Freesurfer

freesurfer@nmr.mgh.harvard.edu

30132 discussions

question about annot files and principal curvatures
by Peter Savadjiev 19 Jan '12

19 Jan '12

Hi, In order to obtain the vertices of lh.curv that belong to a specific freesurfer cortical ROI, such as 'superiortemporal', or 'superiorfrontal', etc., I use the information in lh.aparc.annot, as described for example in http://surfer.mnr.mgh.harvard.edu/fswiki/AnnotFiles/ . However, now I am interested in looking at the principal curvatures in the same cortical ROI. To obtain the principal curvatures, I use mris_curvature -max $SUBJECTS_DIR/caseXYZ/surf/lh.<some_surface> and mris_curvature -min $SUBJECTS_DIR/caseXYZ/surf/lh.<some_surface> My question is, which surface should I use in <some_surface> so that I can still identify the vertices of interest using lh.aparc.annot? In other words, how do I ensure that the output of the mris_curvature command has the surface vertices stored in the same order as lh.curv? Any help will be much appreciated! Thanks, Peter

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Re: [Freesurfer] Fw : Re: get_4dfp_dimoe problem
by LAOUCHEDI MAKHLOUF 19 Jan '12

19 Jan '12

hi everyone i want just to inform you that it is ok with my problem of the huge pathnames generated by our cluster thank you very much --- En date de : Sam 7.1.12, Nick Schmansky <nicks(a)nmr.mgh.harvard.edu> a écrit : De: Nick Schmansky <nicks(a)nmr.mgh.harvard.edu> Objet: Re: [Freesurfer] Fw : Re: get_4dfp_dimoe problem À: "LAOUCHEDI MAKHLOUF" <laoumakhl(a)yahoo.fr> Cc: Freesurfer(a)nmr.mgh.harvard.edu Date: Samedi 7 janvier 2012, 21h28 laouchedi, the file 'endianio.c' is not a module that can be installed by the end-user. it is source code. did you install the files that i referred to in my prior email to the list? those were rebuilt using endianio.c, and are found here: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/linux-centos4_x86… and are named *4dfp. copy those files to your $FREESURFER_HOME/bin. n. On Fri, 2012-01-06 at 14:29 +0000, LAOUCHEDI MAKHLOUF wrote: > > > --- En date de : Ven 6.1.12, LAOUCHEDI MAKHLOUF <laoumakhl(a)yahoo.fr> a > écrit : > > De: LAOUCHEDI MAKHLOUF <laoumakhl(a)yahoo.fr> > Objet: Re: [Freesurfer] get_4dfp_dimoe problem > À: "AviSnyder" <avi(a)npg.wustl.edu> > Date: Vendredi 6 janvier 2012, 15h28 > > hi everyone > i just remind you of my problem of the file > name which was too long on our cloud; you advised us to > download the endianio.c module, we did this and we installed > it then we've run recon-all but we still have an error > message : > > $Id: imgreg_4dfp.c,v 1.4 2010/02/27 01:41:53 nicks Exp $ > Getifh: /var/spool/pbs/tmpdir/171598.gridgate.scg.nuigalway.ie/https_3a_2f_2falbalonga.cnaf.infn.it_3a9000_2ff_5f9HZFcSVMqQu-a5r7O6fQ/ws28210/.tmp/d924f86d-ff81-451c-9d0b-f655f3361f66/systemExecTask5971557784595886118/freesurfer/average/711-2B_as_mni_average_305_mnone.4dfp.ifh read error, imgfile='/var/spool/pbs/tmpdir/171598.gridgate.scg.nuigalway.ie/https_3a_2f_2falbalonga.cnaf.infn.it_3a9000_2ff_5f9HZFcSVMqQu-a5r7O6fQ/ws28210/.tmp/d924f86d-ff81-451c-9d0b-f655f3361f66/systemExecTask5971557784595886118/freesurfer/average/711-2B_as_mni_average_305_mnone.4dfp.img' > Segmentation fault > ERROR: > 'imgreg_4dfp /var/spool/pbs/tmpdir/171598.gridgate.scg.nuigalway.ie/https_3a_2f_2falbalonga.cnaf.infn.it_3a9000_2ff_5f9HZFcSVMqQu-a5r7O6fQ/ws28210/.tmp/d924f86d-ff81-451c-9d0b-f655f3361f66/systemExecTask5971557784595886118/freesurfer/average/711-2C_as_mni_average_305 /var/spool/pbs/tmpdir/171598.gridgate.scg.nuigalway.ie/https_3a_2f_2falbalonga.cnaf.infn.it_3a9000_2ff_5f9HZFcSVMqQu-a5r7O6fQ/ws28210/.tmp/d924f86d-ff81-451c-9d0b-f655f3361f66/systemExecTask5971557784595886118/freesurfer/average/711-2B_as_mni_average_305_mask talsrcimg_g11 none talsrcimg_to_711-2C_as_mni_average_305_t4 4355' failed! status=139 > ERROR: mpr2mni305 execution aborted > > i've attached the recon-all.log contained in the