Freesurfer

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30132 discussions

TBSS doubts
by Anupa AV 23 Aug '13

23 Aug '13

Dear All, I was trying to do TBSS analysis. But I encountered with some problems.I attached a ppt which shows raw DWI, FA map generated using FDT FSL toolbox and the TBSS results. If you see the FA and TBSS results,..some brain areas got removed. I'm wondering where I made the mistake?? Can you please help me out?? Thanks in advance.!!

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Problem with mris_ca_label (seg fault)
by Demian Wassermann 22 Aug '13

22 Aug '13

Dear Support line of free surfer, I have a problem when I try to apply a new atlas to the surfaces. Even with the standard free surfer atlases it segfaults Environment: FREESURFER_HOME: /projects/schiz/software/freesurfer-v4.5/freesurfer Build stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v4.5.0 RedHat release: Fedora release 18 (Spherical Cow) Kernel info: Linux 3.9.2-200.fc18.x86_64 x86_64 Command: $FREESURFER_HOME/bin/mris_ca_label -t $FREESURFER_HOME/average/colortable_desikan_killiany.txt case01009 lh lh.sphere.reg $FREESURFER_HOME/average/lh.curvature.buckner40.filled.desikan_killiany.2009-03-04.gcs lh.test.annot Output: $Id: mris_ca_label.c,v 1.23 2007/03/23 20:00:07 fischl Exp $ $Id: mrisurf.c,v 1.557.2.19 2009/08/05 22:10:21 nicks Exp $ reading atlas from /projects/schiz/software/freesurfer-v4.5/freesurfer/average/lh.curvature.buckner40.filled.desikan_killiany.2009-03-04.gcs... reading color table from GCSA file.... average std = 1.0 using min determinant for regularization = 0.011 0 singular and 384 ill-conditioned covariance matrices regularized Segmentation fault (core dumped) Am I doing something wrong? How can I diagnose and fix this? Thanks D -- Demian Wassermann, PhD demian(a)bwh.harvard.edu LMI / PNL / SPL Labs Harvard Medical School Brigham and Women's Hospital 1249 Boylston, Boston, MA, USA http://lmi.bwh.harvard.edu/~wassermann/

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gradient table question for Tracula
by Salil Soman 22 Aug '13

22 Aug '13

Hi Anastasia, A question I had about the gradient tables for Tracula - I recently came across this passage from Hui Zhang: "To correct for any errors that you identify, you need to first modify the gradient table, then repeat the tensor reconstruction. The modification of the gradient table typically involves flipping the signs of the x or y component of all gradient vectors. To determine the correct flipping of the signs in a systematic way, it is necessary to understand why this happens. The reason is that the gradient directions are always defined with respect to some right-handed frame of reference, while the frame of reference of the acquired image data is typically NOT right-handed. This mismatch is the cause of the problem. The sign flipping intends to fix this mismatch and the key is to identify the difference between the two frames of reference in question. In our experience, if the data is acquired on SIEMENS scanners, the signs of x gradient components need to be flipped; for GE scanners, it is usually the y components." (from http://dti-tk.sourceforge.net/pmwiki/pmwiki.php?n=Documentation.Visualizati… ). Does this mean that the gradient tables i get from dcm2nii need to have the Y component flipped for my GE acquisitions or is this adjusted in the tracula processing? Thank you. -- Salil Soman, MD, MS Postdoctoral Research Fellow - Stanford Radiological Sciences Laboratory Fellow - Palo Alto War Related Illness and Injury Study Center WOC Neuroradiology Attending - Veterans Affairs Palo Alto Health Care System

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Error message of Ubuntu 13.04 and Centos4 & Centos6
by JoJo 22 Aug '13

