Thanks Anastasia! You seemed to have caught the issue. the dtifit files were mistakenly generated from the anisotropic preprocessed image. I will ensure the same voxel dimensions among all inputs and re-run. Will let you know if that doesn't fix it!
All the best, Derek On Tue, Jan 17, 2017 at 10:31 AM, Yendiki, Anastasia < ayend...@mgh.harvard.edu> wrote: > Hi Derek - There's an inconsistency among the output volumes that are > supposed to be in diffusion space; some have 2mm iso resolution and some > have .9x.9x3mm. From the logs it looks like you reran some of the > pre-processing steps separately. If you ran some before resampling and some > after, this may be causing the mix-up. I would just start from scratch in a > new subject directory and see if that fixes it. > > Best, > a.y > > ------------------------------ > *From:* freesurfer-boun...@nmr.mgh.harvard.edu [ > freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Derek A Pisner [ > dpis...@utexas.edu] > *Sent:* Sunday, January 15, 2017 3:01 PM > > *To:* Freesurfer support list > *Subject:* Re: [Freesurfer] TRACULA in FreeSurfer 6.0 trac-paths error > > Uploaded: > > https://gate.nmr.mgh.harvard.edu/filedrop2/index.php?p=6cwuw1zwaag > > Also, I've included a dwi_TRfixed.nii.gz file with the TR in the header > fixed. Curious to see if that one works! > > mri_convert --in_type nii --out_type nii --out_orientation RAS dwi.nii.gz > -tr 1000 dwi_TRfixed.nii.gz > > On Sun, Jan 15, 2017 at 1:44 PM, Yendiki, Anastasia < > ayend...@mgh.harvard.edu> wrote: > >> Hi Derek - It looks like it fails, but I suspect that it may be something >> unrelated to the warning. Can you please upload a zip file with this >> subject's TRACULA directories (dmri, dmri.bedpostX, dlabel, dpath, scripts) >> for me here: >> >> https://gate.nmr.mgh.harvard.edu/filedrop2/ >> >> Thanks! >> >> a.y >> >> ------------------------------ >> *From:* freesurfer-boun...@nmr.mgh.harvard.edu [ >> freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Derek A Pisner [ >> dpis...@utexas.edu] >> *Sent:* Sunday, January 15, 2017 2:36 PM >> *To:* Freesurfer support list >> >> *Subject:* Re: [Freesurfer] TRACULA in FreeSurfer 6.0 trac-paths error >> >> Hi Anastasia, >> >> >> >> See attached log. Hard to tell, but it does seem that trac-all fails >> after this warning. >> >> >> >> Thanks for taking a look! >> >> >> >> Derek Pisner >> >> Doctoral Student >> >> CLA 4.600 >> >> Mood Disorders Laboratory (MDL) >> >> Department of Psychology | The University of Texas at Austin >> >> >> >> On Sun, Jan 15, 2017 at 1:27 PM, Yendiki, Anastasia < >> ayend...@mgh.harvard.edu> wrote: >> >>> Hi Derek - It sounds like the programs that you used to convert from >>> dicom to nifti and to resample from anisotropic nifti to isotropic nifti >>> don't copy the TE and TR info in the header correctly. This information is >>> not needed to run -paths, however. Does trac-all stop running after this >>> warning, or does it keep going? Can you attach your entire trac-all.log >>> file? Thanks! >>> >>> a.y >>> >>> ------------------------------ >>> *From:* freesurfer-boun...@nmr.mgh.harvard.edu [ >>> freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Derek A Pisner [ >>> dpis...