Freesurfer

freesurfer@nmr.mgh.harvard.edu

30132 discussions

Re: [Freesurfer] [Tracula] error running trac-all –path –c Configuration_file.txt
by Anastasia Yendiki 19 Aug '13

19 Aug '13

Hi Francesco - The bedpostx files are created when you run trac-all -bedp. Then you need to run trac-all -path to reconstruct the paths under dpath/... as the final step. Did you run this? a.y On Mon, 19 Aug 2013, Francesco Siciliano wrote: > Thank you! > > Is it normal, however, not to have a dpath folder with summary statistics? I have all of the bedpostx output files, however, I seem to be missing the dpath folder as well as a script confirming that -path was completed. > > Thanks, > Francesco > ________________________________________ > From: Anastasia Yendiki [ayendiki(a)nmr.mgh.harvard.edu] > Sent: Monday, August 19, 2013 1:56 PM > To: Francesco Siciliano > Cc: freesurfer(a)nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] [Tracula] error running trac-all –path –c Configuration_file.txt > > Hi Francesco - There's a list of bedpostx output files here: > http://fsl.fmrib.ox.ac.uk/fsl/fsl4.0/fdt/fdt_bedpostx.html > > The best way to determine if bedpostx finished running properly is to > check if those files were created in the dmri.bedpostX directory. > > a.y > > On Mon, 19 Aug 2013, Francesco Siciliano wrote: > >> Hello, >> I received an error on several terminals running trac-all –path –c Configuration_file.txt >> >> 55 slices processed >> 56 slices processed >> 56 slices processed >> 57 slices processed >> 57 slices processed >> 58 slices processed >> 59 slices processed >> 60 slices processed >> 61 slices processed >> Queuing post processing stage >> 70 slices processed >> For some reason the bedpostX process DOES NOT appear >> to have successfully completed. Please examine your >> results carefully. >> /Users/jonathanposner/Desktop/MRI_Software/FSL_installer/fsl/bin/bedpostx: line 262: kill: (15849) - No such process >> >> Is this an indication that the processing did not finish? Could this have anything to do with limited computer >> memory? >> >> > > > 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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Curvature/folding stats
by Michael Kranz 19 Aug '13

19 Aug '13

Hi all, What's the difference between the curvature and folding measures outputted in the aparc stats files (i.e. mean, gaussian, folding index, and curvature index)? Additionally, which measures are the most reliable for individual differences? Thanks, Mike Michael Kranz Graduate Research Assistant |Beckman Institute University of Illinois 314-323-1329

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Re: [Freesurfer] trac-all inquiry
by Anastasia Yendiki 19 Aug '13

