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30088 discussions

FWHM smoothing for surface based
by Charlotte Bernard 18 Apr '12

18 Apr '12

Dear Freesurfer users, I would like to know what is the level of smooth recommanded to use for surface-based group analysis? Thank you, All the best, Charlotte

3 2

Segmentation
by Jordan Pierce 18 Apr '12

18 Apr '12

Hi, We're trying to edit the aseg segmentation and reconstruct it. If we run 'recon-all -s subject -make all' does that depend on any information from the surfaces or brainmask volume, or are the stats independent of that? Thank you, Jordan Pierce Graduate Student Behavioral and Brain Sciences Program Psychology Department The University of Georgia

4 6

Mapping of fsaverage surface to native volume
by René Besseling 18 Apr '12

18 Apr '12

That gives the same scattered appearance as before, see attachment. So I guess it's not a viewer issue. Maybe something to do with missing header information of the original T1 scan? By the way: strange that the overlay contains so many zeros; one would expect (transparent) NaNs... Best regards, Rene On Thu, Apr 12, 2012 at 7:38 PM, Douglas N Greve <greve(a)nmr.mgh.harvard.edu>wrote: > Try loading it in tkmedit, something like: > > tkmedit sub01 orig.mgz -overlay sig_2subj01_volumetric.nii > > doug > > > On 04/12/2012 03:46 AM, René Besseling wrote: > >> Hi Doug, >> >> Sorry, missed your reply. I assumed the --identity argument was used for >> looking up the surface-to-volume mapping somewhere in the predefined folder >> structure of this subject. Anyhow, my last command was >> mri_surf2vol --surfval sig_2subj01.mgh --hemi rh --fillribbon --identity >> sub01 --template subj01/mri/orig.mgz --o sig_2subj01_volumetric.nii >> so I guess no transformation is needed since the surface is already in >> the proper space (that of subj01). >> About my tkmedit command: I'm not using that. I usually visualize my >> results in Matlab, for the pics I send I used Freeview and tksurfer (so >> commands such as "mrview T1.mgz" and "tksurfer fsaverage lh inflated") >> Best regards, >> René >> >> >> 2012/4/5 Douglas N Greve <greve(a)nmr.mgh.harvard.edu <mailto: >> greve(a)nmr.mgh.harvard.**edu <greve(a)nmr.mgh.harvard.edu>>> >> >> >> The template specifies the output geometry. When you specify >> --identity, you specify a particular transformation between the >> volume and the surface, so you can't change the target volume >> without specifying a different transform. I'm at a bit of a loss >> as to why this is not working. What is your tkmedit command? >> doug >> >> >> On 04/05/2012 06:04 AM, René Besseling wrote: >> >> Hi Doug, >> >> I'm using tksurfer to visualize the surface maps; this looks >> OK for both the original map overlaid on fsaverage and the >> mapped surface (generated using mri_surf2surf) overlaid on >> subj01. The mapping from surface to cortical ribbon also works >> well for fsaverage but goes haywire for subj01, see pics in >> attachment. >> >> I noticed that mri_surf2vol gives different results when using >> different --template volumes. Why is that? I assumed that the >> --template image essentially provides the range of voxel >> coordinates to which the surface values can be mapped. In >> other words: when providing a template with a bigger field of >> view, I'd expect the center of the resulting output to look >> the same as the output generating when using a small FOV >> template. Does it matter whether you write your output as .mgz >> or .nii? >> >> Best regards, >> >> Rene >> >> On Wed, Apr 4, 2012 at 10:42 PM, Douglas N Greve >> <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu> >> > >> <mailto:greve@nmr.mgh.harvard.**edu <greve(a)nmr.mgh.harvard.edu> >> >> <mailto:greve@nmr.mgh.harvard.**edu <greve(a)nmr.mgh.harvard.edu>>>> >> wrote: >> >> How are you visualizing the results? Can you send a pic? >> You should be >> using tkmedit. >> doug >> >> On 04/04/2012 09:59 AM, René Besseling wrote: >> > Dear Freesurfer users, >> > >> > I've been trying to map a Qdec contrast sig.mgh to the >> native volume >> > of a subject using mri_surf2surf (to get from Qdec fsaverage >> surface >> > to native surface) and mri_surf2vol (to map from native >> surface to >> > native volume cortical ribbon). However, the last step goes >> wrong: I >> > get a nii with the same range of values as were in the >> surface, but >> > the nonzero voxels are scattered all over, so I guess there is >> > something wrong with the surface-to-voxel coordinate mapping. >> Below is >> > my code, any ideas on what goes wrong? >> > >> > Best regards, >> > >> > Rene >> > >> > mri_surf2surf --hemi rh --srcsubject fsaverage --noreshape >> --sval >> > sig.mgh --trgsubject subj01 --tval sig_2subj01.mgh >> > >> > mri_surf2vol --surfval sig_2subj01.mgh --hemi rh --fillribbon >> > --identity sub01 --template subj01/mri/orig.mgz --o >> > sig_2subj01_volumetric.nii >> > >> > >> > ______________________________**_________________ >> > Freesurfer mailing list >> > Freesurfer(a)nmr.mgh.harvard.edu >> <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer(a)nmr.mgh.harvard.edu> >> > >> <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer(a)nmr.mgh.harvard.edu> >> >> <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer(a)nmr.mgh.harvard.edu> >> >> >> >> > https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> >> >> -- >> Douglas N. Greve, Ph.D. >> MGH-NMR Center >> greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu> >> > >> <mailto:greve@nmr.mgh.harvard.**edu <greve(a)nmr.mgh.harvard.edu> >> >> <mailto:greve@nmr.mgh.harvard.**edu <greve(a)nmr.mgh.harvard.edu>>> >> Phone Number: 617-724-2358 <tel:617-724-2358> >> <tel:617-724-2358 <tel:617-724-2358>> >> Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 >> >> <tel:617-726-7422>> >> >> Bugs: surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >> <http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >> > >> <http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >> > >> FileDrop: >> www.nmr.mgh.harvard.edu/**facility/filedrop/index.html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >> <http://www.nmr.mgh.harvard.**edu/facility/filedrop/index.**html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >> > >> <http://www.nmr.mgh.harvard.**edu/facility/filedrop/index.**html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >> > >> >> ______________________________**_________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer(a)nmr.mgh.harvard.edu> >> > >> <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer(a)nmr.mgh.harvard.edu> >> >> <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer(a)nmr.mgh.harvard.edu> >> >> >> >> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer<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<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 <mailto:greve@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu> >> > >> Phone Number: 617-724-2358 <tel:617-724-2358> >> Fax: 617-726-7422 <tel:617-726-7422> >> >> Bugs: surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >> <http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >> > >> FileDrop: www.nmr.mgh.harvard.edu/**facility/filedrop/index.html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >> <http://www.nmr.mgh.harvard.**edu/facility/filedrop/index.**html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >> > >> >> >> > -- > 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<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: www.nmr.mgh.harvard.edu/**facility/filedrop/index.html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > >

