Freesurfer

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30134 discussions

Optimizing 2 jitters in one design with OPTSEQ?
by Hoorn, J. van 07 Feb '14

07 Feb '14

Dear Freesurfer mailinglist, I am developing a fMRI task in which I would like to include 2 jitters. One trial looks like this: Stimulus (5000ms) >> Waiting screen (jitter1) >> Feedback (2000 ms) >> Fixation (jitter2) There will be three types of trials, and in one of those trial-types the feedback displayed is contingent on the choice made during the stimulus-screen. We are interested in the both events stimulus and feedback. How can we optimize the two jitters in this design? As far as I know, OPTSEQ can provide one optimal jitter, but I could not figure out whether OPTSEQ can provide two lists of optimal jitters for one trial, when the time between the jitters is not the same. Is this possible? And in other words, does it even make sense to make two separate, independent jitterlists with OPTSEQ or is it not useful because only one of the two lists is optimal anyway? I would really like to have your input. Thanks in advance! Jorien

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Segmentation/cortical thickness
by Erik Lindberg 07 Feb '14

07 Feb '14

Dear FS expersts! I have two questions: 1) I am looking at the output from a FS run. When looking at the red and yellow lines it appears as the cortical thickness has bin estimated too thin. But when I take away the two lines and just look at the segmentation it looks quite god (and much thicker than the estimation of cortical thickness). How should I interpret this: Can it be that the cortical thickness measure is not completely correct while the cortical volumes from the segmentation is OK? I have run this dataset in both 5.3 and 5.1 FS versions. To me it looks like the 5.3 is making the cortex even thinner than the 5.1. In the 5.3 version I am using -mprage and -3T flags - while no flags was used in the 5.1 run. Is there any logical explanation for this? Is there any trick to make affect the program so that the yellow line (white matter border) is more consistent with what I see in the segmentation. Thanks in advance! Erik

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Re: [Freesurfer] Freesurfer Digest, Vol 120, Issue 8
by Muhammad Naveed Iqbal Qureshi 07 Feb '14