19 Aug '13

Hi David - Thank you very much for your kind words. Does the DWI volume for this subject have 65 frames (as many as the entries in bvecs/bvals)? You can check this by running: mri_info dmri/dwi.nii.gz a.y On Fri, 16 Aug 2013, David Soto wrote: > hi Anastasia, I am pleased that trac-all > has completed and the output looks pretty cool > so thanks for this amazing piece of software! > Just an issue with one subject, the preprocessing > stage is giving an error data and bvals/bvecs do not contain the same number > of entries, however I checked the files and do seem to > have the same number (all files attached). > Related or unrelated to this issue, not all the dlabel/diff output files > are generated, only these ... any advise appreciated, cheers - ds > anat_brain_mask.bbr.nii.gz > lh.cst_AS_avg33_mni_bbr_cpts_6.nii.gz > rh.cst_AS_avg33_mni_bbr_cpts_6.nii.gz > anat_brain_mask-vent.bbr.nii.gz > lh.cst_AS_avg33_mni_bbr_cpts_6_std.txt > rh.cst_AS_avg33_mni_bbr_cpts_6_std.txt > aparc+aseg+2mm.bbr.nii.gz > lh.cst_AS_avg33_mni_bbr_cpts_6.txt > rh.cst_AS_avg33_mni_bbr_cpts_6.txt > aparc+aseg.bbr.nii.gz > lh.ilf_AS_avg33_mni_bbr_cpts_5.nii.gz > rh.ilf_AS_avg33_mni_bbr_cpts_5.txt > aparc+aseg_mask.bbr.nii.gz > lh.ilf_AS_avg33_mni_bbr_cpts_5_std.txt > White-Matter.bbr.nii.gz > cortex+2mm.bbr.nii.gz > lh.ilf_AS_avg33_mni_bbr_cpts_5.txt > White-Matter++.bbr.nii.gz > cortex+2mm+bs.bbr.nii.gz > lowb_brain_mask.nii.gz > cortex.bbr.nii.gz > notventricles.bbr.nii.gz > > http://www1.imperial.ac.uk/medicine/people/d.soto/ > On 12/08/13 09:57, David Soto wrote: > Thanks Anastasia, understood - the issue is that would be very > time consuming at this stage for several reasons.. > I found the issue with MRIConverter can be solved just by > doing fslmaths on the diffusion output image > fslmaths output data > This should not change the diffusion image yet is fine for processing > in FS > cheers > d.s. > http://www1.imperial.ac.uk/medicine/people/d.soto/ > > On 10 Aug 2013, at 00:43, Anastasia Yendiki > <ayendiki(a)nmr.mgh.harvard.edu> wrote: > > > I didn't mean run mri_convert on the nifti output of > another program. I meant run mri_convert directly on the > original dicom to convert it to nifti: > mri_convert yourimage.dcm yourimage.nii.gz > > On Fri, 9 Aug 2013, Soto, David wrote: > > I see - as said the diffusion output.nii from > MRIConverter > http://lcni.uoregon.edu/~jolinda/MRIConvert/ > [to not confound it with mri_converter) > is not read by Freeview and mri_converter does > not like it either > --------------------------------------------------------------------------- > ------------ > MD00071523-2:RSDTI_WMGUI/ACH_AMO/diff] dsoto% > mri_convert output.nii data.mgz > mri_convert output.nii data.mgz > $Id: mri_convert.c,v 1.179.2.7 2012/09/05 > 21:55:16 mreuter Exp $ > reading from output.nii... > nifti1Read(): unsupported slice timing pattern > 5 in > /Users/dsoto/Documents/fMRI/RSDTI_WMGUI/ACH_AMO/diff/output.nii > No such file or directory > --------------------------------------------------------------------------- > ------------ > > NOW, I find that if I use FSL and run bet with > a fractional intensity threshold of 0, > I get an output file which is read by > Freeview- which should allow me to proceed > with all the necessary preprocessing steps in > trac-all > > would this be fine? I dont think the bet I run > will affect the image > > cheers > ds > http://www1.imperial.ac.uk/medicine/people/d.soto/ > > ________________________________________ > From: Anastasia Yendiki > [ayendiki(a)nmr.mgh.harvard.edu] > Sent: 09 August 2013 23:15 > To: Soto, David > Cc: freesurfer(a)nmr.mgh.harvard.edu > Subject: RE: [Freesurfer] trac-all inquiry > > When you apply a rotation to the DWIs (as > eddy_correct does), you need to > apply the same rotation to the corresponding > gradient vectors. See for > example: Leemans, A., Jones, D. K., Jun 2009. > The B-matrix must be rotated > when correcting for subject motion in DTI > data. Magn Reson Med 61 (6), > 1336–49. > > If you don't want to pass the dicoms to > trac-all directly, you can use > mri_convert to convert from dicom to nifti. > > On Fri, 9 Aug 2013, Soto, David wrote: > > hi - am afraid not because I am > feeding to trac-all > already eddycorrected images then > in the config file > I have > > # Perform registration-based > eddy-current compensation? > # Default: 1 (yes) > set doeddy = 0 > # Rotate diffusion gradient > vectors to match eddy-current > compensation? > # Only used if doeddy = 1 > # Default: 1 (yes) > > is this critical?? > > unfortunately, this is the only > way I manage to get it to work > as said my diffusion outputs from > mriconverter > are not read by FS, only through > mediation > of some FSL operation on the > files, then FS > likes