2 2

mri_robust_template
by Arman Eshaghi 17 Apr '12

17 Apr '12

Hi, I have bias-corrected and co-registered longitudinal images, and I'm interested to use Freesurfer to construct unbiased within-subject templates (to be used in SPM). Using mri_roubust_template, I get the following error message on some (not all) of the subjects. I was wondering whether I could use options/flags to avoid this. -------------------------------------------------------- ERROR: All entries are zero! Images do not overlap (anymore?). This can have several reasons (i.e. different modalities, different intensity scales, large non-linearities, too diff. voxel sizes ...) Maybe use --transform <init.lta> with an approx. alignment obtained from tkregister or another registration program. Or do some prior intensity correction? -------------------------------------------------------- All the best, Arman

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request for dicom sequences on phantoms
by Satrajit Ghosh 17 Apr '12

17 Apr '12

howdy brain imagers, we are trying to put together a vocabulary of DICOM terms and their definitions related to brain imaging. unfortunately, a lot of the useful info is often in private tags and these differ from sequence to sequence and from scanner to scanner. to help us get at these tags, this is a shout out to folks to see if they can make available a DICOM dataset (***without anonymizing***) collected using their favorite current sequences on a phantom (no worries about privacy - or so i hope). for time series/gradient direction sequences a couple of volumes will do. we are interested in the DICOM header only not the content of the images. if you have such images or are willing to acquire them, please send me an email *off the list* at: satra(a)mit.edu and i will point you to an appropriate location and method to upload your DICOM data. cheers, satra ps. please do not reply all as you may not have post permissions on all the lists.