07 Feb '14

Hi Douglas Greve, Can you help me to run the following command properly bmssa-server:/> set subj=/home/bmssa-server/freesurfer/subjects/CHR01 bmssa-server:/> mri_surf2vol --surfval {$subj}/surf/rh.thickness --hemi rh --fillribbon --template mri/orig.mgz --volregidentity {$subj} --outvol {$subj}_rh.ribbon.niigdiagno = -1 Using identity matrix for registration mghRead(mri/orig.mgz, -1): could not open file mri_surf2vol ERROR: reading mri/orig.mgz header bmssa-server:/> mghRead {$subj}/mri/orig.mgz Thank you Best Regards, Muhammad Naveed Iqbal Qureshi P please don't print this e-mail unless you really need to > From: freesurfer-request(a)nmr.mgh.harvard.edu > Subject: Freesurfer Digest, Vol 120, Issue 8 > To: freesurfer(a)nmr.mgh.harvard.edu > Date: Thu, 6 Feb 2014 12:00:02 -0500 > > Send Freesurfer mailing list submissions to > freesurfer(a)nmr.mgh.harvard.edu > > To subscribe or unsubscribe via the World Wide Web, visit > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > or, via email, send a message with subject or body 'help' to > freesurfer-request(a)nmr.mgh.harvard.edu > > You can reach the person managing the list at > freesurfer-owner(a)nmr.mgh.harvard.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Freesurfer digest..." > > > Today's Topics: > > 1. hippocampus misestimation (Adam Mezher) > 2. Re: hippocampus misestimation (Bruce Fischl) > 3. 3D thickness scale (Jonathan Holt) > 4. Re: 3D thickness scale (Louis Nicholas Vinke) > 5. Actual Thickness Values (Natasha Haris) > 6. Re: WM editing and longitudinal processing v5.3.0 (Derin J Cobia) > 7. Re: WM editing and longitudinal processing v5.3.0 (Bruce Fischl) > 8. Re: upgrading to freesurfer 5.3 (Anastasia Yendiki) > 9. Re: Tracula: from anatomical to diffusion space and FSL > probtracx (Anastasia Yendiki) > 10. Re: Fwd: Tracula Error: bvecs and bvals don't have the same > number of entries (Anastasia Yendiki) > 11. Re: Fwd: trac-all -path error (Anastasia Yendiki) > 12. Re: Tracula only outputs merged flt file (and missing bbr) > (Anastasia Yendiki) > 13. Re: Outputting all tracula statistics to table (Anastasia Yendiki) > 14. Re: dmri_motion Error bvals (Anastasia Yendiki) > 15. Cluster Summary (Natasha Haris) > 16. Re: TRACULA error: pre-processing (Anastasia Yendiki) > 17. Re: SLFP (Anastasia Yendiki) > 18. Re: "trac-all -prior" giving "Segmentation fault (core > dumped) (Anastasia Yendiki) > 19. Re: TRACULA -stat (Anastasia Yendiki) > 20. Re: Cluster Summary (Douglas Greve) > 21. Re: upgrading to freesurfer 5.3 (Laura Christine Anderson) > 22. Linear Mixed Effects Models (Eric Cunningham) > 23. tracula and libnetcdf (Satrajit Ghosh) > 24. Re: Linear Mixed Effects Models (jorge luis) > 25. Re: tracula and libnetcdf (Satrajit Ghosh) > 26. thickness visualization in SPM (Muhammad Naveed Iqbal Qureshi) > 27. Re: thickness visualization in SPM (Douglas Greve) > 28. Tracula shows some tracks with bbr and others with flt > (Salil Soman) > 29. Re: Tracula only outputs merged flt file (and missing bbr) > (Salil Soman) > 30. possible to render hippocampal subfield segmentations as 3D > structures? (Salil Soman) > 31. Rotation involved in recon-all (Ed Gronenschild) > 32. Re: dmri_motion Error bvals (Liliana Maia) > 33. A question on fsaverage (peng) > 34. Fwd: A question on fsaverage (peng) > 35. Re: Rotation involved in recon-all (Bruce Fischl) > 36. Re: calculating spc on lobes annotation in longitudinal > structural analysis (Jeremy Young) > 37. Re: A question on fsaverage (Bruce Fischl) > 38. Re: Rotation involved in recon-all (Ed Gronenschild) > 39. Re: Rotation involved in recon-all (Harms, Michael) > 40. Re: Rotation involved in recon-all (Ed Gronenschild) > 41. Re: Rotation involved in recon-all (Harms, Michael) > 42. Re: A question on fsaverage (peng) > 43. basic math operations for volume labels? (Kami Koldewyn) > 44. Re: basic math operations for volume labels? (Maritza Ebling) > 45. FSFAST surface-based analysis to w-file (Caspar M. Schwiedrzik) > 46. Re: Mean diffusivity (Rotem Saar) > 47. Re: Actual Thickness Values (Douglas N Greve) > 48. Re: Fwd: trac-all -path error (Jon Wieser) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 5 Feb 2014 10:10:06 -0800 > From: Adam Mezher <adammezher(a)gmail.com> > Subject: [Freesurfer] hippocampus misestimation > To: freesurfer(a)nmr.mgh.harvard.edu > Message-ID: > <CAO6KwZ6HXJqzOcAhY+ABUGJphBfr+q-j+u0gQmC_ccd=HsN5Aw(a)mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Hi all, > > I was curious to know if anyone has been able to use edits to correct > hippocampal under- or over-estimation. I've experienced a number of cases > in which about half of the left hippocampus is labeled as ctx-lh-unknown or > Left-Cerebral-White-Matter (for reference, I'm using FreeSurfer version 5.1 > for these projects). If anyone has any suggestions to correct this error, > it would be much appreciated. > > Thank you, > Adam > > > > > > > > > *Adam MezherStaff Research Associate IICenter for Imaging of > Neurodegenerative DiseasesSan Francisco VA Medical Center4150 Clement St. > (114M)San Francisco, CA 94121Tel: 415-221-4810 Ext. 4629 Fax: 415-668-2864* > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20140205/2… > > ------------------------------ > > Message: 2 > Date: Wed, 5 Feb 2014 13:14:35 -0500 (EST) > From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] hippocampus misestimation > To: Adam Mezher <adammezher(a)gmail.com> > Cc: freesurfer(a)nmr.mgh.harvard.edu > Message-ID: <alpine.LRH.2.03.1402051314180.24528(a)nmr.mgh.harvard.edu> > Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed > > Hi Adam > > if you upload an example we will take a look > cheers > Bruce > > On Wed, 5 Feb 2014, Adam Mezher wrote: > > > Hi all, > > > > I was curious to know if anyone has been able to use edits to correct > > hippocampal under- or over-estimation. I've experienced a number of cases in > > which about half of the left hippocampus is labeled as ctx-lh-unknown or > > Left-Cerebral-White-Matter (for reference, I'm using FreeSurfer version 5.1 > > for these projects). If anyone has any suggestions to correct this error, it > > would be much appreciated. > > > > Thank you, > > Adam > > > > Adam Mezher > > Staff Research Associate II > > Center for Imaging of Neurodegenerative Diseases > > San Francisco VA Medical Center > > 4150 Clement St. (114M) > > San Francisco, CA 94121 > > Tel: 415-221-4810 Ext. 4629 > > Fax: 415-668-2864 > > > > > > > ------------------------------ > > Message: 3 > Date: Wed, 5 Feb 2014 14:10:29 -0500 > From: Jonathan Holt <whatsdac(a)umich.edu> > Subject: [Freesurfer] 3D thickness scale > To: freesurfer(a)nmr.mgh.harvard.edu > Message-ID: <0E08548B-3C11-43BA-AD97-3858E19A5D93(a)umich.edu> > Content-Type: text/plain; charset="windows-1252" > > Hi all, > > I?ve pulled up a 3D inflated thickness figure by loading the following into freeview > > lh.inflated:overlay=lh.thickness:overlay_threshold=0.1,3::name=inflated_thickness:visible=0 > > I?m wondering how the colors correspond to thickness and whether or not I can generate a scale to help interpret the figure. > > best, > > Jon > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20140205/6… > > ------------------------------ > > Message: 4 > Date: Wed, 5 Feb 2014 14:29:32 -0500 (EST) > From: Louis Nicholas Vinke <vinke(a)nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] 3D thickness scale > To: Jonathan Holt <whatsdac(a)umich.edu> > Cc: freesurfer(a)nmr.mgh.harvard.edu > Message-ID: <alpine.LRH.2.03.1402051427100.64459(a)nmr.mgh.harvard.edu> > Content-Type: text/plain; charset="windows-1252" > > Hi Jon, > If it's the colorbar you are looking for then right-click on the viewing > window, then Show Color Bar -> inflated_thickness. There are some > additional options under Configure Overlay located on the left sidebar. > -Louis > > On Wed, 5 Feb 2014, Jonathan Holt wrote: > > > Hi all, > > I?ve pulled up a 3D inflated thickness figure by loading the following into freeview > > > > lh.inflated:overlay=lh.thickness:overlay_threshold=0.1,3::name=inflated_thickness:visible=0 > > > > I?m wondering how the colors correspond to thickness and whether or not I can generate a scale to help > > interpret the figure. > > > > best, > > > > Jon > > > > > > ------------------------------ > > Message: 5 > Date: Wed, 5 Feb 2014 14:07:48 -0800 > From: Natasha Haris <harisnatasha(a)gmail.com> > Subject: [Freesurfer] Actual Thickness Values > To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: > <CALWaFcQBmEDn6AR0W+cjtE9yBUP3C9FAWNhtpq-c8_Q9U5PQtQ(a)mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Dear Freesurfers, > > My measure is thickness and I want to be able to get a list of all the > maximum thickness values at the centers of each significant cluster - is > there any simple way to do that on QDEC? Also, I would like to get an > average of all of the thickness values at each voxel for each cluster - is > there a way to do that as well? > > Many thanks, > Natasha > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20140205/c… > > ------------------------------ > > Message: 6 > Date: Wed, 5 Feb 2014 22:50:14 +0000 > From: Derin J Cobia <d-cobia(a)northwestern.edu> > Subject: Re: [Freesurfer] WM editing and longitudinal processing > v5.3.0 > To: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > Cc: FreeSurfer Listserve <freesurfer(a)nmr.mgh.harvard.edu>, Martin > Reuter <mreuter(a)nmr.mgh.harvard.edu>, Ed Gronenschild > <ed.gronenschild(a)maastrichtuniversity.nl> > Message-ID: <0CADD9C5-98F3-4D10-A98E-57E66BCE3B0F(a)northwestern.edu> > Content-Type: text/plain; charset="us-ascii" > > Could you clarify this a little more Bruce? I was under the same impression as Ed that 110s could be used in editing the wm volume (but cannot recall why/how I know that). We've edited using 110s and 255s with some limited success for both (rerunning occasionally deletes these manual edits or surface does not follow them) - maybe it is related to the mixing of intensities? In a sense does using 110s trigger the stream to think a control point was placed there (absent the Voronoi diagram, etc)? > > So, if manual 255s are always used, how are they differentiated from ventricle or internal capsule ones? Does this even matter? Broadly, does using a variety of intensity values affect other volumes (e.g. aseg, brainfinalsurfs, etc)? > > Thanks, > Derin > > > On Feb 4, 2014, at 11:25 AM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> wrote: > > > Hi Ed > > > > it was never the case that an edited on wm.mgz voxel had the value of 110. It was always 255. 110 is the value that locations have when they are either an automatically or manually added control point > > > > cheers > > Bruce > > On Tue, 4 Feb 2014, Ed Gronenschild wrote: > > > >> Hi Martin, > >> One thing I want to be sure of: > >> should the edited wm voxels really have a value of either 1 or 255. > >> In previous versions an added wm voxel had a value of about 110, > >> this is not anymore the case? > >> I'm asking this because I want to edit wm by using results from another > >> application that segments wm, so not by means of manually editing > >> with freeview. > >> Cheers, > >> Ed > >> On 4 Feb 2014, at 17:00, Martin Reuter wrote: > >> > >> Hi Ed, > >> take a look at this wiki page about edits in the long stream: > >> https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalEdits > >> everything should work. for long, you'd edit the base. If that is not > >> sufficient, you can edit the cross or the long. Edits from the cross > >> should be transferred to the long, except if the long already contain > >> manual edits. > >> Best, Martin > >> On Feb 4, 2014, at 9:06 AM, Ed Gronenschild > >> <ed.gronenschild(a)maastrichtuniversity.nl> wrote: > >> > >> Hi Bruce, > >> > >> When I have a look in the recon-all script I see that it > >> is tested if > >> there > >> are voxels present in wm.mgz with value 1 or 255. Both > >> indicate > >> wm editing. The comment in recon-all says that 1 means > >> remove > >> and 255 means add. > >> And concerning my second question: are these edited voxels > >> correcly processed with the option autorecon2-wm and > >> subsequently > >> with longitudinal processing? > >> > >> Cheers, > >> ed > >> > >> On 4 Feb 2014, at 14:27, Bruce Fischl wrote: > >> > >> Hi Ed, > >> > >> yes, although we reserve the values under 5 I > >> think for editing > >> changes, > >> I believe we only use 1 at the moment. > >> > >> cheers > >> Bruce > >> On Tue, 4 Feb 2014, Ed Gronenschild > >> wrote: > >> > >> Hi, > >> > >> From what I can read in the wiki > >> about wm editing, I understand > >> that edited wm voxels have values > >> of either 255 (added) or > >> 1 (removed) and no other values. > >> These are stored in the file > >> wm.mgz. Is that correct? > >> Before processing a lot of data I > >> want to be sure that running > >> recon-all with the option > >> autorecon2-wm will recognize these > >> voxels, also during longitudinal > >> processing. Can you confirm > >> this. > >> > >> FreeSurfer v5.3.0 Mac OSX10.6 > >> > >> Kind regards, > >> Ed > >> > >> _______________________________________________ > >> 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. > >> > >> _______________________________________________ > >> Freesurfer mailing list > >> Freesurfer(a)nmr.mgh.harvard.edu > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >> --------------------------------- > >> Dr. Martin Reuter > >> Assistant in Neuroscience - Massachusetts General Hospital > >> Instructor in Neurology - Harvard Medical School > >> MGH / HMS / MIT > >> A.A.Martinos Center for Biomedical Imaging > >> 149 Thirteenth Street, Suite 2301 > >> Charlestown, MA 02129 > >> Phone: +1-617-724-5652 > >> Email: > >> mreuter(a)nmr.mgh.harvard.edu > >> reuter(a)mit.edu > >> Web : http://reuter.mit.edu > > _______________________________________________ > > 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. > > > > > ------------------------------ > > Message: 7 > Date: Wed, 5 Feb 2014 18:08:25 -0500 (EST) > From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] WM editing and longitudinal processing > v5.3.0 > To: Derin J Cobia <d-cobia(a)northwestern.edu> > Cc: FreeSurfer Listserve <freesurfer(a)nmr.mgh.harvard.edu>, Martin > Reuter <mreuter(a)nmr.mgh.harvard.edu>, Ed Gronenschild > <ed.gronenschild(a)maastrichtuniversity.nl> > Message-ID: <alpine.LRH.2.03.1402051807520.24528(a)nmr.mgh.harvard.edu> > Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed > > Hi Derin > > we replace all 255s with 254 I think and 1 with 5 or something like that. > I'd have to go dig up the code. If you add 110 it will work, but if you > rerun it will not be retained. > > cheers > Bruce > > > On Wed, 5 Feb 2014, Derin J Cobia wrote: > > > Could you clarify this a little more Bruce? I was under the same impression as Ed that 110s could be used in editing the wm volume (but cannot recall why/how I know that). We've edited using 110s and 255s with some limited success for both (rerunning occasionally deletes these manual edits or surface does not follow them) - maybe it is related to the mixing of intensities? In a sense does using 110s trigger the stream to think a control point was placed there (absent the Voronoi diagram, etc)? > > > > So, if manual 255s are always used, how are they differentiated from ventricle or internal capsule ones? Does this even matter? Broadly, does using a variety of intensity values affect other volumes (e.g. aseg, brainfinalsurfs, etc)? > > > > Thanks, > > Derin > > > > > > On Feb 4, 2014, at 11:25 AM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> wrote: > > > >> Hi Ed > >> > >> it was never the case that an edited on wm.mgz voxel had the value of 110. It was always 255. 110 is the value that locations have when they are either an automatically or manually added control point > >> > >> cheers > >> Bruce > >> On Tue, 4 Feb 2014, Ed Gronenschild wrote: > >> > >>> Hi Martin, > >>> One thing I want to be sure of: > >>> should the edited wm voxels really have a value of either 1 or 255. > >>> In previous versions an added wm voxel had a value of about 110, > >>> this is not anymore the case? > >>> I'm asking this because I want to edit wm by using results from another > >>> application that segments wm, so not by means of manually editing > >>> with freeview. > >>> Cheers, > >>> Ed > >>> On 4 Feb 2014, at 17:00, Martin Reuter wrote: > >>> > >>> Hi Ed, > >>> take a look at this wiki page about edits in the long stream: > >>> https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalEdits > >>> everything should work. for long, you'd edit the base. If that is not > >>> sufficient, you can edit the cross or the long. Edits from the cross > >>> should be transferred to the long, except if the long already contain > >>> manual edits. > >>> Best, Martin > >>> On Feb 4, 2014, at 9:06 AM, Ed Gronenschild > >>> <ed.gronenschild(a)maastrichtuniversity.nl> wrote: > >>> > >>> Hi Bruce, > >>> > >>> When I have a look in the recon-all script I see that it > >>> is tested if > >>> there > >>> are voxels present in wm.mgz with value 1 or 255. Both > >>> indicate > >>> wm editing. The comment in recon-all says that 1 means > >>> remove > >>> and 255 means add. > >>> And concerning my second question: are these edited voxels > >>> correcly processed with the option autorecon2-wm and > >>> subsequently > >>> with longitudinal processing? > >>> > >>> Cheers, > >>> ed > >>> > >>> On 4 Feb 2014, at 14:27, Bruce Fischl wrote: > >>> > >>> Hi Ed, > >>> > >>> yes, although we reserve the values under 5 I > >>> think for editing > >>> changes, > >>> I believe we only use 1 at the moment. > >>> > >>> cheers > >>> Bruce > >>> On Tue, 4 Feb 2014, Ed Gronenschild > >>> wrote: > >>> > >>> Hi, > >>> > >>> From what I can read in the wiki > >>> about wm editing, I understand > >>> that edited wm voxels have values > >>> of either 255 (added) or > >>> 1 (removed) and no other values. > >>> These are stored in the file > >>> wm.mgz. Is that correct? > >>> Before processing a lot of data I > >>> want to be sure that running > >>> recon-all with the option > >>> autorecon2-wm will recognize these > >>> voxels, also during longitudinal > >>> processing. Can you confirm > >>> this. > >>> > >>> FreeSurfer v5.3.0 Mac OSX10.6 > >>> > >>> Kind regards, > >>> Ed > >>> > >>> _______________________________________________ > >>> 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. > >>> > >>> _______________________________________________ > >>> Freesurfer mailing list > >>> Freesurfer(a)nmr.mgh.harvard.edu > >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >>> --------------------------------- > >>> Dr. Martin Reuter > >>> Assistant in Neuroscience - Massachusetts General Hospital > >>> Instructor in Neurology - Harvard Medical School > >>> MGH / HMS / MIT > >>> A.A.Martinos Center for Biomedical Imaging > >>> 149 Thirteenth Street, Suite 2301 > >>> Charlestown, MA 02129 > >>> Phone: +1-617-724-5652 > >>> Email: > >>> mreuter(a)nmr.mgh.harvard.edu > >>> reuter(a)mit.edu > >>> Web : http://reuter.mit.edu > >> _______________________________________________ > >> 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. > > > > > > > > > > > ------------------------------ > > Message: 8 > Date: Wed, 5 Feb 2014 18:56:55 -0500 (EST) > From: Anastasia Yendiki <ayendiki(a)nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] upgrading to freesurfer 5.3 > To: Laura Christine Anderson <lander10(a)umd.edu> > Cc: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: <alpine.LRH.2.03.1402051854351.28556(a)nmr.mgh.harvard.edu> > Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed > > > Hi Laura - In case you're still having this problem, it potentially means > that you're using the centos6 build of 5.3 when you should be using the > centos4 build instead. Can you please check which build of 5.1 you were > using? > > Thanks, > a.y > > On Mon, 13 Jan 2014, Laura Christine Anderson wrote: > > > Hi Anastasia, thanks so much