@utexas.edu] >>> *Sent:* Sunday, January 15, 2017 11:47 AM >>> *To:* freesurfer@nmr.mgh.harvard.edu >>> *Subject:* Re: [Freesurfer] TRACULA in FreeSurfer 6.0 trac-paths error >>> >>> Hi Anastasia, >>> >>> Thanks for the quick response! >>> >>> The TE and the TR are both listed as 0.00 with mri_info. Of note, these >>> dwi images have been resampled from anisotropic to isotropic voxels using >>> an in-house python script. I noticed that this error comes up only for the >>> resampled, but not the original image. I am guessing this is the underlying >>> source of the problem and has less to do with trac-all. What does trac-all >>> need from the header to successfully run -paths? How can the header be >>> corrected in freesurfer so that it will run successfully? Strangely, the TE >>> also comes up as being equal to 0 in the original, anisotropic, image... >>> The TR is what appears to be different and perhaps that is the source of >>> the niiRead() warning? See below. >>> >>> Many Thanks, >>> >>> Derek >>> >>> *vlogin03.ls5(69)$ *mri_info dwi.nii.gz >>> >>> niiRead(): NIFTI_UNITS_UNKNOWN, assuming mm >>> >>> WARNING: niiRead(): unknown time units 0 in >>> /work/04171/dpisner/data/ABM/TRACULA/tractography_output/s00 >>> 2/dmri/dwi.nii.gz >>> >>> Volume information for dwi.nii.gz >>> >>> type: nii >>> >>> dimensions: 115 x 115 x 56 x 55 >>> >>> voxel sizes: 2.000000, 2.000000, 2.000000 >>> >>> type: FLOAT (3) >>> >>> fov: 230.000 >>> >>> dof: 0 >>> >>> xstart: -115.0, xend: 115.0 >>> >>> ystart: -115.0, yend: 115.0 >>> >>> zstart: -56.0, zend: 56.0 >>> >>> * TR: 0.00 msec, TE: 0.00 msec,* TI: 0.00 msec, flip angle: >>> 0.00 degrees >>> >>> nframes: 55 >>> >>> PhEncDir: UNKNOWN >>> >>> FieldStrength: 0.000000 >>> >>> ras xform present >>> >>> xform info: x_r = -1.0000, y_r = 0.0000, z_r = 0.0000, c_r = >>> -0.4490 >>> >>> : x_a = 0.0000, y_a = 1.0000, z_a = 0.0000, c_a = >>> 40.5440 >>> >>> : x_s = 0.0000, y_s = 0.0000, z_s = 1.0000, c_s = >>> 55.0398 >>> >>> Orientation : LAS >>> >>> Primary Slice Direction: axial >>> >>> >>> voxel to ras transform: >>> >>> -2.0000 0.0000 0.0000 114.5510 >>> >>> 0.0000 2.0000 0.0000 -74.4560 >>> >>> 0.0000 0.0000 2.0000 -0.9602 >>> >>> 0.0000 0.0000 0.0000 1.0000 >>> >>> >>> voxel-to-ras determinant -8 >>> >>> >>> ras to voxel transform: >>> >>> -0.5000 -0.0000 -0.0000 57.2755 >>> >>> -0.0000 0.5000 -0.0000 37.2280 >>> >>> -0.0000 -0.0000 0.5000 0.4801 >>> >>> -0.0000 -0.0000 -0.0000 1.0000 >>> >>> >>> *vlogin03.ls5(84)$ *mri_info aniso_eddy_corrected_data_denoised.nii.gz >>> >>> Volume information for eddy_corrected_data_denoised.nii.gz >>> >>> type: nii >>> >>> dimensions: 256 x 256 x 37 x 55 >>> >>> voxel sizes: 0.898400, 0.898400, 3.000002 >>> >>> type: FLOAT (3) >>> >>> fov: 229.990 >>> >>> dof: 0 >>> >>> xstart: -115.0, xend: 115.0 >>> >>> ystart: -115.0, yend: 115.0 >>> >>> zstart: -55.5, zend: 55.5 >>> >>> * TR: 1000.00 msec, TE: 0.00 msec,* TI: 0.00 msec, flip >>> angle: 0.00 degrees >>> >>> Yendiki, Anastasia >>> <https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=from:%22Yendiki%2C+Anastasia%22> >>> Fri, 13 Jan 2017 07:12:39 -0800 >>> <https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=date:20170113> >>> >>> Hi Derek - Thanks for testing the 6.0 release candidate. Does it keep >>> running >>> after this message? Since this is a warning and not an error, it may not be >>> critical. If you run mri_info on your dwi.nii.gz, does the TE show up as >>> zero? >>> >>> Best, >>> a.y >>> >>> >>> >>> On Thu, Jan 12, 2017 at 9:06 PM, Derek A Pisner <dpis...