Freesurfer September 2012

freesurfer@nmr.mgh.harvard.edu

89 participants
154 discussions

Freesurfer and FSL
by Ana Arruda 10 Oct '12

10 Oct '12

Dear experts, I'm an MSc student and part of my final project is related to the measurement of the volume of the hippocampus. The last thing I have to do is to compare two softwares, FSL and Freesurfer. On Freesurfer, I've used the following commands: recon-all -i where_my_subject_is -autorecon1 -s output_name then, related to the same subject recon-all -autorecon2 -s output_name After approximately 12 hours, and after comparing the results of Freesurfer and FSL, I found that those obtained with Freesurfer are bigger than those obtained with FSL. According to the literature the results are the reverse. Do you know any idea what I'm doing wrong? Thank you for your attention, Ana Arruda

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Re: [Freesurfer] integrating FSL and Freesurfer
by noam Schneck 09 Oct '12

09 Oct '12

Hi Doug Here are more detailed versions of my first two questions. 1) I used tkmedit to look at the mean_func produced by a gfeat analysis of one subject's three functional runs overlayed onto the anatomical image produced by recon-all on that same subject(bert/mri/orig.mgz). The registration matrix I used was the anat2std.dat that was produced by running reg-feat2anat on all three of the feat analyses from the individual runs. When I did this I saw that the mean_func image was outside the boundaries of the anatomical image. Correspondingly, when I overlayed the zstat.nii.gz from the gfeat analysis onto the anatomical image I had activation outside of the anatomical image brain. 2) Originally, I ran BBR on a subject that I had run Recon-all for. I used BBR to register the example_func.nii.gz to the bert/mri/orig.mgz. I had BBR output an fsl.mat. I then used ApplyXFM in fsl to apply BBR's fsl.mat to register the example_func.nii.gz onto a T1 image that had been created by converting bert/mri/brainmask.mgz into niftii with mri_convert. I tried it again, this time converting the orig.mgz to niftii. In both cases the example_func in T1 space image produced by ApplyXFM is rotated about 90 degrees and also inverted. This is viewed in fslview, The corresponding T1 images created by mri_convert are not. What can I do to allow me to use BBR's fsl.mat within ApplyXFM?

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bad tissue segmentation, WM/GM boundary
by EK Kim 06 Oct '12

06 Oct '12

Dear all expert, Hello, I have been trying to solve this WM/GM boundary error. The data I attached here have a lots of problems, especially WM/GM boundary was not detected in temporal areas. Using mri_cnr function, I calculated the gray/white CNR of the norm.mgz. --------------------------------- norm.mgz white = 97.3+-10.3, gray = 77.3+-14.8, csf = 55.6+-19.5 gray/white CNR = 1.222, gray/csf CNR = 0.790 lh CNR = 1.006 white = 97.0+-11.2, gray = 76.9+-15.1, csf = 55.9+-19.3 gray/white CNR = 1.139, gray/csf CNR = 0.737 rh CNR = 0.938 total CNR = 0.972 ---------------------------------- 1. Does the low CNR affect the bad tissue segmentation results? How can I solve the problem? Is there a way to improve the low CNR value? 2. How can I delete the continuous areas, indicated by red arrow (axial, 134)? I use freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0. Thank you for any comments or replies in advance. Best, EK

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More than two time-points in longitudinal base = Memory allocation error?
by Liz Bowman 03 Oct '12

03 Oct '12

Hello, I have several patients scans taken over multiple time points (up to nine time points in some patients). I thought I might be able to use these to create a base template for longitudinal processing, however the process fails and exits with errors if I try to create a base with more than two time points from a patient. This is a sample of the error log of the most recent attempt, with three timepoints: Resolution: 1 S( 128 128 128 ) T( 128 128 128 ) Iteration(f): 1 -- diff. to prev. transform: 0.876663 Iteration(f): 2 -- diff. to prev. transform: 0.0148738 Iteration(f): 3 -- diff. to prev. transform: 0.00156813 < 0.01 :-) Resolution: 0 S( 256 256 256 ) T( 256 256 256 ) Iteration(f): 1 -- diff. to prev. transform: 0.263086 Iteration(f): 2mri_robust_template(1035) malloc: *** mmap(size=262144) failed (error code=12)*** error: can't allocate region*** set a breakpoint in malloc_error_break to debugMRIalloc(256, 256, 256): could not allocate 262144 bytes for 68th slice Cannot allocate memoryDarwin 550D-UOM88670.local 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 recon-all -s KSx3 exited with ERRORS at Mon Jul 23 10:15:13 EST 2012 For more details, see the log file /Applications/freesurfer/subjects/KSx3/scripts/recon-all.logTo report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting I would be grateful for any advice. Regards, EA Bowman