scripts dir > and the log file contained in mri/transforms dir > > > thank you very much > > > > --- En date de : Mer 4.1.12, Snyder, Avi <avi(a)npg.wustl.edu> a > écrit : > > De: Snyder, Avi <avi(a)npg.wustl.edu> > Objet: Re: [Freesurfer] get_4dfp_dimoe problem > À: "Bruce Fischl" <fischl(a)nmr.mgh.harvard.edu> > Cc: "LAOUCHEDI MAKHLOUF" <laoumakhl(a)yahoo.fr>, > "Freesurfer(a)nmr.mgh.harvard.edu" > <Freesurfer(a)nmr.mgh.harvard.edu> > Date: Mercredi 4 janvier 2012, 1h31 > > I don't think there are any special env variables. > It may be that the environment in which FreeSurfer is > being run simply > generates huge pathnames. > A few months ago I revised the module containing > get_4dfp_dimoe() to > double the size of filename buffers. > This module (endianio.c) is attached. Theoretically, > compiling with this > revised source could fix the problem. > > Avi > ----------------------------- > On 1/3/12 6:04 PM, "Bruce Fischl" > <fischl(a)nmr.mgh.harvard.edu> wrote: > > >Hi Avi > > > >just running recon-all I think. Is there an env > variable you use to > >specify > >a tmp dir or something? > > > >thanks > >Bruce > > > >On Tue, 3 Jan 2012, Snyder, Avi wrote: > > > >> It looks like both the command (imgreg_4dfp) and > argument > >> (.../711-2B_as_mni_average_305_mask.4dfp.img) > fields are garbled. > >> Evidently, operating system paths have not been > correctly set. > >> The 4dfp suite of tools is available and probably > could be installed but > >> I'm not sure that is what is wanted. > >> I don't understand what LAOUCHEDI MAKHLOUF is > trying to do. > >> > >> AZS > >> > ----------------------------------------------------- > >> On 1/3/12 10:40 AM, "Bruce Fischl" > <fischl(a)nmr.mgh.harvard.edu> wrote: > >> > >>> this is actually not part of FreeSurfer proper, > but rather something > >>>that > >>> Avi Synder (ccd) was kind enough to contribute. > Avi: can you comment? > >>> > >>> thanks > >>> Bruce > >>> On > >>> Tue, 3 Jan 2012, LAOUCHEDI MAKHLOUF wrote: > >>> > >>>> hi everyone > >>>> we run recon-all on a cloud and we obtained this > error: > >>>> > >>>> mpr2mni305 failed, see > transforms/talairach_avi.log > >>>> > >>>> The log says the file name is too long perhaps > because of the tmp dir > >>>> file > >>>> names: > >>>> > >>>> > >>>> > >>>>get_4dfp_dimoe:/var/spool/pbs/tmpdir/169536.gridgate.scg.nuigalway.ie/h > >>>>tt > >>>> ps_3a_2f_2fwms01. > >>>> > >>>> > >>>>ihep.ac.cn_3a9000_2fM72N6GZlEC95pE7rgch5YQ/ws15158/.tmp/8d3aa62d-5994-4 > >>>>7e > >>>> 5- > >>>> > >>>> > >>>>ba6d-031806ec9ffb/systemExecTask8201883777111446775/freesurfer/average/ > >>>>71 > >>>> 1- > >>>> 2B_as_mni_average_305_mask.4dfp.img filename too > long > >>>> ERROR: > >>>> > >>>>'imgreg_4dfp/var/spool/pbs/tmpdir/169536.gridgate.scg.nuigalway.ie/http > >>>>s_ > >>>> 3a_2f_2fwms01. > >>>> > >>>> > >>>>ihep.ac.cn_3a9000_2fM72N6GZlEC95pE7rgch5YQ/ws15158/.tmp/8d3aa62d-5994-4 > >>>>7e > >>>> 5- > >>>> > >>>> > >>>>ba6d-031806ec9ffb/systemExecTask8201883777111446775/freesurfer/average/ > >>>>71 > >>>> 1- > >>>> 2C_as_mni_average_305 > >>>> /var/spool/pbs/tmpdir/169536.gridgate.scg.nuigalway.i > >>>> > >>>> > >>>>e/https_3a_2f_2fwms01.ihep.ac.cn_3a9000_2fM72N6GZlEC95pE7rgch5YQ/ws1515 > >>>>8/ > >>>> .t > >>>> > >>>> > >>>>mp/8d3aa62d-5994-47e5-ba6d-031806ec9ffb/systemExecTask82018837771114467 > >>>>75 > >>>> /f > >>>> > reesurfer/average/711-2B_as_mni_average_305_masktalsrcimg_g11 none > >>>> talsrcimg_to_711-2C_as_mni_average_305_t4 4355' > failed! status=255 > >>>> > >>>> > >>>> knowing that it is difficult for us to do things > differently (to > >>>>change > >>>> the > >>>> path); is it possible to do something in > freesurfer to work with > >>>>thesse > >>>> filenames ? > >>>> > >>>> thanks for your help > >> > >> > >> > >> > > > > > >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 _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] Freesurfer Digest, Vol 75, Issue 15
by Sebastian Moeller 19 Jan '12

