Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30099 discussions

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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Linear Mixed Effects Models
by franziska baier 21 Nov '14

21 Nov '14

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Re: [Freesurfer] Odd thing about mris_convert? Position changed from freesurfer format to .stl
by ting xu 21 Nov '14

21 Nov '14

Hi Bruce, Thank you for your reply! Would you please give me a hint how does it work, save ras2vox or ras xform into to FS surface file? I searched the archive, googled, did not figure out yet. All the function such as read_susrf.m and write_surf.m only deal with coordinates and faces information. Thank you! Ting On Fri, Nov 21, 2014 05:21 Hi Ting STL may not contain the info for ras2vox transform as it is not a medicalimaging format. We've only supported it in the past for 3D printing and such. You might need to keep track of the ras2vox and restore it when you convert back (e.g. in matlab) cheers Bruce On Fri, Nov 21, 2014 at 12:18 AM, ting xu <xutingxt(a)gmail.com> wrote: > Hi there, > > In my understanding, mris_convert does not change any information > (vertices coordinates and triangles) during converting, right? However, I > observed odd thing as bellow, > > Command I used:* mris_convert subjid/surf/lh.white > subjid/surf/lh.white.stl* > > I convert the white surface to .stl format, then load original white > surface and .stl file in freeview, with subjid/mri/brainmask.mgz as volume > underlay. The shape of lh.white.stl mesh looks the same as original one, > but the position of lh.white.stl was displaced. I attached a screenshot > (yellow one is original white surface, red one is .stl format one). > > I also used freesurfer_read_surf function to read the coordinates and the > faces in matlab, then compare it to .stl coordinate, they are the same. > > I need to use .stl format for my analysis outside freesurfer, then convert > result back to freesurfer format. I am worried whether this would cause any > problems? > > PS, if it is fsaverage template surface, no position shift after format > transform. > > Many thanks if anyone help with this, > > Ting > > >

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qdec and recon-all crashes
by Jon Alan Wieser 21 Nov '14

21 Nov '14

hi freesurfer folks, when I try to run qdec or recon-all, they crash recon-all -s MJ0001 -qcache if: Expression Syntax. qdec cd: Too many arguments. we have determined that because the subjects_directory name has spaces and ()'s in it, it is causing the two programs to crash echo $SUBJECTS_DIR /Users/wieser/Dropbox (UWM BraIN Lab)/ImagingSuite/Blackbird/MJMRI/MJ0001 I know that linux doesn't like spaces and ()'s in the directory name, and I usually avoid them, but we have recently started using dropbox to backup our data, in Dropbox is causing the spaces and ()'s to be in the directory name. Is there any way to make recon-all and qdec run in directories that have these characters in the directory name thanks Jon

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repost: recon-all failure due to header
by Ashley Stillman 21 Nov '14

21 Nov '14

Hi Freesurfer team, Any ideas for the below issue we are having? We are having issues running recon-all on our dicom files, as they are saved as a mosaic. When we open the original dicom file (attached) it lists out the rows, columns and slices. However, when we run mriparsesdcmdir, it just posts 0’s for the rows and columns (screen shot attached). We are able to recreate the output file necessary to run recon-all (basically fill in the missing 0’s). Is there a way to tell recon-all to call on this file to retrieve the missing data manually? Thank you, Ashley Ashley N. Stillman Clinical Psychology Graduate Research Assistant University of Tulsa, T.R.A.P.T. Lab Laureate Institute for Brain Research email: anstillman(a)laureateinstitute.org<mailto:anstillman@laureateinstitute.org> | ashley-stillman(a)utulsa.edu<mailto:ashley-stillman@utulsa.edu>

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Odd thing about mris_convert? Position changed from freesurfer format to .stl
by ting xu 21 Nov '14

21 Nov '14

Hi there, In my understanding, mris_convert does not change any information (vertices coordinates and triangles) during converting, right? However, I observed odd thing as bellow, Command I used:* mris_convert subjid/surf/lh.white subjid/surf/lh.white.stl* I convert the white surface to .stl format, then load original white surface and .stl file in freeview, with subjid/mri/brainmask.mgz as volume underlay. The shape of lh.white.stl mesh looks the same as original one, but the position of lh.white.stl was displaced. I attached a screenshot (yellow one is original white surface, red one is .stl format one). I also used freesurfer_read_surf function to read the coordinates and the faces in matlab, then compare it to .stl coordinate, they are the same. I need to use .stl format for my analysis outside freesurfer, then convert result back to freesurfer format. I am worried whether this would cause any problems? PS, if it is fsaverage template surface, no position shift after format transform. Many thanks if anyone help with this, Ting

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