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Error with mri_volcluster
by Antonella Kis 01 Oct '12

01 Oct '12

Dear Doug, I was running the mri_glmfit-sim \ --glmdir GroupAnalysis_abs.glmdir \ --sim perm 1000 3 permcsd \ --sim-sign abs \ --cwpvalthresh .05 just to get an idea of how my FA Group Analysis data is looking and I got an error before to get the permcsd.sig.cluster.summary file from the mri_volcluster: mri_volcluster --in GroupAnalysis_abs.glmdir/contrast/sig.mgh --mask GroupAnalysis_abs.glmdir/mask.mgh --reg /usr/local/freesurfer/subjects/fsaverage/mri.2mm/reg.2mm.dat --no-fixmni --cwsig GroupAnalysis_abs.glmdir/contrast/permcsd.sig.cluster.mgh --sum GroupAnalysis_abs.glmdir/contrast/permcsd.sig.cluster.summary --ocn GroupAnalysis_abs.glmdir/contrast/permcsd.sig.ocn.mgh --cwpvalthresh .05 --seg fsaverage aparc+aseg.mgz --csdpdf GroupAnalysis_abs.glmdir/contrast/permcsd.pdf.dat --csd GroupAnalysis_abs.glmdir/csd/permcsd.j001-contrast.csd --vwsig GroupAnalysis_abs.glmdir/contrast/permcsd.sig.voxel.mgh ERROR: cannot find /media/2Tra/Antonella_2011/DTI_FS/GLM_CVS/fsaverage/mri/aparc+aseg.mgz I replaced the fsaverage/mri/aparc+aseg.mgz with the cvs_avg35/mri/aseg.mgz and to get the cluster summary I was running: mri_volcluster --in GroupAnalysis_abs.glmdir/contrast/sig.mgh --mask GroupAnalysis_abs.glmdir/mask.mgh --reg /usr/local/freesurfer/subjects/fsaverage/mri.2mm/reg.2mm.dat --no-fixmni --cwsig GroupAnalysis_abs.glmdir/contrast/permcsd.sig.cluster.mgh --sum GroupAnalysis_abs.glmdir/contrast/permcsd.sig.cluster.summary --ocn GroupAnalysis_abs.glmdir/contrast/permcsd.sig.ocn.mgh --cwpvalthresh .05 --seg cvs_avg35 aseg.mgz --csdpdf GroupAnalysis_abs.glmdir/contrast/permcsd.pdf.dat --csd GroupAnalysis_abs.glmdir/csd/permcsd.j001-contrast.csd --vwsig GroupAnalysis_abs.glmdir/contrast/permcsd.sig.voxel.mgh but then I am getting the following error: NOT Adjusting threshold for 1-tailed test Using defalt ctab /usr/local/freesurfer/FreeSurferColorLUT.txt INFO: loading mask volume: GroupAnalysis_abs.glmdir/mask.mgh INFO: MRIbinarize01(): nhits = 961260 Found 961260 voxels in mask ERROR: Input volume voxel dimensions do not match those in the registration file. If the input volume is in bshort/bfloat format, check that there is an accompanying bhdr file. Can you please help me to solve this problem. I am not sure what to do. Thank you very much! Antonella PS. Just to remember you that I registered my FA data over the CVS space but I have for each subject from dt_recom the register.dat file so I suppose I need to keeo the fsaverage in the --reg COMMAND-LINE ARGUMENTS.

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Re: [Freesurfer] CT Method Comparison
by Douglas N Greve 01 Oct '12

