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mri_convert -ait
by Don Hagler 06 Feb '07

06 Feb '07

I was trying to warp a volume in atlas space (i.e. an ROI) to single subject space using mri_convert -ait ... (version = stable3) and ran into trouble. I found that mri_convert will quit if the data type is int (type 1) and will give strange results if data type is float (type 3). I was able to do what I needed by converting my input volume to uchar (type 0). For what I want to do, uchar works just fine, but is there some reason why it fails for floats? It might be helpful to include some kind of message in the help and maybe quit it the -ait option is used and the input datatype is not uchar. _________________________________________________________________ Laugh, share and connect with Windows Live Messenger http://clk.atdmt.com/MSN/go/msnnkwme0020000001msn/direct/01/?href=http://im…

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surface back to the subject native space
by anqi 06 Feb '07

06 Feb '07

I wonder whether there is a way to convert surfaces back to the subject native space. Thanks! Anqi Qiu Center for Imaging Science The Johns Hopkins University -----Original Message----- From: freesurfer-bounces(a)nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of freesurfer-request(a)nmr.mgh.harvard.edu Sent: Tuesday, February 06, 2007 11:43 AM To: freesurfer(a)nmr.mgh.harvard.edu Subject: Freesurfer Digest, Vol 36, Issue 10 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. Re: tkregister2:views mixed up. (Chacko Cherian) 2. Re: tkregister2:views mixed up. (Doug Greve) 3. Re: brainmask.mgz problems (Bruce Fischl) 4. error with mri_ca_register (Binyam Nardos) ---------------------------------------------------------------------- Message: 1 Date: Mon, 5 Feb 2007 15:47:55 -0800 (PST) From: Chacko Cherian <chacko_cherian(a)yahoo.com> Subject: Re: [Freesurfer] tkregister2:views mixed up. To: Doug Greve <greve(a)nmr.mgh.harvard.edu> Cc: Freesurfer <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <570151.930.qm(a)web35315.mail.mud.yahoo.com> Content-Type: text/plain; charset=iso-8859-1 Yes,It is perfectly fine with the --regheader optionmwhich means no problem with geometry info. But how do I fix the talairach.xfm? Thanks a lot! Chacko. --- Doug Greve <greve(a)nmr.mgh.harvard.edu> wrote: > I mean to just load the orig.mgz into tkmedit and see if it is > oriented correctly. Assuming that it is oriented correctly, then it > sounds like the talairach transform is messed up pretty badly. > When you run > tkregister2, try adding --regheader. This will ignore the info in the > talairaach.xfm file and force it to use the geometry info. it will > likely be very far off, but the basic orientation should be ok. > > Chacko Cherian wrote: > > >It has the problem in tkmedit,after I load the transform..i checked > >brainmask.img and T1.img after loading the transform and they had > >this > problem..The > >header and geometry info look fine.. > > > > > >--- Doug Greve <greve(a)nmr.mgh.harvard.edu> wrote: > > > > > > > >>That means that the geometry info in the file is messed up. Where > >>did the data come from? Are the dicoms messed up too? > >> > >>Chacko Cherian wrote: > >> > >> > >> > >>>No, It has the same problem in tkmedit too. > >>> > >>> > >>>--- Doug Greve <greve(a)nmr.mgh.harvard.edu> wrote: > >>> > >>> > >>> > >>> > >>> > >>>>Does it view correctly in tkmedit? > >>>> > >>>>Chacko Cherian wrote: > >>>> > >>>> > >>>> > >>>> > >>>> > >>>>>Hello ALL, > >>>>> > >>>>>Has anybody had trouble with tkregister2..I > >>>>> > >>>>> > >>loaded > >> > >> > >>>>> > >>>>> > >>>>> > >>>>> > >>>>the > >>>> > >>>> > >>>> > >>>> > >>>>>transform