Freesurfer August 2012

freesurfer@nmr.mgh.harvard.edu

110 participants
170 discussions

Talairach coordinates
by peka Savayan 14 Aug '12

14 Aug '12

Hi FreeSurfer, My fMRI time series come from Brain Voyager and x,y,z-coordinates are in Talairach space. Thank you. Peka

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Talairach coordinates
by peka Savayan 14 Aug '12

14 Aug '12

Hi FreeSurfer, I would like to know the x,y,z- coordinates of all atlas ROIs in Talairach space. I have the x, y z coordinates of the voxel time series of an fMRI task. I would like to know which of these voxels belong to a particular ROI. Can you give me advice, please? Thank you. Peka

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analyzeto4dfp to get a talsrcimg.4dfp.ifh file
by Jeff Thompson 14 Aug '12

14 Aug '12

Hi,I have run talairach_avi with the template I have made, and an input file that is manually skull stripped. I ran: talairach_avi --i <input>.nii.gz --atlas <avgeragetemplate> --xfm talairach_avitest.xfmI had put the <averagetemplate>.nii.gz file in the average folder in freesurfer for this to work. I also have <averagetemplate>.4dfp.hdr , <averagetemplate>.4dfp.img , <averagetemplate>.4dfp.mat in the average folder.Running this creates talsrcimg.hdr, talsrcimg.img, talsrcimg.mat in the folder where I ran the script. However in the talairach_avi log it gives an error saying /Applications/freesurfer/average/<averagetemplate>.4dfp.ifh does not exist! How can I create this file?I found a brief note in a mailing list that mentioned analyzeto4dfp talsrcimg -O0 -y:$Id: ifh2hdr.c,v 1.3 2007/05/05 10:45:03 nicks Exp $ Sat Dec 31 03:27:10 2011 Writing: talsrcimg.4dfp.hdr $Id: analyzeto4dfp.c,v 1.2 2007/05/05 00:00:06 nicks Exp $ Reading: talsrcimg.hdr header size 348 bytes hdr.dime.datatype offset=70 value=2 hdr.dime.bitpix offset=72 value=8 hdr.hist.orient offset=252 value=-1 dimensionality 4 dimensions 256 256 256 1 Reading: talsrcimg.img Writing: talsrcimg.4dfp.img Writing: talsrcimg.4dfp.ifh ifh2hdr talsrcimg -r0to255 ori=2 However, I don't know what I need to run this. Will I need to install analyze and 4dfp to be able to run analyzeto4dfp? Or is there another way to get this <averagetemplate>.4dfp.ifh file?Thanks,-Jeff

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Re: [Freesurfer] Creating and using an atlas from scratch‏
by Jeff Thompson 14 Aug '12

14 Aug '12

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Re: [Freesurfer] mri_cnr
by prasser 14 Aug '12

14 Aug '12

Hi, I was wondering if there is any documentation on mri_cnr, particularly how the noise is calculated. Thank you, Paul > > thanks Dr. B.....that helped a lot > > ----- Original Message ----- > From: "Bruce Fischl" <fischl(a)nmr.mgh.harvard.edu> > To: "Kushal Kapse" <kkapse(a)mail.med.upenn.edu> > Cc: "freesurfer" <freesurfer(a)nmr.mgh.harvard.edu> > Sent: Monday, June 18, 2012 2:27:29 PM > Subject: Re: [Freesurfer] mri_cnr > > Hi KK > > this is something i wrote for myself, but you are welcome to try it out. > YOu don't need to give it the slope stuff, that is optional. The "vol" > command line parms are the volumes that you want to assess CNR in. For > example: > > mri_cnr ~/local_subjects/bruce/surf ~/local_subjects/bruce/mri/norm.mgz > processing MRI volume /homes/4/fischl/local_subjects/bruce/mri/norm.mgz... > white = 95.8+-9.7, gray = 65.3+-17.9, csf = 40.1+-17.2 > gray/white CNR = 2.241, gray/csf CNR = 1.026 > lh CNR = 1.633 > white = 95.7+-9.9, gray = 65.5+-17.8, csf = 41.5+-17.4 > gray/white CNR = 2.205, gray/csf CNR = 0.937 > rh CNR = 1.571 > total CNR = 1.602 > > > On Mon, > 18 Jun 2012, Kushal Kapse wrote: > > > hi fellas, > > > > i am trying to run mri_cnr command in freesurfer to compute and see CNR for gray/white/csf.... the command gives following info as help: > > > > -bash-3.2$ mri_cnr > > usage: mri_cnr [options] <surf directory> <vol 1> <vol 2> ... > > -s <slope fname> <dist in> <dist out> <step in> <step out> > > > > > > i understand that 'surf directory'= subjects 'surf' folder ; but i am not able to figure out what it means by vol1, vol2 and slope fname......it doesnt show any error but just doesnt do anything even if i mention the surf directory to this command..... > > > > i checked on freesurfer mail archive, but no info since 2009 about any update on this command..... > > > > may someone please give an info if anyone ever used this command > > > > > > thanks > > kk > > _______________________________________________ > > 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 > > > 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 >

