Freesurfer

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30088 discussions

Crippled fiber tracts in healthy subjects (TRACULA)
by Ansgar Furst 27 Mar '12

27 Mar '12

Dear All, Please ignore my earlier incomplete message with the same title! We are using the ADNI Acc 3D FSPGR for structurals and a 30 directional (5 B0s) dual-spin repeat sequence for DTI (on a 3T GE 750 discovery) which so far rendered really nice results. However, recently I encountered data from several healthy young subjects where the TRACULA fiber tract estimations would suggest severely "crippled" tracts which, however, is not consistent with their FA maps. The crippling is most visible when comparing left vs right cingulate gyri. In some cases either the left or right side is almost completely gone. Has anyone else experienced similar issues and found a remedy? Thanks a lot, Ansgar

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Re: [Freesurfer] Error in fast_selxavg3 (line 254) XCond = cond(XtX);
by Douglas N Greve 27 Mar '12

27 Mar '12

FSFAST assumes that you do. A silly way around this is to just replicate your polar runs and call them eccen runs. doug On 03/27/2012 12:35 PM, Kiley Seymour wrote: > no I don't. > > On Tue, Mar 27, 2012 at 6:17 PM, Douglas N Greve > <greve(a)nmr.mgh.harvard.edu> wrote: >> Do you not have any eccen runs? >> doug >> >> On 03/27/2012 06:55 AM, Kiley Seymour wrote: >>> Dear Doug, >>> >>> I am aware I am becoming a regular pain. But I now encounter the >>> following problem when running selxavg3-sess -a rtopy.self.lh -s >>> CMRU1711. I have also attached my analysis.info and Xtmp.mat files >>> >>> Thanks for all of your suggestions. >>> >>> K >>> >>> #@# CMRU1711 ############################### >>> /media/sf_DATA1/RETINOTOPY/CMRU1711 >>> ------------------------- >>> $Id: fast_selxavg3.m,v 1.100 2011/03/02 16:14:38 greve Exp $ >>> /home/virtualuser/freesurfer/fsfast/toolbox/fast_selxavg3.m >>> /home/virtualuser/freesurfer/fsfast/toolbox/fast_ldanaflac.m >>> /home/virtualuser/freesurfer/matlab/MRIread.m >>> ------------------------- >>> outtop = /media/sf_DATA1/RETINOTOPY >>> Extension format = nii.gz >>> nruns = 3 >>> autostimdur = >>> >>> >>> outanadir = /media/sf_DATA1/RETINOTOPY/CMRU1711/bold/rtopy.self.lh >>> Found 138599/149490 (92.7) voxels in mask >>> Creating Design Matrix >>> ... creation time = 0.008 sec >>> DoMCFit = 1 >>> ntptot = 369, nX = 33, DOF = 336 >>> Saving X matrix to >>> /media/sf_DATA1/RETINOTOPY/CMRU1711/bold/rtopy.self.lh/Xtmp.mat >>> Error using svd >>> Input to SVD must not contain NaN or Inf. >>> >>> Error in cond (line 39) >>> s = svd(A); >>> >>> Error in fast_selxavg3 (line 254) >>> XCond = cond(XtX); >>> >>> >>> >>> >>> >>> >>> _______________________________________________ >>> 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html >> >> _______________________________________________ >> 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. >> > -- 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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trac-all -prep error
by Sarina Sacco 27 Mar '12