01 Oct '12

hi Gari, looking at this I don't really see a problem. Yes, the t-test is very significant, but I would expect that from a paired t looking across different methods. the size of the effect is very small, about 1.5%. Do you see this as a problem? doug On 09/28/2012 05:14 AM, Garikoitz Lerma-Usabiaga wrote: > Hi Doug, > I think that the differences are significant enough, but just in case > please find attached an excel file with the data and the t-test. > > Some of the ROI-s are small (Triangularis, Operculum, Orbitalis and > then all together in the IFG). I attached images for each of them for > reference. > > > If in any case you assume that there are going to be differences, > which method would you recommend and why? > > Thanks! > Gari > > PS after mri_preproc I didn't smooth the surface as in the qdec > example, ¿should I do that? > > > > > > > On Fri, Sep 28, 2012 at 4:24 AM, Douglas Greve > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: > > > OK, got it (finally). I would not expect the answers to be > identical, but I would expect them to be "close". How close are > they? If the ROI is very small, there might be appreciable > differences between the two. > > doug > > > > On 9/27/12 6:26 PM, Garikoitz Lerma-Usabiaga wrote: >> Hi, >> You are right, this was one of the methods. The second one is as >> follows (I copy the repeated steps): >> >>> For a given ROI, you have a nifti file (roi.nii) in 2mm space >>> defined on colin27. This ROI volume has a voxel value == 1 if it >>> is in the ROI or 0 if it is out. >>> >>> You have a registration between roi.nii and orig.mgz >>> >>> You run mri_vol2surf on roi.nii to get lh.roi.mgh >> >> I run mris_preproc for every subject to Colin27: mris_preproc >> --out /subject/surf/ROI_toColin27.mgh --target Colin27 --hemi lh >> --meas thickness --s subject >> >> mri_segstats --seg /Colin27/surf/lh.roi.mgh --in >> /subject/surf/ROI_to_Colin127.mgh --sum >> subject/stats/target_lh.ROI.stats >> >> >> Thanks for your help, >> Gari >> >> >> Note: >> You said: You run mri_cor2label (with --surf option) to convert >> lh.roi.mgh into lh.roi.label >> Just in case, this is how I run it: >> >> * mri_cor2label --i /subjects/Colin27/lh.ROI.mgh --surf Colin27 >> lh --id 1 --l /subjects/Colin27/lh.ROI.label >> * mri_label2label --srclabel >> /subjects/Colin27/lh.ROI.label --srcsubject Colin27 >> --trgsubject subject --trglabel lh.ROI_Colin27_to_bert >> --regmethod surface --hemi lh >> >> >> >> >> On 26/09/2012, at 23:56, Douglas N Greve >> <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: >> >>> Sorry, I'm still a little lost. Let me see if I have it right: >>> >>> For a given ROI, you have a nifti file (roi.nii) in 2mm space >>> defined on colin27. This ROI volume has a voxel value == 1 if it >>> is in the ROI or 0 if it is out. >>> >>> You have a registration between roi.nii and orig.mgz >>> >>> You run mri_vol2surf on roi.nii to get lh.roi.mgh >>> >>> You run mri_cor2label (with --surf option) to convert lh.roi.mgh >>> into lh.roi.label >>> >>> You run mri_label2label on lh.roi.label to map it into an >>> individual subject >>> >>> You run mris_anatomical_stats on the individual lh.roi.label file >>> >>> Does this describe one of your processing streams correctly? If >>> so, what is the other processing stream (given in this kind of >>> detail)? >>> >>> doug >>> >>> >>> >>> On 09/25/2012 04:43 PM, Garikoitz Lerma-Usabiaga wrote: >>>> I have both. In origin, the ROI-s are 2mm volume based .nii >>>> that I convert to FS .mgh with register.dat I obtained with >>>> bbregister. >>>> -- In the case of label2label method I create the surface >>>> version with mri_vol2surf (and the correspondence is perfect), >>>> and then use mri_label2label in order to get the CT averages. >>>> -- In the case of surf2surf, I use the volume based .mgh with >>>> mri_preproc (mri_surf2surf) >>>> >>>> thanks! >>>> Gari >>>> >>>> On Tue, Sep 25, 2012 at 5:57 PM, Douglas N Greve >>>> <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> >>>> <mailto:greve@nmr.mgh.harvard.edu>> wrote: >>>> >>>> So you have ROIs in Colin27 space and you want to map them into >>>> your CT space and compute average CT intensities over them? Are >>>> the ROIs volume-based or surface-based? >>>> doug >>>> >>>> >>>> On 09/25/2012 05:09 AM, Garikoitz Lerma-Usabiaga wrote: >>>> >>>> Hi Doug, >>>> many thanks for your answer, I try to detail it more: >>>> >>>> 1.