I visualize this error: > > ERROR: fio_pushd: > > /Applications/freesurfer/subjects/subject_prova/Diff01/dlabel/mni > > ERROR: must specify brain mask volume for output subject > > > > Thanks, > > > > Stefano > > > > > _______________________________________________ > 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 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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recon-all INVALID=766 and other error
by stdp82＠virgilio.it 04 Feb '13

04 Feb '13

Hi list, I'm running :recon-all -all -i $SUBJECTS_DIR/MPRAGE.nii.gz -subject $SUBJECTS_DIR/hptu_sub001In bold the error that I'm visualizing: Subject Stamp: freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0Current Stamp: freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0INFO: SUBJECTS_DIR is /Applications/freesurfer/subjects/subject_prova/Diff01Actual FREESURFER_HOME /Applications/freesurferDarwin iMac-di-Stefano.local 12.2.1 Darwin Kernel Version 12.2.1: Thu Oct 18 12:13:47 PDT 2012; root:xnu-2050.20.9~1/RELEASE_X86_64 x86_64/Applications/freesurfer/subjects/subject_prova/Diff01/hptu_sub001\n mri_convert /Applications/freesurfer/subjects/subject_prova/Diff01/MPRAGE.nii.gz /Applications/freesurfer/subjects/subject_prova/Diff01/hptu_sub001/mri/orig/001.mgz \nmri_convert /Applications/freesurfer/subjects/subject_prova/Diff01/MPRAGE.nii.gz /Applications/freesurfer/subjects/subject_prova/Diff01/hptu_sub001/mri/orig/001.mgz $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $reading from /Applications/freesurfer/subjects/subject_prova/Diff01/MPRAGE.nii.gz...TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00i_ras = (-0.998454, 0.00426797, -0.0554224)j_ras = (0.0151969, 0.980022, -0.198308)k_ras = (-0.0534688, 0.198844, 0.978572)writing to /Applications/freesurfer/subjects/subject_prova/Diff01/hptu_sub001/mri/orig/001.mgz...#--------------------------------------------#@# MotionCor Mon Feb 4 20:34:08 CET 2013Found 1 runs/Applications/freesurfer/subjects/subject_prova/Diff01/hptu_sub001/mri/orig/001.mgzChecking for (invalid) multi-frame inputs...WARNING: only one run found. This is OK, but motioncorrection cannot be performed on one run, so I'llcopy the run to rawavg and continue.\n cp /Applications/freesurfer/subjects/subject_prova/Diff01/hptu_sub001/mri/orig/001.mgz /Applications/freesurfer/subjects/subject_prova/Diff01/hptu_sub001/mri/rawavg.mgz \n/Applications/freesurfer/subjects/subject_prova/Diff01/hptu_sub001\n mri_convert /Applications/freesurfer/subjects/subject_prova/Diff01/hptu_sub001/mri/rawavg.mgz /Applications/freesurfer/subjects/subject_prova/Diff01/hptu_sub001/mri/orig.mgz --conform \nmri_convert /Applications/freesurfer/subjects/subject_prova/Diff01/hptu_sub001/mri/rawavg.mgz /Applications/freesurfer/subjects/subject_prova/Diff01/hptu_sub001/mri/orig.mgz --conform $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $reading from /Applications/freesurfer/subjects/subject_prova/Diff01/hptu_sub001/mri/rawavg.mgz...TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00i_ras = (-0.998454, 0.00426797, -0.0554224)j_ras = (0.0151969, 0.980022, -0.198308)k_ras = (-0.0534688, 0.198844, 0.978572)Original Data has (0.8, 2, 0.8) mm size and (320, 85, 320) voxels.Data is conformed to 1 mm size and 256 voxels for all directionschanging data type from float to uchar (noscale = 0)...MRIchangeType: Building histogram Reslicing using trilinear interpolation writing to /Applications/freesurfer/subjects/subject_prova/Diff01/hptu_sub001/mri/orig.mgz...