those. > > I could start from scratch using > dicoms but would prefer > not to as the data is already > well organised > > cheers > ds > http://www1.imperial.ac.uk/medicine/people/d.soto/ > > ________________________________________ > From: Anastasia Yendiki > [ayendiki(a)nmr.mgh.harvard.edu] > Sent: 09 August 2013 22:44 > To: Soto, David > Subject: Re: [Freesurfer] > trac-all inquiry > > Are you rotating the gradient > vectors accordingly? This is done > in > trac-all after running > eddy_correct. > > On Fri, 9 Aug 2013, Soto, David > wrote: > > Hi Anastasia, stuff is > running smoothly at > last one quick > question, is there > any 'disadvantage' in > using FSL to do the > eddy correct and then > feed > those images to > trace-all ? > cheers > ds > http://www1.imperial.ac.uk/medicine/people/d.soto/ > > On 9 Aug 2013, at > 15:33, David Soto > <dsoto(a)imperial.ac.uk> > wrote: > > hi, for some > reason FS does not > like the > nii file from > Mriconverter, ( I saw > a post about this > http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg19526.ht > ml > ) but does like > the nii.gz > outputs from FSL... > > I'll try to debug > the bepostx error > > thanks! > > ds > > http://www1.imperial.ac.uk/medicine/people/d.soto/ > On 09/08/13 14:26, > Anastasia Yendiki > wrote: > > There is no > reason to conevrt to > .mnc. You should use > your > original .nii, if > that shows up > correctly in freeview. > > As for the > bedpostx error, this > is an Ubuntu issue > that > has come to my > attention very > recently. In Ubuntu > /bin/sh > is not a bash > shell any more. To get > around this, you'll > have to edit the > first line of the > scripts > $FREESURFER_HOME/bin/bedpostx_mgh > and > $FREESURFER_HOME/bin/fsl_sub_mgh. > You'll have to replace > "/bin/sh" with > "/bin/bash" on the > first line of those > two > scripts. > > On Fri, 9 Aug > 2013, David Soto > wrote: > > hi- I tried > to convert from nii to > mnc becos > that is > what i did when > I did > recon-all > > but I also > tried with nii at the > beggining and > got the > same issues. > In fact in > my last post (pasted > below > again)the > input was a nii file > could you > please check the stuff > below? > thanks! ds > > > Hi, further > to my prior email > I made some > progress. I noted that > nii2mnc > does not > seem to work on the > diffusion > output.nii > that I got from > Mriconverter as the > output.mnc > brain has parts > chopped in > Freeview. > > (I think > there may be something > funny about > this, as > the recon-all does > like the T1 output > form > Mriconverter) > > HENCE I > tried use the output > of eddycorrect > from FSL > (which I already run > for other thing) > Then I > created a new folder > where i placed the > output of > FSL eddycorrect and in > the > configuration > file I did > (i) set > dcmlist = > (fsleddycorrectoutput.nii.gz) > (ii) turned > 'set doeddy = 0' > > then run it > trac-all -c > traculatest.txt -prep > -log > trac_from_fsleddy > > > it seemed > to complete without > errors (log > attached)n > and I checked the > preprocessing > outputs in > Freeview (FA, masks > and > aparc+asegs) > and all seemed > fine. > > However > when I attempt the > next stage in > trac-all > i.e. > trac-all -c > traculatest.txt -bedp > -log > trac_from_fsleddy_bedp > it fails > saying the following > /usr/local/freesurfer/bin/bedpostx_mgh: > 131: > /usr/local/freesurfer/bin/bedpostx_mgh: > Syntax > error: "(" > unexpected > > > the log is > also attached. > > any advise > appreciated! > > cheers > ds > http://www1.imperial.ac.uk/medicine/people/d.soto/ > http://www1.imperial.ac.uk/medicine/people/d.soto/ > On 09/08/13 > 14:02, Anastasia > Yendiki wrote: > > Why > are you converting > from .nii > to > .mnc? Why are you not > using the > .nii > directly? > > On > Fri, 9 Aug 2013, David > Soto > wrote: > > hi > - thanks for the > feedback > > weirdly, > the nii2mnc > transform > of the > diffusion > data > falters, I get a > part > of the brain > chopped > have > no idea why this > is > the case, as it > worked > fine > before > for the T1 for > recon-all...I > am using > Ubuntu > 12.04 > > anyway > am trying to > sort > this out now, if > you > have any > advise > that would much > appreciated!! > cheers > ds > > > http://www1.imperial.ac.uk/medicine/people/d.soto/ > On > 08/08/13 17:03, > Anastasia > Yendiki > wrote: > > Hi > David - > The > fact > that > it's > taking > so > many > tries > to > initialize > the > left > ILF > tells > me > that > something > has > gone > wrong > with > the > data, > either > with > the > T1 > to DWI > registration, > or > with > the > mask, > or > something > like > that. > Have > you > looked > at > any > of the > output > files > of > the > pre-processing? > The > FA > map, > the > aparc+aseg, > etc? > > a.y > > On > Wed, 7 > Aug > 2013, > Soto, > David > wrote: > > Hi > Anastasia, > I > checked > the > becs > and > bvals > files, > there > was > a > bug > in > the > transposition > of > the > columns > into > 3 > rows > in > the > bvecs. > But > i > still > have > problems.. > I > rerun > trac-all > -prep > and > seemed > fine > but > ended > with > a > Segmentation > fault > (core > dumped) > which > however > is > not > present > in > the > last > line > of > the > trac-all.log > (Attached). > Writing > output > files > to/home/dsoto/Documents/fmri/rsdtianawmg > ui/02ST/dlabel/mni/lh.ilf_AS_avg33_mn > i_bbr_* > Writing > spline > volume > to/home/dsoto/Documents/fmri/rsdtianawmg > ui/02ST/dlabel/mni/lh.ilf_AS_avg33_mn > i_bbr_cpts_5.nii.gz > Segmentation > fault > (core > dumped) > Just > in > case > I > tried > trac-all > -bedp > complains > like > these > below, > any > advise > appreciated, > cheers > - > ds > /home/dsoto/Documents/fmri/rsdtianawmgui > /02ST/diffree/tracula02ST.txt > -bedp > INFO: > SUBJECTS_DIR > is > /home/dsoto/Documents/fmri/rsdtianawmgui > > INFO: > Diffusion > root > is > /home/dsoto/Documents/fmri/rsdtianawmgui > > Actual > FREESURFER_HOME > /usr/local/freesurfer > WARN: > Running > FSL's > bedbost > locally > - > this > might > take > a > while > WARN: > It > is > recommended > to > run > this > step > on > a > cluster > bedpostx_mgh > -n > 2 > /home/dsoto/Documents/fmri/rsdtianawmgui > /02ST/dmri > /usr/local/freesurfer/bin/bedpostx_mgh: > 131: > /usr/local/freesurfer/bin/bedpostx_mgh: > Syntax > error: > "(" > unexpected > http://www1.imperial.ac.uk/medicine/peop > le/d.soto/ > > ________________________________________ > > From: > Anastasia > Yendiki > [ayendiki(a)nmr.mgh.harvard.edu] > Sent: > 07 > August > 2013 > 17:22 > To: > Soto, > David > Cc: > freesurfer(a)nmr.mgh.harvard.edu > Subject: > RE: > [Freesurfer] > trac-all > inquiry > > Hi > David > - > Every > time > you > run > trac-all, > the > results > get > appended > to > this > file, > so > you > need > to > look > for > error > messages > only > in > the > more > recent > invocation > of > trac-all. > The > first > error > there > seems > to > be: > > > Error: > bvecs > and > bvals > don't > have > the > same > number > of > entries > > Do > you > have > the > same > number > of > b-values > and > gradient > vectors > and > volumes > in > your > DWI > series? > > a.y > > On > Tue, > 6 > Aug > 2013, > Soto, > David > wrote: > > hi > > I > upgraded > to > FS > 5.3 > but > still > encountering > issues > with > trac-all > prep. > > The > log > is > attached, > things > I > noted > after > inspecting > it > > 1) > INFO: > FreeSurfer > build > stamps > do > not > match > Subject > Stamp: > freesurfer-Linux-centos4_x86_64-st > able-pub-v5.1.0 > Current > Stamp: > freesurfer-Linux-centos4_x86_64-st > able-pub-v5.3.0 > > 2) > Error: > input > image > /home/dsoto/Documents/fmri/rsdtian > awmgui/02ST/dmri/lowb > not > valid > 3) > Image > Exception > : > #22 > :: > ERROR: > Could > not > open > image > /home/dsoto/Documents/fmri/rsdtian > awmgui/02ST/dmri/lowb_brain > 4) > Image > Exception > : > #22 > :: > ERROR: > Could > not > open > image > /home/dsoto/Documents/fmri/rsdtian > awmgui/02ST/dlabel/diff/White-Matter++. > 5) > ERROR: > Could > not > read > /home/dsoto/Documents/fmri/rsdtian > awmgui/02ST/dmri/dtifit_FA.nii.gz > but > despite > all > this > it > says: > trac-preproc > finished > without > error > at > Tue > Aug > 6 > 21:27:30 > BST > 2013 > > thanks > for > your > help > > cheers > ds > > http://www1.imperial.ac.uk/medicin > e/people/d.soto/ > > > > > __________________________________ > ______ > From: > Anastasia > Yendiki > [ayendiki(a)nmr.mgh.harvard.edu] > Sent: > 06 > August > 2013 > 19:30 > To: > Soto, > David > Cc: > freesurfer(a)nmr.mgh.harvard.edu > Subject: > RE: > [Freesurfer] > trac-all > inquiry > > I > see, > you're > using > the > old > version > of > tracula > (from > freesurfer > 5.1). > In > that > version, > you > had > to > define > the > number > of > low-b > images > in > the > configuration > file. > I > strongly > recommend > updating > to > freesurfer > 5.3. > A > lot > of > things > have > improved > in > tracula > since > then. > > Also, > in > the > future > please > attach > any > log > files > as > separate > attachments > instead > of > pasting > them > into > the > body > of > your > email > - > this > causes > the > body > of > the > email > to > exceed > the > limit > allowable > on > the > list. > > Thanks, > a.y > > > 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/compliance > line > . > 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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RAS to Talairach
by sujith vijayan 19 Aug '13