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Problems with ICV
by Wisse, L.E.M. 14 Aug '12

14 Aug '12

Dear freesurfers, I tried to calculate ICV with FreeSurfer, but I encountered some problems. I first ran autorecon 1, 2 and 3, but I noticed afterwards that a few ICV values were really off. The values were really high and when I looked at brain.finalsurfs.mgz, the segmentation also included skull, eyes and sometimes even the nose and ears. (I am not sure that I should look at the brainfinal.surfs.mgz for ICV segmentation, but the segmentations seemed to correlate with the ICV values.) So, I decided to try adjusting the watershed parameters and I also tried using gcut. I noticed that the segmentation brain.finalsurfs improved a lot, however in aseg.stats the ICV values did not change at all! Can anyone help me with this problem? Kind regards, Laura Wisse ------------------------------------------------------------------------------ De informatie opgenomen in dit bericht kan vertrouwelijk zijn en is uitsluitend bestemd voor de geadresseerde. Indien u dit bericht onterecht ontvangt, wordt u verzocht de inhoud niet te gebruiken en de afzender direct te informeren door het bericht te retourneren. Het Universitair Medisch Centrum Utrecht is een publiekrechtelijke rechtspersoon in de zin van de W.H.W. (Wet Hoger Onderwijs en Wetenschappelijk Onderzoek) en staat geregistreerd bij de Kamer van Koophandel voor Midden-Nederland onder nr. 30244197. Denk s.v.p aan het milieu voor u deze e-mail afdrukt. ------------------------------------------------------------------------------ This message may contain confidential information and is intended exclusively for the addressee. If you receive this message unintentionally, please do not use the contents but notify the sender immediately by return e-mail. University Medical Center Utrecht is a legal person by public law and is registered at the Chamber of Commerce for Midden-Nederland under no. 30244197. Please consider the environment before printing this e-mail.

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longitudinal analysis: rate of change
by Shannon Kogachi 13 Aug '12

13 Aug '12

Hi, I had a question about the rate of change (thickening in mm/year) for the longitudinal processing. How is this value calculated when there are more than two timepoints per subject? Thank you! -Shannon K.

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Radial Distance from Tessellated Hippocampus Surface
by Jared Saletin 13 Aug '12

13 Aug '12

Hi Freesurfer folks, I was wondering if anyone knew an automated or semi-automated method for calculating radial distance along the longitudinal axis of the hippocampus from a surface generated by tessellating the segmentation from aseg. I know radial distance is used to examine local changes in morphology in cases such as aging and dementia - I was curious if there anyone has done so using the freesurfer Hipp segmentation as the starting point. Thanks so much! Jared

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Tracula: pathway #7
by Chris Watson 13 Aug '12

13 Aug '12

Hello, When I go through trac-prep, pathway #7 always takes much much longer than any of the others. And for that pathway it always displays this: INFO: Distances between consecutive points are 34 37 34 40 WARN: Could not find satisfactory control point fit - try 90 Has anyone else had this problem? Visually, they look right to me. Thanks, Chris

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Re: [Freesurfer] Freesurfer Digest, Vol 102, Issue 10
by Linda Douw 13 Aug '12

13 Aug '12

Hi Doug, I first parcellate fsaverage5 using ico4 (all my functional data are morphed to fsaverage5 surface): mris_make_face_parcellation /fsaverage5/rh.inflated $FREESURFER_HOME/lib/bem/ic4.tri rh.ico4.annot Then I extract the waveforms using mri_segstats mri_segstats --i rh.functional.nii.gz --avgwf rh_ico4.txt --annot fsaverage5c rh ico4 --sum ico4_rh.sum Hope this clarifies the problem! Linda > ------------------------------ > > Message: 25 > Date: Fri, 10 Aug 2012 11:18:38 -0400 > From: Douglas N Greve <greve(a)nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] ico4 parcellation and mri_segstats > To: freesurfer(a)nmr.mgh.harvard.edu > Message-ID: <5025264E.3030801(a)nmr.mgh.harvard.edu> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > what are your command lines? > doug > > On 08/09/2012 01:21 PM, Linda Douw wrote: >> Dear Freesurfers, >> >> I'm trying to extract the average waveforms from all 2562 ROIs in an >> annotation constructed using mris_make_face_parcellation with ico4. >> However, I get only 2460 waveforms after doing mri_segstats, and the >> summary files show that several ROIs are 'skipped' for some reason. Am I >> missing something? >> >> Thanks, >> > > -- > 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 > > > > ------------------------------ > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > End of Freesurfer Digest, Vol 102, Issue 10 > ******************************************* > > >

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Freesurfer August 2012