Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30083 discussions

mri_convert and image orientation; Analyze format
by Watson, Christopher 18 Sep '08

18 Sep '08

Hello Freesurfers, Lately I've been scratching my head about image orientation problems. What I do here is take the DICOM images and use mri_convert to convert them into SPM Analyze format. The command I use is: mri_convert.x86_64.dev -dicomread2 "$experiment" --nskip ${nskip} \ "path/to/subj/dir/image" --out_type spm So the output files we get are imageXXX.{hdr,img,mat}. So, I assume these truly are Analyze format and not NIfTI (if i'm incorrect please tell me, this would be very important). There are weird things SPM does concerning image orientation, so it's *very* important that I get this right (we do functional imaging on surgery candidates): *Does mri_convert flip the images in any way?* That is, if my DICOM images are in radiological convention, will the imageXXX images still be in radiological convention? I've been searching far and wide and have hit a wall. With patients, we can see the water pill on the right side of the forehead easily, but with the EPI functional images for our research subjects it's pretty much impossible to tell. Thanks very much, Chris Watson

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neuroimaging job announcement
by Paymon Hosseini 18 Sep '08

18 Sep '08

Greetings, The MIT Center for Neuroeconomics is seeking a technical assistant who will take a lead role in the design, implementation, and analysis of functional MRI studies. A candidate with FreeSurfer/FSL experience will have a distinct advantage. Here is a link to the full job description and online application page: https://sh.webhire.com/servlet/av/jd?ai=631&ji=2275928&sn=I

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RE: [Freesurfer] freesurfer
by Bruce Fischl 17 Sep '08

17 Sep '08

they are listed in $FREESURFER_HOME/FreeSurferColorLUT.txt cheers, Bruce On Wed, 17 Sep 2008, Hwee Ling Lee wrote: > Hi Bruce, > > Thanks for the advice. > It works well. > I was wondering if there's any way I could check what values of the label > correspond to a particular brain region. > Thanks. > > Cheers, > HL > > > > -----Original Message----- > From: freesurfer-bounces(a)nmr.mgh.harvard.edu > [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl > Sent: 16 September 2008 22:51 > To: Hwee Ling Lee > Cc: freesurfer(a)nmr.mgh.harvard.edu; 'Doug Greve' > Subject: Re: [Freesurfer] freesurfer > > Hi HweeLing, > > you can use mri_extract_label aparc+aseg.mgz <label> <output volume> > > then the command line Jenni posted before to transform it to MNI space (or > you can try giving the talairach.xfm to mri_extract_label with -t, but I'm > not positive that works) > > cheers, > Bruce > > > > On Tue, 16 Sep 2008, Hwee Ling Lee wrote: > >> >> Hi, >> >> I wanted to write out a mask image for left and right STS as Analyze > format file. >> Using this, I plan to plot the parameter estimates along the STS, > posteriorly to anteriorly. >> I know this is an unusual way of doing things, however, I thought this > might be best suited to customize each STS mask for individual subjects as > many studies have shown differences in STS morphology. >> >> Thanks, >> HweeLing >> >> >> On Tue, 16 Sep 2008 15:44:11 -0400 (EDT) >> Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> wrote: >>> can you tell us exactly what you would like to do with it? >>> On Tue, 16 Sep 2008, Hwee Ling Lee wrote: >>> >>>> Hi, >>>> >>>> I'm re-posting a question. >>>> >>>> Pardon my ignorance. >>>> >>>> How do I use this mri_vol2vol command? I tried to follow the notes, > however, >>>> I'm not quite sure, hence I was not able to write a ROI mask. >>>> >>>> Cheers, >>>> HL >>>> >>>> >>>> -----Original Message----- >>>> From: freesurfer-bounces(a)nmr.mgh.harvard.edu >>>> [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Doug Greve >>>> Sent: 12 September 2008 18:10 >>>> To: Bruce Fischl >>>> Cc: freesurfer(a)nmr.mgh.harvard.edu; Hwee Ling Lee >>>> Subject: Re: [Freesurfer] freesurfer >>>> >>>> You can also skip the 1st two steps and just convert aparc+aseg.mgz to >>>> MNI with mri_vol2vol (make sure to use the --interp nearest flag). Then >>>> look for voxels with values 1030 (left STG) or 2030 (right STG). >>>> >>>> doug >>>> >>>> Bruce Fischl wrote: >>>> >>>>> Hi HweeLing, >>>>> >>>>> I think the aparc.a2005s has the STS labeled in it, so you should >>>>> already have what you need in individual space. You could use >>>>> mri_annot2label, mri_label2vol and mri_vol2vol to transform this into >>>>> MNI if you need to. >>>>> >>>>> cheers, >>>>> Bruce >>>>> >>>>> >>>>> >>>>> On Fri, 12 Sep 2008, Hwee Ling Lee wrote: >>>>> >>>>>> >>>>>> Hi All, >>>>>> >>>>>> I was looking for methods to create a superior temporal sulcus >>>>>> mask (upper and lower boundary). >>>>>> >>>>>>> From my understanding, Freesurfer does a pretty good job in labeling >>>>>>> the >>>>>> >>>>>> sulcus, hence I was wondering if there are possible ways to write the >>>>>> particular ROI as a mask image for each individual subject, and >>>>>> preferably >>>>>> to be in the MNI space or if not, at least in the native space. >>>>>> >>>>>> Thank you. >>>>>> >>>>>> Best wishes, >>>>>> HweeLing >>>>>> >>>>>> >>>>>> >>>>>> > ----------------------------------------------------------------------- >>>>>> Hwee Ling, Lee >>>>>> Max-Planck Institute for Biological Cybernetics >>>>>> Cognitive Neuroimaging >>>>>> Spemannstrasse 41 >>>>>> 72076 Tuebingen >>>>>> Germany >>>>>> Tel: +49-70701-601-1785 >>>>>> Fax: +49-7071-601-616 >>>>>> hwee-ling.lee(a)tuebingen.mpg.de >>>>>> hweeling.lee(a)gmail.com >>>>>> http://www.kyb.mpg.de/~hweeling >>>>>> > ----------------------------------------------------------------------- >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> _______________________________________________ >>>>>> 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 >>>>> >>>>> >>>> >>>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer(a)nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> Hwee Ling, Lee >> >> PhD student >> http://www.kyb.mpg.de/~hweeling >> Max-Planck Institute for Biological Cybernetics >> NWG Noppeney >> Spemannstr 41 >> 72076 Tuebingen >> >> >> > _______________________________________________ > 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
by Bruce Fischl 17 Sep '08