19 Aug '13

I am looking at intracranial electrode recordings from some epileptic patients. The locations of the electrodes have been determined using a preoperative MRI and a postoperative CT scan. The locations are in RAS coordinates. Is there some sort of function that will allow me to translate the RAS coordinates to Talairach coordiantes? Or some sort of function that will output an anatomical label for each of the RAS coordinates? Please let me know what I need in addition to the RAS coordinates as a .mat file. For example, do I need to install FreeSurfer? What additional files do I need? My preference would be to do this all in Matlab. Sincerely, Sujith

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[Tracula] error running trac-all –path –c Configuration_file.txt
by Francesco Siciliano 19 Aug '13

19 Aug '13

Hello, I received an error on several terminals running trac-all –path –c Configuration_file.txt 55 slices processed 56 slices processed 56 slices processed 57 slices processed 57 slices processed 58 slices processed 59 slices processed 60 slices processed 61 slices processed Queuing post processing stage 70 slices processed For some reason the bedpostX process DOES NOT appear to have successfully completed. Please examine your results carefully. /Users/jonathanposner/Desktop/MRI_Software/FSL_installer/fsl/bin/bedpostx: line 262: kill: (15849) - No such process Is this an indication that the processing did not finish? Could this have anything to do with limited computer memory?

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few questions regarding qdec
by Binod Thapa-Chhetry 19 Aug '13

19 Aug '13

HI all, We had submitted a paper based on cortical thickness analysis in Qdec. The reviewer's had couple concerns regarding the QDec analysis. We would appreciate your help to address/resolve those issues. Here are the concerns: (1) What was the rationale of using 10mm smoothing? The typical fMRI values for volumteric work is 2-3 x the original voxel size. What's the reason for this value? Our response so far: A smoothing kernel of 10 mm was chosen because this setting had been published recently in articles that performed similar analyses. 10 mm therefore was a typical parameter for this type of analysis. This setting was also the default in the QDEC GUI, also suggesting that it was a typical setting. We only performed analyses of the data for this project using this setting and did not iteratively test multiple kernel widths. Also, the FWHM for cortical thickness analyses is somewhat larger than that used in fMRI analyses because it is applied to surface, as opposed to volume-based data. Surface based data are not prone to the same artifacts of including white matter, csf or brain tissue on the other side of a sulcus as volume-based data are. (2) What's the p-value to get in for a cluster-wise analysis and what size is a significant cluster? It's important to know these non cluster-wise values to get a sense of the parameters that determine significance. Our response so far: QDEC does not have a parameter that can be adjusted for cluster size or extent as other whole brain analyses such as Statistical Parametric Mapping do. The researcher can only indicate a statistical cutoff. We used a p value cutoff of 0.05 after a correction for multiple comparisons that was based on the Monte Carlo permutation cluster analysis with 10,000 iterations. Additionally, our findings comprise of pretty large clusters. This obviates the reason for cluster-thresholding based on size. Thanks in advance for the response. Binod

