Freesurfer April 2012

freesurfer@nmr.mgh.harvard.edu

123 participants
192 discussions

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

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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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Please help: Registering to FSL feat- example_func2standard
by Michelle Umali 17 Apr '12

17 Apr '12

Hi Freesurfers, I ran reg-feat2anat to register freesurfer data to FSL feat in order to generate some binary masks. Afterwards I edited the FEAT registration to standard space via: reg-feat2anat --feat subjectX.feat --manxfm func2std and saved the registration. i want to use these example_func2standard edits, but I just now realized that I didn't add the -overwrite-exf2std flag. Is there anyway to generate a new example_func2standard.mat from the exf2std.register.dat that has the edits to replace the FSL-generated one? I would love to avoid re-editing everything. Many thanks for any help. Michelle

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subtracting segmented volumes
by Adil Javed 17 Apr '12

17 Apr '12

Hi, Is there a way to subtract segmented files in freesurfer? For example, aparc+aseg.mgz - aseg.mgz= aparc.mgz only? I am interested in looking only at the cortex. I find that label to volume conversion doesn't give me a nice segmented cortex, with some patchy areas of intensities lost. thanks, AJ

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reg-feat2anat --feat --manxfm func2std
by Michelle Umali 17 Apr '12

17 Apr '12

Hi Freesurfers, I ran reg-feat2anat and am now checking registration. For some subjects I had to edit the registration of feat to standard space. So, do I have to replace the example_func2standard.mat fsl's example_func2standard.mat in the reg folder or is this done automatically? Is this the only file that has to be copied over? Thanks. Michelle

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Longitudinal Edits, skull strip and wmcp, how to do this longitudinally
by Mark Fletcher 16 Apr '12

16 Apr '12

For some of my subjects, I need to make many different types of edits on my longitudinal data, but have a few questions regarding the order/how to do this. I have read the details of this website ( http://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalProcessing) but wanted to confirm a few things. In regards to the following questions, I have not yet run the "create base" yet for anything. Also, I am asking these questions because I already made all of the following edits (and others) on the cross-sectionals as described at ( http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TroubleshootingData) and need to know if this was the right time to do this, and what to do after? *For subjects that just need white matter control points:* For subjects that just need white matter control points, I have added them on each cross-sectional time point, and reprocessed them via the command (recon-all -autorecon2-cp -autorecon3 -subjid cp_before). Is the next step to simply run (recon-all -base <templateid> -tp <tp1id> -tp <tp2id> ... -all) pointing to the subjects that have been corrected with control points? Do I need to add any flags or additional commands for the base creation to take the white matter control points into account? Should I need to make any further edits to the "base" or longitudinals after this? *For subjects needing skull stripping and white matter control points*: A few of my subjects need both WMCP's and skull stripping adjustments? I'm assuming that you should do the skull stripping first and then the WMCP, is this correct? Does it matter? I am doing this to the cross sectionals only. * After reprocessing these, is the next step to simply run (recon-all -base <templateid> -tp <tp1id> -tp <tp2id> ... -all) pointing to the subjects that have been corrected with control points and skull strip? Do I need to add any flags or additional commands for the base creation to take the white matter control points into account? Should I need to make any further edits to the "base" or longitudinals after this?* *Does all this hold true if making manual edits of the skull* *Subjects that need Pial Edits amidst other things*: A few subjects need pial edits? I've done this to the crossectionals, is this appropriate (I couldn't tell from the longitudinal edits page? Any order that this should fit in? After reprocessing them for the edits, *is the next step to simply run (recon-all -base <templateid> -tp <tp1id> -tp <tp2id> ... -all) pointing to the subjects that have been corrected with the pial edits? Do I need to add any flags or additional commands for the base creation to take the white matter control points into account? Should I need to make any further edits to the "base" or longitudinals after this?* *Making Edits to White Matter:* One of my subjects seem to have lesions similar to those described here ( http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/WhiteMatterEdits) When/where do I edit this in the longitudinal processing stream? These subject also needs WMCP, is their an important order for doing these. *After reprocessing them for the edits, is the next step to simply run (recon-all -base <templateid> -tp <tp1id> -tp <tp2id> ... -all) pointing to the subjects that have been corrected to the white matter? Do I need to add any flags or additional commands for the base creation to take the white matter control points into account? Should I need to make any further edits to the "base" or longitudinals after this?* *Correcting Topological Defects:* When should I correct topological defects as described here ( http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TopologicalDefect ). Same end questions as ones above about what to do after fixing these. *Filling Lateral Ventricle: *Another question about White matter edits. One of my subjects needs to have its lateral ventricle filled (aka, adding it to the white matter). When/where should I do this. After processing it, what commands to run to create base? Thanks for answering my many questions. I am very impressed at the functionality of FreeSurfer, but want to be sure I am using them correctly.

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Job offer for neuroscientist with focus on MR image analysis
by Prof. Dr. Michael Deppe 16 Apr '12

16 Apr '12

On behalf of the Medical Faculty of the University of Münster I forward the following offer for a postdoctoral position in Neuroimaging research: Kind regards, Michael Deppe ---------------------------------------------------------------------- Prof. Dr. rer. medic. Dipl.-Phys. Michael Deppe Universität Münster Klinik und Poliklinik für Neurologie Funktionelle Bildgebung Albert-Schweitzer-Campus 1, Gebäude A1 48129 Münster, Germany Tel. +49 (0)251-83-48174 FAX +49 (0)251-83-52064 deppe(a)uni-muenster.de ----------------------------------------------------------------------

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Re: [Freesurfer] mri_compute_volume_fractions
by Bruce Fischl 14 Apr '12

14 Apr '12

Hi Adrian this will create a voxel map with the % of each tissue class in each voxel. If you want the total %s, just read them out of the stats files and compute them directly. cheers Bruce On Sat, 14 Apr 2012, Adrian Garcia wrote: > Dear Bruce, > > thank you for the reply. So this function creates an image for wm/gm/csf. I was hoping for a table of values (i.e. percent of wm/gm/csf in the volume), is this possible or should I be looking at another function? > > Best wishes > Adrian > > >

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mri_compute_volume_fractions
by Adrian Garcia 14 Apr '12

14 Apr '12

I would like to have Freesurfer calculate the percentage of wm/gm/csf from an MRI volume (produced with mri_volsynth). I have run recon-all to completion and have a registration matrix from the MRI to the Freesurfer anatomical (tkregister2). It looks like mri_compute_volume_fractions will do what I want, but I am not sure what parameters to supply, particularly the <output stem>. Would somebody be able to point me to some documentation for this function or an example of the command line to output the segmentation information? Best wishes Adrian

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Freesurfer April 2012