27 Mar '12

quando avvio il trac-all (relase FS5.1) mi crea questo errore: /opt/freesurfer/bin/trac-preproc #------------------------------------- #@# Image corrections Tue Mar 27 11:17:27 CEST 2012 mri_convert /opt/freesurfer/subjects/subjects_trac_all/Diff001_F.B./orig/1.2.840.113619.2.260.6945.224896.29441.1274773115.263.dcm /opt/freesurfer/subjects/subjects_trac_all/Diff001_F.B./dmri/dwi_orig.nii.gz mri_convert /opt/freesurfer/subjects/subjects_trac_all/Diff001_F.B./orig/1.2.840.113619.2.260.6945.224896.29441.1274773115.263.dcm /opt/freesurfer/subjects/subjects_trac_all/Diff001_F.B./dmri/dwi_orig.nii.gz $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from /opt/freesurfer/subjects/subjects_trac_all/Diff001_F.B./orig/1.2.840.113619.2.260.6945.224896.29441.1274773115.263.dcm... Starting DICOMRead2() dcmfile = /opt/freesurfer/subjects/subjects_trac_all/Diff001_F.B./orig/1.2.840.113619.2.260.6945.224896.29441.1274773115.263.dcm dcmdir = /opt/freesurfer/subjects/subjects_trac_all/Diff001_F.B./orig Ref Series No = 7 Found 2242 files, checking for dicoms Found 2240 dicom files in series. First Sorting Computing Slice Direction Vs: 0.029 0.321 1.9739 Vs: 0.0144997 0.160497 0.98693 Second Sorting Counting frames nframes = 28 nslices = 80 ndcmfiles = 2240 PE Dir = COL (dicom read) TransferSyntaxUID: --1.2.840.10008.1.2-- jpegUID: --1.2.840.10008.1.2.4-- Loading pixel data TR=10050.00, TE=87.10, TI=0.00, flip angle=90.00 i_ras = (-0.999859, -0.0058291, -0.0157782) j_ras = (0.00830111, -0.987041, -0.160255) k_ras = (-0.0144997, -0.160497, 0.98693) writing to /opt/freesurfer/subjects/subjects_trac_all/Diff001_F.B./dmri/dwi_orig.nii.gz... mri_probedicom --i /opt/freesurfer/subjects/subjects_trac_all/Diff001_F.B./orig/1.2.840.113619.2.260.6945.224896.29441.1274773115.263.dcm > /opt/freesurfer/subjects/subjects_trac_all/Diff001_F.B./dmri/dcminfo.dat flip4fsl /opt/freesurfer/subjects/subjects_trac_all/Diff001_F.B./dmri/dwi_orig.nii.gz /opt/freesurfer/subjects/subjects_trac_all/Diff001_F.B./dmri/dwi_orig_flip.nii.gz INFO: input image orientation is LPS INFO: input image determinant is 2 fslswapdim /opt/freesurfer/subjects/subjects_trac_all/Diff001_F.B./dmri/dwi_orig.nii.gz x -y z /opt/freesurfer/subjects/subjects_trac_all/Diff001_F.B./dmri/dwi_orig_flip.nii.gz fslorient -forceradiological /opt/freesurfer/subjects/subjects_trac_all/Diff001_F.B./dmri/dwi_orig_flip.nii.gz fslorient: Command not found. mv -f /opt/freesurfer/subjects/subjects_trac_all/Diff001_F.B./dmri/dwi_orig_flip.mghdti.bvecs /opt/freesurfer/subjects/subjects_trac_all/Diff001_F.B./dmri/bvecs mv: cannot stat `/opt/freesurfer/subjects/subjects_trac_all/Diff001_F.B./dmri/dwi_orig_flip.mghdti.bvecs': No such file or directory Linux thunder 2.6.38-8-generic #42-Ubuntu SMP Mon Apr 11 03:31:24 UTC 2011 x86_64 x86_64 x86_64 GNU/Linux trac-preproc exited with ERRORS at Tue Mar 27 11:18:21 CEST 2012 Non riesco a capire perchè,da cosa può dipendere?