17 Sep '08

can you tell us exactly what you would like to do with it? On Tue, 16 Sep 2008, Hwee Ling Lee wrote: > Hi, > > I'm re-posting a question. > > Pardon my ignorance. > > How do I use this mri_vol2vol command? I tried to follow the notes, however, > I'm not quite sure, hence I was not able to write a ROI mask. > > Cheers, > HL > > > -----Original Message----- > From: freesurfer-bounces(a)nmr.mgh.harvard.edu > [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Doug Greve > Sent: 12 September 2008 18:10 > To: Bruce Fischl > Cc: freesurfer(a)nmr.mgh.harvard.edu; Hwee Ling Lee > Subject: Re: [Freesurfer] freesurfer > > You can also skip the 1st two steps and just convert aparc+aseg.mgz to > MNI with mri_vol2vol (make sure to use the --interp nearest flag). Then > look for voxels with values 1030 (left STG) or 2030 (right STG). > > doug > > Bruce Fischl wrote: > >> Hi HweeLing, >> >> I think the aparc.a2005s has the STS labeled in it, so you should >> already have what you need in individual space. You could use >> mri_annot2label, mri_label2vol and mri_vol2vol to transform this into >> MNI if you need to. >> >> cheers, >> Bruce >> >> >> >> On Fri, 12 Sep 2008, Hwee Ling Lee wrote: >> >>> >>> Hi All, >>> >>> I was looking for methods to create a superior temporal sulcus >>> mask (upper and lower boundary). >>> >>>> From my understanding, Freesurfer does a pretty good job in labeling >>>> the >>> >>> sulcus, hence I was wondering if there are possible ways to write the >>> particular ROI as a mask image for each individual subject, and >>> preferably >>> to be in the MNI space or if not, at least in the native space. >>> >>> Thank you. >>> >>> Best wishes, >>> HweeLing >>> >>> >>> >>> ----------------------------------------------------------------------- >>> Hwee Ling, Lee >>> Max-Planck Institute for Biological Cybernetics >>> Cognitive Neuroimaging >>> Spemannstrasse 41 >>> 72076 Tuebingen >>> Germany >>> Tel: +49-70701-601-1785 >>> Fax: +49-7071-601-616 >>> hwee-ling.lee(a)tuebingen.mpg.de >>> hweeling.lee(a)gmail.com >>> http://www.kyb.mpg.de/~hweeling >>> ----------------------------------------------------------------------- >>> >>> >>> >>> >>> >>> _______________________________________________ >>> 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] Multiple flat surfaces
by SHRIKANTH KULASHEKHAR 17 Sep '08

17 Sep '08

Hi Bruce , In that case would it be possible to flatten one whole hemisphere in freesurfer ? what is the best possible way to do this ? Thanks. shriks Unlimited freedom, unlimited storage. Get it now, on http://help.yahoo.com/l/in/yahoo/mail/yahoomail/tools/tools-08.html/