19 Jan '12

Hi Fred, yu probably checked the following already, but on the off chance you have not... Maybe you have set X11 to 256 color mode? Start X11.app (from /Applications/Utilities) go to the X11 menu, select Preferences..., switch to the tab called output and see what is selected for Colors. If it is set to 256 Colors you have your root cause, just switch to something higher and all should be fine. best Sebastian On May 9, 2010, at 9:00 AM, freesurfer-request(a)nmr.mgh.harvard.edu wrote: > 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. tksurfer/tkmedit display color fix in OSX 10.6? (Fred Dick) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Sun, 9 May 2010 15:34:35 +0100 > From: Fred Dick <fdick(a)crl.ucsd.edu> > Subject: [Freesurfer] tksurfer/tkmedit display color fix in OSX 10.6? > To: freesurfer(a)nmr.mgh.harvard.edu > Message-ID: <873B33F2-3339-4871-9395-1EFEEC1EFAAB(a)crl.ucsd.edu> > Content-Type: text/plain; charset="us-ascii" > > Dear all > > This is a pretty minor issue (except for figure making) - but has anyone experienced and then fixed a display problem in tksurfer/tkmedit in OSX 10.6 (possibly also 10.5) where graphics seem to be drawn only with 256 colors, thereby giving images a kind of contour-plot look? (See attached image below). [Running 10.6.3, i686-apple-darwin10-gcc-4.2.1, tksurfer 1.309 (yes, older), tkmedit v 1.330] > > I looked around the mail archives but didn't see anyone else commenting on this, but do know someone else having the same issue, so would be happy for any suggestions. > > Thanks, > Fred > > >

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Re: [Freesurfer] Freesurfer flips brains?
by Léoné, F.T.M. (Frank) 19 Jan '12

19 Jan '12

Hi Douglas, Ah, makes sense, sorry for that. I do most of the work in SPM, so: - I have a highres structural scan, nii file format - I convert it to a surface using recon-all - Coregister the highres structural to the functional scan, so it is in the voxel size and orientation as the functional scans (SPM) - I try to bbregister the coregistered and resliced T1 with the surface using something like: bbregister --s S7_FS --mov ~/Data/Exp1_Saccades_phase/S7_FS/mri/orig/flipped_rmasked_str_S2_seler20090508.nii --init-spm --reg ~/Data/Exp1_Saccades_phase/S7_FS/mri/orig/register.partial.auto.dat --t1 and view it with vglrun tkregister2 --mov /home/action/fraleo/Data/Exp1_Saccades_phase/S7_FS/mri/orig/flipped_rmasked_str_S2_seler20090508.nii --reg /home/action/fraleo/Data/Exp1_Saccades_phase/S7_FS/mri/orig/register.partial.auto.dat --surf Here you see that I already use a flipped structural scan. If I do it like this, bbregister converges to a nice and correct solution (everything aligns). If I don't, tkregister2 showms unregistered struc and func, while it is obvious it would be roughly aligned if you would flip either of them. In addition/in general: What would be the recommended way to do the coregistration etc. if you do all you analyses in SPM? Would it for example be better to coregistrate and reslice all functionals with the structural, so they are automatically aligned with the surface? Now I have a structural which is coregistered with the funcional and I realign that one, but that makes for one extra step where it can go wrong. Don't think this is related to the flip, but I also have a few alignment problems for other subjects. Thanks a lot in advance, best, Frank ----- "Douglas N Greve" <greve(a)nmr.mgh.harvard.edu> schreef: > Van: "Douglas N Greve" <greve(a)nmr.mgh.harvard.edu> > Aan: "Frank Leoné" <f.leone(a)donders.ru.nl> > Cc: freesurfer(a)nmr.mgh.harvard.edu > Verzonden: Woensdag 18 januari 2012 18:34:31 > Onderwerp: Re: [Freesurfer] Freesurfer flips brains? > > Hi Frank, we'll need a lot more detail. Are you doing all of this in > FreeSurfer? What are your command lines? How are you evaluating > whether > volumes are flipped? > doug > > Léoné wrote: > > Dear all, > > > > I must be missing something really obvious, but it seems my brains > are flipped. What I do: > > > > - I have a highres structural scan, nii file format > > - I convert it to a surface using recon-all > > - Coregister the highres structural to the functional scan, so it is > in the voxel size and orientation as the functional scans > > - I try to bbregister the coregistered and resliced T1 with the > surface > > > > But then: hey, it doesn't fit, my low-res T1 is flipped compared to > my y surface, hence to my original T1. So is it indeed true that my T1 > might have been flipped? If so, does it make a wrong assumption on > neurological vs radiological convention, or what is going on? > > > > Thanks in advance, > > > > best, > > > > Frank > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > > > The information in this e-mail is intended only for the person to whom > it is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you > in error > but does not contain patient information, please contact the sender > and properly > dispose of the e-mail.