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Help data check: problem with neck and skull stripping
by Charlotte Bernard 17 Apr '12

17 Apr '12

From: chakeba(a)live.fr To: freesurfer(a)nmr.mgh.harvard.edu Subject: Date: Tue, 17 Apr 2012 15:50:11 +0200 Dear Freesurfer users, I have a question about data check. In my sample, the most of my subjects have lot of neck or a bad skull stripping. I give you three examples. Is it acceptable for analysis? I will really help me, Thanks for all, charlotte

2 1

Re: [Freesurfer] trac-all -prep error
by Anastasia Yendiki 17 Apr '12

17 Apr '12

Hi Sarina - You'll have to specify the list of gradient directions (bvecfile) and b-values (bvalfile), see here for more info: http://surfer.nmr.mgh.harvard.edu/fswiki/dmrirc Please send email to the freesurfer list and not to me directly. Emails sent to the freesurfer list are saved in a searchable archive so that other users can benefit from these pearls of wisdom. http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/ a.y On Wed, 11 Apr 2012, Sarina Sacco wrote: > Ciao Anastasia ho risolto il problema di FSL,ora l'installazione è > corretta,però mi si presenta sempre un errore inerente al bvecs non li > trova,potrebbe forse dipendere dai files DICOM che utilizzo? > Questo è l'errore: > sarina@thunder:/opt/freesurfer/subjects$ trac-all -prep -c > $SUBJECTS_DIR/subjects_trac_all/scripts/dmrircFiles/dmrirc_Diff001_F.B. > INFO: SUBJECTS_DIR is /opt/freesurfer/subjects/subjects_recon_all > INFO: Diffusion root is /opt/freesurfer/subjects/subjects_trac_all > Actual FREESURFER_HOME /opt/freesurfer > trac-preproc -c > /opt/freesurfer/subjects/subjects_trac_all/Diff001_F.B./scripts/dmrirc.local > -log /opt/freesurfer/subjects/subjects_trac_all/Diff001_F.B./scripts/trac-all.log > -cmd /opt/freesurfer/subjects/subjects_trac_all/Diff001_F.B./scripts/trac-all.cmd > #------------------------------------- > /opt/freesurfer/bin/trac-preproc > #------------------------------------- > #@# Image corrections Wed Apr 11 18:01:15 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 > INFO: left-right orientation was flipped by fslswapdim > fslorient -forceradiological > /opt/freesurfer/subjects/subjects_trac_all/Diff001_F.B./dmri/dwi_orig_flip.nii.gz > 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 Wed Apr 11 18:03:33 CEST 2012 > > > 2012/3/27 Anastasia Yendiki <ayendiki(a)nmr.mgh.harvard.edu>: >> >> Ciao Sarina - The problem is here "fslorient: Command not found." You have >> to make sure that FSL is properly installed and the FSL executables are in >> your path, as trac-all calls a few of them. >> >> Hope this helps, >> a.y >> >> >> On Tue, 27 Mar 2012, Sarina Sacco wrote: >> >>> 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? >>> >>> _______________________________________________ >>> 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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Re: [Freesurfer] trakula segmentation fault
by Viviana Siless 17 Apr '12