for your help. I downloaded the update to > > calculate motion parameters for each participant. I now have Freesurfer > > 5.3 installed on my server but all the preprocessing was completed in > > Freesurfer 5.1 (not 5.2 like I originally said). Can I run the motion > > calculation step (trac-all -qa) using preprocessed data from 5.1? > > > > I tried and am getting this error message: > > > > brain:/export/data/brain1/RSTOM: trac-all -qa -c > > /export/data/brain1/RSTOM/dmrirc.example_NEW_5.3 > > INFO: SUBJECTS_DIR is /export/data/brain1/RSTOM > > INFO: Diffusion root is /export/data/brain1/RSTOM > > Actual FREESURFER_HOME > > /afs/glue.umd.edu/software/freesurfer/5.3.0/Linux-x64 > > INFO: FreeSurfer build stamps do not match > > Subject Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 > > Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 > > /cell_root/software/freesurfer/new/sys/bin/dmri_motion: error while > > loading shared libraries: libnetcdf.so.6: cannot open shared object file: > > No such file or directory > > /cell_root/software/freesurfer/new/sys/bin/dmri_group: error while loading > > shared libraries: libnetcdf.so.6: cannot open shared object file: No such > > file or directory > > INFO: current FREESURFER_HOME does not match that of previous processing. > > Current: /cell_root/software/freesurfer/new/sys > > Previous: /software/brain/Freesurfer/5.1.0/freesurfer/ > > trac-preproc -c /export/data/brain1/RSTOM/TLR103/scripts/dmrirc.local -log > > /export/data/brain1/RSTOM/TLR103/scripts/trac-all.log -cmd > > /export/data/brain1/RSTOM/TLR103/scripts/trac-all.cmd > > #------------------------------------- > > /cell_root/software/freesurfer/new/sys/bin/trac-preproc > > #------------------------------------- > > #@# Image quality assessment Mon Jan 13 15:19:04 EST 2014 > > /cell_root/software/freesurfer/new/sys/bin/dmri_motion --dwi > > /export/data/brain1/RSTOM/TLR103/dmri/dwi_orig.nii.gz --mat > > /export/data/brain1/RSTOM/TLR103/dmri/dwi.ecclog --bval > > /export/data/brain1/RSTOM/TLR103/dmri/bvals --out > > /export/data/brain1/RSTOM/TLR103/dmri/dwi_motion.txt > > /cell_root/software/freesurfer/new/sys/bin/dmri_motion: error while > > loading shared libraries: libnetcdf.so.6: cannot open shared object file: > > No such file or directory > > Linux brain.umd.edu 2.6.32-358.6.2.el6.x86_64 #1 SMP Tue May 14 15:48:21 > > EDT 2013 x86_64 x86_64 x86_64 GNU/Linux > > > > trac-preproc exited with ERRORS at Mon Jan 13 15:19:04 EST 2014 > > > > Thanks for your help! > > > > > > Laura C. Anderson, B.A. > > Graduate Student > > Clinical & Developmental Psychology > > University of Maryland > > College Park, MD 20742 > > BPS 0112 > > > > > > > > > > On 12/17/13 4:33 PM, "Anastasia Yendiki" <ayendiki(a)nmr.mgh.harvard.edu> > > wrote: > > > >> > >> Hi Laura - Please read the information on the wiki page: > >> http://surfer.nmr.mgh.harvard.edu/fswiki/Tracula#Updates > >> > >> Tracula in 5.2 and 5.3 is identical. The motion measures are not in 5.3 > >> but in a newer update, that you can download from that wiki page. > >> > >> As an aside, you should not be using recon-all from 5.2, since 5.3 was > >> released immediately after to fix a bug in 5.2. > >> > >> Hope this helps, > >> a.y > >> > >> On Fri, 13 Dec 2013, Laura Christine Anderson wrote: > >> > >>> Hi Anastasia, I was hoping to upgrade to Freesurfer 5.3 in order to use > >>> the > >>> new motion detection feature of Tracula. The issue is that all of the > >>> preprocessing has already been completed in Freesurfer 5.2 with the > >>> older > >>> version of Tracula. Would I need to redo all the preprocessing in 5.3 in > >>> order to use the new motion detection feature? > >>> > >>> Thanks for your help! > >>> Laura > >>> > >>> Laura C. Anderson, B.A. > >>> Graduate Student > >>> Clinical & Developmental Psychology > >>> University of Maryland > >>> College Park, MD 20742 > >>> BPS 0112 > >>> > >>> > >> > >> > >> 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. > > > > > > > > > > > ------------------------------ > > Message: 9 > Date: Wed, 5 Feb 2014 19:11:12 -0500 (EST) > From: Anastasia Yendiki <ayendiki(a)nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] Tracula: from anatomical to diffusion space > and FSL probtracx > To: Garikoitz Lerma-Usabiaga <garikoitz(a)gmail.com> > Cc: Freesurfer <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: <alpine.LRH.2.03.1402051859280.28556(a)nmr.mgh.harvard.edu> > Content-Type: text/plain; charset="iso-8859-1" > > > Hi Gari - You're talking about thresholding the probtrackx maps, right? If > so the 20% at which the tracula maps are thresholded by default is > probably too high for probtrackx, I'd try something like 2%. (Tracula is > global and probtrackx is local tractography, so their outputs are > different beasts.) > > Are the waytotal values very different among subjects? Are the anatomical > seed mask sizes very different? Did you take that into account? Probtrackx > will generate X sample paths for each voxel in the seed mask. Did you > threshold the tracula tracts before using them as waymasks? > > a.y > > On Tue, 14 Jan 2014, Garikoitz Lerma-Usabiaga wrote: > > > Hi Anastasia,?it worked perfectly and I could run probtrack between my anatomical seed > > and using waypoints from Tracula tracts. > > > > I have another doubt right now. The probabilities in each new tract are very different. > > I divided every value with waytotal using fslmaths -div in order to normalize them, and > > obtained something like this:? > > subject: S_20, Max Value after normalizing with waytotal: 0.75533 > > subject: S_23, Max Value?after normalizing with waytotal: 0.27883 > > subject: S_25, Max Value?after normalizing with waytotal: 0.60251 > > subject: S_27, Max Value after normalizing with waytotal: 0.32355? > > > > > > Should I consider the same absolute value for all tracts in order to threshold them or > > should I threshold all tracts independently with the 20%? > > > > I want to check visually the existence of the tract between the anatomical and the > > tract, with the same probability across subjects, and afterwards obtain the FA values > > in order to correlate with behavior. > > > > Thanks again! > > Gari > > > > > > > > > > > > > > > > On Mon, Jan 13, 2014 at 7:55 PM, Anastasia Yendiki <ayendiki(a)nmr.mgh.harvard.edu> > > wrote: > > > > Hi Gari - Yes, fslmaths should be able to do it, with -thrp 20. > > > > a.y > > > > On Mon, 13 Jan 2014, Garikoitz Lerma-Usabiaga wrote: > > > > Thanks Anastasia, I finally got it, I had to do mri_vol2vol > > twice to have it > > in the diffusion space.? > > I have an additional question:? > > I want to create waypoint masks for probtracx from Tracula > > tracts (for > > example, uncinate).? > > > > Should I use mri_binarize on path.pd.nii to create the mask? > > Should I use 20% of the maximum value as the threshold in order > > to do so? (a > > little help with the command line will be greatly appreciated) > > > > thanks again! > > Gari > > > > > > On Sun, Jan 12, 2014 at 3:08 AM, Anastasia Yendiki > > <ayendiki(a)nmr.mgh.harvard.edu> wrote: > > > > ? ? ? Has mri/hippo_subfield_in_diffusion_space.nii been > > actually > > ? ? ? transformed to diffusion space by applying the > > anatorig2diff > > ? ? ? transformation? I'm assuming that your diffusion data is > > not > > ? ? ? 0.5mm resolution? You can search for the name of the > > ? ? ? transformation in trac-all.log to see examples of how it > > is > > ? ? ? applied to volumes. > > > > ? ? ? On Sat, 11 Jan 2014, Garikoitz Lerma-Usabiaga wrote: > > > > ? ? ? ? ? ? Hi Anastasia,the problem is > > ? ? ? ? ? ? with?mri/hippo_subfield_in_diffusion_space.nii, > > ? ? ? ? ? ? which originally is mri/hippo_subfield.mgz, the > > ? ? ? ? ? ? output of running recon-all > > ? ? ? ? ? ? -hippo-subfields. So as far as I understand it is > > ? ? ? ? ? ? not in anatomical space, > > ? ? ? ? ? ? according to MRI info, it is (one example): > > ? ? ? ? ? ? - LIA > > ? ? ? ? ? ? - 85x97x141 > > ? ? ? ? ? ? - 0.5x0.5x0.5 > > > > ? ? ? ? ? ? So, how could I convert it to the diffussion space > > ? ? ? ? ? ? in FSL format in order to > > ? ? ? ? ? ? be able to use it in probtrackx? > > ? ? ? ? ? ? Should I do 2 steps or 3 steps? > > ? ? ? ? ? ? 1.- mri_convert to anatorig space (brainmask.mgz > > ? ? ? ? ? ? space, LIA, 256x256x256) > > ? ? ? ? ? ? 2.- anatorig2diff in order to change to FSL format > > ? ? ? ? ? ? and to diffusion space?? > > ? ? ? ? ? ? (3.- would be the previous one in two steps, first > > ? ? ? ? ? ? from anatorig to anat and > > ? ? ? ? ? ? then from anat to diff) > > > > ? ? ? ? ? ? Any indication of the best programs to do all the > > ? ? ? ? ? ? change will be appreciated > > ? ? ? ? ? ? (I've seen in trac-all.log that mostly fsl programs > > ? ? ? ? ? ? are being used to do the > > ? ? ? ? ? ? flips, and then tkregister2 and bbregister for the > > ? ? ? ? ? ? registrations) > > > > ? ? ? ? ? ? Thanks for the help! > > ? ? ? ? ? ? Gari? > > > > > > > > ? ? ? ? ? ? On Sat, Jan 11, 2014 at 1:31 AM, Anastasia Yendiki > > ? ? ? ? ? ? <ayendiki(a)nmr.mgh.harvard.edu> wrote: > > > > ? ? ? ? ? ? ? ? ? Hi Gari - So if I understand correctly, your > > ? ? ? ? ? ? inputs to > > ? ? ? ? ? ? ? ? ? probtrackx are: > > ? ? ? ? ? ? ? ? ? ? ? ? ? > > ? ? ? ? ? ? mri/hippo_subfield_in_diffusion_space.nii > > ? ? ? ? ? ? ? ? ? ? ? ? ? dmri.bedpostX/merged > > ? ? ? ? ? ? ? ? ? ? ? ? ? dmri.bedpostX/nodif_brain_mask > > > > ? ? ? ? ? ? ? ? ? If these all come from the output of tracula, > > ? ? ? ? ? ? aren't these all > > ? ? ? ? ? ? ? ? ? in LAS orientation? > > > > ? ? ? ? ? ? ? ? ? a.y > > > > ? ? ? ? ? ? ? ? ? On Thu, 9 Jan 2014, Garikoitz Lerma-Usabiaga > > ? ? ? ? ? ? wrote: > > > > ? ? ? ? ? ? ? ? ? ? ? ? Hi Anastasia,I want to use a > > hippocampal > > ? ? ? ? ? ? subfield as > > ? ? ? ? ? ? ? ? ? ? ? ? a seed in FSL. I am having problems > > ? ? ? ? ? ? understanding > > ? ? ? ? ? ? ? ? ? ? ? ? how > > ? ? ? ? ? ? ? ? ? ? ? ? to change spaces around... > > > > ? ? ? ? ? ? ? ? ? ? ? ? 1.- Is this command ok? > > ? ? ? ? ? ? ? ? ? ? ? ? mri_vol2vol --mov dmri/dtifit_FA.nii.gz > > ? ? ? ? ? ? --targ > > ? ? ? ? ? ? ? ? ? ? ? ? > > ? ? ? ? ? ? mri/hippo_subfield_in_anatomical_space.mgz --inv > > ? ? ? ? ? ? ? ? ? ? ? ? --interp > > ? ? ? ? ? ? ? ? ? ? ? ? nearest --o > > ? ? ? ? ? ? ? ? ? ? ? ? > > ? ? ? ? ? ? mri/hippo_subfield_in_diffusion_space.nii --reg > > ? ? ? ? ? ? ? ? ? ? ? ? dmri/xfms/anatorig2diff.bbr.dat > > ? ? ? ? ? ? --no-save-reg > > > > ? ? ? ? ? ? ? ? ? ? ? ? 2.- I would like to visualize it in > > ? ? ? ? ? ? freeview in > > ? ? ? ? ? ? ? ? ? ? ? ? anatomical space to check if it is ok, > > ? ? ? ? ? ? if I load > > ? ? ? ? ? ? ? ? ? ? ? ? nu.mgz and > > ? ? ? ? ? ? ? ? ? ? ? ? hippo_subfield_in_anatomical_space.mgz > > ? ? ? ? ? ? and then load > > ? ? ? ? ? ? ? ? ? ? ? ? hippo_subfield_in_diffusion_space.nii > > ? ? ? ? ? ? with the > > ? ? ? ? ? ? ? ? ? ? ? ? registration file > > ? ? ? ? ? ? dmri/xfms/anatorig2diff.bbr.dat, > > ? ? ? ? ? ? ? ? ? ? ? ? should I visualize it ok? > > ? ? ? ? ? ? ? ? ? ? ? ? If I don't register it, they show to be > > ? ? ? ? ? ? displaced > > ? ? ? ? ? ? ? ? ? ? ? ? (more than expected). > > > > > > ? ? ? ? ? ? ? ? ? ? ? ? 3.- Afterwards I want to run probtracx > > ? ? ? ? ? ? with the > > ? ? ? ? ? ? ? ? ? ? ? ? following command (my doubt is mainly > > ? ? ? ? ? ? about the > > ? ? ? ? ? ? ? ? ? ? ? ? files to > > ? ? ? ? ? ? ? ? ? ? ? ? use, since FSL files are RAS, > > freesurfer > > ? ? ? ? ? ? anatomical > > ? ? ? ? ? ? ? ? ? ? ? ? are LIA and freesurfer diffusion are > > ? ? ? ? ? ? LIA, are all > > ? ? ? ? ? ? ? ? ? ? ? ? the > > ? ? ? ? ? ? ? ? ? ? ? ? files in the same format and FSL is ok > > ? ? ? ? ? ? with it?): > > ? ? ? ? ? ? ? ? ? ? ? ? /usr/local/fsl/bin/probtrackx > > ? ? ? ? ? ? --mode=seedmask > > ? ? ? ? ? ? ? ? ? ? ? ? > > ? ? ? ? ? ? -x?mri/hippo_subfield_in_diffusion_space.nii?-s > > ? ? ? ? ? ? ? ? ? ? ? ? dmri.bedpostX/merged -m > > ? ? ? ? ? ? ? ? ? ? ? ? dmri.bedpostX/nodif_brain_mask -o > > ? ? ? ? ? ? ? ? ? ? ? ? fdt_paths_hippo_subfields > > ? ? ? ? ? ? ? ? ? ? ? ? --dir=FSL_ConnResults_Hipp -c 0.2 -S > > ? ? ? ? ? ? 2000 > > ? ? ? ? ? ? ? ? ? ? ? ? --steplength=0.5 -P 5000 --opd > > > > ? ? ? ? ? ? ? ? ? ? ? ? many thanks! > > ? ? ? ? ? ? ? ? ? ? ? ? Gari? > > > > > > > > > > ? ? ? ? ? ? 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. > > > > > > > > > > > > > > > > > > ------------------------------ > > Message: 10 > Date: Wed, 5 Feb 2014 19:18:16 -0500 (EST) > From: Anastasia Yendiki <ayendiki(a)nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] Fwd: Tracula Error: bvecs and bvals don't > have the same number of entries > To: Francesco Baldacchini <frankbald(a)gmail.com> > Cc: freesurfer(a)nmr.mgh.harvard.edu > Message-ID: <alpine.LRH.2.03.1402051915020.28556(a)nmr.mgh.harvard.edu> > Content-Type: text/plain; charset="iso-8859-1" > > > Hi Francesco - Which version of tracula are you running? To be able to use > bvecs files that are in 3 rows instead of 3 columns, you need to make sure > that you have the latest update to tracula, see here: > http://surfer.nmr.mgh.harvard.edu/fswiki/Tracula/#Updates > > This option was not available in the previous releases of tracula. > > Hope this helps, > a.y > > On Mon, 20 Jan 2014, Francesco Baldacchini wrote: > > > Hi,? > > Sorry Anastasia, I'm seeing that my question was not so clear. The files I sent you in > > the first mail are the bvecs and bvals saved by trac-all -prep in the dmri directory. > > The original files are in attachment in this mail, > > > > Francesco Baldacchini > > > > > > 2014/1/13 Anastasia Yendiki <ayendiki(a)nmr.mgh.harvard.edu> > > > > Hi Francesco - The bvecs file that you're attaching has only 3 vectors, > > while the bvals file has 65 b-values. Are these your original files, or the > > ones saved by trac-all in the dmri/ directory? > > > > a.y > > > > On Mon, 13 Jan 2014, Francesco Baldacchini wrote: > > > > Hi everybody, > > I'm trying to run the trac all -prep command but after some > > times I get this > > error "bvecs and bvals don't have the same number of entries". > > I've checked > > my bvals and bvecs, which are in attach, but they seems to be > > formatted in > > the right way. What can I do? Thanks, > > > > Francesco Baldacchini > > > > > > > > > > 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. > > > > > > > > > > > > ------------------------------ > > Message: 11 > Date: Wed, 5 Feb 2014 19:35:12 -0500 (EST) > From: Anastasia Yendiki <ayendiki(a)nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] Fwd: trac-all -path error > To: Jon Wieser <wieser(a)uwm.edu> > Cc: freesurfer(a)nmr.mgh.harvard.edu > Message-ID: <alpine.LRH.2.03.1402051932460.28556(a)nmr.mgh.harvard.edu> > Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed > > > Hi Jon - You need to look at the aparc+aseg after it has been mapped to > diffusion space. It's possible that it looks fine in its original space > but then maybe something goes wrong with the registration. So you should > look at the aparc+aseg and aparc+aseg_mask files from the tracula > dlabel/diff directory. These are in diffusion space and you can overlay > them on the FA map to see if there's anything strange in the ILF area. > > Hope this helps, > a.y > > On Tue, 14 Jan 2014, Jon Wieser wrote: > > > Hi anastasia > > I looked at the brainmask and the aparc+aseg. I did see anything missing in the area of the left ILF. > > I have attached the files. can you take a look at them? > > Thanks > > JOn > > > > ----- Original Message ----- > > From: "Anastasia Yendiki" <ayendiki(a)nmr.mgh.harvard.edu> > > To: "Jon Wieser" <wieser(a)uwm.edu> > > Cc: "freesurfer" <freesurfer(a)nmr.mgh.harvard.edu> > > Sent: Friday, January 10, 2014 6:15:23 PM > > Subject: Re: [Freesurfer] Fwd: trac-all -path error > > > > > > Hi Jon - Have you checked the brain mask and aparc+aseg for this subject? > > Anything missing there that might affect the left ILF? > > > > a.y > > > > On Wed, 8 Jan 2014, Jon Wieser wrote: > > > >> > >> Dear freesurfer experts > >> I'm getting the following error when runing trac-all -c dmrirc_single_subject -path > >> > >> > >> Loading initial proposal SD's from /BrainLabDocs/Studies/Nicotine_MJ_Ecstasy_Study/Data/MRI/N1084/data/freesurfer/dlabel/diff/lh.ilf_AS_avg23_mni_flt_cpts_5_std.txt > >> Processing pathway 3 of 18... > >> Initializing MCMC > >> Segmentation fault > >> Darwin cerebrum.uwm.edu 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:33:36 PDT 2011; root:xnu-1504.15.3~1/RELEASE_I386 i386 > >> > >> > >> I have attached the trac-all.log and trac-all.error files > >> > >> I am running tracula 5.3 > >> > > > > > > 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. > > > > > > > ------------------------------ > > Message: 12 > Date: Wed, 5 Feb 2014 19:48:13 -0500 (EST) > From: Anastasia Yendiki <ayendiki(a)nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] Tracula only outputs merged flt file (and > missing bbr) > To: Salil Soman <salsoman(a)stanford.edu> > Cc: free surfer <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: <alpine.LRH.2.03.1402051946180.28556(a)nmr.mgh.harvard.edu> > Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed > > > Hi Sal - That sounds strange. Are the individual paths created normally > for the bbr case? So there are subdirectories with path.pd.nii.gz files > for all the tracts? Does the trac-all.log show any commands run or error > messages for the bbr case? > > a.y > > On Sat, 18 Jan 2014, Salil Soman wrote: > > > Hi, > > Is there a specific issue to troubleshoot if Tracula only creates the merged ... flt > > file and not the merged ... bbr file in paths? All of my dmrirc files have both bbr and > > flt =1, and most of my outputs have both, but occasionally I only get 1. > > > > Thanks! > > > > > > -- > > Salil Soman, MD, MS > > Postdoctoral Research Fellow - Stanford Radiological Sciences Laboratory > > Fellow - Palo Alto War Related Illness and Injury Study Center > > WOC Neuroradiology Attending - Veterans Affairs Palo Alto Health Care System > > > > > > > ------------------------------ > > Message: 13 > Date: Wed, 5 Feb 2014 19:50:58 -0500 (EST) > From: Anastasia Yendiki <ayendiki(a)nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] Outputting all tracula statistics to table > To: Salil Soman <salsoman(a)stanford.edu> > Cc: free surfer <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: <alpine.LRH.2.03.1402051948270.28556(a)nmr.mgh.harvard.edu> > Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed > > > Hi Sal - Have you checked the tutorial? > http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TraculaStatistics > > One is for grouping the pathstats.overall.txt files, the other for the > pathstats.byvoxel.txt files. So average measures over the whole tract vs. > measures as a function of position along the tract. > > Hope this helps, > a.y > > On Mon, 20 Jan 2014, Salil Soman wrote: > > > Hi, > > What is the proper way to generate a single table containing all tracula generated > > statistics for all subjects in a study? I tought tractstats2table was the way to do > > this, I am confused as to how trac-all -stat factors into this process in the latest > > (12-09-13 version)? > > > > Thank you. > > > > -Sal > > > > > > > ------------------------------ > > Message: 14 > Date: Wed, 5 Feb 2014 19:56:51 -0500 (EST) > From: Anastasia Yendiki <ayendiki(a)nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] dmri_motion Error bvals > To: Liliana Maia <limaia.25(a)gmail.com> > Cc: freesurfer(a)nmr.mgh.harvard.edu > Message-ID: <alpine.LRH.2.03.1402051953100.28556(a)nmr.mgh.harvard.edu> > Content-Type: text/plain; charset="iso-8859-15" > > > Hi Liliana - This error indicates that it could not find the > /home/lapsi/test/bvals file at all, not that the file had the wrong > format. Does that file exist? > > Also, if you run "trac-all -prep -noqa", you're telling trac-all NOT to do > the QA step that calculates the motion measures, so