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dividing a label into equal parts
by Ritobrato Datta 18 Jan '12

18 Jan '12

Is there a way to divide a surface label like V1 into equal parts (say 10 parts) either along its length or width and save each part as a separate label ? Drawing them in tkmedit is quite crude and not very accurate. Please let me know. Thanks Ri

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Re: [Freesurfer] Thanks so much!
by Lilla Zollei 18 Jan '12

18 Jan '12

Yes, but then you would not use --reg $TUTORIAL_DIR/$subj/dtrecon/register.dat with mri_vol2vol. --Lilla On Wed, 18 Jan 2012, Antonella Kis wrote: > Finally I understood! THANKS so much Lilla! > > So I can use the nearst interp if while resampling in the CVS space my input (--mov) volume is replaced from --mov $TUTORIAL_DIR/$subj/dtrecon/fa-masked.mgz \ > with for example /media/2Tra/Antonella_2011/DTI_FS/dtrecon_cvs/P04_cvs/P04/mri/wmparc.mgz? > > > THANKS SO MUCH! > Antonella > > ___________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________ > From: Lilla Zollei <lzollei(a)nmr.mgh.harvard.edu> > To: Antonella Kis <atorok9(a)yahoo.com> > Cc: freesurfer(a)nmr.mgh.harvard.edu > Sent: Wednesday, January 18, 2012 4:02 PM > Subject: Re: [Freesurfer] THANKS > > > Yes, that is right. > > > On Wed, 18 Jan 2012, Antonella Kis wrote: > > > Thanks so much now I more clear. So based on my understanding when resampling on CVS space we will use the nears interpolation if instead of the fa-masked.mgz we have a segmentation volume such as wmparc.mgz or the aparc+aseg.mgz but if I have fa-masked.mgz no > matter > > how I defined my mask I will have use the --interp trilin while resampling since the fa-masked.mgz is not a segmentation file. > > > > Is this right? > > > > Sorry for asking so many silly questions. > > > > Thanks. > > Antonella > > > >__________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________ > _ > > From: Lilla Zollei <lzollei(a)nmr.mgh.harvard.edu> > > To: Antonella Kis <atorok9(a)yahoo.com> > > Cc: freesurfer(a)nmr.mgh.harvard.edu > > Sent: Wednesday, January 18, 2012 3:46 PM > > Subject: Re: [Freesurfer] How to define the FA-mask > > > > > > fa-masked is a masked volume and not a segmentation file. A segmentation file contains labels that correspond to certain anatomical areas. The fa-masked file is the same as your fa volume but some background regions are eliminated from it using the mask volume. > > > > > > On Wed, 18 Jan 2012, Antonella Kis wrote: > > > > > Thank you Lilla, this is very helpful. Just one more question please: why it says it is not a segmented volume the input volume which in fact you mentioned is the fa-masked.mgz if this was defined using the wmparc? > > > > > > THANKS and have a great day! > > > Antonella > > > > >>_________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________ > _ > > _ > > > From: Lilla Zollei <lzollei(a)nmr.mgh.harvard.edu> > > > To: Antonella Kis <atorok9(a)yahoo.com> > > > Cc: freesurfer(a)nmr.mgh.harvard.edu > > > Sent: Wednesday, January 18, 2012 3:38 PM > > > Subject: Re: [Freesurfer] How to define the FA-mask > > > > > > > > > Hi, > > > > > > > Many thanks for your reply. Can ypu please advise me how I should calculate the mask if I want to do the masking based upon intensity values found in the fa image? > > > > > > > > I tried to run (without wmparc) but it gave me error: > > > > > > > > mri_mask $TUTORIAL_DIR/$subj/dtrecon/fa.nii \ > > > > $TUTORIAL_DIR/$subj/dtrecon/fa-masked.mgz > > > > > > > > > > Sorry, you should use mri_threshold if you want to do intensity > > > thresholding and mri_mask if you want to use a mask. In the above the > > > second argument, the mask, is missing. > > > > > > > > > > On the tutorial site which is the input volume that it says is not a segmented volume during resampling on the CVS: > > > > > > > > > mri_vol2vol --targ $FREESURFER_HOME/subjects/cvs_avg35/mri/norm.mgz \ > > > > > --m3z $SUBJECTS_DIR/$subj/cvs/combined_tocvs_avg35_elreg_afteraseg-norm.m3z \ > > > > > --noDefM3zPath --reg $TUTORIAL_DIR/$subj/dtrecon/register.dat \ > > > > > --mov $TUTORIAL_DIR/$subj/dtrecon/fa-masked.mgz \ > > > > > --o $TUTORIAL_DIR/$subj/dtrecon/fa-masked.ANAT+CVS-to-avg35.mgz \ > > > > > --interp trilin --no-save-reg > > > > > > It is "$TUTORIAL_DIR/$subj/dtrecon/fa-masked.mgz" > > > > > > > Based on your experience What will be the best to use when I define my voxels the parcellation map or an intensity threshol? > > > > > > It really depends on your data. You might want to look at both outputs on > > > a couple of data sets and then decide. > > > > > > --Lilla > > > > > > > > > > From: Lilla Zollei <lzollei(a)nmr.mgh.harvard.edu> > > > > To: Antonella Kis <atorok9(a)yahoo.com> > > > > Cc: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> > > > > Sent: Wednesday, January 18, 2012 2:34 PM > > > > Subject: Re: [Freesurfer] How to define the FA-mask > > > > > > > > > > > > > mri_mask $TUTORIAL_DIR/$subj/dtrecon/fa.nii \ > > > > > $SUBJECTS_DIR/$subj/mri/wmparc2diff.mgz \ > > > > > $TUTORIAL_DIR/$subj/dtrecon/fa-masked.mgz > > > > > and when it follows the resampling on the CVS space I see: > > > > > > > > > > mri_vol2vol --targ $FREESURFER_HOME/subjects/cvs_avg35/mri/norm.mgz \ > > > > > --m3z $SUBJECTS_DIR/$subj/cvs/combined_tocvs_avg35_elreg_afteraseg-norm.m3z \ > > > > > --noDefM3zPath --reg $TUTORIAL_DIR/$subj/dtrecon/register.dat \ > > > > > --mov $TUTORIAL_DIR/$subj/dtrecon/fa-masked.mgz \ > > > > > --o $TUTORIAL_DIR/$subj/dtrecon/fa-masked.ANAT+CVS-to-avg35.mgz \ > > > > > --interp trilin --no-save-reg > > > > > with the following explanation: The '--interp' flag indicates the type of interpolation we want to use for our resampling. We are not using a segmented volume as an input so we use the default trilinear (trilin) interpolation option. If you wanted to resample > a > > > > > segmentation volume (such as wmparc or aseg) in CVS space, you would want to use the nearest neighbor (nearest) interpolation option. > > > > > > > > > > I don't understand what exactly means: "We are not using a segmented volume as an input" since the fa-masked is defined using the wmparc2diff? > > > > > > > > When you masked the FA volume, you eliminated some values that are outside of the mask but did not create a binary volume, the original FA values remained in the volume. > > > > > > > > > I understood there two masking options: (option 1) using the wmparc to guide my masking or (option 2) if I want to do the masking based upon intensity values found in the fa image. > > > > > I am not sure how will be the best to define my FA-mask if I was running the CVS registration with the option --noaseg and also I want to do a group study and see if my Fa values increases or decreases in controls vs. patients. Can you please give me an > advise? > > > > > > > > These two things are not related. When considering the masking the only thing you need to think about is whethe ryou trust the parcellation map or an intensity threshold better in order to define voxels that you would like to keep in your input volume. > > > > > > > > > Also, I am not sure if I am mixing things or not but can I define my mask using the wmparc if I did the registration with the --noaseg option? > > > > > > > > Again, these deceisions are not related. > > > > > > > > Lilla > > > > > > > > > > > > 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 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 information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the e-mail > contains patient information, please contact the Partners Compliance HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in error > but does not contain patient information, please contact the sender and properly > dispose of the e-mail. > > > >