22 Aug '13

Dear Freesurfer experts, I installed FS Centos4-64(and also tried Centos6) on Ubuntu 13.04. I tried the commands in tutorial and got error message, listed as follows. Nevertheless, FS can read in volume and surface from GUI. Another question is, which one of Centos4 or Centos6 is more suitable for Ubuntu 13.04? 1. tkmedit bert orig.mgz Couldn't create output file .xdebug_tkmeditReading /usr/local/freesurfer/tktools/tkm_common.tcl 2. tkmedit -segmentation mri/aseg.mgz \ $FREESURFER_HOME/FreeSurferColorLUT.txt bert norm.mgz Couldn't create output file .xdebug_tkmeditmghRead(/usr/local/freesurfer/subjects/bert/mri/mri/aseg.mgz, -1): could not open file a window pop up: Error: loading segmentation mri/aseg.mgz Couldn't import the segmentation volume. Tkmedit couldn't read the segmentation specified. This could be because the segmentation volume wasn't a valid COR volume directory. Note: In fact, I can load segmentation volume from window. 3. tksurfer bert rh pial Couldn't create output file .xdebug_tksurfersubject is bert Thanks for your help, JoJo

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FW: Contrast and F-test
by Jacobs H (NP) 22 Aug '13

22 Aug '13

Dear Doug, Thank you for the information. Sorry for not sending this to the list. Do you mean that I then have to include the three variables (covariate 1, covariate 2, product of these two) or only the product in the fsgd file? If I need to include all three of them, can you advise me on the contrasts? If it is only the product, I think I can use the same contrasts as before, right? Thanks Heidi ================================================ Dr. Heidi Jacobs Postdoc researcher Faculty of Health, Medicine and Life Sciences School for Mental Health and Neurosciences Division Cognitive Neuropsychiatry and Clinical Neurosciences Alzheimer Center Limburg h.jacobs(a)maastrichtuniversity.nl www.maastrichtuniversity.nl www.heidijacobs.nl Dr. Tanslaan 12, 6229 ET Maastricht P.O. Box 616, 6200 MD Maastricht, The Netherlands T +31 43 38 84 090 F +31 43 38 84 092 ================================================ ________________________________________ Van: freesurfer-bounces(a)nmr.mgh.harvard.edu [freesurfer-bounces(a)nmr.mgh.harvard.edu] namens Douglas N Greve [greve(a)nmr.mgh.harvard.edu] Verzonden: donderdag 22 augustus 2013 16:34 Aan: freesurfer(a)nmr.mgh.harvard.edu Onderwerp: Re: [Freesurfer] Contrast and F-test If you want to test for an interaction between continuous variables, then you should create a new regressor by multiplying them together then test that regressor doug On 08/22/2013 08:09 AM, Jacobs H (NP) wrote: > Hi all, > > I my manuscript, I examined the association between cognition and cortical thickness. I first did this in three groups separately and then ran a F-test. > One of the reviewers, now wants me to examine the interaction between cognition and education (all continuous). > > Would this be the correct contrast for each group separately (last two zeros are for covariates, also continuous) > > 0 1 -1 0 0 > > Would this be the correct way for the F-test: > > 0 0 0 0 0 1 -1 0 -1 1 0 0 0 0 0 0 0 > 0 0 0 1 0 -1 -1 0 1 0 0 0 0 0 0 > > Thanks! > > Heidi > > ================================================ > Dr. Heidi Jacobs > Postdoc researcher > Faculty of Health, Medicine and Life Sciences > School for Mental Health and Neurosciences > Division Cognitive Neuropsychiatry and Clinical Neurosciences > Alzheimer Center Limburg > h.jacobs(a)maastrichtuniversity.nl > www.maastrichtuniversity.nl > www.heidijacobs.nl > > Dr. Tanslaan 12, 6229 ET Maastricht > P.O. Box 616, 6200 MD Maastricht, The Netherlands > T +31 43 38 84 090 F +31 43 38 84 092 > ================================================ > _______________________________________________ > 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: https://gate.nmr.mgh.harvard.edu/filedrop2 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.

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Contrast and F-test
by Jacobs H (NP) 22 Aug '13

22 Aug '13

Hi all, I my manuscript, I examined the association between cognition and cortical thickness. I first did this in three groups separately and then ran a F-test. One of the reviewers, now wants me to examine the interaction between cognition and education (all continuous). Would this be the correct contrast for each group separately (last two zeros are for covariates, also continuous) 0 1 -1 0 0 Would this be the correct way for the F-test: 0 0 0 0 0 1 -1 0 -1 1 0 0 0 0 0 0 0 0 0 0 1 0 -1 -1 0 1 0 0 0 0 0 0 Thanks! Heidi ================================================ Dr. Heidi Jacobs Postdoc researcher Faculty of Health, Medicine and Life Sciences School for Mental Health and Neurosciences Division Cognitive Neuropsychiatry and Clinical Neurosciences Alzheimer Center Limburg h.jacobs(a)maastrichtuniversity.nl www.maastrichtuniversity.nl www.heidijacobs.nl Dr. Tanslaan 12, 6229 ET Maastricht P.O. Box 616, 6200 MD Maastricht, The Netherlands T +31 43 38 84 090 F +31 43 38 84 092 ================================================