I'm confused about > what exactly you ran. The log file from scripts/trac-all.log should show > you what steps were run and what the command line was. > > a.y > > On Wed, 22 Jan 2014, Liliana Maia wrote: > > > Hi, > > > > Within the new Tracula update and with outputs resulted from trac-all -prep -noqa I ran: > > > > dmri_motion --out './test.txt' --dwi './dwi_orig.nii.gz' --bval './bvals' --mat './dwi.ecclog' > > > > And an error message appears: > > > > machine? x86_64 > > > > Output motion measure file: /home/lapsi/test/motion.txt > > Input transform file: /home/lapsi/test/dwi.ecclog > > Input DWI file: /home/lapsi/test/dwi_orig.nii.gz > > Input b-value table: /home/lapsi/test/bvals > > Low-b image intensity threshold: 100 > > Nominal diffusivity: 0.001 > > Loading volume-to-baseline affine transformations > > Computing between-volume head motion measures > > INFO: Processed transforms for 33 volumes > > Loading DWI volume series from /home/lapsi/test/dwi_orig.nii.gz > > Loading b-value table from /home/lapsi/test/bvals > > ERROR: Could not open /home/lapsi/test/bvals for reading > > > > > > I tried with the b-values one value for each line in file bvalsT (see attachments): > > dmri_motion --out 'teste.txt' --dwi 'dwi_orig.nii.gz' --bval './bvalsT' --mat 'dwi.ecclog' > > ,but the same error occurred. > > > > What can I do to verify this head motion? > > > > Thank you > > ?Best, > > > > -- > > > > Liliana Maia > > MEng Biomedical Engineering > > > > > > > > ------------------------------ > > Message: 15 > Date: Wed, 5 Feb 2014 16:59:04 -0800 > From: Natasha Haris <harisnatasha(a)gmail.com> > Subject: [Freesurfer] Cluster Summary > To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: > <CALWaFcRSNQVbNaiSGjqFZ7jrc+Da0NDy2iApUqKpUGX_pP1CkA(a)mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Hello Freesurfers, > > Is there any way to get a list of all the clusters (with information on > their location, x/y/z vertices, t statistic etc) from QDEC? > > Thanks , > Natasha > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20140205/6… > > ------------------------------ > > Message: 16 > Date: Wed, 5 Feb 2014 20:03:51 -0500 (EST) > From: Anastasia Yendiki <ayendiki(a)nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] TRACULA error: pre-processing > To: Won Sang Jung <wonrad(a)gmail.com> > Cc: Freesurfer(a)nmr.mgh.harvard.edu > Message-ID: <alpine.LRH.2.03.1402052001210.28556(a)nmr.mgh.harvard.edu> > Content-Type: text/plain; charset="utf-8" > > > Hi Wonsang - The new tutorial data has subjects named elmo.2005, > elmo.2008, and elmo.2012 - not Diff001, which was from the old tutorial > data. So if you're using the new tutorial data you need to set your > configuration file accordingly with the new subject names, as shown on the > tutorial page: > > http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula > > Hope this helps, > a.y > > On Thu, 23 Jan 2014, Won Sang Jung wrote: > > > Hi, > > ? > > I have a problem running TRACULA in the pre-processing stage.? > > ? > > The error message is the following; > > ? > > Loading streamline start ROI from > > /usr/local/freesurfer/subjects/tracula/tutorialdata/diffusion_tutorial/Diff001/dlabel/mni/lh.cst_AS_roi1.flt.nii.gz > > niiRead(): error opening file > > /usr/local/freesurfer/subjects/tracula/tutorialdata/diffusion_tutorial/Diff001/dlabel/mni/lh.cst_AS_roi1.flt.nii.gz > > ERROR: Could not read > > /usr/local/freesurfer/subjects/tracula/tutorialdata/diffusion_tutorial/Diff001/dlabel/mni/lh.cst_AS_roi1.flt.nii.gz > > Linux localhost.localdomain 2.6.18-371.1.2.el5 #1 SMP Tue Oct 22 12:51:53 EDT 2013 x86_64 x86_64 x86_64 GNU/Linux > > ? > > trac-preproc exited with ERRORS at 2014. 01. 23. (?) 18:32:17 KST > > ? > > ? > > I guess this error started to happen after I updated Freesurfer version 5.3.0 > > ? > > (I could successfully run TRACULA with same data with the prior version of Freesurfer) > > ? > > ? > > In my setting, > > ? > > $TUTORIAL_DATA? --> /usr/local/freesurfer/subjects/tracula/tutorialdata > > ? > > ? > > I tried re-download the file, diffusion_tutorial.tar.gz, from freesurfer server and extracted file again, but still I > > couldn't find the file "lh.cst_AS_roi1.flt.nii.gz" in Diff001/dlabel/mni folder. > > ? > > ? > > Thank you in advance for your advice. > > ? > > ? > > Wonsang Jung > > > > > > ------------------------------ > > Message: 17 > Date: Wed, 5 Feb 2014 20:06:08 -0500 (EST) > From: Anastasia Yendiki <ayendiki(a)nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] SLFP > To: stdp82(a)virgilio.it > Cc: freesurfer(a)nmr.mgh.harvard.edu > Message-ID: <alpine.LRH.2.03.1402052004020.28556(a)nmr.mgh.harvard.edu> > Content-Type: text/plain; charset="utf-8" > > > Hi Stefano - Yes, the SLFP contains mostly SLF III. You cannot get other > tracts that are not included in the tracula atlas. It'd be similar to > trying to get a new label with freesurfer that's not included in the > freesurfer parcellation atlas. > > a.y > > On Fri, 24 Jan 2014, stdp82(a)virgilio.it wrote: > > > Hi list,? > > > > SLFP is SLF III? > > > > Is there a way to obtain by TRACULA also SLF I and II, knowing the the cortical targets of the tracts? > > > > Thanks,? > > > > > > Stefano > > > > > > ------------------------------ > > Message: 18 > Date: Wed, 5 Feb 2014 20:09:03 -0500 (EST) > From: Anastasia Yendiki <ayendiki(a)nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] "trac-all -prior" giving "Segmentation fault > (core dumped) > To: Yong-Hwan Kim <whiteneng(a)gmail.com> > Cc: freesurfer(a)nmr.mgh.harvard.edu > Message-ID: <alpine.LRH.2.03.1402052007590.28556(a)nmr.mgh.harvard.edu> > Content-Type: text/plain; charset="iso-8859-1" > > > Hi Yong-Hwan - Can you please send your entire trac-all.log file? It's > possible that something went wrong earlier in the processing even if the > other steps didn't fail explicitly. > > Thanks, > a.y > > On Tue, 28 Jan 2014, Yong-Hwan Kim wrote: > > > Hello, FreeSurfer community, > > I'm trying to run TRACULA sequentially. > > > > After running, "trac-all -prior -s <subject> -i <input_DWI.nii> -c <tracula_conf.txt>" > > that shows an error "Segmentation fault (core dumped)" in my server. > > (Other options, "-corr, -qa, -intra, -inter, -masks, -tensor", were have done without error) > > > > Server was configured as, > > 1. Fedora 13 - 64bit > > 2. FreeSurfer v5.1 > > 3. Tracula v5.3 (updated from v5.1) > > > > Can anyone suggest a reason why this would be the case? > > > > Thank you, > > Yong-Hwan Kim > > > > > > Captured Shell logs > > -------------------------------------------------------------------------------------------------- > > . > > . > > . > > Loading cortex mask from /usr/local/freesurfer/trctrain/trc033/dlabel/mni/cortex+2mm.nii.gz > > Processing pathway 1 of 18... > > Matching streamline ends > > INFO: ?Have 4657 non-truncated streamlines (min/mean/max length: 60/99/137) > > . > > . > > . > > Finding center streamline > > INFO: Step is 5 voxels > > Segmentation fault (core dumped) > > Linux localhost 2.6.33.3-85.fc13.x86_64 #1 SMP Thu May 6 18:09:49 ... > > > > trac-preproc exited with ERRORS at Tue Jan 28 21:30:52 KST 2014 > > > > -------------------------------------------------------------------------------------------------- > > > > > > Error Log from <subject>/scripts/trac-all.error > > -------------------------------------------------------------------------------------------------- > > SUBJECT G001 > > DATE Tue Jan 28 21:30:52 KST 2014 > > USER user > > HOST localhost > > PROCESSOR x86_64 > > OS Linux > > Linux localhost 2.6.33.3-85.fc13.x86_64 #1 SMP Thu May 6 18:09:49 UTC 2010 x86_64 x86_64 x86_64 GNU/Linux > > $Id: trac-preproc,v 1.46 2013/12/04 17:02:25 ayendiki Exp $ > > /usr/local/freesurfer/bin/trac-preproc > > PWD /usr/local/freesurfer/subjects/G001 > > CMD /usr/local/freesurfer/bin/dmri_train --outdir /usr/local/freesurfer/subjects/G001/dlabel/mni --out > > lh.cst_AS_avg33_mni_bbr rh.cst_AS_avg33_mni_bbr lh.ilf_AS_avg33_mni_bbr rh.ilf_AS_avg33_mni_bbr lh.unc_AS_avg33_mni_bbr > > rh.unc_AS_avg33_mni_bbr fmajor_PP_avg33_mni_bbr fminor_PP_avg33_mni_bbr lh.atr_PP_avg33_mni_bbr rh.atr_PP_avg33_mni_bbr > > lh.ccg_PP_avg33_mni_bbr rh.ccg_PP_avg33_mni_bbr lh.cab_PP_avg33_mni_bbr rh.cab_PP_avg33_mni_bbr lh.slfp_PP_avg33_mni_bbr > > rh.slfp_PP_avg33_mni_bbr lh.slft_PP_avg33_mni_bbr rh.slft_PP_avg33_mni_bbr --slist /tmp/subj33.G001.14153.txt --trk > > dlabel/mni/lh.cst_AS.bbr.trk dlabel/mni/rh.cst_AS.bbr.trk dlabel/mni/lh.ilf_AS.bbr.trk dlabel/mni/rh.ilf_AS.bbr.trk > > dlabel/mni/lh.unc_AS.bbr.trk dlabel/mni/rh.unc_AS.bbr.trk dlabel/mni/fmajor_PP.bbr.trk dlabel/mni/fminor_PP.bbr.trk > > dlabel/mni/lh.atr_PP.bbr.trk dlabel/mni/rh.atr_PP.bbr.trk dlabel/mni/lh.ccg_PP.bbr.trk dlabel/mni/rh.ccg_PP.bbr.trk > > dlabel/mni/lh.cab_PP.bbr.trk dlabel/mni/rh.cab_PP.bbr.trk dlabel/mni/lh.slfp_PP.bbr.trk dlabel/mni/rh.slfp_PP.bbr.trk > > dlabel/mni/lh.slft_PP.bbr.trk dlabel/mni/rh.slft_PP.bbr.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.bbr.nii.gz > > dlabel/mni/lh.cst_AS_roi2.bbr.nii.gz dlabel/mni/rh.cst_AS_roi1.bbr.nii.gz dlabel/mni/rh.cst_AS_roi2.bbr.nii.gz > > dlabel/mni/lh.ilf_AS_roi1.bbr.nii.gz dlabel/mni/lh.ilf_AS_roi2.bbr.nii.gz dlabel/mni/rh.ilf_AS_roi1.bbr.nii.gz > > dlabel/mni/rh.ilf_AS_roi2.bbr.nii.gz dlabel/mni/lh.unc_AS_roi1.bbr.nii.gz dlabel/mni/lh.unc_AS_roi2.bbr.nii.gz > > dlabel/mni/rh.unc_AS_roi1.bbr.nii.gz dlabel/mni/rh.unc_AS_roi2.bbr.nii.gz dlabel/mni/fmajor_PP_roi1.bbr.nii.gz > > dlabel/mni/fmajor_PP_roi2.bbr.nii.gz dlabel/mni/fminor_PP_roi1.bbr.nii.gz dlabel/mni/fminor_PP_roi2.bbr.nii.gz > > dlabel/mni/lh.atr_PP_roi1.bbr.nii.gz dlabel/mni/lh.atr_PP_roi2.bbr.nii.gz dlabel/mni/rh.atr_PP_roi1.bbr.nii.gz > > dlabel/mni/rh.atr_PP_roi2.bbr.nii.gz dlabel/mni/lh.ccg_PP_roi1.bbr.nii.gz dlabel/mni/lh.ccg_PP_roi2.bbr.nii.gz > > dlabel/mni/rh.ccg_PP_roi1.bbr.nii.gz dlabel/mni/rh.ccg_PP_roi2.bbr.nii.gz dlabel/mni/lh.cab_PP_roi1.bbr.nii.gz > > dlabel/mni/lh.cab_PP_roi2.bbr.nii.gz dlabel/mni/rh.cab_PP_roi1.bbr.nii.gz dlabel/mni/rh.cab_PP_roi2.bbr.nii.gz > > dlabel/mni/lh.slfp_PP_roi1.bbr.nii.gz dlabel/mni/lh.slfp_PP_roi2.bbr.nii.gz dlabel/mni/rh.slfp_PP_roi1.bbr.nii.gz > > dlabel/mni/rh.slfp_PP_roi2.bbr.nii.gz dlabel/mni/lh.slft_PP_roi1.bbr.nii.gz dlabel/mni/lh.slft_PP_roi2.bbr.nii.gz > > dlabel/mni/rh.slft_PP_roi1.bbr.nii.gz dlabel/mni/rh.slft_PP_roi2.bbr.nii.gz --bmask > > /usr/local/freesurfer/subjects/G001/dlabel/mni/aparc+aseg_mask.nii.gz --fa > > /usr/local/freesurfer/subjects/G001/dmri/dtifit_FA.nii.gz --cptdir /usr/local/freesurfer/subjects/G001/dlabel/diff --reg > > /usr/local/freesurfer/subjects/G001/dmri/xfms/mni2diff.bbr.mat --ncpts 6 6 5 5 5 5 7 5 5 5 5 5 4 4 5 5 5 5 --trunc > > -------------------------------------------------------------------------------------------------- > > > > > > > > ------------------------------ > > Message: 19 > Date: Wed, 5 Feb 2014 20:10:52 -0500 (EST) > From: Anastasia Yendiki <ayendiki(a)nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] TRACULA -stat > To: stdp82(a)virgilio.it > Cc: freesurfer(a)nmr.mgh.harvard.edu > Message-ID: <alpine.LRH.2.03.1402052009260.28556(a)nmr.mgh.harvard.edu> > Content-Type: text/plain; charset="utf-8" > > > Hi Stefano - It's the same dmrirc file that you used for all the other > steps. It should contain all the subjects that you want to combine stats > from. > > a.y > > On Sun, 2 Feb 2014, stdp82(a)virgilio.it wrote: > > > > > Hi list, > > > > I don?t understand how I can use the -stat option for TRACULA tool. > > > > From the guide, I should use a dmrirc file. What it should contains? > > > > Thanks, > > > > > > Stefano > > > > > > > > ------------------------------ > > Message: 20 > Date: Wed, 05 Feb 2014 20:26:36 -0500 > From: Douglas Greve <greve(a)nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] Cluster Summary > To: freesurfer(a)nmr.mgh.harvard.edu > Message-ID: <52F2E4CC.20905(a)nmr.mgh.harvard.edu> > Content-Type: text/plain; charset="iso-8859-1" > > > look in the QDEC output folder. in each contrast subfolder you'll see a > "summary" file. This has most of the info you request. > doug > > > On 2/5/14 7:59 PM, Natasha Haris wrote: > > Hello Freesurfers, > > > > Is there any way to get a list of all the clusters (with information > > on their location, x/y/z vertices, t statistic etc) from QDEC? > > > > Thanks , > > Natasha > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20140205/c… > > ------------------------------ > > Message: 21 > Date: Thu, 6 Feb 2014 01:29:04 +0000 > From: Laura Christine Anderson <lander10(a)umd.edu> > Subject: Re: [Freesurfer] upgrading to freesurfer 5.3 > To: Anastasia Yendiki <ayendiki(a)nmr.mgh.harvard.edu> > Cc: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: <9FF1335F-3511-41A2-BA8E-3178703C123F(a)umd.edu> > Content-Type: text/plain; charset="us-ascii" > > Hi Anastasia, you are correct- that was the issue. All figured out now, thanks! > > Laura > > Sent from my iPhone > > > On Feb 5, 2014, at 6:57 PM, "Anastasia Yendiki" <ayendiki(a)nmr.mgh.harvard.edu> wrote: > > > > > > Hi Laura - In case you're still having this problem, it potentially means that you're using the centos6 build of 5.3 when you should be using the centos4 build instead. Can you please check which build of 5.1 you were using? > > > > Thanks, > > a.y > > > >> On Mon, 13 Jan 2014, Laura Christine Anderson wrote: > >> > >> Hi Anastasia, thanks so much for your help. I downloaded the update to > >> calculate motion parameters for each participant. I now have Freesurfer > >> 5.3 installed on my server but all the preprocessing was completed in > >> Freesurfer 5.1 (not 5.2 like I originally said). Can I run the motion > >> calculation step (trac-all -qa) using preprocessed data from 5.1? > >> > >> I tried and am getting this error message: > >> > >> brain:/export/data/brain1/RSTOM: trac-all -qa -c > >> /export/data/brain1/RSTOM/dmrirc.example_NEW_5.3 > >> INFO: SUBJECTS_DIR is /export/data/brain1/RSTOM > >> INFO: Diffusion root is /export/data/brain1/RSTOM > >> Actual FREESURFER_HOME > >> /afs/glue.umd.edu/software/freesurfer/5.3.0/Linux-x64 > >> INFO: FreeSurfer build stamps do not match > >> Subject Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 > >> Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 > >> /cell_root/software/freesurfer/new/sys/bin/dmri_motion: error while > >> loading shared libraries: libnetcdf.so.6: cannot open shared object file: > >> No such file or directory > >> /cell_root/software/freesurfer/new/sys/bin/dmri_group: error while loading > >> shared libraries: libnetcdf.so.6: cannot open shared object file: No such > >> file or directory > >> INFO: current FREESURFER_HOME does not match that of previous processing. > >> Current: /cell_root/software/freesurfer/new/sys > >> Previous: /software/brain/Freesurfer/5.1.0/freesurfer/ > >> trac-preproc -c /export/data/brain1/RSTOM/TLR103/scripts/dmrirc.local -log > >> /export/data/brain1/RSTOM/TLR103/scripts/trac-all.log -cmd > >> /export/data/brain1/RSTOM/TLR103/scripts/trac-all.cmd > >> #------------------------------------- > >> /cell_root/software/freesurfer/new/sys/bin/trac-preproc > >> #------------------------------------- > >> #@# Image quality assessment Mon Jan 13 15:19:04 EST 2014 > >> /cell_root/software/freesurfer/new/sys/bin/dmri_motion --dwi > >> /export/data/brain1/RSTOM/TLR103/dmri/dwi_orig.nii.gz --mat > >> /export/data/brain1/RSTOM/TLR103/dmri/dwi.ecclog --bval > >> /export/data/brain1/RSTOM/TLR103/dmri/bvals --out > >> /export/data/brain1/RSTOM/TLR103/dmri/dwi_motion.txt > >> /cell_root/software/freesurfer/new/sys/bin/dmri_motion: error while > >> loading shared libraries: libnetcdf.so.6: cannot open shared object file: > >> No such file or directory > >> Linux brain.umd.edu 2.6.32-358.6.2.el6.x86_64 #1 SMP Tue May 14 15:48:21 > >> EDT 2013 x86_64 x86_64 x86_64 GNU/Linux > >> > >> trac-preproc exited with ERRORS at Mon Jan 13 15:19:04 EST 2014 > >> > >> Thanks for your help! > >> > >> > >> Laura C. Anderson, B.A. > >> Graduate Student > >> Clinical & Developmental Psychology > >> University of Maryland > >> College Park, MD 20742 > >> BPS 0112 > >> > >> > >> > >> > >> On 12/17/13 4:33 PM, "Anastasia Yendiki" <ayendiki(a)nmr.mgh.harvard.edu> > >> wrote: > >> > >>> > >>> Hi Laura - Please read the information on the wiki page: > >>> http://surfer.nmr.mgh.harvard.edu/fswiki/Tracula#Updates > >>> > >>> Tracula in 5.2 and 5.3 is identical. The motion measures are not in 5.3 > >>> but in a newer update, that you can download from that wiki page. > >>> > >>> As an aside, you should not be using recon-all from 5.2, since 5.3 was > >>> released immediately after to fix a bug in 5.2. > >>> > >>> Hope this helps, > >>> a.y > >>> > >>>> On Fri, 13 Dec 2013, Laura Christine Anderson wrote: > >>>> > >>>> Hi Anastasia, I was hoping to upgrade to Freesurfer 5.3 in order to use > >>>> the > >>>> new motion detection feature of Tracula. The issue is that all of the > >>>> preprocessing has already been completed in Freesurfer 5.2 with the > >>>> older > >>>> version of Tracula. Would I need to redo all the preprocessing in 5.3 in > >>>> order to use the new motion detection feature? > >>>> > >>>> Thanks for your help! > >>>> Laura > >>>> > >>>> Laura C. Anderson, B.A. > >>>> Graduate Student > >>>> Clinical & Developmental Psychology > >>>> University of Maryland > >>>> College Park, MD 20742 > >>>> BPS 0112 > >>> > >>> > >>> 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. > >> > >> > >> > >> > > > > ------------------------------ > > Message: 22 > Date: Wed, 5 Feb 2014 15:39:31 -1000 > From: Eric Cunningham <etc42(a)hawaii.edu> > Subject: [Freesurfer] Linear Mixed Effects Models > To: free surfer <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: > <CAH3UtpC3sBp1KmkUvnpqfuavdhSD7tAwFNLtbRWJdpiG8QGfuA(a)mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Hello Freesurfer Experts, > > I am currently trying to run the Linear Mixed Effects Models described in > the wiki here: > http://surfer.nmr.mgh.harvard.edu/fswiki/LinearMixedEffectsModels > > And I am running into difficulties that are fairly well described by the > last message in this previous mail thread: > https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg25787.html > > Can you please clarify the variable "ni"? > > the following command: > *[M,Y,ni] = sortData(M,1,Y,sID);* > results in: > ??? Error: File: sortData.m Line: 59 Column: 6 > Expression or statement is incorrect--possibly unbalanced (, {, or [. > > do i need to build "ni" ahead of time? > > You probably don't need to know this, but I am using data generated by > Freesurfer version 5.1, on matlab 7.8.0 (R2009a), which I gather will cause > a few problems further down the line. > > Thank you for your help, > -Eric > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20140205/f… > > ------------------------------ > > Message: 23 > Date: Wed, 5 Feb 2014 21:02:46 -0500 > From: Satrajit Ghosh <satra(a)mit.edu> > Subject: [Freesurfer] tracula and libnetcdf > To: Freesurfer Mailing List <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: > <CA+A4wOmdqHka0tyC4vyb_nRstUYhsTD9zoJDhPE5hMPoF9LGuQ(a)mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > hi a.y., > > when running trac-preproc i'm getting this error (for dmri_motion and > dmri_group), but it continues running: > > /software/freesurfer/bin/dmri_motion: error while loading shared libraries: > libnetcdf.so.6: cannot open shared object file: No such file or directory > > what will this fail to do? > > also is libnetcdf now a dependency for freesurfer? the reason i ask is that > i'm running this on a remote cluster for which i don't have admin > privileges. > > cheers, > > satra > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20140205/3… > > ------------------------------ > > Message: 24 > Date: Thu, 6 Feb 2014 02:34:21 +0000 (GMT) > From: jorge luis <jbernal0019(a)yahoo.es> > Subject: Re: [Freesurfer] Linear Mixed Effects Models > To: Eric Cunningham <etc42(a)hawaii.edu>, free surfer > <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: > <1391654061.76590.YahooMailNeo(a)web28703.mail.ir2.yahoo.com> > Content-Type: text/plain; charset="iso-8859-1" > > Hi Eric > > The meaning of the variable ni is > explained in the header of each script that have it either as an input > or output. But you can also download the sample data from the wiki page (ftp://surfer.nmr.mgh.harvard.edu/pub/data/long_mixed_effects_tools-data.tar… you will find instances of that > variable and how it relates to the design matrix. > > Best > -Jorge > > > > El Mi?rcoles 5 de febrero de 2014 20:40, Eric Cunningham <etc42(a)hawaii.edu> escribi?: > > Hello Freesurfer Experts, > > > >I am currently trying to run the Linear Mixed Effects Models described in the wiki here: > >http://surfer.nmr.mgh.harvard.edu/fswiki/LinearMixedEffectsModels > > > >And I am running into difficulties that are fairly well described by the last message in this previous mail thread: > > > >https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg25787.html > > > > > >Can you please clarify the variable "ni"?? > > > > > >the following command: > >[M,Y,ni] = sortData(M,1,Y,sID); > >results in: > >??? Error: File: sortData.m Line: 59 Column: 6 > >Expression or statement is incorrect--possibly unbalanced (, {, or [. > > > > > >do i need to build "ni" ahead of time? > > > > > >You probably don't need to know this, but I am using data generated by Freesurfer version 5.1, on matlab 7.8.0 (R2009a), which I gather will cause a few problems further down the line.? > > > > > >Thank you for your help, > > > >-Eric > > > >_______________________________________________ > >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. > > > > > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20140206/5… > > ------------------------------ > > Message: 25 > Date: Wed, 5 Feb 2014 23:07:48 -0500 > From: Satrajit Ghosh <satra(a)mit.edu> > Subject: Re: [Freesurfer] tracula and libnetcdf > To: Freesurfer Mailing List <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: > <CA+A4wOkX7FA8d+qy0Peq+iGhV8JG8GptY+ob=GtA50V6Q-HVHQ(a)mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > update: the lack of libnetcdf eventually makes it fail. > > i found a libnetcdf.so.7 on the cluster and soft linked it to > libnetcdf.so.6 and added the path to LD_LIBRARY_PATH. > > that let trac-all -prep run to completion. > > cheers, > > satra > > > On Wed, Feb 5, 2014 at 9:02 PM, Satrajit Ghosh <satra(a)mit.edu> wrote: > > > hi a.y., > > > > when running trac-preproc i'm getting this error (for dmri_motion and > > dmri_group), but it continues running: > > > > /software/freesurfer/bin/dmri_motion: error while loading shared > > libraries: libnetcdf.so.6: cannot open shared object file: No such file or > > directory > > > > what will this fail to do? > > > > also is libnetcdf now a dependency for freesurfer? the reason i ask is > > that i'm running this on a remote cluster for which i don't have admin > > privileges. > > > > cheers, > > > > satra > > > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20140205/5… > > ------------------------------ > > Message: 26 > Date: Thu, 6 Feb 2014 13:31:08 +0900 > From: Muhammad Naveed Iqbal Qureshi <mniqureshi(a)hotmail.com> > Subject: [Freesurfer] thickness visualization in SPM > To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: <BLU174-W12FC93D1A2DD4554A6157FC4940(a)phx.gbl> > Content-Type: text/plain; charset="ks_c_5601-1987" > > > Hi, > > How can I convert freesurfer .thickness files into .nii volume data to analyze in SPM > I have already converted the .thickness files into .nii format by using mri_convert command but the converted files can not be visualize in spm > probably I need to project the thickness on anatomical volume to visualize it correctly in spm > can anyone help me > > waiting for your replies > Thank you > > > > Best Regards, > > Muhammad > Naveed Iqbal Qureshi > > P please don't print this e-mail unless > you really need to > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20140206/5… > > ------------------------------ > > Message: 27 > Date: Wed, 05 Feb 2014 23:38:44 -0500 > From: Douglas Greve <greve(a)nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] thickness visualization in SPM > To: freesurfer(a)nmr.mgh.harvard.edu > Message-ID: <52F311D4.4020405(a)nmr.mgh.harvard.edu> > Content-Type: text/plain; charset="iso-8859-1" > > > Use mri_surf2vol > doug > > > > > On 2/5/14 11:31 PM, Muhammad Naveed Iqbal Qureshi wrote: > > > > > > Hi, > > > > How can I convert freesurfer .thickness files into .nii volume data to > > analyze in SPM > > I have already converted the .thickness files into .nii format by > > using mri_convert command but the converted files can not be visualize > > in spm > > probably I need to project the thickness on anatomical volume to > > visualize it correctly in spm > > can anyone help me > > > > waiting for your replies > > Thank you > > > > *Best Regards,* > > *Muhammad Naveed Iqbal Qureshi* > > Pplease don't print this e-mail unless you really need to > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20140205/2… > > ------------------------------ > > Message: 28 > Date: Wed, 5 Feb 2014 21:39:46 -0800 > From: Salil Soman <salsoman(a)stanford.edu> > Subject: [Freesurfer] Tracula shows some tracks with bbr and others > with flt > To: free surfer <freesurfer(a)nmr.mgh.harvard.edu>, Anastasia Yendiki > <ayendiki(a)nmr.mgh.harvard.edu> > Message-ID: > <CABd6wRVc5b=7YZrak_FfvAh2wGvjJGriz9+qefMp=mx91iNuYQ(a)mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Hi, > > I have a couple of dti cases where bbr will include forceps major and > missing forceps minor and flt will be the opposite. Similar things have > occurred for anterior thalamic tracts and cingulum bundles. Any > suggestions on what I may be doing incorrectly? > > Best wishes, > > Sal > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20140205/4… > > ------------------------------ > > Message: 29 > Date: Wed, 5 Feb 2014 21:40:53 -0800 > From: Salil Soman <salsoman(a)stanford.edu> > Subject: Re: [Freesurfer] Tracula only outputs merged flt file (and > missing bbr) > To: Anastasia Yendiki <ayendiki(a)nmr.mgh.harvard.edu>, free surfer > <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: > <CABd6wRVGojBARF7AdM4uFwHWXEuFQuhL2bOfFPRc4u0UnHw8VA(a)mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > This had only occurred for 1 case lot of the last 100. I will look into > your suggestions. > > Thank you. > > Sal > On Feb 5, 2014 4:48 PM, "Anastasia Yendiki" <ayendiki(a)nmr.mgh.harvard.edu> > wrote: > > > > > Hi Sal - That sounds strange. Are the individual paths created normally > > for the bbr case? So there are subdirectories with path.pd.nii.gz files for > > all the tracts? Does the trac-all.log show any commands run or error > > messages for the bbr case? > > > > a.y > > > > On Sat, 18 Jan 2014, Salil Soman wrote: > > > > Hi, > >> Is there a specific issue to troubleshoot if Tracula only creates the > >> merged ... flt > >> file and not the merged ... bbr file in paths? All of my dmrirc files > >> have both bbr and > >> flt =1, and most of my outputs have both, but occasionally I only get 1. > >> > >> Thanks! > >> > >> > >> -- > >> Salil Soman, MD, MS > >> Postdoctoral Research Fellow - Stanford Radiological Sciences Laboratory > >> Fellow - Palo Alto War Related Illness and Injury Study Center > >> WOC Neuroradiology Attending - Veterans Affairs Palo Alto Health Care > >> System > >> > >> > >> > > > > 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. > > > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20140205/5… > > ------------------------------ > > Message: 30 > Date: Thu, 6 Feb 2014 01:04:52 -0800 > From: Salil Soman <salsoman(a)stanford.edu> > Subject: [Freesurfer] possible to render hippocampal subfield > segmentations as 3D structures? > To: free surfer <freesurfer(a)nmr.mgh.harvard.edu>, Koen Van Leemput > <koen(a)nmr.mgh.harvard.edu> > Message-ID: > <CABd6wRVRVLG0i1fF+VycHCVwZGCDcEgeFv0GGT8DV5pkO_E52w(a)mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Hi, > > I generated hippocampal subfield segmentations, can generate statistics, > but was wondering if there was a way to visualized the subfield > segmentations as a 3D structure? (e.g. like the figure in this paper: > http://niacal.northwestern.edu/projects/17) > > Thank you for your consideration. > > Best wishes, > > -- > Salil Soman, MD, MS > Postdoctoral Research Fellow - Stanford Radiological Sciences Laboratory > Fellow - Palo Alto War Related Illness and Injury Study Center > WOC Neuroradiology Attending - Veterans Affairs Palo Alto Health Care System > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20140206/1… > > ------------------------------ > > Message: 31 > Date: Thu, 6 Feb 2014 10:24:44 +0100 > From: Ed Gronenschild <ed.gronenschild(a)maastrichtuniversity.nl> > Subject: [Freesurfer] Rotation involved in recon-all > To: freesurfer(a)nmr.mgh.harvard.edu > Message-ID: > <76B83C93-89F0-433C-956B-FF3644935EF7(a)maastrichtuniversity.nl> > Content-Type: text/plain; charset=us-ascii > > Hi, > > Using recon-all (freesurfer v5.1.0, MacOSX10.6) I noticed a rotation > of the T1 data early in the pipeline, i.e., converting rawavg.mgz to > orig.mgz., see excerpt of output of mri_info below > > rawavg.mgz: > > xform info: x_r = 0.0081, y_r = -0.0913, z_r = 0.9958, c_r = 0.0813 > : x_a = -0.9999, y_a = -0.0066, z_a = 0.0076, c_a = 14.8386 > : x_s = 0.0059, y_s = -0.9958, z_s = -0.0913, c_s = 13.1335 > > orig.mgz: > > xform info: x_r = -1.0000, y_r = -0.0000, z_r = 0.0000, c_r = 0.0813 > : x_a = 0.0000, y_a = -0.0000, z_a = 1.0000, c_a = 14.8386 > : x_s = 0.0000, y_s = -1.0000, z_s = 0.0000, c_s = 13.1335 > > > Is that the default way of processing the data? > > Cheers, > Ed > > > > > ------------------------------ > > Message: 32 > Date: Thu, 6 Feb 2014 09:40:09 +0000 > From: Liliana Maia <limaia.25(a)gmail.com> > Subject: Re: [Freesurfer] dmri_motion Error bvals > To: Anastasia Yendiki <ayendiki(a)nmr.mgh.harvard.edu> > Cc: freesurfer(a)nmr.mgh.harvard.edu > Message-ID: > <CAAQiZcbtdCuOnKS8AUNG-hs0zcozRc-eU90uHogw59uaAMj6Mg(a)mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Hi anastasia, > > Thanks for your answer! > I've already find where is my bug. > I've downloaded other tracula update (Centos4). After I download Centos6, > tracula runs without problems with the files used before. > Thanks again > No dia 6 de Fev de 2014 00:56, "Anastasia Yendiki" < > ayendiki(a)nmr.mgh.harvard.edu> escreveu: > > > > > Hi Liliana - This error indicates that it could not find the > > /home/lapsi/test/bvals file at all, not that the file had the wrong format. > > Does that file exist? > > > > Also, if you run "trac-all -prep -noqa", you're telling trac-all NOT to do > > the QA step that calculates the motion measures, so I'm confused about what > > exactly you ran. The log file from scripts/trac-all.log should show you > > what steps were run and what the command line was. > > > > a.y > > > > On Wed, 22 Jan 2014, Liliana Maia wrote: > > > > Hi, > >> > >> Within the new Tracula update and with outputs resulted from trac-all > >> -prep -noqa I ran: > >> > >> dmri_motion --out './test.txt' --dwi './dwi_orig.nii.gz' --bval './bvals' > >> --mat './dwi.ecclog' > >> > >> And an error message appears: > >> > >> machine x86_64 > >> > >> Output motion measure file: /home/lapsi/test/motion.txt > >> Input transform file: /home/lapsi/test/dwi.ecclog > >> Input DWI file: /home/lapsi/test/dwi_orig.nii.gz > >> Input b-value table: /home/lapsi/test/bvals > >> Low-b image intensity threshold: 100 > >> Nominal diffusivity: 0.001 > >> Loading volume-to-baseline affine transformations > >> Computing between-volume head motion measures > >> INFO: Processed transforms for 33 volumes > >> Loading DWI volume series from /home/lapsi/test/dwi_orig.nii.gz > >> Loading b-value table from /home/lapsi/test/bvals > >> ERROR: Could not open /home/lapsi/test/bvals for reading > >> > >> > >> I tried with the b-values one value for each line in file bvalsT (see > >> attachments): > >> dmri_motion --out 'teste.txt' --dwi 'dwi_orig.nii.gz' --bval './bvalsT' > >> --mat 'dwi.ecclog' > >> ,but the same error occurred. > >> > >> What can I do to verify this head motion? > >> > >> Thank you > >> Best, > >> > >> -- > >> > >> Liliana Maia > >> MEng Biomedical Engineering > >> > >> > >> > >> > > > > 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. > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20140206/a… > > ------------------------------ > > Message: 33 > Date: Thu, 6 Feb 2014 11:00:12 +0100 > From: peng <prion.w(a)gmail.com> > Subject: [Freesurfer] A question on fsaverage > To: Freesurfer(a)nmr.mgh.harvard.edu > Message-ID: > <CABd61DEpChYyTdhpCnO6GwXSqu5e0SHhSp+ozkq+4uqHz_wXWA(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hi everyone, > > I am a new user of freesurfer. As a first step, I wrote a script (see > below between ---) to run recon-all on the anatomical data. Since I found > it very slow, and our server has multi-cores, I run this script manually > several times, thus it appeared to be parallel.Then I have several > questions: > > 1 From the screen output, I guess if a certain subject folder exists, > freesurfer will refuse to work on this subject. Then I have assumption that > if I run the same script multiple times would not overwrite results from > previous session. Can I hold this believe? > 2 After certain time, I found new folders with name such as [fsaverage], > which I assumed as kind of average of subjects. Then I worry this was > generated from one session (either the first one or the last one, > depending on overwriting policy of this folder). For example, if session > one worked on subject 1 4 7 ... and session two worked on subject 2 5 8... > and session three worked on subject 3 6 9 ... ; is this [fsaverage] an > average of (subject 1, 4, 7) or (subject 3, 6, 9)? Or I am so lucky that > it is the average all processed subjects? > 3 Is there a proper way to work in parallel than my stone-age way? > 4 I searched the wiki and found some slides and pages which may help but > not answering the above question. Would you please suggest an example > "full" script of analysis? > Thank you very much! > ======= > My environment: 64-bit Linux with OpenSUSE. 8-CPUs/32G mem > Script: > ------------- > #!/bin/csh > echo "beginning ..." > > #environment setup > source ~/1tests/FreeSurferEnv.csh > > #Set environment and get the filelist > set raw_dir = '~/2rawdata/' > set fileNameList = `ls {$raw_dir}` > > #Try all the subjects in a loop > foreach file ($fileNameList) > echo "Now processing file ($file): ..." > echo "" > set inName = ($raw_dir$file) > recon-all -i $inName -s $file -autorecon-all > end > > echo "done!" > ------------- > ======= > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20140206/f… > > ------------------------------ > > Message: 34 > Date: Thu, 6 Feb 2014 11:06:14 +0100 > From: peng <prion.w(a)gmail.com> > Subject: [Freesurfer] Fwd: A question on fsaverage > To: Freesurfer(a)nmr.mgh.harvard.edu > Message-ID: > <CABd61DEr39F46WZRjRdUH5DxuPnkBVikJWfOzOCEM6s66b1Rqw(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hi everyone, > > I just re-checked the folder [fsaverage], their modified date was quite > old, probably they are just copies from freesurfer installation folder > rather than results of my scripts. Then my question 2 become void... > > best! > Peng > > ---------- Forwarded message ---------- > From: peng <prion.w(a)gmail.com> > Date: Thu, Feb 6, 2014 at 11:00 AM > Subject: A question on fsaverage > To: Freesurfer(a)nmr.mgh.harvard.edu > > > Hi everyone, > > I am a new user of freesurfer. As a first step, I wrote a script (see > below between ---) to run recon-all on the anatomical data. Since I found > it very slow, and our server has multi-cores, I run this script manually > several times, thus it appeared to be parallel.Then I have several > questions: > > 1 From the screen output, I guess if a certain subject folder exists, > freesurfer will refuse to work on this subject. Then I have assumption that > if I run the same script multiple times would not overwrite results from > previous session. Can I hold this believe? > 2 After certain time, I found new folders with name such as [fsaverage], > which I assumed as kind of average of subjects. Then I worry this was > generated from one session (either the first one or the last one, > depending on overwriting policy of this folder). For example, if session > one worked on subject 1 4 7 ... and session two worked on subject 2 5 8... > and session three worked on subject 3 6 9 ... ; is this [fsaverage] an > average of (subject 1, 4, 7) or (subject 3, 6, 9)? Or I am so lucky that > it is the average all processed subjects? > 3 Is there a proper way to work in parallel than my stone-age way? > 4 I searched the wiki and found some slides and pages which may help but > not answering the above question. Would you please suggest an example > "full" script of analysis? > Thank you very much! > ======= > My environment: 64-bit Linux with OpenSUSE. 8-CPUs/32G mem > Script: > ------------- > #!