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Re: [Freesurfer] THANKS
by Lilla Zollei 18 Jan '12

18 Jan '12

Yes, that is right. On Wed, 18 Jan 2012, Antonella Kis wrote: > Thanks so much now I more clear. So based on my understanding when resampling on CVS space we will use the nears interpolation if instead of the fa-masked.mgz we have a segmentation volume such as wmparc.mgz or the aparc+aseg.mgz but if I have fa-masked.mgz no matter > how I defined my mask I will have use the --interp trilin while resampling since the fa-masked.mgz is not a segmentation file. > > Is this right? > > Sorry for asking so many silly questions. > > Thanks. > Antonella > > ___________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________ > From: Lilla Zollei <lzollei(a)nmr.mgh.harvard.edu> > To: Antonella Kis <atorok9(a)yahoo.com> > Cc: freesurfer(a)nmr.mgh.harvard.edu > Sent: Wednesday, January 18, 2012 3:46 PM > Subject: Re: [Freesurfer] How to define the FA-mask > > > fa-masked is a masked volume and not a segmentation file. A segmentation file contains labels that correspond to certain anatomical areas. The fa-masked file is the same as your fa volume but some background regions are eliminated from it using the mask volume. > > > On Wed, 18 Jan 2012, Antonella Kis wrote: > > > Thank you Lilla, this is very helpful. Just one more question please: why it says it is not a segmented volume the input volume which in fact you mentioned is the fa-masked.mgz if this was defined using the wmparc? > > > > THANKS and have a great day! > > Antonella > > > >__________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________ > _ > > From: Lilla Zollei <lzollei(a)nmr.mgh.harvard.edu> > > To: Antonella Kis <atorok9(a)yahoo.com> > > Cc: freesurfer(a)nmr.mgh.harvard.edu > > Sent: Wednesday, January 18, 2012 3:38 PM > > Subject: Re: [Freesurfer] How to define the FA-mask > > > > > > Hi, > > > > > Many thanks for your reply. Can ypu please advise me how I should calculate the mask if I want to do the masking based upon intensity values found in the fa image? > > > > > > I tried to run (without wmparc) but it gave me error: > > > > > > mri_mask $TUTORIAL_DIR/$subj/dtrecon/fa.nii \ > > > $TUTORIAL_DIR/$subj/dtrecon/fa-masked.mgz > > > > > > > Sorry, you should use mri_threshold if you want to do intensity > > thresholding and mri_mask if you want to use a mask. In the above the > > second argument, the mask, is missing. > > > > > > > On the tutorial site which is the input volume that it says is not a segmented volume during resampling on the CVS: > > > > > > > mri_vol2vol --targ $FREESURFER_HOME/subjects/cvs_avg35/mri/norm.mgz \ > > > > --m3z $SUBJECTS_DIR/$subj/cvs/combined_tocvs_avg35_elreg_afteraseg-norm.m3z \ > > > > --noDefM3zPath --reg $TUTORIAL_DIR/$subj/dtrecon/register.dat \ > > > > --mov $TUTORIAL_DIR/$subj/dtrecon/fa-masked.mgz \ > > > > --o $TUTORIAL_DIR/$subj/dtrecon/fa-masked.ANAT+CVS-to-avg35.mgz \ > > > > --interp trilin --no-save-reg > > > > It is "$TUTORIAL_DIR/$subj/dtrecon/fa-masked.mgz" > > > > > Based on your experience What will be the best to use when I define my voxels the parcellation map or an intensity threshol? > > > > It really depends on your data. You might want to look at both outputs on > > a couple of data sets and then decide. > > > > --Lilla > > > > > > > From: Lilla Zollei <lzollei(a)nmr.mgh.harvard.edu> > > > To: Antonella Kis <atorok9(a)yahoo.com> > > > Cc: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> > > > Sent: Wednesday, January 18, 2012 2:34 PM > > > Subject: Re: [Freesurfer] How to define the FA-mask > > > > > > > > > > mri_mask $TUTORIAL_DIR/$subj/dtrecon/fa.nii \ > > > > $SUBJECTS_DIR/$subj/mri/wmparc2diff.mgz \ > > > > $TUTORIAL_DIR/$subj/dtrecon/fa-masked.mgz > > > > and when it follows the resampling on the CVS space I see: > > > > > > > > mri_vol2vol --targ $FREESURFER_HOME/subjects/cvs_avg35/mri/norm.mgz \ > > > > --m3z $SUBJECTS_DIR/$subj/cvs/combined_tocvs_avg35_elreg_afteraseg-norm.m3z \ > > > > --noDefM3zPath --reg $TUTORIAL_DIR/$subj/dtrecon/register.dat \ > > > > --mov $TUTORIAL_DIR/$subj/dtrecon/fa-masked.mgz \ > > > > --o $TUTORIAL_DIR/$subj/dtrecon/fa-masked.ANAT+CVS-to-avg35.mgz \ > > > > --interp trilin --no-save-reg > > > > with the following explanation: The '--interp' flag indicates the type of interpolation we want to use for our resampling. We are not using a segmented volume as an input so we use the default trilinear (trilin) interpolation option. If you wanted to resample a > > > > segmentation volume (such as wmparc or aseg) in CVS space, you would want to use the nearest neighbor (nearest) interpolation option. > > > > > > > > I don't understand what exactly means: "We are not using a segmented volume as an input" since the fa-masked is defined using the wmparc2diff? > > > > > > When you masked the FA volume, you eliminated some values that are outside of the mask but did not create a binary volume, the original FA values remained in the volume. > > > > > > > I understood there two masking options: (option 1) using the wmparc to guide my masking or (option 2) if I want to do the masking based upon intensity values found in the fa image. > > > > I am not sure how will be the best to define my FA-mask if I was running the CVS registration with the option --noaseg and also I want to do a group study and see if my Fa values increases or decreases in controls vs. patients. Can you please give me an advise? > > > > > > These two things are not related. When considering the masking the only thing you need to think about is whethe ryou trust the parcellation map or an intensity threshold better in order to define voxels that you would like to keep in your input volume. > > > > > > > Also, I am not sure if I am mixing things or not but can I define my mask using the wmparc if I did the registration with the --noaseg option? > > > > > > Again, these deceisions are not related. > > > > > > Lilla > > > > > > > > > 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 information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the e-mail > contains patient information, please contact the Partners Compliance HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in error > but does not contain patient information, please contact the sender and properly > dispose of the e-mail. > > > >

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Re: [Freesurfer] How to define the FA-mask
by Lilla Zollei 18 Jan '12