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subcortical segmentation
by abel cruz vadell 17 Sep '08

17 Sep '08

Hi I have done the three recon-all steps of cortical segmentation in my data and I corrected manually the segmentation errors. Now, I will check the subcortical structures. The correction of this subcortical segmentation will afect the previous cortical segmentation? Thanks Abel

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Multiple flat surfaces
by SHRIKANTH KULASHEKHAR 17 Sep '08

17 Sep '08

Hi, Is there a way to visualize multiple flat surfaces from the same brain in a single tksurfer window ? Thanks in advance. shriks Unlimited freedom, unlimited storage. Get it now, on http://help.yahoo.com/l/in/yahoo/mail/yahoomail/tools/tools-08.html/

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Re: [Freesurfer] MNI152
by Doug Greve 16 Sep '08

16 Sep '08

yep, you can use that one. Cherif Sahyoun wrote: > Thx Doug! > What should I use as --temp? > I have the MNI152 that fsl uses, but I'm not sure it's the one you > used (orientation-wise) to create the reg file. > > ------------------------------------------------------------------------------------------ > Cherif P. Sahyoun HST-MEMP > > Developmental Neuroimaging of Cognitive Functions > > C: 617 688 8048 > H: 617 424 6956 > cherif(a)mit.edu <mailto:cherif@mit.edu> > > "Live as if this were your last day. Learn as if you'll live forever" > Ghandi > ------------------------------------------------------------------------------------------- > > > On Fri, Sep 12, 2008 at 12:08 PM, Doug Greve > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: > > You can use mri_label2vol and spec > $FREESURFER_HOME/average/mni152.register.dat as the registration file. > > Cherif Sahyoun wrote: > >> Hi, >> >> I'd like to morph ROIs drawn on the fsaverage surface onto the >> MNI152 volume. Any ideas on how to do it? >> Usually I'd mri_label2label and then mri_label2vol, but I don't >> think there is a surface version of MNI152, is there? >> >> Thanks! >> Cherif >> ------------------------------------------------------------------------------------------ >> Cherif P. Sahyoun HST-MEMP >> >> Developmental Neuroimaging of Cognitive Functions >> >> C: 617 688 8048 >> H: 617 424 6956 >> cherif(a)mit.edu <mailto:cherif@mit.edu> >> >> "Live as if this were your last day. Learn as if you'll live forever" >> Ghandi >> ------------------------------------------------------------------------------------------- >> >>------------------------------------------------------------------------ >> >>_______________________________________________ >>Freesurfer mailing list >>Freesurfer(a)nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >>https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> > >-- >Douglas N. Greve, Ph.D. >MGH-NMR Center >greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> >Phone Number: 617-724-2358 >Fax: 617-726-7422 > >In order to help us help you, please follow the steps in: >surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > > > > -- 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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FindFacePath
by j janssen 16 Sep '08

16 Sep '08

Hi, using Freesurfer version 4.05 i have a brain that runs through autorecon1 (without errors according to log) but exits with errors during autorecon2. the error given is: "ERROR: _FindFacePath: could not find path!" other brains in the same set do not give this error message, therefore i assume it must have something to do with the specific brain. i´ve attached the log-file. i realize this is little info, let me know what else you need for diagnosis. thanks, -joost

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follow-up to automation of TkMedit
by Jared Price 16 Sep '08

16 Sep '08

Hi everyone. This is Jared over at Brigham and Women's. I have a follow-up question on the question I asked earlier about automating TkMedit such that it will switch between the segmentation overlay view and the gray-scale MRI view automatically. I was able to find a scripting option that I believe should allow me to switch the view from a command-line prompt. The command is listed in the TkMedit Guide. It is "SetDisplayFlag *flag value" *where flag is equal to one of various display options and value is equal to 0 or 1, presumably on or off. We use Mac OS X and run freesurfer through the Terminal command prompt using X11 as our graphical display program. Anyway, when I enter the command "SetDisplayFlag 15 1" which I believe should do the same thing as the keystroke control-g (turn on the segmentation overlay) my command prompt shows me no error messages, apparently accepts the command, but nothing changes on my display. The view remains exactly as it was before regardless of whether or not the segmentation volume was initially on or off when I ran the command. If anyone knows how to turn the segmentation overlay on or off from a command prompt or can correct any missteps that I may have taken please let me know. Thanks and all the best to each of you, Jared Price Center for Neurological Imaging Brigham and Women's Hospital Harvard Medical School 1249 Boylston Street Boston, MA 02115 617-525-6076 jcp44(a)bwh.harvard.edu

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