\n mri_add_xform_to_header -c /Applications/freesurfer/subjects/subject_prova/Diff01/hptu_sub001/mri/transforms/talairach.xfm /Applications/freesurfer/subjects/subject_prova/Diff01/hptu_sub001/mri/orig.mgz /Applications/freesurfer/subjects/subject_prova/Diff01/hptu_sub001/mri/orig.mgz \nINFO: extension is mgz#--------------------------------------------#@# Talairach Mon Feb 4 20:34:17 CET 2013/Applications/freesurfer/subjects/subject_prova/Diff01/hptu_sub001/mri\n talairach_avi --i orig.mgz --xfm transforms/talairach.auto.xfm \n\n cp transforms/talairach.auto.xfm transforms/talairach.xfm \n#--------------------------------------------#@# Talairach Failure Detection Mon Feb 4 20:34:49 CET 2013/Applications/freesurfer/subjects/subject_prova/Diff01/hptu_sub001/mri\n talairach_afd -T 0.005 -xfm transforms/talairach.xfm \ntalairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.4903, pval=0.1531 >= threshold=0.0050)\n awk -f /Applications/freesurfer/bin/extract_talairach_avi_QA.awk /Applications/freesurfer/subjects/subject_prova/Diff01/hptu_sub001/mri/transforms/talairach_avi.log \nTalAviQA: 0.96699z-score: -2#-------------------------------------------- IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 008: -log(p) = 1145838.5 tol 0.000000final transform: 1.009 0.068 0.121 -29.003;-0.086 0.984 0.166 -21.039;-0.120 -0.163 1.074 15.915; 0.000 0.000 0.000 1.000; writing output transformation to transforms/talairach_with_skull.lta...registration took 14 minutes and 43 seconds.\n mri_watershed -T1 -brain_atlas /Applications/freesurfer/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull.lta T1.mgz brainmask.auto.mgz \n Mode: T1 normalized volumeMode: Use the information of atlas (default parms, --help for details)gcaAllocMax: node dims 64 64 64gcaAllocMax: prior dims 128 128 128gcaAllocMax: max_labels 0 *********************************************************The input file is T1.mgzThe output file is brainmask.auto.mgzWeighting the input with atlas information before watershed ********FINAL ITERATIVE TEMPLATE DEFORMATION********Compute Local values csf/grayFine Segmentation...38 iterations mri_strip_skull: done peeling brain Brain Size = 1931109 voxels, voxel volume = 1.000 mm3 = 1931109 mmm3 = 1931.109 cm3 dt = 5.00e-06, momentum=0.80, tol=1.00e-05l_intensity = 1.0000Aligning input volume to GCA...Transform matrix 0.97624 0.08548 0.05852 -18.68727;-0.08544 1.05705 -0.07489 3.31129;-0.06540 0.06526 0.99572 -9.04030; 0.00000 0.00000 0.00000 1.00000;nsamples 2772Quasinewton: input matrix 0.97624 0.08548 0.05852 -18.68727;-0.08544 1.05705 -0.07489 3.31129;-0.06540 0.06526 0.99572 -9.04030; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 007: -log(p) = 7093.2 tol 0.000010Resulting transform: 0.976 0.085 0.059 -18.687;-0.085 1.057 -0.075 3.311;-0.065 0.065 0.996 -9.040; 0.000 0.000 0.000 1.000;************************************************** EM alignment process ... Computing final MAP estimate using 312841 samples. **************************************************dt = 5.00e-06, momentum=0.80, tol=1.00e-07l_intensity = 1.0000Aligning input volume to GCA...Transform matrix 0.97624 0.08548 0.05852 -18.68727;-0.08544 1.05705 -0.07489 3.31129;-0.06540 0.06526 0.99572 -9.04030; 0.00000 0.00000 0.00000 1.00000;nsamples 312841Quasinewton: input matrix 0.97624 0.08548 0.05852 -18.68727;-0.08544 1.05705 -0.07489 3.31129;-0.06540 0.06526 0.99572 -9.04030; 0.00000 0.00000 0.00000 1.00000;dfp_em_step_func: 008: -log(p) = 844596.4after pass:transform: ( 0.98, 0.09, 0.06, -18.69) ( -0.08, 1.06, -0.07, 3.31) ( -0.07, 0.06, 1.00, -9.04) IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESpass 2 through quasi-newton minimization... IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 010: -log(p) = 844596.4 tol 0.000000final transform: 0.984 0.092 0.065 -18.687;-0.079 1.063 -0.069 3.311;-0.066 0.064 0.996 -9.040; 0.000 0.000 0.000 1.000; **************** pass 1 of 1 ************************setting smoothness coefficient to 0.039blurring input image with Gaussian with sigma=2.000...0000: dt=0.000, rms=0.876, neg=0, invalid=766gcamFindOptimalTimeStep: Complete in 18445.328 ms0001: dt=129.472000, rms=0.781 (10.831%), neg=0, invalid=766gcamFindOptimalTimeStep: Complete in 19654.701 ms0002: dt=369.920000, rms=0.748 (4.319%), neg=0, invalid=766gcamFindOptimalTimeStep: Complete in 19650.012 ms0003: dt=129.472000, rms=0.730 (2.388%), neg=0, invalid=766gcamFindOptimalTimeStep: Complete in 19766.332 ms0004: dt=73.984000, rms=0.729 (0.156%), neg=0, invalid=7660005: dt=73.984000, rms=0.726 (0.308%), neg=0, invalid=7660006: dt=73.984000, rms=0.722 (0.547%), neg=0, invalid=7660007: dt=73.984000, rms=0.718 (0.635%), neg=0, invalid=7660008: dt=73.984000, rms=0.713 (0.737%), neg=0, invalid=766 Thanks, Stefano