17 Apr '12

Hi Anastasia, My mistake with the expiration date. Please try with this link: https://transfert.inria.fr/fichiers/0b1013b5de0fc0cc9e8dd2d6101a054b/testDa… Thanks! Viviana Siless -- Parietal Team, INRIA Saclay Neurospin, Centre CEA de Saclay 91191 Gif sur Yvette – FRANCE On Tue, Apr 17, 2012 at 6:03 PM, Anastasia Yendiki < ayendiki(a)nmr.mgh.harvard.edu> wrote: > > Hi Viviana - I was away from email for some time and it looks like the > uploaded file has expired. Could you reupload it? I apologize for the delay. > > Thanks, > a.y > > > On Fri, 6 Apr 2012, Viviana Siless wrote: > > Hi Anastasia, >> Here is the data: https://transfert.inria.fr/**fichiers/** >> 4531ddb4948dff7223febc5a5b4f7e**7d/testData.tar.gz<https://transfert.inria.fr/fichiers/4531ddb4948dff7223febc5a5b4f7e7d/testDa…>Let me know if you have any >> trouble. >> I changed to the other track-all, and the error is the same. >> Please let me know if I'm doing anything wrong! >> Thank you! >> >> Viviana Siless >> -- >> Parietal Team, INRIA Saclay >> Neurospin, Centre CEA de Saclay >> 91191 Gif sur Yvette – FRANCE >> >> >> On Thu, Apr 5, 2012 at 7:38 PM, Anastasia Yendiki < >> ayendiki(a)nmr.mgh.harvard.edu> wrote: >> >> Hi Viviana - If you upload this data set I'm happy to look at it. >> >> Also, I strongly recommend getting the updated version of trac-all >> from the wiki (I'm guessing from the log file that >> you're probably not using that?) See 2012/01/09 update here: >> http://surfer.nmr.mgh.**harvard.edu/fswiki/Tracula<http://surfer.nmr.mgh.harvard.edu/fswiki/Tracula> >> >> Thanks, >> a.y >> >> >> On Wed, 4 Apr 2012, Viviana Siless wrote: >> >> Hello, >> I'm trying to run trac-all prec and I'm getting a segmentation fault >> error. >> >> Loading streamlines from /media/vivi/code/freesurfer/** >> trctrain/trc032/dlabel/mni/lh.**cst_AS.flt.trk >> Loading streamline start ROI from /media/vivi/code/freesurfer/** >> trctrain/trc033/dlabel/mni/lh.**cst_AS_roi1.flt.nii.gz >> Loading streamline end ROI from /media/vivi/code/freesurfer/** >> trctrain/trc033/dlabel/mni/lh.**cst_AS_roi2.flt.nii.gz >> Loading streamlines from /media/vivi/code/freesurfer/** >> trctrain/trc033/dlabel/mni/lh.**cst_AS.flt.trk >> INFO: Rejected 0 streamlines for straying off mask >> INFO: Rejected 0 streamlines for reversing direction >> Segmentation fault >> Linux vivi-ThinkStation-C20X 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 Wed Apr 4 18:24:21 CEST 2012 >> >> >> - When I look at the trak-all.error I see this error: >> >> ------------------------------ >> SUBJECT 000000112288Proc >> DATE Wed Apr 4 18:24:21 CEST 2012 >> USER vivi >> HOST vivi-ThinkStation-C20X >> PROCESSOR x86_64 >> OS Linux >> Linux vivi-ThinkStation-C20X 2.6.38-8-generic #42-Ubuntu SMP Mon Apr >> 11 03:31:24 UTC 2011 x86_64 x86_64 x86_64 >> GNU/Linux >> $Id: trac-preproc,v 1.17.2.5 2011/05/20 06:51:51 ayendiki Exp $ >> /media/vivi/code/freesurfer/**bin/trac-preproc >> PWD /media/vivi/code/freesurfer >> CMD /media/vivi/code/freesurfer/**bin/dmri_train --outdir >> /media/vivi/images/freesurfer/**000000112288Proc/dlabel/mni >> --out >> lh.cst_AS_avg33_mni_flt rh.cst_AS_avg33_mni_flt >> lh.unc_AS_avg33_mni_flt rh.unc_AS_avg33_mni_flt >> lh.ilf_AS_avg33_mni_flt >> rh.ilf_AS_avg33_mni_flt fmajor_PP_avg33_mni_flt >> fminor_PP_avg33_mni_flt lh.atr_PP_avg33_mni_flt >> rh.atr_PP_avg33_mni_flt >> lh.ccg_PP_avg33_mni_flt rh.ccg_PP_avg33_mni_flt >> lh.cab_PP_avg33_mni_flt rh.cab_PP_avg33_mni_flt >> lh.slfp_PP_avg33_mni_flt >> rh.slfp_PP_avg33_mni_flt lh.slft_PP_avg33_mni_flt >> rh.slft_PP_avg33_mni_flt --slist >> /tmp/subj33.000000112288Proc.