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Re: [Freesurfer] [tracula] error running trac-all -prep
by Borsodi Florian 22 Aug '13

22 Aug '13

Hi Anastasia, I checked the dmri.bedpostx directory. Unless "nodif_brain", all files are there. Sincerely, Florian >>> Anastasia Yendiki 22.08.13 15.06 Uhr >>> Hi Florian - My guess is that everything ran fine and you don't need to change anything else. Check that all the output files were created in the dmri.bedpostX directory: http://fsl.fmrib.ox.ac.uk/fsl/fsl4.0/fdt/fdt_bedpostx.html a.y On Thu, 22 Aug 2013, Borsodi Florian wrote: > Hi Anastasia, > > This Ubuntu-related error is a tricky one. > I changed the first line in those files you told me and reran trac-all. All > three steps of trac-all ran without any errrors. I checked the FA maps and > the MNI registration and everything looks fine. > > After running trac-all -bedp, the step stopped with the following line: > "Queuing post processing stage > /usr/local/freesurfer/bin/bedpostx_mgh: line 439: 9381 Terminated > ${subjdir}.bedpostX/monitor." > I think it's fine, because line 439 is the last line of the script, so it > worked well. > Maybe I have to change all ".sh" in the files to ".bash" to get all > messages. > > Thank you so much for your big help. > I hope I didn't cause you much trouble with my problems and questions. > > Sincerely, > Florian > > >>> Anastasia Yendiki 20.08.13 17.56 Uhr >>> > > This is an Ubuntu-related error that has surfaced recently because in > Ubuntu /bin/sh is not a bash shell any more. To get around this, you can > 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 Tue, 20 Aug 2013, Borsodi Florian wrote: > > > Hi Anastasia, > > > > Yes, i am running this on ubuntu 12.04. > > > > Sincerely, > > Florian > > > > >>> Anastasia Yendiki 20.08.13 17.38 Uhr > >>> > > > > Hi Florian - Are you running this on an ubuntu system by any chance? > > > > a.y > > > > On Tue, 20 Aug 2013, Borsodi Florian wrote: > > > > > Hi Anastasia, > > > > > > Thank you for your help. > > > I changed the commas in "/dmri/bvecs" to dots and reran trac-all. But > the command "xfmrot" changed the dots back to > > > commas. So, I changed our system language from de_AUT.UTF-8 to > en_US.UTF-8 and reran trac-all. After changing the > > > system language everything was genereted correctly and trac-all -prep > ran without any errors. > > > I'm so glad. > > > > > > Then, I started the next step "trac-all -bedp" and got a syntax error > "/usr/local/freesurfer/bin/bedpostx_mgh: 131: > > > /usr/local/freesurfer/bin/bedpostx_mgh: Syntax error: "(" unexpected. " > I also attached the the logfile. I was > > reading > > > about this error in the mail archive. Would I have to run "bedpostx" > outside of tracula ? > > > > > > Sincerely, > > > Florian > > > > > > >>> Anastasia Yendiki 19.08.13 17.54 Uhr > >>> > > > > > > Hi Florian - Can you please change the decimal commas to points and try > > > again? > > > > > > a.y > > > > > > On Mon, 19 Aug 2013, Borsodi Florian wrote: > > > > > > > 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.bve > c > > > > > s > > > > > > > > > > > > > > > > > >>>/data/physics/florian/nii/1020000485074_20080319/dmri/dwi_orig.mghdti.bva > l > > > > > 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 > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > _______________________________________________ > > > Freesurfer mailing list > > > Freesurfer(a)nmr.mgh.harvard.edu > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >

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Re: [Freesurfer] [tracula] error running trac-all -prep
by Borsodi Florian 22 Aug '13

