Freesurfer

freesurfer@nmr.mgh.harvard.edu

15 participants
30097 discussions

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

2 1

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

1 0

"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

3 4

Out of memory error in selxavg3....
by Joseph Andreano 21 Aug '13

21 Aug '13

I'm trying to run selxavg on a dataset with a rather large number (930) of timepoints. Selxavg keeps erroring out with an 'out of memory. Type HELP MEMORY for your options' error. I see that this problem has been discussed on the mailing list previously, and the advice was to split the file into multiple runs for analysis. For reasons having to do with the design of the experiment, this is not a viable option for me. Is there any other way around the memory limitation? Thanks, Joe Andreano _________________________________ Joseph M. Andreano, PhD Postdoctoral Researcher Interdisciplinary Affective Science Laboratory Massachusetts General Hospital _________________________________

2 1

Group thickness analysis, 2x2x2
by Chris Watson 20 Aug '13

20 Aug '13

Dear Doug et al., I have 2 groups, 2 genders, and 2 scanners (A and B). (I also have Age as a covariate). In my FSGD they are listed in this order: ControlFemaleA ControlFemaleB ControlMaleA ControlMaleB CaseFemaleA CaseFemaleB CaseMaleA CaseMaleB I used the following contrast to test for a group X scanner interaction: [1 -1 1 -1 -1 1 -1 1 0] And I also looked at a group X scanner X gender interaction: [1 -1 -1 1 -1 1 1 -1 0] For both, there are no significant results in either hemi. Would this mean that I can instead just have 4 groups (Control/Case Female/Male), or even just 2 groups (Control/Case)? Is that even appropriate? Thanks, Chris

1 0

Out of memory error in selxavg3....
by Joseph Andreano 20 Aug '13

20 Aug '13

1 0

Re: [Freesurfer] [tracula] error running trac-all -prep
by Borsodi Florian 20 Aug '13

20 Aug '13

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

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Re: [Freesurfer] Fornix labelled as corpus callosum in patient with periventricular leukomalacia
by Corinna Bauer 20 Aug '13

20 Aug '13

Hi Bruce, I was just wondering if you had any suggestions on how to fix the corpus callosum labels? Corinna On Wed, Aug 14, 2013 at 11:49 AM, Corinna Bauer <corinnab83(a)gmail.com>wrote: > In general, it mostly looks ok. There are regions which are labelled as > hypointensities, but should be CSF or gray matter, particularly around the > parieto-occipital fissure (see attached). Much of the fornix and corpus > callosum is also just labelled as left/right cerebral white matter. > > > > > On Wed, Aug 14, 2013 at 11:37 AM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu > > wrote: > >> Hi Corinna >> >> how does the rest of the aseg.mgz look? Is it accurate? >> Bruce >> >> On Wed, 14 Aug 2013, Corinna Bauer wrote: >> >> Hello all, >>> I am examining diffusion tracking in the corpus callosum of individuals >>> with >>> periventricular leukomalacia (PVL). The corpus callosum is particularly >>> small and the anterior and mid-anterior labels are being applied to the >>> fornix (see attached Fornix_labelled_as_CC.png). The midposterior and >>> posterior look ok, while the central is very small, maybe one voxel in >>> size. >>> >>> The wm segmentation, seen with ?l.white, also shows segmentation defaults >>> with the anterior corpus callosum (see attached images). I tried to >>> correct >>> this using control points, which you can see did not fix the >>> segmentation. >>> >>> Any suggestions? >>> >>> Corinna >>> >>> >>> >>> >> >> 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<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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