and the coronal and horizontal views > >>>>> > >>>>> > >>are > >> > >> > >>>>>mixed up.Coronal view of the subject is coupled > >>>>> > >>>>> > >>>>> > >>>>> > >>>>with > >>>> > >>>> > >>>> > >>>> > >>>>>the horizontal view of the talairach volume. > >>>>> > >>>>>Thanks in advance > >>>>>Regards, > >>>>> > >>>>>Chacko. > >>>>> > >>>>> > >>>>> > >>>>> > >>>>> > >>>>> > >>>>> > >>>_____________________________________________________________________ >>>_______________ > >>> > >>> > >>>> > >>>> > >>>> > >>>> > >>>>>TV dinner still cooling? > >>>>>Check out "Tonight's Picks" on Yahoo! TV. > >>>>>http://tv.yahoo.com/ > >>>>>_______________________________________________ > >>>>>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 > >>>> > >>>>In order to help us help you, please follow the steps in: > >>>>surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > >>>> > >>>> > >>>>_______________________________________________ > >>>>Freesurfer mailing list > >>>>Freesurfer(a)nmr.mgh.harvard.edu > >>>> > >>>> > >>>> > >>>> > >>>> > >>https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >> > >> > >>> > >>> > >>> > >>> > >>> > >>> > >>> > >>> > >>______________________________________________________________________ >>______________ > >> > >> > >>>Never miss an email again! > >>>Yahoo! Toolbar alerts you the instant new Mail > >>> > >>> > >>arrives. > >> > >>http://tools.search.yahoo.com/toolbar/features/mail/ > >> > >> > >>> > >>> > >>> > >>> > >>-- > >>Douglas N. Greve, Ph.D. > >>MGH-NMR Center > >>greve(a)nmr.mgh.harvard.edu > >>Phone Number: 617-724-2358 > >>Fax: 617-726-7422 > >> > >>In order to help us help you, please follow the steps in: > >>surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > >> > >> > >> > >> > >>>_______________________________________________ > >>> > >>> > >>Freesurfer mailing list > >>Freesurfer(a)nmr.mgh.harvard.edu > >> > >> > >> > >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > >_______________________________________________________________________ >_____________ > >Never miss an email again! > === message truncated === ____________________________________________________________________________ ________ Finding fabulous fares is fun. Let Yahoo! FareChase search your favorite travel sites to find flight and hotel bargains. http://farechase.yahoo.com/promo-generic-14795097 ------------------------------ Message: 2 Date: Mon, 05 Feb 2007 20:20:04 -0500 From: Doug Greve <greve(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] tkregister2:views mixed up. To: Chacko Cherian <chacko_cherian(a)yahoo.com> Cc: Freesurfer <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <45C7D7C4.2070908(a)nmr.mgh.harvard.edu> Content-Type: text/plain; charset="us-ascii" You can start with that one and fix it by hand (which is a hassle). We are working on ways to make the talairach more robust. BTW, if you run tkregister2 again after fixing it, you should not include the --regheader as that will ignore your previous edits. doug Chacko Cherian wrote: >Yes,It is perfectly fine with the --regheader optionmwhich means no >problem with geometry info. >But how do I fix the talairach.xfm? > >Thanks a lot! > >Chacko. >--- Doug Greve <greve(a)nmr.mgh.harvard.edu> wrote: > > > >>I mean to just load the orig.mgz into tkmedit and see if it is >>oriented correctly. Assuming that it is oriented correctly, then it >>sounds like the talairach transform is messed up pretty badly. >>When you run >>tkregister2, try adding --regheader. This will ignore the info in the >>talairaach.xfm file and force it to use the geometry info. it will >>likely be very far off, but the basic orientation should be ok. >> >>Chacko Cherian wrote: >> >> >> >>>It has the problem in tkmedit,after I load the transform..i checked >>>brainmask.img and T1.img after loading the transform and they had >>>this >>> >>> >>problem..The >> >> >>>header and geometry info look fine.. >>> >>> >>>--- Doug Greve <greve(a)nmr.mgh.harvard.edu> wrote: >>> >>> >>> >>> >>> >>>>That means that the geometry info in the file is messed up. Where >>>>did the data come from? Are the dicoms messed up too? >>>> >>>>Chacko Cherian wrote: >>>> >>>> >>>> >>>> >>>> >>>>>No, It has the same problem in tkmedit too. >>>>> >>>>> >>>>>--- Doug Greve <greve(a)nmr.mgh.harvard.edu> wrote: >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>>>Does it view correctly in tkmedit? >>>>>> >>>>>>Chacko Cherian wrote: >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>>>Hello ALL, >>>>>>> >>>>>>>Has anybody had trouble with tkregister2..I >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>loaded >>>> >>>> >>>> >>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>the >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>>>transform and the coronal and horizontal views >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>are >>>> >>>> >>>> >>>> >>>>>>>mixed up.Coronal view of the subject is coupled >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>with >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>>>the horizontal view of the talairach volume. >>>>>>> >>>>>>>Thanks in advance >>>>>>>Regards, >>>>>>> >>>>>>>Chacko. >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>____________________________________________________________________ >>>>________________ >>>> >>>> >>>>> >>>>> >>>>> >>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>>>TV dinner still cooling? >>>>>>>Check out "Tonight's Picks" on Yahoo! TV. >>>>>>>http://tv.yahoo.com/ >>>>>>>_______________________________________________ >>>>>>>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 >>>>>> >>>>>>In order to help us help you, please follow the steps in: >>>>>>surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>>>>> >>>>>> >>>>>>_______________________________________________ >>>>>>Freesurfer mailing list >>>>>>Freesurfer(a)nmr.mgh.harvard.edu >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >>>> >>>> >>>> >>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>_____________________________________________________________________ >>>_______________ >>> >>> >>>> >>>> >>>> >>>> >>>>>Never miss an email again! >>>>>Yahoo! Toolbar alerts you the instant new Mail >>>>> >>>>> >>>>> >>>>> >>>>arrives. >>>> >>>> >>>> >>>http://tools.search.yahoo.com/toolbar/features/mail/ >>> >>> >>>> >>>> >>>> >>>> >>>>> >>>>> >>>>> >>>>> >>>>-- >>>>Douglas N. Greve, Ph.D. >>>>MGH-NMR Center >>>>greve(a)nmr.mgh.harvard.edu >>>>Phone Number: 617-724-2358 >>>>Fax: 617-726-7422 >>>> >>>>In order to help us help you, please follow the steps in: >>>>surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>>> >>>> >>>> >>>> >>>> >>>> >>>>>_______________________________________________ >>>>> >>>>> >>>>> >>>>> >>>>Freesurfer mailing list >>>>Freesurfer(a)nmr.mgh.harvard.edu >>>> >>>> >>>> >>>> >>>> >>https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >>> >>> >>> >>> >>______________________________________________________________________ >>______________ >> >> >>>Never miss an email again! >>> >>> >=== message truncated === > > > > >_______________________________________________________________________ >_____________ >Finding fabulous fares is fun. >Let Yahoo! FareChase search your favorite travel sites to find flight and hotel bargains. >http://farechase.yahoo.com/promo-generic-14795097 > > > > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