**16360.txt --trk >> dlabel/mni/lh.cst_AS.flt.trk dlabel/mni/rh.cst_AS.flt.trk >> dlabel/mni/lh.unc_AS.flt.trk dlabel/mni/rh.unc_AS.flt.trk >> dlabel/mni/lh.ilf_AS.flt.trk dlabel/mni/rh.ilf_AS.flt.trk >> dlabel/mni/fmajor_PP.flt.trk dlabel/mni/fminor_PP.flt.trk >> dlabel/mni/lh.atr_PP.flt.trk dlabel/mni/rh.atr_PP.flt.trk >> dlabel/mni/lh.ccg_PP.flt.trk dlabel/mni/rh.ccg_PP.flt.trk >> dlabel/mni/lh.cab_PP.flt.trk dlabel/mni/rh.cab_PP.flt.trk >> dlabel/mni/lh.slfp_PP.flt.trk >> dlabel/mni/rh.slfp_PP.flt.trk >> dlabel/mni/lh.slft_PP.flt.trk dlabel/mni/rh.slft_PP.flt.trk --seg >> dlabel/mni/aparc+aseg.nii.gz --cmask >> dlabel/mni/cortex+2mm.nii.gz >> --lmask 16 16 0 0 0 0 0 0 10 49 0 0 0 0 0 0 0 0 --rois >> dlabel/mni/lh.cst_AS_roi1.flt.**nii.gz >> dlabel/mni/lh.cst_AS_roi2.flt.**nii.gz >> dlabel/mni/rh.cst_AS_roi1.flt.**nii.gz >> dlabel/mni/rh.cst_AS_roi2.flt.**nii.gz dlabel/mni/lh.unc_AS_roi1.flt.** >> nii.gz >> dlabel/mni/lh.unc_AS_roi2.flt.**nii.gz >> dlabel/mni/rh.unc_AS_roi1.flt.**nii.gz dlabel/mni/rh.unc_AS_roi2.flt.** >> nii.gz >> dlabel/mni/lh.ilf_AS_roi1.flt.**nii.gz >> dlabel/mni/lh.ilf_AS_roi2.flt.**nii.gz dlabel/mni/rh.ilf_AS_roi1.flt.** >> nii.gz >> dlabel/mni/rh.ilf_AS_roi2.flt.**nii.gz >> dlabel/mni/fmajor_PP_roi1.flt.**nii.gz dlabel/mni/fmajor_PP_roi2.flt.** >> nii.gz >> dlabel/mni/fminor_PP_roi1.flt.**nii.gz >> dlabel/mni/fminor_PP_roi2.flt.**nii.gz dlabel/mni/lh.atr_PP_roi1.flt.** >> nii.gz >> dlabel/mni/lh.atr_PP_roi2.flt.**nii.gz >> dlabel/mni/rh.atr_PP_roi1.flt.**nii.gz dlabel/mni/rh.atr_PP_roi2.flt.** >> nii.gz >> dlabel/mni/lh.ccg_PP_roi1.flt.**nii.gz >> dlabel/mni/lh.ccg_PP_roi2.flt.**nii.gz dlabel/mni/rh.ccg_PP_roi1.flt.** >> nii.gz >> dlabel/mni/rh.ccg_PP_roi2.flt.**nii.gz >> dlabel/mni/lh.cab_PP_roi1.flt.**nii.gz dlabel/mni/lh.cab_PP_roi2.flt.** >> nii.gz >> dlabel/mni/rh.cab_PP_roi1.flt.**nii.gz >> dlabel/mni/rh.cab_PP_roi2.flt.**nii.gz dlabel/mni/lh.slfp_PP_roi1.** >> flt.nii.gz >> dlabel/mni/lh.slfp_PP_roi2.**flt.nii.gz dlabel/mni/rh.slfp_PP_roi1.* >> *flt.nii.gz dlabel/mni/rh.slfp_PP_roi2.**flt.nii.gz >> dlabel/mni/lh.slft_PP_roi1.**flt.nii.gz dlabel/mni/lh.slft_PP_roi2.* >> *flt.nii.gz dlabel/mni/rh.slft_PP_roi1.**flt.nii.gz >> dlabel/mni/rh.slft_PP_roi2.**flt.nii.gz --bmask >> /media/vivi/images/freesurfer/**000000112288Proc/dlabel/mni/**aparc+aseg_mask.nii.gz >> --fa >> /media/vivi/images/freesurfer/**000000112288Proc/dmri/mni/**dtifit_FA.flt.nii.gz >> --ncpts 5 --debug >> >> >> - If I run that command, I get the same (of course): >> >> INFO: Rejected 0 streamlines for straying off mask >> INFO: Rejected 0 streamlines for reversing direction >> Segmentation fault >> >> >> Can anybody give me an idea of the problem? I run recon-all and >> finished without errors. >> I attach the log file, the error file, and my dmrirc file. Please >> let me know if you need anything else. >> >> Thanks in advance! >> >> Viviana Siless >> -- >> Parietal Team, INRIA Saclay >> Neurospin, Centre CEA de Saclay >> 91191 Gif sur Yvette – FRANCE >> >> >> >> >> >> >> 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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How to create a circle ROI centered at certain coordinate?
by zhang mingxia 17 Apr '12