18 Jan '12

fa-masked is a masked volume and not a segmentation file. A segmentation file contains labels that correspond to certain anatomical areas. The fa-masked file is the same as your fa volume but some background regions are eliminated from it using the mask volume. On Wed, 18 Jan 2012, Antonella Kis wrote: > Thank you Lilla, this is very helpful. Just one more question please: why it says it is not a segmented volume the input volume which in fact you mentioned is the fa-masked.mgz if this was defined using the wmparc? > > THANKS and have a great day! > Antonella > > ___________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________ > From: Lilla Zollei <lzollei(a)nmr.mgh.harvard.edu> > To: Antonella Kis <atorok9(a)yahoo.com> > Cc: freesurfer(a)nmr.mgh.harvard.edu > Sent: Wednesday, January 18, 2012 3:38 PM > Subject: Re: [Freesurfer] How to define the FA-mask > > > Hi, > > > Many thanks for your reply. Can ypu please advise me how I should calculate the mask if I want to do the masking based upon intensity values found in the fa image? > > > > I tried to run (without wmparc) but it gave me error: > > > > mri_mask $TUTORIAL_DIR/$subj/dtrecon/fa.nii \ > > $TUTORIAL_DIR/$subj/dtrecon/fa-masked.mgz > > > > Sorry, you should use mri_threshold if you want to do intensity > thresholding and mri_mask if you want to use a mask. In the above the > second argument, the mask, is missing. > > > > On the tutorial site which is the input volume that it says is not a segmented volume during resampling on the CVS: > > > > > mri_vol2vol --targ $FREESURFER_HOME/subjects/cvs_avg35/mri/norm.mgz \ > > > --m3z $SUBJECTS_DIR/$subj/cvs/combined_tocvs_avg35_elreg_afteraseg-norm.m3z \ > > > --noDefM3zPath --reg $TUTORIAL_DIR/$subj/dtrecon/register.dat \ > > > --mov $TUTORIAL_DIR/$subj/dtrecon/fa-masked.mgz \ > > > --o $TUTORIAL_DIR/$subj/dtrecon/fa-masked.ANAT+CVS-to-avg35.mgz \ > > > --interp trilin --no-save-reg > > It is "$TUTORIAL_DIR/$subj/dtrecon/fa-masked.mgz" > > > Based on your experience What will be the best to use when I define my voxels the parcellation map or an intensity threshol? > > It really depends on your data. You might want to look at both outputs on > a couple of data sets and then decide. > > --Lilla > > > > From: Lilla Zollei <lzollei(a)nmr.mgh.harvard.edu> > > To: Antonella Kis <atorok9(a)yahoo.com> > > Cc: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> > > Sent: Wednesday, January 18, 2012 2:34 PM > > Subject: Re: [Freesurfer] How to define the FA-mask > > > > > > > mri_mask $TUTORIAL_DIR/$subj/dtrecon/fa.nii \ > > > $SUBJECTS_DIR/$subj/mri/wmparc2diff.mgz \ > > > $TUTORIAL_DIR/$subj/dtrecon/fa-masked.mgz > > > and when it follows the resampling on the CVS space I see: > > > > > > mri_vol2vol --targ $FREESURFER_HOME/subjects/cvs_avg35/mri/norm.mgz \ > > > --m3z $SUBJECTS_DIR/$subj/cvs/combined_tocvs_avg35_elreg_afteraseg-norm.m3z \ > > > --noDefM3zPath --reg $TUTORIAL_DIR/$subj/dtrecon/register.dat \ > > > --mov $TUTORIAL_DIR/$subj/dtrecon/fa-masked.mgz \ > > > --o $TUTORIAL_DIR/$subj/dtrecon/fa-masked.ANAT+CVS-to-avg35.mgz \ > > > --interp trilin --no-save-reg > > > with the following explanation: The '--interp' flag indicates the type of interpolation we want to use for our resampling. We are not using a segmented volume as an input so we use the default trilinear (trilin) interpolation option. If you wanted to resample a > > > segmentation volume (such as wmparc or aseg) in CVS space, you would want to use the nearest neighbor (nearest) interpolation option. > > > > > > I don't understand what exactly means: "We are not using a segmented volume as an input" since the fa-masked is defined using the wmparc2diff? > > > > When you masked the FA volume, you eliminated some values that are outside of the mask but did not create a binary volume, the original FA values remained in the volume. > > > > > I understood there two masking options: (option 1) using the wmparc to guide my masking or (option 2) if I want to do the masking based upon intensity values found in the fa image. > > > I am not sure how will be the best to define my FA-mask if I was running the CVS registration with the option --noaseg and also I want to do a group study and see if my Fa values increases or decreases in controls vs. patients. Can you please give me an advise? > > > > These two things are not related. When considering the masking the only thing you need to think about is whethe ryou trust the parcellation map or an intensity threshold better in order to define voxels that you would like to keep in your input volume. > > > > > Also, I am not sure if I am mixing things or not but can I define my mask using the wmparc if I did the registration with the --noaseg option? > > > > Again, these deceisions are not related. > > > > Lilla > > > > > > 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. > > > > > > > > > > >