22 Aug '13

Hi Anastasia, This Ubuntu-related error is a tricky one. I changed the first line in those files you told me and reran trac-all. All three steps of trac-all ran without any errrors. I checked the FA maps and the MNI registration and everything looks fine. After running trac-all -bedp, the step stopped with the following line: "Queuing post processing stage /usr/local/freesurfer/bin/bedpostx_mgh: line 439: 9381 Terminated ${subjdir}.bedpostX/monitor." I think it's fine, because line 439 is the last line of the script, so it worked well. Maybe I have to change all ".sh" in the files to ".bash" to get all messages. Thank you so much for your big help. I hope I didn't cause you much trouble with my problems and questions. Sincerely, Florian >>> Anastasia Yendiki 20.08.13 17.56 Uhr >>> This is an Ubuntu-related error that has surfaced recently because in Ubuntu /bin/sh is not a bash shell any more. To get around this, you can 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 Tue, 20 Aug 2013, Borsodi Florian wrote: > Hi Anastasia, > > Yes, i am running this on ubuntu 12.04. > > Sincerely, > Florian > > >>> Anastasia Yendiki 20.08.13 17.38 Uhr >>> > > Hi Florian - Are you running this on an ubuntu system by any chance? > > a.y > > On Tue, 20 Aug 2013, Borsodi Florian wrote: > > > Hi Anastasia, > > > > Thank you for your help. > > I changed the commas in "/dmri/bvecs" to dots and reran trac-all. But the command "xfmrot" changed the dots back to > > commas. So, I changed our system language from de_AUT.UTF-8 to en_US.UTF-8 and reran trac-all. After changing the > > system language everything was genereted correctly and trac-all -prep ran without any errors. > > I'm so glad. > > > > Then, I started the next step "trac-all -bedp" and got a syntax error "/usr/local/freesurfer/bin/bedpostx_mgh: 131: > > /usr/local/freesurfer/bin/bedpostx_mgh: Syntax error: "(" unexpected. " I also attached the the logfile. I was > reading > > about this error in the mail archive. Would I have to run "bedpostx" outside of tracula ? > > > > Sincerely, > > Florian > > > > >>> Anastasia Yendiki 19.08.13 17.54 Uhr >>> > > > > Hi Florian - Can you please change the decimal commas to points and try > > again? > > > > a.y > > > > On Mon, 19 Aug 2013, Borsodi Florian wrote: > > > > > 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 > > > > > > > > > > > > > > > > > > > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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procedure to install QDEC
by Muhammad Naveed Iqbal Qureshi 21 Aug '13

21 Aug '13

Dear List members, Please guide me about installing qdec on Ubuntu. Best Regards, Muhammad Naveed Iqbal Qureshi please don't print this e-mail unless you really need to

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"segmentation fault" - recon-all
by Mark Plantz 21 Aug '13

21 Aug '13

Hello all, While running recon-all for a subject, I ran into the following error message: *reading aseg from /Users/IngvalsonLab/Desktop/avgseg_seg_test/mri/aseg.auto_noCCseg.mgz* *reading norm from /Users/IngvalsonLab/Desktop/avgseg_seg_test/mri/norm.mgz* *0 voxels in left wm, 0 in right wm, xrange [-1, 257]* *searching rotation angles z=[-7 7], y=[83 97]* *searching scale 1 Z rot 6.8 global minimum found at slice 0.0, rotations (90.00, -0.00)* *final transformation (x=0.0, yr=90.000, zr=-0.000):* *-0.000 0.000 1.000 128.000;* *-0.000 1.000 -0.000 128.000;* *-1.000 0.000 0.000 128.000;* * 0.000 0.000 0.000 1.000;* *Segmentation fault* *Darwin dhcp-165-124-23-248.prevmed.northwestern.edu 12.4.0 Darwin Kernel Version 12.4.0: Wed May 1 17:57:12 PDT 2013; root:xnu-2050.24.15~1/RELEASE_X86_64 x86_64* *recon-all -s avgseg_seg_test exited with ERRORS at Mon Aug 19 13:32:28 CDT 2013* * * I don't know if this error is directly related to the actual brain segmentation, but recon-all was run with a different gca atlas. The command was: recon-all -gca atlas.gca -all -s <subjID> My best guess is that the .gca file is the source of the problem, but I am not sure why recon-all would make it to the final transformation and then throw an error. Any ideas? Thanks in advance. MP

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