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Re: [Freesurfer] volume mapping
by Johnson 27 Mar '12

27 Mar '12

OK T1 space is the space acquired from the machine, original anatomical space regards JG On 03/26/2012 2:25 PM, Bruce Fischl wrote: > can you post to the list so others can answer? And can you clarify > what you mean by "T1" space? > > On Mon, 26 Mar 2012, Johnson wrote: > >> Hi >> well, I had to transfer the fiber tracts coordinates from DWI space >> to T1 space, I used the b0 and the T1 for the registration process, I >> got the transformation matrix and applied it onto the tracts and they >> fit very well. >> Now I want to transform the tracts from T1 space to the freesurfer >> space, I need to know the transformation matrix that was used during >> the processing if it was saved in any of the logs >> thanks >> Johnson >> On 03/26/2012 2:09 PM, Bruce Fischl wrote: >>> Hi Johnson >>> >>> what T1 did you register to? Most of the ones we generate (T1.mgz, >>> brainmask.mgz, ...) are in a common coordinate system and you shouldn't >>> have to transform from one to another. >>> cheers >>> Bruce >>> >>> >>> On Mon, 26 Mar 2012, Johnson wrote: >>> >>>> Hi >>>> Let me re-phrase my question: >>>> I already did registration from DWI to T1, this step is OK. >>>> Now I want to go from T1 to FreeSurfer space (aparc+aseg.mgz file not >>>> the aparc+aseg-in-rawavg file). I know I have two choices: >>>> 1) do registration using bbregister >>>> 2) since Freesurfer during processing have already done this step, the >>>> transformation matrix is there somewhere, the question is where to >>>> find >>>> it? which log or which file? this choice is better since it is more >>>> accurate. >>>> >>>> Thanks >>>> JG >>>> >>>> On 03/26/2012 12:41 PM, Anastasia Yendiki wrote: >>>>> If you want to register your DWI to T1, you should register to >>>>> mri/brain.mgz. You can do this with bbregister, or with any affine >>>>> registration tool of your choice. >>>>> >>>>> On Mon, 26 Mar 2012, Johnson wrote: >>>>> >>>>>> Hi >>>>>> I found it in a 256x256x256 space while the T1 we use is in >>>>>> different >>>>>> space, I found this page on the registration step: >>>>>> http://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat >>>>>> I wish to know how this script work? >>>>>> >>>>>> mri_label2vol --seg aseg.mgz --temp rawavg.mgz --o >>>>>> aseg-in-rawavg.mgz >>>>>> --regheader aseg.mgz >>>>>> >>>>>> what is the transformation used ? >>>>>> JG >>>>>> >>>>>> >>>>>> On 03/26/2012 12:24 PM, Anastasia Yendiki wrote: >>>>>>> Hi Johnson - The aparc+aseg.mgz is in the same space as the T1 >>>>>>> used as >>>>>>> input to freesurfer. >>>>>>> >>>>>>> a.y >>>>>>> >>>>>>> On Mon, 26 Mar 2012, Johnson wrote: >>>>>>> >>>>>>>> Hi FS expert >>>>>>>> I need to know the transformation matrix itself since I will do >>>>>>> the> transformation in matlab. >>>>>>>> I successfully transformed white matter fibers coordinates to T1 >>>>>>> using> AIR 5.0 from LONI lab. >>>>>>>> They provide a transformation matrix. >>>>>>>> Now I want to transform the coordinates from T1 to Freesurfer >>>>>>> space, so >>>>>>>> my question is: what is the transformation matrix that relates >>>>>>> the T1 >>>>>>>> which FS have used for parcellation and segmentation with the> >>>>>>> aparc+aseg.mgz file? >>>>>>>> I searched the logs but couldn't find such matrix. >>>>>>>> I don't want to do a registration step since it will be less >>>>>>> accurate> than the one that was generated during the segmentation >>>>>>> process. >>>>>>>> Also is it just one transformation or a combination of >>>>>>> transformations? >>>>>>>>> thanks >>>>>>>>> >>>>>>> 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 >>> >> >> >> > -- Johnson J. GadElkarim Research Assistant, Department Of Psychiatry, PhD Candidate, Department Of Electrical& Computer Eng., University Of Illinois at Chicago Mob: 312 - 376 - 7322 Email: jgadel2(a)uic.edu