@utexas.edu> >>> wrote: >>> >>>> Hi Anastasia, >>>> >>>> I am getting the following error when running trac-all –paths on all of >>>> my diffusion images using the newly updated TRACULA: >>>> >>>> *vlogin03.ls5(97)$* /work/04171/dpisner/stampede/A >>>> pplications/freesurfer/bin/trac-all -no-isrunning -path -c >>>> /work/04171/dpisner/data/ABM/TRACULA/tractography_output/s00 >>>> 2/trac_config.txt >>>> >>>> niiRead(): NIFTI_UNITS_UNKNOWN, assuming mm >>>> >>>> WARNING: niiRead(): unknown time units 0 in >>>> /work/04171/dpisner/data/ABM/TRACULA/tractography_output/s00 >>>> 2/dmri/dwi.nii.gz >>>> >>>> >>>> >>>> Any idea what’s going on here? >>>> >>>> >>>> >>>> Thanks as always, >>>> >>>> >>>> >>>> Derek Pisner >>>> >>>> Doctoral Student >>>> >>>> CLA 4.600 >>>> >>>> Mood Disorders Laboratory (MDL) >>>> >>>> Department of Psychology | The University of Texas at Austin >>>> >>>> >>>> >>>> P.S. Here is the header information on my dwi.nii.gz file: >>>> >>>> *vlogin03.ls5(105)$* fslhd dwi.nii.gz >>>> >>>> filename dwi.nii.gz >>>> >>>> sizeof_hdr 348 >>>> >>>> data_type FLOAT32 >>>> >>>> dim0 4 >>>> >>>> dim1 115 >>>> >>>> dim2 115 >>>> >>>> dim3 56 >>>> >>>> dim4 55 >>>> >>>> dim5 1 >>>> >>>> dim6 1 >>>> >>>> dim7 1 >>>> >>>> vox_units Unknown >>>> >>>> time_units Unknown >>>> >>>> datatype 16 >>>> >>>> nbyper 4 >>>> >>>> bitpix 32 >>>> >>>> pixdim0 0.000000 >>>> >>>> pixdim1 2.000000 >>>> >>>> pixdim2 2.000000 >>>> >>>> pixdim3 2.000000 >>>> >>>> pixdim4 1.000000 >>>> >>>> pixdim5 1.000000 >>>> >>>> pixdim6 1.000000 >>>> >>>> pixdim7 1.000000 >>>> >>>> vox_offset 352 >>>> >>>> cal_max 0.0000 >>>> >>>> cal_min 0.0000 >>>> >>>> scl_slope 1.000000 >>>> >>>> scl_inter 0.000000 >>>> >>>> phase_dim 0 >>>> >>>> freq_dim 0 >>>> >>>> slice_dim 0 >>>> >>>> slice_name Unknown >>>> >>>> slice_code 0 >>>> >>>> slice_start 0 >>>> >>>> slice_end 0 >>>> >>>> slice_duration 0.000000 >>>> >>>> time_offset 0.000000 >>>> >>>> intent Unknown >>>> >>>> intent_code 0 >>>> >>>> intent_name >>>> >>>> intent_p1 0.000000 >>>> >>>> intent_p2 0.000000 >>>> >>>> intent_p3 0.000000 >>>> >>>> qform_name Unknown >>>> >>>> qform_code 0 >>>> >>>> qto_xyz:1 2.000000 0.000000 0.000000 0.000000 >>>> >>>> qto_xyz:2 0.000000 2.000000 0.000000 0.000000 >>>> >>>> qto_xyz:3 0.000000 0.000000 2.000000 0.000000 >>>> >>>> qto_xyz:4 0.000000 0.000000 0.000000 1.000000 >>>> >>>> qform_xorient Left-to-Right >>>> >>>> qform_yorient Posterior-to-Anterior >>>> >>>> qform_zorient Inferior-to-Superior >>>> >>>> sform_name Aligned Anat >>>> >>>> sform_code 2 >>>> >>>> sto_xyz:1 -2.000000 0.000000 0.000000 114.551003 >>>> >>>> sto_xyz:2 0.000000 2.000000 0.000000 -74.456001 >>>> >>>> sto_xyz:3 0.000000 0.000000 2.000000 -0.960182 >>>> >>>> sto_xyz:4 0.000000 0.000000 0.000000 1.000000 >>>> >>>> sform_xorient Right-to-Left >>>> >>>> sform_yorient Posterior-to-Anterior >>>> >>>> sform_zorient Inferior-to-Superior >>>> >>>> file_type NIFTI-1+ >>>> >>>> file_code 1 >>>> >>>> descrip >>>> >>>> aux_file >>>> >>>> -- >>>> Derek Pisner >>>> >>> >>> >>> >>> -- >>> Derek Pisner >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@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. >>> >>> >> >> >> -- >> Derek Pisner >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@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. >> >> > > > -- > Derek Pisner > > _______________________________________________ > Freesurfer mailing list > Freesurfer@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. > > -- Derek Pisner
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