- bbregister is registering two Colin27 brains. First >>>> one is >>>> a 2mm found in spm/canonical/single_subject_T1.nii, and >>>> second >>>> one is the FS_spm_Canonical found in SurfRend >>>> distribution. It >>>> was in .COR format and I run recon-all to have a modern >>>> version of it. As they are almost the same brain the >>>> registration matrix is quite simple and the registration was >>>> perfect. This way I had exactly the same ROI-s for Colin27 in >>>> SPM and in FS (it did not work that well for fsaverage, >>>> that's >>>> why I took this approach). >>>> >>>> 2.- In any case, I have several ROI-s in Colin27 space in FS, >>>> and then when I try to obtain average CT values from my >>>> subjects I use these 2 different approaches: label2label and >>>> surf2surf. >>>> mri_anatomical_stats is run on the labels created by >>>> mri_label2label. >>>> >>>> >>>> If you think it will be of help I can send the detailed >>>> command line calls, >>>> thanks! >>>> Gari >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> On Sat, Sep 22, 2012 at 12:47 AM, Douglas N Greve >>>> <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> >>>> <mailto:greve@nmr.mgh.harvard.edu> >>>> <mailto:greve@nmr.mgh.harvard.edu >>>> <mailto:greve@nmr.mgh.harvard.edu>>> wrote: >>>> >>>> Hi Gari, I'll need more information. I can't tell >>>> what you >>>> are doing. >>>> Eg, what is being registered with BBR? what is >>>> mris_anatomical_stats run >>>> on? Where does Colin27 come into it and why? >>>> doug >>>> >>>> On 09/19/2012 06:15 PM, Garikoitz Lerma-Usabiaga >>>> (Gari) wrote: >>>>> Dear Freesurfers, >>>>> We've been comparing 2 different methods to obtain CT averages >>>> for 4 Volume ROI-s (volume ROI-s were in Colin27 space). >>>>> We've used the 40 buckner subjects for the comparisons. >>>>> >>>>> METHOD L2L: bbregister>> mri_vol2surf (mgh)>> >>>> mri_binarize (mgh)>> mri_cor2label (label)>> >>>> mri_label2label>> >>>> mris_anatomical_stats >>>>> METHOD S2S: bbregister>> mri_vol2surf>> mri_preproc >>>> (mri_surf2surf)>> mri_segstats >>>>> >>>>> >>>>> After performing t-test-s over the results, we can observe that >>>> the results are in many cases different. >>>>> >>>>> -- Is there a way to choose the "best" method? Which one should >>>> we use for our work and why? >>>>> >>>>> Many thanks again for your help, >>>>> Gari >>>>> >>>>> PD We've tabulated a third method as well: >>>>> METHOD SurfRend: Surfrend (.w)>> mri_surf2surf(.mgh)>> >>>> mri_binarize(.mgh)>> mri_cor2label (.label)>> >>>> mris_anatomical_stats >>>>> _______________________________________________ >>>>> Freesurfer mailing list >>>>> Freesurfer(a)nmr.mgh.harvard.edu >>>>> <mailto:Freesurfer@nmr.mgh.harvard.edu> >>>> <mailto:Freesurfer@nmr.mgh.harvard.edu> >>>> <mailto:Freesurfer@nmr.mgh.harvard.edu >>>> <mailto:Freesurfer@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 <mailto:greve@nmr.mgh.harvard.edu> >>>> <mailto:greve@nmr.mgh.harvard.edu> >>>> <mailto:greve@nmr.mgh.harvard.edu >>>> <mailto:greve@nmr.mgh.harvard.edu>> >>>> Phone Number: 617-724-2358 <tel:617-724-2358> >>>> <tel:617-724-2358 <tel:617-724-2358>> >>>> Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 >>>> <tel:617-726-7422>> >>>> >>>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>>> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >>>> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >>>> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >>>> FileDrop: >>>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>>> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >>>> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >>>> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >>>> >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer(a)nmr.mgh.harvard.edu >>>> <mailto:Freesurfer@nmr.mgh.harvard.edu> >>>> <mailto:Freesurfer@nmr.mgh.harvard.edu> >>>> <mailto:Freesurfer@nmr.mgh.harvard.edu >>>> <mailto:Freesurfer@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. >>>> >>>> >>>> >>>> -- Douglas N. Greve, Ph.D. >>>> MGH-NMR Center >>>> greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> >>>> <mailto:greve@nmr.mgh.harvard.edu> >>>> Phone Number: 617-724-2358 <tel:617-724-2358> >>>> Fax: 617-726-7422 <tel:617-726-7422> >>>> >>>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>>> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >>>> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >>>> FileDrop: >>>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>>> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >>>> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >>>> >>>> >>> >>> -- >>> Douglas N. Greve, Ph.D. >>> MGH-NMR Center >>> greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> >>> Phone Number: 617-724-2358 >>> Fax: 617-726-7422 >>> >>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >>> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >>> > > -- 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