2 1

mkbrainmask-sess
by Kiley Seymour 27 Mar '12

27 Mar '12

Dear Freesurfers, I am currently trying to do some retinotopic mapping. I have been successful in running the reconstruction commands and setting everything up for the analysis, but I have run into problems when using the selxavg3-sess command. i.e. selxavg3-sess -a rtopy.self.lh -s IFEE2211 -no-preproc ( -no-preproc since I have co-registered and motion corrected my files in SPM). I was unable to run this command as freesurfer could not find /media/sf_DATA1/RETINOTOPY/IFEE2211/bold/001/global.meanval.dat So I ran mktemplate - sess, which was successfully completed. And then I ran mkbrainmask-sess (see below). Any help with this would be much appreciated. Thanks Kiley FreeSurfer:~/data1/RETINOTOPY> mkbrainmask-sess -s IFEE2211 -d ~/data1/RETINOTOPY ------------------------------------------------ /media/sf_DATA1/RETINOTOPY/IFEE2211 Fri Mar 23 09:42:26 EDT 2012 mkbrainmask -i template.nii.gz -o masks/brain.nii.gz -thresh 0.1 -ndil 1 -nerode 0 FSLMATHSfslmaths.fsl Scratch Dir is /tmp/mkbrainmask_7930 /media/sf_DATA1/RETINOTOPY/IFEE2211/bold mri_convert template.nii.gz /tmp/mkbrainmask_7930/in.nii mri_convert template.nii.gz /tmp/mkbrainmask_7930/in.nii $Id: mri_convert.c,v 1.179.2.1 2011/03/22 16:37:02 nicks Exp $ reading from template.nii.gz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.998558, -0.0534653, -0.00482299) j_ras = (-0.0536701, 0.992375, 0.110955) k_ras = (0.00114604, -0.111054, 0.993814) writing to /tmp/mkbrainmask_7930/in.nii... # ---------- Using FSL's BET to Extract Brain------------------ # /media/sf_DATA1/RETINOTOPY/IFEE2211/bold bet.fsl /tmp/mkbrainmask_7930/in.nii /tmp/mkbrainmask_7930/brain -m -f 0.1 /home/virtualuser/freesurfer/bin/bet.fsl: 150: /bin/remove_ext: not found /home/virtualuser/freesurfer/bin/bet.fsl: 151: /bin/remove_ext: not found /home/virtualuser/freesurfer/bin/bet.fsl: 158: /bin/imtest: not found [: 158: =: unexpected operator /home/virtualuser/freesurfer/bin/bet.fsl: 380: /bin/bet2: not found mri_binarize --i /tmp/mkbrainmask_7930/brain_mask.nii --min .01 --o /tmp/mkbrainmask_7930/brain_mask.nii niiRead(): error opening file /tmp/mkbrainmask_7930/brain_mask.nii $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /media/sf_DATA1/RETINOTOPY/IFEE2211/bold cmdlinemri_binarize --i /tmp/mkbrainmask_7930/brain_mask.nii --min .01 --o /tmp/mkbrainmask_7930/brain_mask.nii sysname Linux hostnameFreeSurfer machine i686 user virtualuser input /tmp/mkbrainmask_7930/brain_mask.nii frame 0 nErode3d 0 nErode2d 0 output /tmp/mkbrainmask_7930/brain_mask.nii Binarizing based on threshold min 0.01 max +infinity binval 1 binvalnot 0

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Failure to convert DICOM files
by Ed Gronenschild 27 Mar '12

27 Mar '12

Hi, I got an error during the first step in recon-all (Mac OS 10.6.8, FreeSurfer v5.1.0). The eror message in the log file is: WARNING: file ...../MR.1.3.12.2.1107.5.2.18.41016.201008031106017688438785.dcm does not contain a Siemens ASCII header has this file been anonymized? ERROR: cannot unpack mosiacs without ASCII header. This is strange because it is no mosaic file and all the files can be converted without any problems with e.g., dcm2nii and viewed with OSIRIX. Cheers, Ed