17 Apr '12

Dear Freesurfer experts, Recently, I was creating ROI. But I just knew how to create it manually as this website introduce: http://surfer.nmr.mgh.harvard.edu/fswiki/tksurfer_labeledit. Does Freesurfer provide the way to create ROI by using of certain coordinate? That is, if I know the MNI or Talairach coordinate of the ROI, I want to define an 10mm circle ROI centered at that certain coordinate, is there any way? Thank you very much! Mingxia Zhang

2 1

Re: [Freesurfer] How can I get the mean thickness of the significant cluster
by Douglas N Greve 17 Apr '12

17 Apr '12

There should be an ocn.dat file that corresponds to the CSD base name that you passed to mri_glmfit-sim. The cache just uses a pre-computed table. The computations are pretty simple. It synthesizes white gaussian noise on the surface, smooths it by a certain amount, then finds clusters at various thresholds and signs. It tabulates how likely a cluster of a given size is given the smoothing level, threshold, and sign. doug On 04/16/2012 09:10 PM, zhang mingxia wrote: > Hi Doug, > > Thanks. I have done Clusterwise Correction for Multiple Comparisons, > so there is some file like mc-z.positive.y.ocn.dat. I have seen the > column. > > By the way, I just know the clusterwise correction(which I get > the mc-z. files) use the permutation method. What about the "--cache" > one? Is there any introduction on website? I have not seen any. > > Thanks again. > > Mingxia > > On Thu, Apr 12, 2012 at 10:33 AM, Douglas N Greve > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: > > Hi Zhang, there should be a file named something like > "cache.th13.abs.y.ocn.dat" that is output as part of the > correction for > multiple comparisons. This will have a column for each significant > cluster in the order that the clusters are in. Each row is a > subject. So > you can take the mean over the subjects to get the number you want. > doug > > > On 04/10/2012 08:01 PM, zhang mingxia wrote: > > Dear Freesurfer experts, > > > > I have done the whole brain analysis and get some significant > > clusters. How can I get the mean thickness of these clusters of > every > > subject? > > > > Thank you very much. > > > > Mingxia Zhang > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > <mailto:Freesurfer@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 <mailto:greve@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 <tel:617-724-2358> > Fax: 617-726-7422 <tel:617-726-7422> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu <mailto: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. > > -- 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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