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long_mris_slopes command: temporal average calculation
by Shannon Kogachi 01 Oct '12

01 Oct '12

Hi, I had a question about how the temporal average is calculated for subjects with multiple timepoints. I used the long_mris_slopes command on a longitudinal set of data. However, when I compared the average volumes calculated through this command to the average volumes calculated in excel after extracting the same vertices at the individual timepoints, these values did not match up. The average volumes calculated through long_mris_slopes were smaller. Please let me know if there is a way to explain this discrepancy. Thank you! -Shannon K.

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amira
by Colin Reveley 29 Sep '12

29 Sep '12

It's slightly off topic, but begging your leave: If there is anyone out there who is experienced in amira, and might be willing to offer a little email help for a very tricky segmentation, I'd be very grateful. The segmentation is for use with freesurfer, at least, so it's not a total outrage to ask I hope. best, Colin Reveley, Sussex

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Cerebellar volume correction
by Rachel Steinhorn 29 Sep '12

29 Sep '12

We'd like to obtain total cerebellar volumes. There are errors within the cerebellar segmentation as revealed in the aseg.mgz file. Is there a method to manually edit the cerebellar segmentation? Thank You, Rachel Steinhorn

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Re: [Freesurfer] Tracula Error: bvecs and bvals don't have the same number of entries
by Anastasia Yendiki 28 Sep '12