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error with mri_ca_register
by Binyam Nardos 06 Feb '07

06 Feb '07

hi all, I just ran autorecon2 on one of our subjects (for the second time, after getting a similar error, i.e. ERROR: mri_ca_register with non-zero status. I just rerun recon-all with -autorecon2 without removing/changing anything produced by the previous autorecon2). Is there any logical place to start to fix the problem or do I have to rerun mri_ca_register as shown below: mri_ca_register -align -nobigventricles -mask brainmask.mgz -T transforms/talairach.lta norm.mgz /usr/local/freesurfer//average/RB_all_2006-02-15.gca transforms/talairach.m3z I have attached the recon-all log for reference. Please advise, thanks, Binyam Binyam Nardos Cognitive Rehabilitation Research Group Washington University School of Medicine Box # 8505 4444 Forest Park Blvd St. Louis, MO 63108 Office: (314) 454-7795 Fax: (314) 286-1601 The contents of this e-mail message and any attachments are intended solely for the addressee(s) named in this message. This communication is intended to be and to remain confidential and may be subject to applicable physician/patient and/or work product privileges. If you are not the intended recipient of this message, or if this message has been addressed to you in error, please immediately alert the sender by reply e-mail and then delete this message and its attachments.

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brainmask.mgz problems
by Catherine Hartley 05 Feb '07

05 Feb '07

Hi, I ran autorecon1 on a group of data consisting of a single set of mprage DICOMs per subject, acquired on a Siemens Allegra 3T scanner. Several of the brainmask.mgz images had large portions of the brainstem and cerebellum removed. A couple had portions of the neck which were not removed. The talairach transforms looked fine. A more experiened Freesurfer user suggested that adding control points and re-running the intensity normalization might fix this. I assume that I can follow the instructions here, http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial_2fControlPoints but that I would need to edit the orig.mgz file and then run autorecon1-cp. Is this correct? My intended analysis (cortical thickness in PFC regions) does not depend upon these flawed regions, but I want to make sure these errors aren't indicative of some larger problem. Also, I know there have been issues with gradient warping with the Allegra. Do these problems sound like gradient warping symptoms? Thanks, Cate

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tkregister2:views mixed up.
by Chacko Cherian 05 Feb '07

05 Feb '07

Hello ALL, Has anybody had trouble with tkregister2..I loaded the transform and the coronal and horizontal views are mixed up.Coronal view of the subject is coupled with the horizontal view of the talairach volume. Thanks in advance Regards, Chacko. ____________________________________________________________________________________ TV dinner still cooling? Check out "Tonight's Picks" on Yahoo! TV. http://tv.yahoo.com/

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input registration matrix
by Chacko Cherian 05 Feb '07

05 Feb '07

Hello All, After making changes using tkregister2 the input registration matrix changes.IS there an 'optimum' input registration matrix that i should try to get.I notice that the closer the values(last column of the input reg matrix) are to zero the better the outcome. Thanks in advance. Chacko. ____________________________________________________________________________________ Now that's room service! Choose from over 150,000 hotels in 45,000 destinations on Yahoo! Travel to find your fit. http://farechase.yahoo.com/promo-generic-14795097

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Doubts with region areas on the fsaverage sphere
by jorge luis 05 Feb '07

05 Feb '07

Hello all I have made deep changes in 9 regions of a left hemisfere of a subject surface after maped it onto the fsaverage subject sphere. The changes were made to have areas close to 15 mm^2. I computed the areas by add the areas of the faces inside the regions (computed using the vertexes spherical coordinates). The freesurfer sphere mapping is based in minimal metric distortion, so, why I got the following differences?: Region Computed areas (mm^2) Computed areas (mm^2) uing mri_surfcluster as explained before with the fsaverage sphere 1 27.56 15.0522 2 21.78 15.0946 3 21.41 15.1087 4 20.77 15.1501 5 19.28 15.1797 6 16.60 15.1918 7 15.99 15.2781 8 14.31 15.3373 9 13.89 15.0541 In both cases the same surface vertexes were found to be inside the regions Another thing: Should I use the sig.mgh file resulted from the mri_glm estimation as the input to the mri_surfcluster function in MonteCarlo simulations? (plus the .csd file of course). In advance thank you a lot Jorge ______________________________________________ LLama Gratis a cualquier PC del Mundo. Llamadas a fijos y móviles desde 1 céntimo por minuto. http://es.voice.yahoo.com

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total brain volume
by Derin Cobia 05 Feb '07

05 Feb '07

I would like to calculate total brain volume (defined as: total white, gray, and subcortical altogether). Should I take the BrainSegVol and minus out cerebellum and ventricles, or add the white and gray matter volumes from mris_anatomical_stats (it seems I remember hearing that white matter from mris_anatomical_stats is not reliable)? Thanks. -Derin

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aseg voxels
by Don Hagler 04 Feb '07

04 Feb '07

Hi, I've found that the number of voxels for a given aseg ROI in aseg.stats does not match exactly the number of voxels when I load the aseg.mgz in matlab and find the voxels of the corresponding ROI code. e.g. vol=load_mgh('aseg.mgz'); length(find(vol==17)). Is there a reason for this difference? Don _________________________________________________________________ Get in the mood for Valentine's Day. View photos, recipes and more on your Live.com page. http://www.live.com/?addTemplate=ValentinesDay&ocid=T001MSN30A0701