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Re: [Freesurfer] [Tracula] error running trac-all –path –c Configuration_file.txt
by Francesco Siciliano 19 Aug '13

19 Aug '13

________________________________ From: Francesco Siciliano Sent: Monday, August 19, 2013 12:54 PM To: Francesco Siciliano Subject: RE: [Tracula] error running trac-all –path –c Configuration_file.txt I also noticed that even on those that appeared to finish, there was no dpath folder. Any help would be greatly appreciated! Francesco Siciliano, B.A. Research Assistant Department of Child and Adolescent Psychiatry The New York State Psychiatric Institute Columbia University 1051 Riverside Drive, Unit 74 New York, NY 10032 (212) 543-6155 ________________________________ From: Francesco Siciliano Sent: Monday, August 19, 2013 12:13 PM To: freesurfer(a)nmr.mgh.harvard.edu Subject: [Tracula] error running trac-all –path –c Configuration_file.txt Hello, I received an error on several terminals running trac-all –path –c Configuration_file.txt 55 slices processed 56 slices processed 56 slices processed 57 slices processed 57 slices processed 58 slices processed 59 slices processed 60 slices processed 61 slices processed Queuing post processing stage 70 slices processed For some reason the bedpostX process DOES NOT appear to have successfully completed. Please examine your results carefully. /Users/jonathanposner/Desktop/MRI_Software/FSL_installer/fsl/bin/bedpostx: line 262: kill: (15849) - No such process Is this an indication that the processing did not finish? Could this have anything to do with limited computer memory?

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Two Inquiries
by Liane Hunter 19 Aug '13

19 Aug '13

1. Segmentation of partial brain Dear FreeSurfers, 1. Can I expect recon-all to work on a T1W image where only part of the brain is in FOV? The obvious answer is that I should just try, but it would help to know in case I get unexpected results. Perhaps a more appropriate question is: what should I expect to work and what should I expect to fail. Thank you, ---------------------- 2. Rotated segmentation Dear FreeSurfers, I start with a T1W image in NIFTI format. After running recon-all, I use mri_convert to convert aseg.mgz to aseg.nii. This aseg.nii image does not overlay the original T1W. It is slightly rotated. Is it normal? If I would like to make it overlay what should I do? Register using flirt? Thank you, -- Liane Hunter MD/Ph.D Candidate Albert Einstein College of Medicine

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Orientation/Primary-Slice-Direction
by Mark Plantz 19 Aug '13

19 Aug '13

Hello freesurfers, I have an image that is in RAS orientation with the axial primary slice direction. Is there anyway to change this to LIA orientation with the coronal primary slice direction? I am assuming mri_convert would work, but I'm not sure which flags to use. Thanks in advance. MP

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Re: [Freesurfer] Antw: Re: [tracula] error running trac-all -prep
by Borsodi Florian 19 Aug '13