2 1

Displaying FSL zstats onto FreeSurfer
by Zurcher Nicole 27 Mar '12

27 Mar '12

Hi everyone, I have two questions regarding FreeSurfer and FSL interoperation and it would be great if someone could help. 1) When displaying subject-level FSL FEAT data onto the FS volume using the command "tkmedit blobby orig.mgz lh.white -overlay ./featdir/stats/zstat1.nii.gz -overlay-reg featdir/reg/freesurfer/anat2exf.register.dat fthresh 1.3 -fmid 2.3 -fslope 1” (mentioned on http://www.fmrib.ox.ac.uk/fsl/freesurfer/index.html) What p-value does the threshold of 1.3 correspond to? Is it a zscore? 2) What would be the best way to display FSL group-level FEAT data (zstats) onto the FreeSurfer surface? As far as I understand, the FSL and FreeSurfer Interoperation website explains how to display subject level-feat on the surface. For the group-level data, it only explains how to run group-level analyses using mri_glmfit based on lower-level FSL FEAT directories. Is there a way to directly map the zstats from FSL group-level analyses onto the FreeSurfer surface? Thanks in advance for the help! Nicole

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amount of manual corrections in 5.1 related to aparc+aseg?
by Dorit Kliemann 27 Mar '12

27 Mar '12

Dear FreeSurfers, I'm working on a structural dataset and after running recon-all -all, I had to correct all cases (32 so far) from minimum pial/wm corrections to massive pial corrections (only three cases needed control points). Mostly, the corrections were needed due to remaining dura/skull. Initially, I tried to adjust the skull-stripping (either with changing the wsthresh or gcut for individual cases), however, those corrections were not always too successful (i.e. still remaining dura/skull), so I continued correcting manually. Are there any known/expected problems that could still arise with the aparc+aseg segmentations after (massive) corrections (i.e. all cases), even after redoing respective recon-steps with version 5.1? In the release notes, I only found that control points may adversely affect aseg... I checked the segmentations and so far I couldn't recognize any obvious/consistent flaws. I remember from working with version 4.1. that most cases need at least some corrections, but I don't have any experience with 5.1, yet. I'm specifically interested in the amygdala, but of course amygdala segmentations will be corrected manually. Thanks, Dorit Data were acquired on a 3T Tim Trio dataset (32 channel-coil, TR 1900ms, TE 2.52 ms, 1x1x1 voxel-size, TI 900ms, flip angle 9, ipad grappa2, bandwidth 170Hz/pixel, prescan-normalize). Data were initially processed with recon-all -all with version 5.1 on a linux cluster (scientific linux 6.1). Data were corrected and then re-run with respective recon-steps on a local Mac (OS 10.5.8) with freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0.

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Re: [Freesurfer] Failure to convert DICOM files
by Ed Gronenschild 27 Mar '12

27 Mar '12

Hi Jamaan, Yes, I got the same error. Ed On 27 Mar 2012, at 13:36, Jamaan Alghamdi wrote: > Hi Ed, > > Have you tried using mri_convert command directly without running recon-all. > > Best wishes, > Jamaan > > Hi, > > I got an error during the first step in recon-all (Mac OS 10.6.8, > FreeSurfer v5.1.0). The eror message in the log file is: > > WARNING: file ...../MR.1.3.12.2.1107.5.2.18.41016.201008031106017688438785.dcm does not contain a Siemens ASCII header > has this file been anonymized? > ERROR: cannot unpack mosiacs without ASCII header. > > This is strange because it is no mosaic file and all the files can be converted > without any problems with e.g., dcm2nii and viewed with OSIRIX. > > Cheers, > Ed > > -- > Jamaan Alghamdi > 07779801950 > 0151 795 4627 > Magnetic Resonance & Image Analysis Research Centre (MARIARC) > University of Liverpool > Pembroke place > Liverpool > L69 3GE > > http://www.easyneuroimaging.com/ >

1 0

-mprage flags
by Sabin Khadka 26 Mar '12

26 Mar '12

Hi all, What does -washu_mprage and -mprage flags do in autorecon step. How does it help in segmentation? -SK

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