Freesurfer November 2014

freesurfer@nmr.mgh.harvard.edu

99 participants
144 discussions

tractstats2table for dwi motion
by Chung, Yoonho 21 Nov '14

21 Nov '14

Hi Anastasia, I was wondering if there is a flag in the tractstats2table function that extracts all the variables in the dwi_motion.txt file for all subjects and put them into a single spreadsheet. Thanks! Best, Yoon

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Command '-qa' in TRACULA
by Anri WATANABE 21 Nov '14

21 Nov '14

Dear FreeSurfer experts, I'm running pre-processing steps in TRACULA separatelly and could neither find the context about quality assessment step nor run the command 'trac-all -qa -c <configulation file>. I downloaded TRACULA in FreeSurfer 5.3, MacOSX lion (64-bit). Could anyone solve this problem? Thank you. Anri ********************************************************************** 京都府立医科大学附属病院精神科・心療内科渡辺杏里 ********************************************************************** WATANABE ANRI Department of Psychiatry, University Hospital, Kyoto Prefectural University of Medicine **********************************************************************

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TRACULA - Error: bvecs and bvals don't have the same number of entries
by Tadeu Kubo 21 Nov '14

21 Nov '14

Dear FS Experts, I'm trying to work with the DTI Siemens (non MGH) and is not working. An error occurs in step "Tensor Fit”. II tried a solution that have worked as substitute bvecs values before this step manual (by original bvecs) and it works great (is meant by: continued)!. Surely I'm doing something wrong, but not yet identified. I would like your help. Sorry for the basic question, but I’m starting with TRACULA. Attached files: .log bvecs.txt bvals.txt

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TRACULA bedpost error
by Worker, Amanda 21 Nov '14

21 Nov '14

Hello, I am trying to run the second step of the TRACULA processing which is: trac-all -bedp -c /home/... I am currently using freesurfer v5.3.0 and I get the following error: 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/k1204763/images/PDPLUS_TRACULA/TRACULA_OUTPUT/PDPLUS006/dmri subjectdir is /home/k1204763/images/PDPLUS_TRACULA/TRACULA_OUTPUT/PDPLUS006/dmri Making bedpostx directory structure Queuing preprocessing stages Queuing parallel processing stage Unable to read script file because of error: error opening bedpostx: No such file or directory Queuing post processing stage Unable to run job: denied: "60" is not a valid object name (cannot start with a digit) Exiting. I have read that this may be a bedpostx FSL problem, however I am not familiar with this. Do you have any advice on how to overcome this problem? Thanks in advance, Amanda

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Tracula_average_average center
by Alshikho, Mohamad J. 21 Nov '14

21 Nov '14

Hi Anastasia, One of Tracula's output is the "pathstats.overal.txt" and in this file we have a list of numbers. Kindly what is the difference between the metrics average and the metrics average center also which one do you recommend to do statistic? Thanks, Mohamad

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Re: [Freesurfer] From bedpostX and recon-all to tracula
by Anastasia Yendiki 21 Nov '14

21 Nov '14

Hi Kate - The -prep, -bedp, and -path steps need to be run separately, in that order. You can't run them all at once unfortunately. See: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/RunningTracula a.y On Wed, 29 Oct 2014, Katherine Damme wrote: > Sorry for the delay. I signed up for the course and hoped that it would answer my question, but I am still > unsure what went wrong. > > Thank you. > > On Tue, Sep 9, 2014 at 12:14 PM, Anastasia Yendiki <ayendiki(a)nmr.mgh.harvard.edu> wrote: > > Can you please attach the trac-all.log file, which has the entire output from beginning to end? > Ofter something goes wrong earlier that causes the program to fail later in the process. > > Also, we'll need your original configuration file. Thanks! > > On Mon, 8 Sep 2014, Katherine Damme wrote: > > Hello Freesurfer Community! > > Thank you Anastasia and Christopher, I am still getting ending with errors and the log > file gives no clue that I have been able to detect, see attached. > > Any help would be appreciated! > > > On Thu, Sep 4, 2014 at 4:29 PM, Anastasia Yendiki <ayendiki(a)nmr.mgh.harvard.edu> > wrote: > > Hi Kate - There is an example configuration file for tracula in your > freesurfer distribution ($FREESURFER_HOME/bin/dmrirc.example). The same > file is also here: > http://surfer.nmr.mgh.harvard.edu/fswiki/dmrirc > > If you attach your configuration file and the log file > (scripts/trac-all.log), we can try to troubleshoot. > > a.y > > On Wed, 3 Sep 2014, Katherine Damme wrote: > > > Hello Freesurfer Community! > > I have sucessfully completed diffusion preprocessing in FSL and the > > recon-all of the structural image and would like to use tracula for the > > tract reconstruction. I keep having trouble with my configuration file. > > > > Does anyone have a bedpostX tracula config file they could share as an > > example?H > > > > Thank you! > > > > Kate > > > > > _______________________________________________ > 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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tracula min mid max values
by Cat Chong 21 Nov '14

21 Nov '14

Dear Anastasia, I am trying to visualize the tract p-values along one pathway as shown in the tutorial.http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TraculaStatist… I have implemented the p-values into a text file but I am uncertain of what the settings for the heat scale thresholds ought to be , i.e. I am unsure of what to set the min, mid, max and offset values if I wish to visualize tract segments significant at < 0.05.Thank you very much for your help,cheers,Cat

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TRACULA preprocessing: bvector rotation, negative eigenvalues
by Barbara Kreilkamp 21 Nov '14

21 Nov '14

Dear Freesurfers, I am looking for information on how exactly the b-table gets rotated. 1. It seems that eddy_correct runs once with 12 doF, and then the bmatrix gets updated based on this registration. Would you please confirm? 2. I know that my data has negative eigenvalues (most of them seem to appear in the 'halo' around the images), and I would like to save L2, L3 voxel values within tracts in the pathstats.byvoxel.txt file. How may I edit dmri_pathstats to accommodate this? My aim is to identify MD, RD, FA, AD (L1) voxel values that were biased by a lot of noise. Thank you very much, Best, Barbara

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TRACULA dwi flipping
by Barbara Kreilkamp 21 Nov '14

21 Nov '14

Dear all, Would you please explain why TRACULA is flipping the data so often? And what does the flip4fsl command do? The data I have is already in the right (radiological) orientation. fslswapdim does not seem to have an effect either, as the parameters are just set to 'x y z'. Are these commands only effective if the data is not in radiological convention? Thank you, Barbara flip4fsl /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/bsplineT2bet_all_controls_patients/c3826/dmri/dwi_orig.nii.gz/Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/bsplineT2bet_all_controls_patients/c3826/dmri/dwi_orig_flip.nii.gz INFO: input image orientation is LAS INFO: input image determinant is -5.02198 fslswapdim /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/bsplineT2bet_all_controls_patients/c3826/dmri/dwi_orig.nii.gz x y z /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/bsplineT2bet_all_controls_patients/c3826/dmri/dwi_orig_flip.nii.gz fslorient -forceradiological /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/bsplineT2bet_all_controls_patients/c3826/dmri/dwi_orig_flip.nii.gz

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tracula failure
by Alena Piovar 21 Nov '14

21 Nov '14

Dear freesurfer experts, I am trying to run tracula but it fails on mri conversion of the data, it creates the nifty files from dicoms, but fails to produce bvec file where the problem could be? The terminal info as well as configuration file used for preprocessing is attached. Looking forward to your answer best regards Alena

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Freesurfer November 2014