2 1

upsampling aseg.mgz to dimension and spacing
by Joshua Lee 04 Feb '13

04 Feb '13

I would like to upsample the aseg.mgz to Dimensions: 370X512X512 Spacing 0.5mm in x,y, and z. Any suggestions? - Josh

2 3

cannot find eddy_correct
by Varghese Chikku 04 Feb '13

04 Feb '13

Dear Team, I tried to run dt_recon and the systems says *cannot find eddy_correct,Make sure FSL is installed*. So ,do I need to install the whole FSL package to run this. In Thanks Chikku

2 1

(no subject)
by Linn Mittlestein 04 Feb '13

04 Feb '13

Dear Freesurfer Experts, Are the fsaverage files necessary for qdec analysis? Regards

3 3

head/face surface extraction
by Troebinger, Luzia 04 Feb '13

04 Feb '13

Hi, I have what I suppose is a slightly unusual question - is it possible to get the head/face shape from a subject's MRI using FreeSurfer? I've only ever used it to get the cortical surface, but was wondering if I could somehow extract the head/face shape, as well. Best Luzia

3 2

fsaverage across versions
by Satrajit Ghosh 04 Feb '13

04 Feb '13

hi bruce and others, are there any specific implications we should be worried about (e.g., with qdec or surf2surf) when using an fsaverage that's from a different version that ran the recon. cheers, satra

2 2

read only cvs server is down
by Knut J Bjuland 04 Feb '13

04 Feb '13

When I tries to download Freesurfer 5.2.0 beta source I get this error message. cvs -d :pserver:anonymous@fsvm.nmr.mgh.harvard.edu:/usr/fscvsroot checkout -P dev cvs server: cannot find module `dev' - ignored cvs [checkout aborted]: cannot expand modules Knut J

1 0

[freesurfer] sulci
by angela.favaro＠unipd.it 04 Feb '13

04 Feb '13

Dear experts, I am studying a group of patients with a genetic illness that implies alterations of olfactory tracts and sulci. My aim was to explore the depth of the olfactory sulci in both patients and controls. I draw a ROI following the image of the sulcus in the fsaverage (see the figure) and I extracted measures of 'sulc' and 'thickness' for any subject using this ROI. My problem is that I found only zero or negative values for sulc (also in controls!). This means that there is not a sulcus, but a gyrus? The difference is statistically significant between patients (more negative) and controls (around zero or low negative). What is the problem and how can I measure the depth of the sulcus? Perhaps should I work on an 'average' surface based on my healthy controls? How can I obtain it? Thank you for any help! Angela

2 1

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Freesurfer February 2013