19 Aug '13

Hi Anastasia, Here are the bvec and bval files you asked me about. Sincerely, Florian >>> Anastasia Yendiki 18.08.13 22.52 Uhr >>> Hi Florian - Can you please also attach the bvecs/bvals files from the dmri directory? Thanks, a.y On Sun, 18 Aug 2013, Borsodi Florian wrote: > Hi Anastasia, > > Thanks for your help. I renamed the directories and reran trac-all. It > worked for the moment. > However, then I got another error: "bvecs and bvals don't have the same > number of entries." > I don't know why, because they actually have the same number of entries. > > I attached the logfile so that you may see what is going on. The error > occours at line 1463. > > Thank you in advance for your help. > > Sincerely, > Florian > > > >>> Anastasia Yendiki 15.08.13 18.01 Uhr >>> > > Hi Florian - I see what's going on. Can you please rename the directory > /data/physics/florian/nii into something that doesn't include "nii", and > rerun? Because "nii" is a file extension, this confuses some of the > scripts. > > Thanks, > a.y > > On Thu, 15 Aug 2013, Borsodi Florian wrote: > > > Hi Anastasia > > > > I ran the command you sent me and it runs without any errors. > > I also attached the command line for you. > > > > Furthermore i ran data with 12 diffusion directions and i keep getting the > > same kind of problems. > > > > sincerely > > Florian > > > > >>> Anastasia Yendiki 02.08.13 19.59 Uhr > >>> > > > > Hi Florian - Can you please run this command directly on the command line > > and see if there are any errors? > > > > flip4fsl > > /data/physics/florian/nii/1020000485074_20080319/dmri/dwi_orig.nii.gz > > /data/physics/florian/nii/1020000485074_20080319/dmri/dwi_orig_flip.nii.gz > > > > Thanks, > > a.y > > > > On Fri, 2 Aug 2013, Borsodi Florian wrote: > > > > > Hi Anastasia > > > > > > Thank you for your answer. > > > > > > Yes, those files exist. > > > I also extracted the bvec an bval files with anotther software then > > dcm2nii > > > and i keep getting the same kind of error. > > > Also, about the 6 diffusion direction, those data i sent you, are just > > > testdata for running tracula. > > > > > > sincerely > > > Florian > > > > > > >>> Anastasia Yendiki 02.08.13 0.41 Uhr > >>> > > > > > > Hi Florian - Do these files exist? > >>/data/physics/florian/nii/1020000485074_20080319/dmri/dwi_orig.mghdti.bvec > s > > > > > > >>/data/physics/florian/nii/1020000485074_20080319/dmri/dwi_orig.mghdti.bval > s > > > > > > > > > > > The format of the bvecs and bvals that you sent seems fine, but (and > this > > > has nothing to do with the error you're getting) I have to warn you that > > > you may not be able to get good results running probabilistic > tractography > > > on this data. It looks like you're acquiring the same 6 diffusion > > > directions, repeated 8 times. Six directions is the absolute minimum for > > > reconstructing the tensor model, but will probably not be sufficient for > > > the crossing fiber model that bedpostx reconstructs (and is used by > > > tracula). Your scan time is better spent acquiring 48 different > > > directions, rather than the same 6 directions 8 times. > > > > > > a.y > > > > > > On Mon, 29 Jul 2013, Borsodi Florian wrote: > > > > > > > Hello, > > > > > > > > I have been trying to run tracula on my data and i keep getting the > same > > > > kind of error repeatedly. > > > > For my imput I am using dicoms from a Siemens scanner with a stadard > > > > diffusion protocol. However, tracula cannot read the bvec and bval > data > > > out > > > > of the dicom header. Therefore, I implemented bvec and bval files into > > the > > > > config file. > > > > After doing so, I got the error which says that tracula cannot find > the > > > > "dwi_orig_flip.mghdti.bvecs" and "dwi_orig_flip.mghdti.bvals" files. > > > > I have tried many options, but still cannot find a solution. > > > > I am hoping to get some troubleshooting help. > > > > > > > > I have atteched my log- and config- files, as well as my bvec and bval > > > > files. > > > > To uphold patient confidentiality, I have encode the name patient's > data > > > as > > > > "AAAAAA". > > > > > > > > I believe the problems are the bvec and bval files or their > structures. > > > The > > > > log-file lete me assume this, especially the lines 202 - 205, 264 - > 268 > > > and > > > > 1480 - 1484. > > > > > > > > Thank you in advance for your help, and your speedy response. > > > > > > > > With kind regards, > > > > > > > > Florian Borsodi > > > > Department of Neurology > > > > Medical University of Graz > > > > > > > > > > > > > > > > > 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 > > > > > >

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