1 0

Re: [Freesurfer] How to define the FA-mask
by Lilla Zollei 18 Jan '12

18 Jan '12

Hi, > Many thanks for your reply. Can ypu please advise me how I should calculate the mask if I want to do the masking based upon intensity values found in the fa image? > > I tried to run (without wmparc) but it gave me error: > > mri_mask $TUTORIAL_DIR/$subj/dtrecon/fa.nii \ > $TUTORIAL_DIR/$subj/dtrecon/fa-masked.mgz > Sorry, you should use mri_threshold if you want to do intensity thresholding and mri_mask if you want to use a mask. In the above the second argument, the mask, is missing. > On the tutorial site which is the input volume that it says is not a segmented volume during resampling on the CVS: > > > mri_vol2vol --targ $FREESURFER_HOME/subjects/cvs_avg35/mri/norm.mgz \ > > --m3z $SUBJECTS_DIR/$subj/cvs/combined_tocvs_avg35_elreg_afteraseg-norm.m3z \ > > --noDefM3zPath --reg $TUTORIAL_DIR/$subj/dtrecon/register.dat \ > > --mov $TUTORIAL_DIR/$subj/dtrecon/fa-masked.mgz \ > > --o $TUTORIAL_DIR/$subj/dtrecon/fa-masked.ANAT+CVS-to-avg35.mgz \ > > --interp trilin --no-save-reg It is "$TUTORIAL_DIR/$subj/dtrecon/fa-masked.mgz" > Based on your experience What will be the best to use when I define my voxels the parcellation map or an intensity threshol? It really depends on your data. You might want to look at both outputs on a couple of data sets and then decide. --Lilla > From: Lilla Zollei <lzollei(a)nmr.mgh.harvard.edu> > To: Antonella Kis <atorok9(a)yahoo.com> > Cc: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> > Sent: Wednesday, January 18, 2012 2:34 PM > Subject: Re: [Freesurfer] How to define the FA-mask > > > > mri_mask $TUTORIAL_DIR/$subj/dtrecon/fa.nii \ > > $SUBJECTS_DIR/$subj/mri/wmparc2diff.mgz \ > > $TUTORIAL_DIR/$subj/dtrecon/fa-masked.mgz > > and when it follows the resampling on the CVS space I see: > > > > mri_vol2vol --targ $FREESURFER_HOME/subjects/cvs_avg35/mri/norm.mgz \ > > --m3z $SUBJECTS_DIR/$subj/cvs/combined_tocvs_avg35_elreg_afteraseg-norm.m3z \ > > --noDefM3zPath --reg $TUTORIAL_DIR/$subj/dtrecon/register.dat \ > > --mov $TUTORIAL_DIR/$subj/dtrecon/fa-masked.mgz \ > > --o $TUTORIAL_DIR/$subj/dtrecon/fa-masked.ANAT+CVS-to-avg35.mgz \ > > --interp trilin --no-save-reg > > with the following explanation: The '--interp' flag indicates the type of interpolation we want to use for our resampling. We are not using a segmented volume as an input so we use the default trilinear (trilin) interpolation option. If you wanted to resample a > > segmentation volume (such as wmparc or aseg) in CVS space, you would want to use the nearest neighbor (nearest) interpolation option. > > > > I don't understand what exactly means: "We are not using a segmented volume as an input" since the fa-masked is defined using the wmparc2diff? > > When you masked the FA volume, you eliminated some values that are outside of the mask but did not create a binary volume, the original FA values remained in the volume. > > > I understood there two masking options: (option 1) using the wmparc to guide my masking or (option 2) if I want to do the masking based upon intensity values found in the fa image. > > I am not sure how will be the best to define my FA-mask if I was running the CVS registration with the option --noaseg and also I want to do a group study and see if my Fa values increases or decreases in controls vs. patients. Can you please give me an advise? > > These two things are not related. When considering the masking the only thing you need to think about is whethe ryou trust the parcellation map or an intensity threshold better in order to define voxels that you would like to keep in your input volume. > > > Also, I am not sure if I am mixing things or not but can I define my mask using the wmparc if I did the registration with the --noaseg option? > > Again, these deceisions are not related. > > Lilla > > > 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. > > > >

1 0

How to define the FA-mask
by Antonella Kis 18 Jan '12

18 Jan '12

Dear all, On the FS Tutorial/Diffusion the FA masked is defined as: mri_mask $TUTORIAL_DIR/$subj/dtrecon/fa.nii \ $SUBJECTS_DIR/$subj/mri/wmparc2diff.mgz \ $TUTORIAL_DIR/$subj/dtrecon/fa-masked.mgzand when it follows the resampling on the CVS space I see: mri_vol2vol --targ $FREESURFER_HOME/subjects/cvs_avg35/mri/norm.mgz \ --m3z $SUBJECTS_DIR/$subj/cvs/combined_tocvs_avg35_elreg_afteraseg-norm.m3z \ --noDefM3zPath --reg $TUTORIAL_DIR/$subj/dtrecon/register.dat \ --mov $TUTORIAL_DIR/$subj/dtrecon/fa-masked.mgz \ --o $TUTORIAL_DIR/$subj/dtrecon/fa-masked.ANAT+CVS-to-avg35.mgz \ --interp trilin --no-save-regwith the following explanation: The '--interp' flag indicates the type of interpolation we want to use for our resampling. We are not using a segmented volume as an input so we use the default trilinear (trilin) interpolation option. If you wanted to resample a segmentation volume (such as wmparc or aseg) in CVS space, you would want to use the nearest neighbor (nearest) interpolation option. I don't understand what exactly means: "We are not using a segmented volume as an input" since the fa-masked is defined using the wmparc2diff? I understood there two masking options: (option 1) using the wmparc to guide my masking or (option 2) if I want to do the masking based upon intensity values found in the fa image. I am not sure how will be the best to define my FA-mask if I was running the CVS registration with the option --noaseg and also I want to do a group study and see if my Fa values increases or decreases in controls vs. patients. Can you please give me an advise? Also, I am not sure if I am mixing things or not but can I define my mask using the wmparc if I did the registration with the --noaseg option? Many thanks. Antonella

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