/bin/csh > echo "beginning ..." > > #environment setup > source ~/1tests/FreeSurferEnv.csh > > #Set environment and get the filelist > set raw_dir = '~/2rawdata/' > set fileNameList = `ls {$raw_dir}` > > #Try all the subjects in a loop > foreach file ($fileNameList) > echo "Now processing file ($file): ..." > echo "" > set inName = ($raw_dir$file) > recon-all -i $inName -s $file -autorecon-all > end > > echo "done!" > ------------- > ======= > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20140206/9… > > ------------------------------ > > Message: 35 > Date: Thu, 6 Feb 2014 08:36:56 -0500 (EST) > From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] Rotation involved in recon-all > To: Ed Gronenschild <ed.gronenschild(a)maastrichtuniversity.nl> > Cc: freesurfer(a)nmr.mgh.harvard.edu > Message-ID: <alpine.LRH.2.03.1402060836430.24528(a)nmr.mgh.harvard.edu> > Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed > > yes, we reorient it to be coronal as part of the "conform" process > > cheers > Bruce > On Thu, 6 > Feb 2014, Ed Gronenschild wrote: > > > Hi, > > > > Using recon-all (freesurfer v5.1.0, MacOSX10.6) I noticed a rotation > > of the T1 data early in the pipeline, i.e., converting rawavg.mgz to > > orig.mgz., see excerpt of output of mri_info below > > > > rawavg.mgz: > > > > xform info: x_r = 0.0081, y_r = -0.0913, z_r = 0.9958, c_r = 0.0813 > > : x_a = -0.9999, y_a = -0.0066, z_a = 0.0076, c_a = 14.8386 > > : x_s = 0.0059, y_s = -0.9958, z_s = -0.0913, c_s = 13.1335 > > > > orig.mgz: > > > > xform info: x_r = -1.0000, y_r = -0.0000, z_r = 0.0000, c_r = 0.0813 > > : x_a = 0.0000, y_a = -0.0000, z_a = 1.0000, c_a = 14.8386 > > : x_s = 0.0000, y_s = -1.0000, z_s = 0.0000, c_s = 13.1335 > > > > > > Is that the default way of processing the data? > > > > Cheers, > > Ed > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > ------------------------------ > > Message: 36 > Date: Thu, 6 Feb 2014 13:38:21 +0000 > From: Jeremy Young <J.Young(a)sussex.ac.uk> > Subject: Re: [Freesurfer] calculating spc on lobes annotation in > longitudinal structural analysis > To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: > <36FE7530ED7D584D903129A6602046EB37AAF394(a)EX-SHA-MBX1.ad.susx.ac.uk> > Content-Type: text/plain; charset="us-ascii" > > Sorry seems like my reply didn't go through to the list. Still trying to figure this out if anyone has some ideas on what to do / recommend trying to calculate manually. > > Best, > Jeremy > > > -----Original Message----- > From: Jeremy Young > Sent: Tuesday, February 04, 2014 4:30 PM > To: 'Douglas N Greve' > Subject: RE: [Freesurfer] calculating spc on lobes annotation in longitudinal structural analysis > > Hi Doug, > > It's the symmetrized percent change, it's the rate of change divided by the average thickness between time points; it's the recommended parameter to use according to the longitudinal analysis tutorial (instead of just percent change relative to time point 1). > > Thanks! > Jeremy > > > -----Original Message----- > From: freesurfer-bounces(a)nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve > Sent: Tuesday, February 04, 2014 4:15 PM > To: freesurfer(a)nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] calculating spc on lobes annotation in longitudinal structural analysis > > What is spc? > doug > > On 02/04/2014 07:18 AM, Jeremy Young wrote: > > The Freesurfer version we have installed is 5.1.0 if that helps. > > > > Best, > > Jeremy > > > > > > --- > > Dear all, > > > > I'm trying to get thickness spc stats for the individual lobe labels > > (specifically the frontal lobe) I created per subject per time point > > (in subject's longitudinal analysis template space) using: > > mri_annotation2label --subject $i --hemi ?h --lobesStrict ?h.lobes > > > > I've run mris_anatomical_stats to get out the stats and put them in > > each subject and time point's stats folder: > > mris_anatomical_stats -a lobes.annot -f $i/stats/lh.lobes.stats $i ?h > > > > Now I'm trying to calculate the spc using: > > long_stats_slopes --qdec long.qdec.table.dat --stats lh.lobes --meas > > thickness --do-spc --time years --out-spc lh.spc.lobes.txt > > > > but I'm getting an error (it works when I use the regular aparc and > > aseg stats files though). Here's my output: > > --- > > Parsing the qdec table: long.qdec.table.dat > > > > Working in SUBJECTS_DIR: /home/j/jy/jy72/scratch/AE/FSstruct/ > > > > > > Subject-Template: CISC4962plate > > > > > > INFO: 2 TPs in CISC4962plate , mean age: 0.565 > > > > aparcstats2table --common-parcs --hemi lh --parc lobes --subjects > > CISC4962.long.CISC4962plate CISC4962-2.long.CISC4962plate --meas > > thickness --tablefile > > ./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/long.lh.lobes.thickness- > > stack.dat > > -d space > > > > SUBJECTS_DIR : /home/j/jy/jy72/scratch/AE/FSstruct/ > > Parsing the .stats files > > Building the table.. > > Writing the table to > > ./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/long.lh.lobes.thickness- > > stack.dat > > > > > > Writing ./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/X-long.mat ... > > > > mri_glmfit --table > > ./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/long.lh.lobes.thickness- > > stack.dat --X ./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/X-long.mat > > --allow-zero-dof --no-contrasts-ok --glmdir > > ./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/glm > > > > > > $Id: mri_glmfit.c,v 1.196.2.6 2011/05/05 20:54:25 greve Exp $ cwd > > /mnt/lustre/scratch/jeremy/AE/FSstruct/qdec > > cmdline mri_glmfit --table > > ./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/long.lh.lobes.thickness- > > stack.dat --X ./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/X-long.mat > > --allow-zero-dof --no-contrasts-ok --glmdir > > ./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/glm > > sysname Linux > > hostname apollo-login > > machine x86_64 > > user jy72 > > FixVertexAreaFlag = 1 > > UseMaskWithSmoothing 1 > > OneSampleGroupMean 0 > > y > > /mnt/lustre/scratch/jeremy/AE/FSstruct/qdec/tmp-CISC4962plate_lh.lobes > > _thickness_Hal4Vg/long.lh.lobes.thickness-stack.dat > > logyflag 0 > > X ./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/X-long.mat > > usedti 0 > > glmdir ./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/glm > > IllCondOK 0 > > ReScaleX 1 > > DoFFx 0 > > Creating output directory > > ./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/glm > > Loading y from > > /mnt/lustre/scratch/jeremy/AE/FSstruct/qdec/tmp-CISC4962plate_lh.lobes > > _thickness_Hal4Vg/long.lh.lobes.thickness-stack.dat > > Found 6 data colums > > Found 2 data rows > > Saving design matrix to > > ./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/glm/Xg.dat > > Normalized matrix condition is 1 > > Matrix condition is 1.76991 > > search space = 6.000000 > > DOF = 0 > > Starting fit and test > > Fit completed in 0 minutes > > Writing results > > lh.lobes.thickness > > lh_frontal_thickness > > lh_cingulate_thickness > > lh_occipital_thickness > > lh_temporal_thickness > > lh_parietal_thickness > > lh_insula_thickness > > mri_glmfit done > > > > > > mri_convert --frame 0 > > ./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/glm/beta.mgh > > ./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/beta0.mgh > > > > mri_convert --frame 0 > > ./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/glm/beta.mgh > > ./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/beta0.mgh > > $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading > > from ./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/glm/beta.mgh... > > TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (1, 0, 0) j_ras = > > (0, 1, 0) k_ras = (0, 0, 1) keeping frame 0 writing to > > ./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/beta0.mgh... > > > > > > mri_convert --frame 1 > > ./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/glm/beta.mgh > > ./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/beta1.mgh > > > > mri_convert --frame 1 > > ./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/glm/beta.mgh > > ./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/beta1.mgh > > $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading > > from ./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/glm/beta.mgh... > > TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (1, 0, 0) j_ras = > > (0, 1, 0) k_ras = (0, 0, 1) keeping frame 1 writing to > > ./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/beta1.mgh... > > > > > > mris_calc -o > > ./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/long.lh.lobes.thickness- > > spc.dat.mgh ./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/beta1.mgh > > div ./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/beta0.mgh > > > > ERROR: mris_calc compute sym. pct. change (spc) problem? > > --- > > > > Am I missing a step somewhere when trying to do this? Please help. > > > > Thanks! > > Jeremy > > > > -- > > Jeremy Young > > PhD Researcher > > Behavioural and Clinical Neuroscience > > School of Psychology > > University of Sussex > > Brighton > > BN1 9QH > > 01273 872776 > > J.Young at sussex.ac.uk > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > > > > > > > _______________________________________________ > > 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: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > _______________________________________________ > 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. > > > > > ------------------------------ > > Message: 37 > Date: Thu, 6 Feb 2014 08:39:25 -0500 (EST) > From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] A question on fsaverage > To: peng <prion.w(a)gmail.com> > Cc: Freesurfer(a)nmr.mgh.harvard.edu > Message-ID: <alpine.LRH.2.03.1402060838010.24528(a)nmr.mgh.harvard.edu> > Content-Type: text/plain; charset="utf-8" > > Hi Peng > > the recon-all instances should be able to be run in parallel. The first > time you run one it will see that fsaverage does not exist, and will > symlink it to $FREESURFER_HOME/subjects/fsaverage (which is our existing > coordinate system, NOT an average of your subjects - to make your own > average use the make_average_subject script). > > cheers > Bruce > > > On Thu, 6 Feb 2014, peng > wrote: > > > Hi everyone, > > > > ? ?I am a new user of freesurfer. As a first step, I wrote a script (see > > below between ---) to run recon-all on the anatomical data. Since I found it > > very slow, and our server has multi-cores, I run this script manually > > several times, thus it appeared to be parallel.Then I have several > > questions: > > > > 1 From the screen output, I guess if a certain subject folder exists, > > freesurfer will refuse to work on this subject. Then I have assumption that > > if I run the same script multiple times would not overwrite results from > > previous session. Can I hold this believe? > > 2 After certain time, I found new folders with name such as [fsaverage], > > which I assumed as kind of average of subjects. Then I worry this was > > generated from one ?session (either the first one or the last one, depending > > on overwriting policy of this folder). For example, if session one worked on > > subject 1 4 7 ... and session two worked on subject 2 5 8... and session > > three worked on subject 3 6 9 ... ; is this [fsaverage] an average of > > (subject 1, 4, 7) or ?(subject 3, 6, 9)? Or I am so lucky that it is the > > average all processed subjects? > > 3 Is there a proper way to work in parallel than my stone-age way? > > 4 I searched the wiki and found some slides and pages which may help but not > > answering the above question. Would you please suggest an example "full" > > script of analysis? > > ? ? Thank you very much! > > ======= > > My environment: 64-bit Linux with OpenSUSE. 8-CPUs/32G mem > > Script: > > ------------- > > #!/bin/csh ? > > echo "beginning ..." ? > > > > #environment setup > > source ~/1tests/FreeSurferEnv.csh > > > > #Set environment and get the filelist? > > set raw_dir = '~/2rawdata/' > > set fileNameList = `ls {$raw_dir}`? > > > > #Try all the subjects in a loop > > foreach file ($fileNameList) > > echo "Now processing file ($file): ..." > > echo "" > > set inName = ($raw_dir$file) > > recon-all -i $inName -s $file -autorecon-all > > end > > > > echo "done!" ? > > ------------- > > ======= > > > > > > > > > > ------------------------------ > > Message: 38 > Date: Thu, 6 Feb 2014 14:43:43 +0100 > From: Ed Gronenschild <ed.gronenschild(a)maastrichtuniversity.nl> > Subject: Re: [Freesurfer] Rotation involved in recon-all > To: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > Cc: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: > <818F78A7-9D93-4470-9EC7-053ACC109235(a)maastrichtuniversity.nl> > Content-Type: text/plain; charset=us-ascii > > Hi Bruce, > > Yes, I do understand that is coronal, but there is an actual rotation apart from an orientation to coronal. > You can read it from the off-diagonal matrix elements. > > Cheers, > Ed > > On 6 Feb 2014, at 14:36, Bruce Fischl wrote: > > > yes, we reorient it to be coronal as part of the "conform" process > > > > cheers > > Bruce > > On Thu, 6 > > Feb 2014, Ed Gronenschild wrote: > > > >> Hi, > >> > >> Using recon-all (freesurfer v5.1.0, MacOSX10.6) I noticed a rotation > >> of the T1 data early in the pipeline, i.e., converting rawavg.mgz to > >> orig.mgz., see excerpt of output of mri_info below > >> > >> rawavg.mgz: > >> > >> xform info: x_r = 0.0081, y_r = -0.0913, z_r = 0.9958, c_r = 0.0813 > >> : x_a = -0.9999, y_a = -0.0066, z_a = 0.0076, c_a = 14.8386 > >> : x_s = 0.0059, y_s = -0.9958, z_s = -0.0913, c_s = 13.1335 > >> > >> orig.mgz: > >> > >> xform info: x_r = -1.0000, y_r = -0.0000, z_r = 0.0000, c_r = 0.0813 > >> : x_a = 0.0000, y_a = -0.0000, z_a = 1.0000, c_a = 14.8386 > >> : x_s = 0.0000, y_s = -1.0000, z_s = 0.0000, c_s = 13.1335 > >> > >> > >> Is that the default way of processing the data? > >> > >> Cheers, > >> Ed > >> > >> > >> _______________________________________________ > >> 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. > > > > > > > ------------------------------ > > Message: 39 > Date: Thu, 6 Feb 2014 14:38:23 +0000 > From: "Harms, Michael" <mharms(a)wustl.edu> > Subject: Re: [Freesurfer] Rotation involved in recon-all > To: Ed Gronenschild <ed.gronenschild(a)maastrichtuniversity.nl>, Bruce > Fischl <fischl(a)nmr.mgh.harvard.edu> > Cc: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: <CF18F9CC.2A4AB%harmsm(a)psychiatry.wustl.edu> > Content-Type: text/plain; charset="us-ascii" > > > Hi Ed, > If you want to avoid the rotation (e.g., to avoid an interpolation at the > conform step) then you need to manually alter the input so as to remove > the off-diagonal elements. That is in fact what we do as part of our > DICOM2NIFTI conversion in the HCP. > > cheers, > -MH > > -- > Michael Harms, Ph.D. > > ----------------------------------------------------------- > Conte Center for the Neuroscience of Mental Disorders > Washington University School of Medicine > Department of Psychiatry, Box 8134 > 660 South Euclid Ave. Tel: 314-747-6173 > St. Louis, MO 63110 Email: mharms(a)wustl.edu > > > > > On 2/6/14 7:43 AM, "Ed Gronenschild" > <ed.gronenschild(a)maastrichtuniversity.nl> wrote: > > >Hi Bruce, > > > >Yes, I do understand that is coronal, but there is an actual rotation > >apart from an orientation to coronal. > >You can read it from the off-diagonal matrix elements. > > > >Cheers, > >Ed > > > >On 6 Feb 2014, at 14:36, Bruce Fischl wrote: > > > >> yes, we reorient it to be coronal as part of the "conform" process > >> > >> cheers > >> Bruce > >> On Thu, 6 > >> Feb 2014, Ed Gronenschild wrote: > >> > >>> Hi, > >>> > >>> Using recon-all (freesurfer v5.1.0, MacOSX10.6) I noticed a rotation > >>> of the T1 data early in the pipeline, i.e., converting rawavg.mgz to > >>> orig.mgz., see excerpt of output of mri_info below > >>> > >>> rawavg.mgz: > >>> > >>> xform info: x_r = 0.0081, y_r = -0.0913, z_r = 0.9958, c_r = > >>> 0.0813 > >>> : x_a = -0.9999, y_a = -0.0066, z_a = 0.0076, c_a = > >>>14.8386 > >>> : x_s = 0.0059, y_s = -0.9958, z_s = -0.0913, c_s = > >>>13.1335 > >>> > >>> orig.mgz: > >>> > >>> xform info: x_r = -1.0000, y_r = -0.0000, z_r = 0.0000, c_r = > >>> 0.0813 > >>> : x_a = 0.0000, y_a = -0.0000, z_a = 1.0000, c_a = > >>>14.8386 > >>> : x_s = 0.0000, y_s = -1.0000, z_s = 0.0000, c_s = > >>>13.1335 > >>> > >>> > >>> Is that the default way of processing the data? > >>> > >>> Cheers, > >>> Ed > >>> > >>> > >>> _______________________________________________ > >>> 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. > >> > > > > > >_______________________________________________ > >Freesurfer mailing list > >Freesurfer(a)nmr.mgh.harvard.edu > >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > ________________________________ > The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. > > > > ------------------------------ > > Message: 40 > Date: Thu, 6 Feb 2014 15:50:21 +0100 > From: Ed Gronenschild <ed.gronenschild(a)maastrichtuniversity.nl> > Subject: Re: [Freesurfer] Rotation involved in recon-all > To: "Harms, Michael" <mharms(a)wustl.edu> > Cc: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: > <F9032F82-CCFA-4C5B-9627-EE2312B99ECD(a)maastrichtuniversity.nl> > Content-Type: text/plain; charset=us-ascii > > Hi Harm, > > Thanks for the trick. Will this, however, give not rise to conversion to Talairach > coordinates? > > Cheers, > Ed > > > On 6 Feb 2014, at 15:38, Harms, Michael wrote: > > > > > Hi Ed, > > If you want to avoid the rotation (e.g., to avoid an interpolation at the > > conform step) then you need to manually alter the input so as to remove > > the off-diagonal elements. That is in fact what we do as part of our > > DICOM2NIFTI conversion in the HCP. > > > > cheers, > > -MH > > > > -- > > Michael Harms, Ph.D. > > > > ----------------------------------------------------------- > > Conte Center for the Neuroscience of Mental Disorders > > Washington University School of Medicine > > Department of Psychiatry, Box 8134 > > 660 South Euclid Ave. Tel: 314-747-6173 > > St. Louis, MO 63110 Email: mharms(a)wustl.edu > > > > > > > > > > On 2/6/14 7:43 AM, "Ed Gronenschild" > > <ed.gronenschild(a)maastrichtuniversity.nl> wrote: > > > >> Hi Bruce, > >> > >> Yes, I do understand that is coronal, but there is an actual rotation > >> apart from an orientation to coronal. > >> You can read it from the off-diagonal matrix elements. > >> > >> Cheers, > >> Ed > >> > >> On 6 Feb 2014, at 14:36, Bruce Fischl wrote: > >> > >>> yes, we reorient it to be coronal as part of the "conform" process > >>> > >>> cheers > >>> Bruce > >>> On Thu, 6 > >>> Feb 2014, Ed Gronenschild wrote: > >>> > >>>> Hi, > >>>> > >>>> Using recon-all (freesurfer v5.1.0, MacOSX10.6) I noticed a rotation > >>>> of the T1 data early in the pipeline, i.e., converting rawavg.mgz to > >>>> orig.mgz., see excerpt of output of mri_info below > >>>> > >>>> rawavg.mgz: > >>>> > >>>> xform info: x_r = 0.0081, y_r = -0.0913, z_r = 0.9958, c_r = > >>>> 0.0813 > >>>> : x_a = -0.9999, y_a = -0.0066, z_a = 0.0076, c_a = > >>>> 14.8386 > >>>> : x_s = 0.0059, y_s = -0.9958, z_s = -0.0913, c_s = > >>>> 13.1335 > >>>> > >>>> orig.mgz: > >>>> > >>>> xform info: x_r = -1.0000, y_r = -0.0000, z_r = 0.0000, c_r = > >>>> 0.0813 > >>>> : x_a = 0.0000, y_a = -0.0000, z_a = 1.0000, c_a = > >>>> 14.8386 > >>>> : x_s = 0.0000, y_s = -1.0000, z_s = 0.0000, c_s = > >>>> 13.1335 > >>>> > >>>> > >>>> Is that the default way of processing the data? > >>>> > >>>> Cheers, > >>>> Ed > >>>> > >>>> > >>>> _______________________________________________ > >>>> 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. > >>> > >> > >> > >> _______________________________________________ > >> Freesurfer mailing list > >> Freesurfer(a)nmr.mgh.harvard.edu > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > ________________________________ > > The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. > > > > > ------------------------------ > > Message: 41 > Date: Thu, 6 Feb 2014 14:53:57 +0000 > From: "Harms, Michael" <mharms(a)wustl.edu> > Subject: Re: [Freesurfer] Rotation involved in recon-all > To: Ed Gronenschild <ed.gronenschild(a)maastrichtuniversity.nl>, "Harms, > Michael" <mharms(a)wustl.edu> > Cc: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: <CF18FDAB.2A4B8%harmsm(a)psychiatry.wustl.edu> > Content-Type: text/plain; charset="us-ascii" > > > orig.mgz is not converted to Talairach. The computed Talairach xfm is > used internally by some stages of recon-all, but none of the volumes are > ever converted to Talairach/MNI space. > > cheers, > -MH > > -- > Michael Harms, Ph.D. > > ----------------------------------------------------------- > Conte Center for the Neuroscience of Mental Disorders > Washington University School of Medicine > Department of Psychiatry, Box 8134 > 660 South Euclid Ave. Tel: 314-747-6173 > St. Louis, MO 63110 Email: mharms(a)wustl.edu > > > > > On 2/6/14 8:50 AM, "Ed Gronenschild" > <ed.gronenschild(a)maastrichtuniversity.nl> wrote: > > >Hi Harm, > > > >Thanks for the trick. Will this, however, give not rise to conversion to > >Talairach > >coordinates? > > > >Cheers, > >Ed > > > > > >On 6 Feb 2014, at 15:38, Harms, Michael wrote: > > > >> > >> Hi Ed, > >> If you want to avoid the rotation (e.g., to avoid an interpolation at > >>the > >> conform step) then you need to manually alter the input so as to remove > >> the off-diagonal elements. That is in fact what we do as part of our > >> DICOM2NIFTI conversion in the HCP. > >> > >> cheers, > >> -MH > >> > >> -- > >> Michael Harms, Ph.D. > >> > >> ----------------------------------------------------------- > >> Conte Center for the Neuroscience of Mental Disorders > >> Washington University School of Medicine > >> Department of Psychiatry, Box 8134 > >> 660 South Euclid Ave. Tel: 314-747-6173 > >> St. Louis, MO 63110 Email: mharms(a)wustl.edu > >> > >> > >> > >> > >> On 2/6/14 7:43 AM, "Ed Gronenschild" > >> <ed.gronenschild(a)maastrichtuniversity.nl> wrote: > >> > >>> Hi Bruce, > >>> > >>> Yes, I do understand that is coronal, but there is an actual rotation > >>> apart from an orientation to coronal. > >>> You can read it from the off-diagonal matrix elements. > >>> > >>> Cheers, > >>> Ed > >>> > >>> On 6 Feb 2014, at 14:36, Bruce Fischl wrote: > >>> > >>>> yes, we reorient it to be coronal as part of the "conform" process > >>>> > >>>> cheers > >>>> Bruce > >>>> On Thu, 6 > >>>> Feb 2014, Ed Gronenschild wrote: > >>>> > >>>>> Hi, > >>>>> > >>>>> Using recon-all (freesurfer v5.1.0, MacOSX10.6) I noticed a rotation > >>>>> of the T1 data early in the pipeline, i.e., converting rawavg.mgz to > >>>>> orig.mgz., see excerpt of output of mri_info below > >>>>> > >>>>> rawavg.mgz: > >>>>> > >>>>> xform info: x_r = 0.0081, y_r = -0.0913, z_r = 0.9958, c_r = > >>>>> 0.0813 > >>>>> : x_a = -0.9999, y_a = -0.0066, z_a = 0.0076, c_a = > >>>>> 14.8386 > >>>>> : x_s = 0.0059, y_s = -0.9958, z_s = -0.0913, c_s = > >>>>> 13.1335 > >>>>> > >>>>> orig.mgz: > >>>>> > >>>>> xform info: x_r = -1.0000, y_r = -0.0000, z_r = 0.0000, c_r = > >>>>> 0.0813 > >>>>> : x_a = 0.0000, y_a = -0.0000, z_a = 1.0000, c_a = > >>>>> 14.8386 > >>>>> : x_s = 0.0000, y_s = -1.0000, z_s = 0.0000, c_s = > >>>>> 13.1335 > >>>>> > >>>>> > >>>>> Is that the default way of processing the data? > >>>>> > >>>>> Cheers, > >>>>> Ed > >>>>> > >>>>> > >>>>> _______________________________________________ > >>>>> 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. > >>>> > >>> > >>> > >>> _______________________________________________ > >>> Freesurfer mailing list > >>> Freesurfer(a)nmr.mgh.harvard.edu > >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >> > >> > >> ________________________________ > >> The materials in this message are private and may contain Protected > >>Healthcare Information or other information of a sensitive nature. If > >>you are not the intended recipient, be advised that any unauthorized > >>use, disclosure, copying or the taking of any action in reliance on the > >>contents of this information is strictly prohibited. If you have > >>received this email in error, please immediately notify the sender via > >>telephone or return mail. > > > > > ________________________________ > The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. > > > > ------------------------------ > > Message: 42 > Date: Thu, 6 Feb 2014 16:03:17 +0100 > From: peng <prion.w(a)gmail.com> > Subject: Re: [Freesurfer] A question on fsaverage > To: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > Cc: Freesurfer(a)nmr.mgh.harvard.edu > Message-ID: > <CABd61DEYvR9OH+WGEEke6brRDmcNm6uNdDdr6_EgbGZj4M5JmA(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Bruce, Thanks a lot! > Would you explain more on how to run recon-all in parallel? By run the > script it did not automatically took the advantage of multiple cores (by > checking CPU usage). Is their somewhere I can change the preference or I > shall add some parameters in my code? > > > On Thu, Feb 6, 2014 at 2:39 PM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu>wrote: > > > Hi Peng > > > > the recon-all instances should be able to be run in parallel. The first > > time you run one it will see that fsaverage does not exist, and will > > symlink it to $FREESURFER_HOME/subjects/fsaverage (which is our existing > > coordinate system, NOT an average of your subjects - to make your own > > average use the make_average_subject script). > > > > cheers > > Bruce > > > > > > > > On Thu, 6 Feb 2014, peng wrote: > > > > Hi everyone, > >> > >> I am a new user of freesurfer. As a first step, I wrote a script (see > >> below between ---) to run recon-all on the anatomical data. Since I found > >> it > >> very slow, and our server has multi-cores, I run this script manually > >> several times, thus it appeared to be parallel.Then I have several > >> questions: > >> > >> 1 From the screen output, I guess if a certain subject folder exists, > >> freesurfer will refuse to work on this subject. Then I have assumption > >> that > >> if I run the same script multiple times would not overwrite results from > >> previous session. Can I hold this believe? > >> 2 After certain time, I found new folders with name such as [fsaverage], > >> which I assumed as kind of average of subjects. Then I worry this was > >> generated from one session (either the first one or the last one, > >> depending > >> on overwriting policy of this folder). For example, if session one worked > >> on > >> subject 1 4 7 ... and session two worked on subject 2 5 8... and session > >> three worked on subject 3 6 9 ... ; is this [fsaverage] an average of > >> (subject 1, 4, 7) or (subject 3, 6, 9)? Or I am so lucky that it is the > >> average all processed subjects? > >> 3 Is there a proper way to work in parallel than my stone-age way? > >> 4 I searched the wiki and found some slides and pages which may help but > >> not > >> answering the above question. Would you please suggest an example "full" > >> script of analysis? > >> Thank you very much! > >> ======= > >> My environment: 64-bit Linux with OpenSUSE. 8-CPUs/32G mem > >> Script: > >> ------------- > >> #!/bin/csh > >> echo "beginning ..." > >> > >> #environment setup > >> source ~/1tests/FreeSurferEnv.csh > >> > >> #Set environment and get the filelist > >> set raw_dir = '~/2rawdata/' > >> set fileNameList = `ls {$raw_dir}` > >> > >> #Try all the subjects in a loop > >> foreach file ($fileNameList) > >> echo "Now processing file ($file): ..." > >> echo "" > >> set inName = ($raw_dir$file) > >> recon-all -i $inName -s $file -autorecon-all > >> end > >> > >> echo "done!" > >> ------------- > >> ======= > >> > >> > >> > >> > >> > > > > 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. > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20140206/2… > > ------------------------------ > > Message: 43 > Date: Thu, 6 Feb 2014 15:31:24 +0000 > From: Kami Koldewyn <k.koldewyn(a)bangor.ac.uk> > Subject: [Freesurfer] basic math operations for volume labels? > To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: <CF195B46.27416%pss245(a)bangor.ac.uk> > Content-Type: text/plain; charset="us-ascii" > > Hi All, > > I was thinking that there was a freesurfer tool that performed simple math operations on volumetric labels (similar to those that mris_label_calc performs for surface labels) but I can't seem to find one. Is there such a tool that I am simply missing? I am hoping to easily create non-overlapping labels from a set of currently overlapping labels. > > Thanks, > > > -kami > > > > Rhif Elusen Gofrestredig 1141565 - Registered Charity No. 1141565 > > Gall y neges e-bost hon, ac unrhyw atodiadau a anfonwyd gyda hi, gynnwys deunydd cyfrinachol ac wedi eu bwriadu i'w defnyddio'n unig gan y sawl y cawsant eu cyfeirio ato (atynt). Os ydych wedi derbyn y neges e-bost hon trwy gamgymeriad, rhowch wybod i'r anfonwr ar unwaith a dilewch y neges. Os na fwriadwyd anfon y neges atoch chi, rhaid i chi beidio a defnyddio, cadw neu ddatgelu unrhyw wybodaeth a gynhwysir ynddi. Mae unrhyw farn neu safbwynt yn eiddo i'r sawl a'i hanfonodd yn unig ac nid yw o anghenraid yn cynrychioli barn Prifysgol Bangor. Nid yw Prifysgol Bangor yn gwarantu bod y neges e-bost hon neu unrhyw atodiadau yn rhydd rhag firysau neu 100% yn ddiogel. Oni bai fod hyn wedi ei ddatgan yn uniongyrchol yn nhestun yr e-bost, nid bwriad y neges e-bost hon yw ffurfio contract rhwymol - mae rhestr o lofnodwyr awdurdodedig ar gael o Swyddfa Cyllid Prifysgol Bangor. > > This email and any attachments may contain confidential material and is solely for the use of the intended recipient(s). If you have received this email in error, please notify the sender immediately and delete this email. If you are not the intended recipient(s), you must not use, retain or disclose any information contained in this email. Any views or opinions are solely those of the sender and do not necessarily represent those of Bangor University. Bangor University does not guarantee that this email or any attachments are free from viruses or 100% secure. Unless expressly stated in the body of the text of the email, this email is not intended to form a binding contract - a list of authorised signatories is available from the Bangor University Finance Office. > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20140206/0… > > ------------------------------ > > Message: 44 > Date: Thu, 6 Feb 2014 10:40:40 -0500 (EST) > From: Maritza Ebling <maritza(a)nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] basic math operations for volume labels? > To: Kami Koldewyn <k.koldewyn(a)bangor.ac.uk> > Cc: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: <alpine.LRH.2.03.1402061040110.7836(a)nmr.mgh.harvard.edu> > Content-Type: text/plain; charset="iso-8859-15" > > mris_calc should work for this purpose. Run mris_calc -h to see the > options > > > On Thu, 6 Feb 2014, Kami Koldewyn > wrote: > > > Hi All, > > > > I was thinking that there was a freesurfer tool that performed simple math operations on volumetric labels (similar to > > those that mris_label_calc performs for surface labels) but I can't seem to find one. ?Is there such a tool that I am > > simply missing? I am hoping to easily create non-overlapping labels ?from a set of currently overlapping labels. > > > > Thanks, > > > > > > -kami > > > > ? > > > > Rhif Elusen Gofrestredig 1141565 - Registered Charity No. 1141565 > > > > Gall y neges e-bost hon, ac unrhyw atodiadau a anfonwyd gyda hi, gynnwys deunydd cyfrinachol ac wedi eu bwriadu i'w > > defnyddio'n unig gan y sawl y cawsant eu cyfeirio ato (atynt). Os ydych wedi derbyn y neges e-bost hon trwy gamgymeriad, > > rhowch wybod i'r anfonwr ar unwaith a dilewch y neges. Os na fwriadwyd anfon y neges atoch chi, rhaid i chi beidio a > > defnyddio, cadw neu ddatgelu unrhyw wybodaeth a gynhwysir ynddi. Mae unrhyw farn neu safbwynt yn eiddo i'r sawl a'i > > hanfonodd yn unig ac nid yw o anghenraid yn cynrychioli barn Prifysgol Bangor. Nid yw Prifysgol Bangor yn gwarantu bod y > > neges e-bost hon neu unrhyw atodiadau yn rhydd rhag firysau neu 100% yn ddiogel. Oni bai fod hyn wedi ei ddatgan yn > > uniongyrchol yn nhestun yr e-bost, nid bwriad y neges e-bost hon yw ffurfio contract rhwymol - mae rhestr o lofnodwyr > > awdurdodedig ar gael o Swyddfa Cyllid Prifysgol Bangor. > > > > This email and any attachments may contain confidential material and is solely for the use of the intended recipient(s). > > If you have received this email in error, please notify the sender immediately and delete this email. If you are not the > > intended recipient(s), you must not use, retain or disclose any information contained in this email. Any views or > > opinions are solely those of the sender and do not necessarily represent those of Bangor University. Bangor University > > does not guarantee that this email or any attachments are free from viruses or 100% secure. Unless expressly stated in > > the body of the text of the email, this email is not intended to form a binding contract - a list of authorised > > signatories is available from the Bangor University Finance Office. > > > > > > > -------------- next part -------------- > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > ------------------------------ > > Message: 45 > Date: Thu, 6 Feb 2014 11:42:38 -0500 > From: "Caspar M. Schwiedrzik" <cschwiedrz(a)mail.rockefeller.edu> > Subject: [Freesurfer] FSFAST surface-based analysis to w-file > To: "Freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: > <CA+bX-38mTMnwaPgarB8rBi_79fpTRSMW4enPO9jCsGuW5zXSkg(a)mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Hi! > I need to export results from a surface-based analysis in FSFAST (v5.1) to > another program (Caret) that accepts .w files. I was wondering what the > recommended way of doing this is. > It seems that mri_surf2surf will do the trick? > Do I set the source and the target to be the same? > Thanks, Caspar > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20140206/3… > > ------------------------------ > > Message: 46 > Date: Thu, 6 Feb 2014 18:56:53 +0200 > From: Rotem Saar <saar.rotem(a)gmail.com> > Subject: Re: [Freesurfer] Mean diffusivity > To: freesurfer(a)nmr.mgh.harvard.edu > Message-ID: > <CAMjFEmZYHwMmZE98K5jNamwYaa8+=2kHq7O2Ee58XSJi_QFAPg(a)mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Dear Doug, > > Sorry - I'm probably missing something, as trying to write what u suggested > (see below email history) didn't work (not sure what am I doing wrong). > I'm copying here what I did to get the average FA value to each region. Can > u PLEASE write what do I need to change in order to get the MD value > instead for the FA value, but keep the same format of the output ? > Thanks, I really appreciate the help !! > > dt_recon --i /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/I160.dcm --s > FOLDER-NAME --o /usr/local/freesurfer/subjects/FOLDER-NAME/DTI --b > /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/bvals.bval > /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/bvecs.bvec > > mri_vol2vol --mov /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/lowb.nii \ > --targ > /usr/local/freesurfer/subjects/FOLDER-NAME/mri/wmparc.mgz \ > --inv --interp nearest --o > /usr/local/freesurfer/subjects/FOLDER-NAME/mri/wmparc2diff.mgz \ > --reg > /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/register.dat --no-save-reg > > mri_vol2vol --mov /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/lowb.nii \ > --targ > /usr/local/freesurfer/subjects/FOLDER-NAME/mri/aparc+aseg.mgz \ > --inv --interp nearest --o > /usr/local/freesurfer/subjects/FOLDER-NAME/mri/aparc+aseg2diff.mgz \ > --reg > /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/register.dat --no-save-reg > > mri_mask /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/fa.nii \ > /usr/local/freesurfer/subjects/FOLDER-NAME/mri/wmparc2diff.mgz \ > /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/fa-masked.mgz > > mri_segstats --seg > /usr/local/freesurfer/subjects/FOLDER-NAME/mri/wmparc2diff.mgz --ctab > $FREESURFER_HOME/FreeSurferColorLUT.txt --i > /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/fa-masked.mgz --sum > /usr/local/freesurfer/subjects/FOLDER-NAME/stats/all_stats_fa-masked > > > Message: 26 > Date: Tue, 04 Feb 2014 11:10:25 -0500 > From: Douglas N Greve <greve(a)nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] Mean diffusivity > To: freesurfer(a)nmr.mgh.harvard.edu > Message-ID: <52F110F1.5050007(a)nmr.mgh.harvard.edu> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > > Use mri_label2vol to transfer the wmparc.mgz into the DTI space, then > use mri_segstats with --seg-erode 1 to compute summaries of the MD in > each region > doug > > > On 02/03/2014 10:45 PM, Rotem Saar wrote: > > Dear freesurfer experts, > > > > Can u please advise on how to extract the mean diffusivity value for > > each ROI from the wmparc file ? > > I know how to extract the FA value, but interested in the MD value > > also for the same regions. > > > > Thanks > > Rotem > > Rotem Saar-Ashkenazy > > Department of Brain and Cognitive Science > > Ben Gurion University of the Negev > > Beer-Sheva 84105 > > Israel > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > Rotem Saar-Ashkenazy > Department of Brain and Cognitive Science > Ben Gurion University of the Negev > Beer-Sheva 84105 > Israel > > > 2014-02-04 5:45 GMT+02:00 Rotem Saar <saar.rotem(a)gmail.com>: > > > Dear freesurfer experts, > > > > Can u please advise on how to extract the mean diffusivity value for each > > ROI from the wmparc file ? > > I know how to extract the FA value, but interested in the MD value also > > for the same regions. > > > > Thanks > > Rotem > > Rotem Saar-Ashkenazy > > Department of Brain and Cognitive Science > > Ben Gurion University of the Negev > > Beer-Sheva 84105 > > Israel > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20140206/c… > > ------------------------------ > > Message: 47 > Date: Thu, 06 Feb 2014 11:57:38 -0500 > From: Douglas N Greve <greve(a)nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] Actual Thickness Values > To: freesurfer(a)nmr.mgh.harvard.edu > Message-ID: <52F3BF02.7030509(a)nmr.mgh.harvard.edu> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > > On 02/05/2014 05:07 PM, Natasha Haris wrote: > > Dear Freesurfers, > > > > My measure is thickness and I want to be able to get a list of all the > > maximum thickness values at the centers of each significant cluster - > > is there any simple way to do that on QDEC? > Do you want the maximum across the cluster or the thickness at the > center of the cluster? Either way, you can't do that in QDEC. You can > use matlab to load in the thickness maps and cluster maps and then do > the search you want. > > Also, I would like to get an average of all of the thickness values at > > each voxel for each cluster - is there a way to do that as well? > Same as above > doug > > > > Many thanks, > > Natasha > > > > > > _______________________________________________ > > 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: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > > > ------------------------------ > > Message: 48 > Date: Thu, 6 Feb 2014 10:59:30 -0600 (CST) > From: Jon Wieser <wieser(a)uwm.edu> > Subject: Re: [Freesurfer] Fwd: trac-all -path error > To: Anastasia Yendiki <ayendiki(a)nmr.mgh.harvard.edu> > Cc: freesurfer <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: <1294716909.3155649.1391705970071.JavaMail.root(a)uwm.edu> > Content-Type: text/plain; charset="utf-8" > > > Hi Anastasia, > I looked at the dlabel/diff/Aparc+aseg overlayed on the dmri/dtifit_FA.nii.gz > the alignments is way off (in freeview, in the coronal view, the aparc+seg is rotated 45 degrees anti-clockwise), and parts of the FA map in the L ILF area are missing. the original DTI is not missing data in these areas. I have attached screenshots > Jon > > ----- Original Message ----- > From: "Anastasia Yendiki" <ayendiki(a)nmr.mgh.harvard.edu> > To: "Jon Wieser" <wieser(a)uwm.edu> > Cc: freesurfer(a)nmr.mgh.harvard.edu > Sent: Wednesday, February 5, 2014 6:35:12 PM > Subject: Re: [Freesurfer] Fwd: trac-all -path error > > > Hi Jon - You need to look at the aparc+aseg after it has been mapped to > diffusion space. It's possible that it looks fine in its original space > but then maybe something goes wrong with the registration. So you should > look at the aparc+aseg and aparc+aseg_mask files from the tracula > dlabel/diff directory. These are in diffusion space and you can overlay > them on the FA map to see if there's anything strange in the ILF area. > > Hope this helps, > a.y > > On Tue, 14 Jan 2014, Jon Wieser wrote: > > > Hi anastasia > > I looked at the brainmask and the aparc+aseg. I did see anything missing in the area of the left ILF. > > I have attached the files. can you take a look at them? > > Thanks > > JOn > > > > ----- Original Message ----- > > From: "Anastasia Yendiki" <ayendiki(a)nmr.mgh.harvard.edu> > > To: "Jon Wieser" <wieser(a)uwm.edu> > > Cc: "freesurfer" <freesurfer(a)nmr.mgh.harvard.edu> > > Sent: Friday, January 10, 2014 6:15:23 PM > > Subject: Re: [Freesurfer] Fwd: trac-all -path error > > > > > > Hi Jon - Have you checked the brain mask and aparc+aseg for this subject? > > Anything missing there that might affect the left ILF? > > > > a.y > > > > On Wed, 8 Jan 2014, Jon Wieser wrote: > > > >> > >> Dear freesurfer experts > >> I'm getting the following error when runing trac-all -c dmrirc_single_subject -path > >> > >> > >> Loading initial proposal SD's from /BrainLabDocs/Studies/Nicotine_MJ_Ecstasy_Study/Data/MRI/N1084/data/freesurfer/dlabel/diff/lh.ilf_AS_avg23_mni_flt_cpts_5_std.txt > >> Processing pathway 3 of 18... > >> Initializing MCMC > >> Segmentation fault > >> Darwin cerebrum.uwm.edu 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:33:36 PDT 2011; root:xnu-1504.15.3~1/RELEASE_I386 i386 > >> > >> > >> I have attached the trac-all.log and trac-all.error files > >> > >> I am running tracula 5.3 > >> > > > > > > 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. > > > > > -------------- next part -------------- > A non-text attachment was scrubbed... > Name: FA.jpg > Type: image/jpeg > Size: 55293 bytes > Desc: not available > Url : http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20140206/3… > -------------- next part -------------- > A non-text attachment was scrubbed... > Name: aparc_aseg.jpg > Type: image/jpeg > Size: 73908 bytes > Desc: not available > Url : http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20140206/3… > > ------------------------------ > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > End of Freesurfer Digest, Vol 120, Issue 8 > ******************************************