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mri_convert failure
by Joan Fisher 04 Feb '07

04 Feb '07

Hi all -- I have edited an anatomical volume (using AFNI's 3dcalc and 3dLRflip commands), and the final volume looks good. My reading is that mri_convert should not have trouble recognizing an afni BRIK file. However, the error is: unknown file type for file ... (The original Volume+orig.BRIK file went through the mri_convert step with no problem.) Is there another way to convert the final merged+orig file below into an 001.mgz file? Or should I be using a flagged option that I'm unaware of? Help appreciated. Joan For anyone interested in the steps I took in AFNI to make the transformed brain, they are: History of inputs to 3dcalc === [joan@cronus: Sat Feb 3 16:35:56 2007] === Input a: [joan@cronus: Sat Feb 3 16:35:56 2007] [joan@cronus: Fri Dec 22 16:18:07 2006] to3d -spgr -prefix Volume -session Results -view orig -xFOV 120.003A-119.997P -yFOV 120.0S-120.0I -zSLAB 88.733L-89.767R '3D:0:8432:256:256:1:Volume/I*' [joan@cronus: Sat Feb 3 16:20:52 2007] Dataset Copy {Input: Dataset=005/Results/Volume+orig.HEAD} {Output: Prefix=rotated} {Data Fill: Method=Data [All]} [joan@cronus: Sat Feb 3 16:24:43 2007] plug_nudge: -rotate 0.00I 0.00R -6.00A -ashift 0.31S -2.98L 0.00P [joan@cronus: Sat Feb 3 16:35:56 2007] === Input b: [joan@cronus: Sat Feb 3 16:35:56 2007] [joan@cronus: Fri Dec 22 16:18:07 2006] to3d -spgr -prefix Volume -session Results -view orig -xFOV 120.003A-119.997P -yFOV 120.0S-120.0I -zSLAB 88.733L-89.767R '3D:0:8432:256:256:1:Volume/I*' [joan@cronus: Sat Feb 3 16:20:52 2007] Dataset Copy {Input: Dataset=005/Results/Volume+orig.HEAD} {Output: Prefix=rotated} {Data Fill: Method=Data [All]} [joan@cronus: Sat Feb 3 16:24:43 2007] plug_nudge: -rotate 0.00I 0.00R -6.00A -ashift 0.31S -2.98L 0.00P [joan@cronus: Sat Feb 3 16:31:05 2007] 3dLRflip -prefix flip rotated+orig. [joan@cronus: Sat Feb 3 16:35:56 2007] === Input c: [joan@cronus: Sat Feb 3 16:35:56 2007] [joan@cronus: Fri Dec 22 16:18:07 2006] to3d -spgr -prefix Volume -session Results -view orig -xFOV 120.003A-119.997P -yFOV 120.0S-120.0I -zSLAB 88.733L-89.767R '3D:0:8432:256:256:1:Volume/I*' [joan@cronus: Sun Jan 14 20:52:47 2007] Dataset Copy {Input: Dataset=005/Results/Volume+orig.HEAD} {Output: Prefix=Lesion} {Data Fill: Method=Zero [One]} [joan@cronus: Sat Feb 3 16:25:29 2007] Dataset Copy {Input: Dataset=005/Results/Lesion+orig.HEAD} {Output: Prefix=lesion_rot} {Data Fill: Method=Data [All]} [joan@cronus: Sat Feb 3 16:26:25 2007] plug_nudge: -rotate 0.00I 0.00R -6.00A -ashift 0.00S -3.00L 0.00P [joan@cronus: Sat Feb 3 16:35:56 2007] =================================== [joan@cronus: Sat Feb 3 16:35:56 2007] 3dcalc -a rotated+orig. -b flip+orig. -c lesion_rot+orig. -expr '(1-c)*a+c*b' -prefix merged These steps created merged+orig.BRIK and merged+orig.HEAD that look fine in afni.

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