28 Sep '12

There are 10 empty lines at the end of your Tbvecs.txt file. Can you try removing those and reruning? Hope this helps, a.y On Fri, 28 Sep 2012, Loi wrote: > Hello again, > > Here is the configuration file and some variations of the bvec and > bval files I have tried using. > > Also, I have noticed that the first time I run trac-all (without > specifying the bvecs and bvals), the bval file generated seems to list > the values twice. ie: > > 0 > 0 > 7 > 7 > 7 > 7 > 0 > 0 > 7 > 7 > 7 > 7 > > I hope this make sense. Thank you, > > Joy-Loi > > > On 9/27/12, Anastasia Yendiki <ayendiki(a)nmr.mgh.harvard.edu> wrote: >> >> Thanks, no problem. I'd like to see the actual files on one of our >> machines just to make sure. >> >> On Thu, 27 Sep 2012, Loi wrote: >> >>> Hello Anastasia, >>> >>> I am in Norway and home from work for the evening, but will send you >>> the files first thing tomorrow morning. >>> Meanwhile, here is a copy of the contents in the files (as included in >>> my original e-mail). >>> Thank you for your help! >>> >>> ********************* >>> My configuration file: >>> >>> >>> setenv SUBJECTS_DIR >>> /usit/tsd/nevro-work/projects/Memory_project/TRACULA_test/TRACULA_recons >>> >>> set dtroot = >>> /usit/tsd/nevro-work/projects/Memory_project/TRACULA_test/TRACULA_data >>> >>> set subjlist = id101 >>> set runlist = 1 >>> >>> set dcmroot = >>> /usit/tsd/nevro-work/projects/Memory_project/TRACULA_test/TRACULA_data >>> set dcmlist = id101/orig/1.dcm >>> >>> set bvalfile = >>> /usit/tsd/nevro-work/projects/Memory_project/TRACULA_test/TRACULA_data/id101/dmri/bvals.txt >>> >>> set bvecfile = >>> /usit/tsd/nevro-work/projects/Memory_project/TRACULA_test/TRACULA_data/id101/dmri/bvecs.txt >>> >>> set nb0 = 10 >>> >>> set doeddy = 1 >>> set dorotbvecs = 1 >>> set thrbet = 0.3 >>> set doregflt = 1 >>> set doregbbr = 0 >>> set doregmni = 1 >>> set mnitemp = /psyklab/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz >>> >>> #set trainfile = >>> /usit/tsd/nevro-work/projects/Memory_project/TRACULA_test/TRACULA_data/subj,train,difftutorial123.txt >>> >>> set pathlist = (lh.cst_AS rh.cst_AS \ >>> lh.ilf_AS rh.ilf_AS \ >>> lh.unc_AS rh.unc_AS \ >>> fmajor_PP fminor_PP \ >>> lh.atr_PP rh.atr_PP \ >>> lh.cab_PP rh.cab_PP \ >>> lh.ccg_PP rh.ccg_PP \ >>> lh.slfp_PP rh.slfp_PP \ >>> lh.slft_PP rh.slft_PP) >>> >>> >>> set ncpts = 5 >>> >>> set usetrunc = 1 >>> >>> >>> >>> >>> >>> ********************* >>> My bvals: >>> >>> 0.0000000 >>> 0.0000000 >>> 0.0000000 >>> 0.0000000 >>> 0.0000000 >>> 0.0000000 >>> 0.0000000 >>> 0.0000000 >>> 0.0000000 >>> 0.0000000 >>> 700.0000000 >>> 700.0000000 >>> 700.0000000 >>> 700.0000000 >>> 700.0000000 >>> 700.0000000 >>> 700.0000000 >>> 700.0000000 >>> 700.0000000 >>> 700.0000000 >>> 700.0000000 >>> 700.0000000 >>> 700.0000000 >>> 700.0000000 >>> 700.0000000 >>> 700.0000000 >>> 700.0000000 >>> 700.0000000 >>> 700.0000000 >>> 700.0000000 >>> 700.0000000 >>> 700.0000000 >>> 700.0000000 >>> 700.0000000 >>> 700.0000000 >>> 700.0000000 >>> 700.0000000 >>> 700.0000000 >>> 700.0000000 >>> 700.0000000 >>> >>> ********************* >>> My bvecs: >>> >>> 0.0000000 0.0000000 0.0000000 >>> 0.0000000 0.0000000 0.0000000 >>> 0.0000000 0.0000000 0.0000000 >>> 0.0000000 0.0000000 0.0000000 >>> 0.0000000 0.0000000 0.0000000 >>> 0.0000000 0.0000000 0.0000000 >>> 0.0000000 0.0000000 0.0000000 >>> 0.0000000 0.0000000 0.0000000 >>> 0.0000000 0.0000000 0.0000000 >>> 0.0000000 0.0000000 0.0000000 >>> -0.9998760 0.0011040 0.0157340 >>> -0.7705615 0.6320276 0.0823114 >>> -0.2461791 0.0273479 0.9688392 >>> -0.7953558 0.1076421 0.5965091 >>> 0.4620816 -0.8755928 0.1407778 >>> 0.2261090 -0.8553081 -0.4661796 >>> 0.2601186 0.4095102 -0.8744363 >>> -0.7969547 -0.5877791 0.1392076 >>> -0.5028073 -0.5104712 0.6975709 >>> -0.3073035 0.1334521 -0.9422074 >>> 0.7957742 0.1950272 -0.5733304 >>> 0.8041493 0.5924478 -0.0484727 >>> -0.1867079 -0.9528833 0.2390659 >>> 0.3898569 -0.1063898 0.9147088 >>> 0.1341999 -0.6614532 0.7378819 >>> 0.3382555 0.8823941 0.3270553 >>> -0.7688307 -0.3139264 -0.5570900 >>> -0.4086013 0.6653325 0.6248017 >>> -0.2933309 0.7581020 -0.5824408 >>> 0.7689370 -0.4282441 0.4747016 >>> 0.1800972 0.5296402 0.8288835 >>> 0.7680658 0.3158178 0.5570763 >>> -0.2214999 0.9744585 0.0370050 >>> -0.4175692 -0.8418782 -0.3418731 >>> -0.1784475 -0.4817282 -0.8579599 >>> 0.3361637 0.8554551 -0.3939400 >>> 0.7858656 -0.5091907 -0.3509137 >>> 0.4194232 -0.2589429 -0.8700761 >>> -0.7760561 0.3511497 -0.5238622 >>> 0.9987836 -0.0413076 0.0269219 >>> >>> >>> >>> >>> >>> >>> On Thu, Sep 27, 2012 at 8:14 PM, Anastasia Yendiki >>> <ayendiki(a)nmr.mgh.harvard.edu> wrote: >>>> >>>> Can you please send the original bvals and bvecs files (the ones that >>>> you >>>> specify in the configuration file), and the configuration file itself? >>>> Thanks! >>>> >>>> a.y >>>> >>>> >>>> On Thu, 27 Sep 2012, Loi wrote: >>>> >>>>> Hello, >>>>> >>>>> I generate the files in Linux (using gedit) and they look normal (I >>>>> have compared them to the files in the tutorial). >>>>> >>>>> So far I have tried ending both with and without .txt, transposing the >>>>> files, changing to equal number of decimals and adding 'setenv LC_ALL >>>>> en_US' to the .tchsrc file. >>>>> >>>>> The inputs I am using are dicoms, and even though I specify a path to >>>>> the b-value files and gradient tables I make (I originally didn't >>>>> specify these, and got the same error message), new bvecs and bvals >>>>> are generated in the trac-all -prep process, leading to the error. >>>>> >>>>> Thank you, >>>>> Joy-Loi >>>>> >>>>> >>>>> >>>>> >>>>> On Thu, Sep 27, 2012 at 7:30 PM, Anastasia Yendiki >>>>> <ayendiki(a)nmr.mgh.harvard.edu> wrote: >>>>>> >>>>>> >>>>>> Hi Joy - How were your bvecs and bvals files generated? In the past >>>>>> some >>>>>> people have had problems with files exported from Excel b/c it >>>>>> generates >>>>>> text files with Windows-specific end-of-line characters that cannot be >>>>>> read >>>>>> properly on Linux. Do the files look normal when you run "more" on >>>>>> them >>>>>> on >>>>>> the system where you ran trac-all? >>>>>> >>>>>> a.y >>>>>> >>>>>> >>>>>> On Wed, 26 Sep 2012, Loi wrote: >>>>>> >>>>>>> Dear FreeSurfers, >>>>>>> >>>>>>> I am trying to run trac-all -prep on a single subject, and get the >>>>>>> following error: >>>>>>> >>>>>>> dtifit -k >>>>>>> >>>>>>> /usit/tsd/nevro-work/projects/Memory_project/TRACULA_test/TRACULA_data/id101/dmri/dwi.nii.gz >>>>>>> -m >>>>>>> >>>>>>> /usit/tsd/nevro-work/projects/Memory_project/TRACULA_test/TRACULA_data/id101/dlabel/diff/aparc+aseg_mask.flt.nii.gz >>>>>>> -r >>>>>>> >>>>>>> /usit/tsd/nevro-work/projects/Memory_project/TRACULA_test/TRACULA_data/id101/dmri/bvecs >>>>>>> -b >>>>>>> >>>>>>> /usit/tsd/nevro-work/projects/Memory_project/TRACULA_test/TRACULA_data/id101/dmri/bvals >>>>>>> -o >>>>>>> >>>>>>> /usit/tsd/nevro-work/projects/Memory_project/TRACULA_test/TRACULA_data/id101/dmri/dtifit >>>>>>> Error: bvecs and bvals don't have the same number of entries >>>>>>> >>>>>>> I have searched the message thread, and cannot seem to find a >>>>>>> solution >>>>>>> applicable to my situation: it seems that the trac-all process >>>>>>> generates transposed bvec and bval files. >>>>>>> Therefore, I tried transposing these manually and specifying the >>>>>>> location to these files (as explained in the tutorial: >>>>>>> http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula) but >>>>>>> attempting to run trac-all again still leads to the same result: new >>>>>>> bval and bvec files are generated, and I receive the same error >>>>>>> message. >>>>>>> >>>>>>> Does anyone know how I can solve this problem? >>>>>>> >>>>>>> Thank you, >>>>>>> Joy-Loi >>>>>>> >>>>>>> >>>>>>> ********************* >>>>>>> My configuration file: >>>>>>> >>>>>>> >>>>>>> setenv SUBJECTS_DIR >>>>>>> /usit/tsd/nevro-work/projects/Memory_project/TRACULA_test/TRACULA_recons >>>>>>> >>>>>>> set dtroot = >>>>>>> /usit/tsd/nevro-work/projects/Memory_project/TRACULA_test/TRACULA_data >>>>>>> >>>>>>> set subjlist = id101 >>>>>>> set runlist = 1 >>>>>>> >>>>>>> set dcmroot = >>>>>>> /usit/tsd/nevro-work/projects/Memory_project/TRACULA_test/TRACULA_data >>>>>>> set dcmlist = id101/orig/1.dcm >>>>>>> >>>>>>> set bvalfile = >>>>>>> >>>>>>> /usit/tsd/nevro-work/projects/Memory_project/TRACULA_test/TRACULA_data/id101/dmri/bvals.txt >>>>>>> >>>>>>> set bvecfile = >>>>>>> >>>>>>> /usit/tsd/nevro-work/projects/Memory_project/TRACULA_test/TRACULA_data/id101/dmri/bvecs.txt >>>>>>> >>>>>>> set nb0 = 10 >>>>>>> >>>>>>> set doeddy = 1 >>>>>>> set dorotbvecs = 1 >>>>>>> set thrbet = 0.3 >>>>>>> set doregflt = 1 >>>>>>> set doregbbr = 0 >>>>>>> set doregmni = 1 >>>>>>> set mnitemp = /psyklab/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz >>>>>>> >>>>>>> #set trainfile = >>>>>>> >>>>>>> >>>>>>> /usit/tsd/nevro-work/projects/Memory_project/TRACULA_test/TRACULA_data/subj,train,difftutorial123.txt >>>>>>> >>>>>>> set pathlist = (lh.cst_AS rh.cst_AS \ >>>>>>> lh.ilf_AS rh.ilf_AS \ >>>>>>> lh.unc_AS rh.unc_AS \ >>>>>>> fmajor_PP fminor_PP \ >>>>>>> lh.atr_PP rh.atr_PP \ >>>>>>> lh.cab_PP rh.cab_PP \ >>>>>>> lh.ccg_PP rh.ccg_PP \ >>>>>>> lh.slfp_PP rh.slfp_PP \ >>>>>>> lh.slft_PP rh.slft_PP) >>>>>>> >>>>>>> >>>>>>> set ncpts = 5 >>>>>>> >>>>>>> set usetrunc = 1 >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> ********************* >>>>>>> My bvals: >>>>>>> >>>>>>> 0.000000 >>>>>>> 0.000000 >>>>>>> 0.000000 >>>>>>> 0.000000 >>>>>>> 0.000000 >>>>>>> 0.000000 >>>>>>> 0.000000 >>>>>>> 0.000000 >>>>>>> 0.000000 >>>>>>> 0.000000 >>>>>>> 700.000000 >>>>>>> 700.000000 >>>>>>> 700.000000 >>>>>>> 700.000000 >>>>>>> 700.000000 >>>>>>> 700.000000 >>>>>>> 700.000000 >>>>>>> 700.000000 >>>>>>> 700.000000 >>>>>>> 700.000000 >>>>>>> 700.000000 >>>>>>> 700.000000 >>>>>>> 700.000000 >>>>>>> 700.000000 >>>>>>> 700.000000 >>>>>>> 700.000000 >>>>>>> 700.000000 >>>>>>> 700.000000 >>>>>>> 700.000000 >>>>>>> 700.000000 >>>>>>> 700.000000 >>>>>>> 700.000000 >>>>>>> 700.000000 >>>>>>> 700.000000 >>>>>>> 700.000000 >>>>>>> 700.000000 >>>>>>> 700.000000 >>>>>>> 700.000000 >>>>>>> 700.000000 >>>>>>> 700.000000 >>>>>>> >>>>>>> ********************* >>>>>>> My bvecs: >>>>>>> >>>>>>> 0.0000000 0.0000000 0.0000000 >>>>>>> 0.0000000 0.0000000 0.0000000 >>>>>>> 0.0000000 0.0000000 0.0000000 >>>>>>> 0.0000000 0.0000000 0.0000000 >>>>>>> 0.0000000 0.0000000 0.0000000 >>>>>>> 0.0000000 0.0000000 0.0000000 >>>>>>> 0.0000000 0.0000000 0.0000000 >>>>>>> 0.0000000 0.0000000 0.0000000 >>>>>>> 0.0000000 0.0000000 0.0000000 >>>>>>> 0.0000000 0.0000000 0.0000000 >>>>>>> -0.9998760 0.0011040 0.0157340 >>>>>>> -0.7705615 0.6320276 0.0823114 >>>>>>> -0.2461791 0.0273479 0.9688392 >>>>>>> -0.7953558 0.1076421 0.5965091 >>>>>>> 0.4620816 -0.8755928 0.1407778 >>>>>>> 0.2261090 -0.8553081 -0.4661796 >>>>>>> 0.2601186 0.4095102 -0.8744363 >>>>>>> -0.7969547 -0.5877791 0.1392076 >>>>>>> -0.5028073 -0.5104712 0.6975709 >>>>>>> -0.3073035 0.1334521 -0.9422074 >>>>>>> 0.7957742 0.1950272 -0.5733304 >>>>>>> 0.8041493 0.5924478 -0.0484727 >>>>>>> -0.1867079 -0.9528833 0.2390659 >>>>>>> 0.3898569 -0.1063898 0.9147088 >>>>>>> 0.1341999 -0.6614532 0.7378819 >>>>>>> 0.3382555 0.8823941 0.3270553 >>>>>>> -0.7688307 -0.3139264 -0.5570900 >>>>>>> -0.4086013 0.6653325 0.6248017 >>>>>>> -0.2933309 0.7581020 -0.5824408 >>>>>>> 0.7689370 -0.4282441 0.4747016 >>>>>>> 0.1800972 0.5296402 0.8288835 >>>>>>> 0.7680658 0.3158178 0.5570763 >>>>>>> -0.2214999 0.9744585 0.0370050 >>>>>>> -0.4175692 -0.8418782 -0.3418731 >>>>>>> -0.1784475 -0.4817282 -0.8579599 >>>>>>> 0.3361637 0.8554551 -0.3939400 >>>>>>> 0.7858656 -0.5091907 -0.3509137 >>>>>>> 0.4194232 -0.2589429 -0.8700761 >>>>>>> -0.7760561 0.3511497 -0.5238622 >>>>>>> 0.9987836 -0.0413076 0.0269219 >>>>>>> _______________________________________________ >>>>>>> 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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Freesurfer September 2012