2 1

Yeo parcellation
by stdp82＠virgilio.it 07 Feb '14

07 Feb '14

Hi list, I have download the files of Yeo parcellation from ftp://surfer.nmr.mgh.harvard.edu/pub/data/Yeo_JNeurophysiol11_MNI152.zip. I have two questions, please. A- Which is the directory where I should put these files?B-I have already run by recon-all -all all my subjects. How can I added to them Yeo parcellation?C-I'd like also calculate the cortical thickness for each Yeo's ROI. Is possible with aparcstats2table? Thanks. Regards, Stefano

2 1

Problem with reg-feat2anat and tcshell: Newer version of reg-feat2anat available?
by Greg Reckless 06 Feb '14

06 Feb '14

I am having the same problem with a newer version of tcshell and reg-feat2anat as discussed in threads below. Has this been resolved? If not, could a working link to the updated version mentioned previously be reposted. https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2013-June/030473.html https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2013-September/033521… Thanks, Greg

5 8

Desikan-Killiany parcellations of SI+SII and IPL
by Estephan Moana 06 Feb '14

06 Feb '14

Dear Freesurfer experts, Is it a fair assumption that the Desikan-Killiany parcellations of the postcentral gyrus is roughly equivalent to SI+SII, and that the supramarginal gyrus ≈ inferior parietal lobule? I used SI, SII and IPL ROI masks in some FSL analyses, and would like to use similar ROIs for Freesurfer results. Thank you. Estephan Moana-Filho, D.D.S., M.S. Ph.D. Candidate Clinical Fellow, Oral & Maxillofacial Pain Program Center for Pain Research and Innovation UNC School of Dentistry moana(a)unc.edu

3 2

Re: [Freesurfer] Fwd: trac-all -path error
by Anastasia Yendiki 06 Feb '14

06 Feb '14

So there's your culprit. You need to fix the intra-subject (diffusion-to-T1) registration. Did you use flirt or bbregister for that? On Thu, 6 Feb 2014, Jon Wieser wrote: > Hi Anastasia, > I looked at the dlabel/diff/Aparc+aseg overlayed on the dmri/dtifit_FA.nii.gz > the alignemenst is way off (in freeview, in the coronal view, the aparc+seg is rotated 45 degrees anti-clockwise), and parts of the FA map in the L ILF area are missing. the original DTI is not missing data in these areas. I have attached screenshots > Jon > > > > ----- Original Message ----- > From: "Anastasia Yendiki" <ayendiki(a)nmr.mgh.harvard.edu> > To: "Jon Wieser" <wieser(a)uwm.edu> > Cc: freesurfer(a)nmr.mgh.harvard.edu > Sent: Wednesday, February 5, 2014 6:35:12 PM > Subject: Re: [Freesurfer] Fwd: trac-all -path error > > > Hi Jon - You need to look at the aparc+aseg after it has been mapped to > diffusion space. It's possible that it looks fine in its original space > but then maybe something goes wrong with the registration. So you should > look at the aparc+aseg and aparc+aseg_mask files from the tracula > dlabel/diff directory. These are in diffusion space and you can overlay > them on the FA map to see if there's anything strange in the ILF area. > > Hope this helps, > a.y > > On Tue, 14 Jan 2014, Jon Wieser wrote: > >> Hi anastasia >> I looked at the brainmask and the aparc+aseg. I did see anything missing in the area of the left ILF. >> I have attached the files. can you take a look at them? >> Thanks >> JOn >> >> ----- Original Message ----- >> From: "Anastasia Yendiki" <ayendiki(a)nmr.mgh.harvard.edu> >> To: "Jon Wieser" <wieser(a)uwm.edu> >> Cc: "freesurfer" <freesurfer(a)nmr.mgh.harvard.edu> >> Sent: Friday, January 10, 2014 6:15:23 PM >> Subject: Re: [Freesurfer] Fwd: trac-all -path error >> >> >> Hi Jon - Have you checked the brain mask and aparc+aseg for this subject? >> Anything missing there that might affect the left ILF? >> >> a.y >> >> On Wed, 8 Jan 2014, Jon Wieser wrote: >> >>> >>> Dear freesurfer experts >>> I'm getting the following error when runing trac-all -c dmrirc_single_subject -path >>> >>> >>> Loading initial proposal SD's from /BrainLabDocs/Studies/Nicotine_MJ_Ecstasy_Study/Data/MRI/N1084/data/freesurfer/dlabel/diff/lh.ilf_AS_avg23_mni_flt_cpts_5_std.txt >>> Processing pathway 3 of 18... >>> Initializing MCMC >>> Segmentation fault >>> Darwin cerebrum.uwm.edu 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:33:36 PDT 2011; root:xnu-1504.15.3~1/RELEASE_I386 i386 >>> >>> >>> I have attached the trac-all.log and trac-all.error files >>> >>> I am running tracula 5.3 >>> >> >> >> 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. >> >>

2 2

basic math operations for volume labels?
by Kami Koldewyn 06 Feb '14

06 Feb '14

Hi All, I was thinking that there was a freesurfer tool that performed simple math operations on volumetric labels (similar to those that mris_label_calc performs for surface labels) but I can't seem to find one. Is there such a tool that I am simply missing? I am hoping to easily create non-overlapping labels from a set of currently overlapping labels. Thanks, -kami Rhif Elusen Gofrestredig 1141565 - Registered Charity No. 1141565 Gall y neges e-bost hon, ac unrhyw atodiadau a anfonwyd gyda hi, gynnwys deunydd cyfrinachol ac wedi eu bwriadu i'w defnyddio'n unig gan y sawl y cawsant eu cyfeirio ato (atynt). Os ydych wedi derbyn y neges e-bost hon trwy gamgymeriad, rhowch wybod i'r anfonwr ar unwaith a dilewch y neges. Os na fwriadwyd anfon y neges atoch chi, rhaid i chi beidio a defnyddio, cadw neu ddatgelu unrhyw wybodaeth a gynhwysir ynddi. Mae unrhyw farn neu safbwynt yn eiddo i'r sawl a'i hanfonodd yn unig ac nid yw o anghenraid yn cynrychioli barn Prifysgol Bangor. Nid yw Prifysgol Bangor yn gwarantu bod y neges e-bost hon neu unrhyw atodiadau yn rhydd rhag firysau neu 100% yn ddiogel. Oni bai fod hyn wedi ei ddatgan yn uniongyrchol yn nhestun yr e-bost, nid bwriad y neges e-bost hon yw ffurfio contract rhwymol - mae rhestr o lofnodwyr awdurdodedig ar gael o Swyddfa Cyllid Prifysgol Bangor. This email and any attachments may contain confidential material and is solely for the use of the intended recipient(s). If you have received this email in error, please notify the sender immediately and delete this email. If you are not the intended recipient(s), you must not use, retain or disclose any information contained in this email. Any views or opinions are solely those of the sender and do not necessarily represent those of Bangor University. Bangor University does not guarantee that this email or any attachments are free from viruses or 100% secure. Unless expressly stated in the body of the text of the email, this email is not intended to form a binding contract - a list of authorised signatories is available from the Bangor University Finance Office.

3 4

optseq2 tnullmax
by Wei-chun Wang 06 Feb '14

06 Feb '14

Hi, I am trying to set up a design using optseq2, but the tnullmax command doesn't seem to be functioning. the script runs and outputs files, but they exceed the tnullmax which i specify. is anyone familiar with this issue? this is what i am inputting: --tr 2 --psdwin 0 20 1 --ev easy 4 36 --ev hard 4 36 --nsearch 100000 --nkeep 1000 --ntp 234 --o output --tnullmax 6 --tnullmin 1 thanks. wei-chun

2 1

possible to render hippocampal subfield segmentations as 3D structures?
by Salil Soman 06 Feb '14

06 Feb '14

Hi, I generated hippocampal subfield segmentations, can generate statistics, but was wondering if there was a way to visualized the subfield segmentations as a 3D structure? (e.g. like the figure in this paper: http://niacal.northwestern.edu/projects/17) Thank you for your consideration. Best wishes, -- Salil Soman, MD, MS Postdoctoral Research Fellow - Stanford Radiological Sciences Laboratory Fellow - Palo Alto War Related Illness and Injury Study Center WOC Neuroradiology Attending - Veterans Affairs Palo Alto Health Care System

3 3

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