Freesurfer April 2012

freesurfer@nmr.mgh.harvard.edu

123 participants
192 discussions

Re: [Freesurfer] surf-sess
by Douglas Greve 03 Apr '12

03 Apr '12

what is the content of the df file? On 4/3/12 2:04 PM, Doris Tsao wrote: > freesurfer-Linux-centos4_x86_64-stable-pub-v4.5.0 ---- > > d > On Tue, 3 Apr 2012, > Douglas Greve wrote: > >> what version of FS are you using? If the newer version, use >> tksurfer-sess not surf-sess >> doug >> >> On 4/3/12 1:46 PM, Doris Tsao wrote: >>> Hi Doug, >>> >>> I am having a path problem with surf-sess. >>> >>> I call: surf-sess -sf sf -df df -a rtopy -retinotopy polar -patch >>> patch.flat -hemi rh >>> >>> .. >>> % tksurfer: polar-flat.tcl: read and smooth real Fourier comp >>> MRISreadCurvatureVectorIntoArray(110304Anakin_hauke/polar/map-real-rh.w): >>> fopen failed >>> No such file or directory >>> MRISreadValuesIntoArray: File 110304Anakin_hauke/polar/map-real-rh.w not >>> found >>> >>> >>> For some reason, the function MRISreadValuesIntoArray is not looking in >>> the directory specified by df. >>> >>> thanks for your help, >>> Doris >>> >>> >> _______________________________________________ >> 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] surf-sess
by Douglas Greve 03 Apr '12

03 Apr '12

what version of FS are you using? If the newer version, use tksurfer-sess not surf-sess doug On 4/3/12 1:46 PM, Doris Tsao wrote: > Hi Doug, > > I am having a path problem with surf-sess. > > I call: surf-sess -sf sf -df df -a rtopy -retinotopy polar -patch > patch.flat -hemi rh > > .. > % tksurfer: polar-flat.tcl: read and smooth real Fourier comp > MRISreadCurvatureVectorIntoArray(110304Anakin_hauke/polar/map-real-rh.w): > fopen failed > No such file or directory > MRISreadValuesIntoArray: File 110304Anakin_hauke/polar/map-real-rh.w not > found > > > For some reason, the function MRISreadValuesIntoArray is not looking in > the directory specified by df. > > thanks for your help, > Doris > >

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roi-to-roi functional connectivity analysis
by Lingqiang Kong 03 Apr '12

03 Apr '12

Hi Surfers, Sorry this is the same question again, but has anyone tried ROI-to-ROI functional connectivity analysis in Freesurfer? Instead of computing seed-to-voxel correlation map for the whole brain, is there a way to compute the correlation between the average time course of two ROIs? One way I presume can work is to take the average time courses generated from the fcseed-sess of each ROI and do it manually for each ROI pair. For example, just compute the correlation coefficient between "lh.hippo.dat" and "rh.hippo.dat". But does that regress out the white matter and ventricles? Is there a way to do this properly? What should go to the mkanalysis-sess in this case? Thank you for your help. Lingqiang -- Lingqiang Kong Ph.D candidate Auditory Neuroscience Laboratory Perceptual Neuroimaging Laboratory Boston University 677 Beacon St. Boston, MA 02215 http://www.cns.bu.edu/~shinn/ANL/index.html http://people.bu.edu/fmri/

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piping contrast enhanced MPRAGES
by Ritobrato Datta 03 Apr '12

03 Apr '12

Hi, Is it advisable to run recon-all on contrast enhanced T1 MPRAGEs ? Or is there a separate pipe to process such images ? If yes, is there a way to combine contrast enhanced and regular (non-contrast enhanced) MPRAGEs to increase SNR for purposes of morphometry ? I have attached a pic for reference. Thanks Ri

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Problem with output size of segmented GM and WM files
by Fellhauer, Iven 03 Apr '12

03 Apr '12

Dear all, I followed the steps described here: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg21266.html and here: https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2009-September/01178… to create GM and WM output files. The size of the input file is 176 x 256 x 256 (native space) but the output file has the size 256 x 256 x 256. Is it possible that the output size is equal to the input size? If it is possible how can I do this? Best regards, Iven

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question about fsaverage
by Charlotte Bernard 03 Apr '12

03 Apr '12

Dear Freesurfer experts, I would like to know if it is necessary to have exactly the same number of subjects in my fsaverage and in my qdec.table.dat? If it is a problem how can I eliminate the subjects I don't study from the fsaverage? Thanks for all, Charlotte

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Rejoindre mon réseau sur LinkedIn
by Max Gunther via LinkedIn 03 Apr '12

03 Apr '12

LinkedIn ------------ Max Gunther souhaite se connecter à vous sur LinkedIn : ------------------------------------------ Je vous invite à faire partie de mon réseau professionnel en ligne sur le site LinkedIn. Accepter l'invitation de Max Gunther http://www.linkedin.com/e/-qq80um-h0kxjfmi-1w/qaAr-Z_86TRZ5lXG-dA9kZQ49qSe5… Voir l'invitation de Max Gunther http://www.linkedin.com/e/-qq80um-h0kxjfmi-1w/qaAr-Z_86TRZ5lXG-dA9kZQ49qSe5… ------------------------------------------ Quel est l'intérêt de faire partie du réseau de Max Gunther ? Le réseau de Max Gunther développera votre propre réseau : Si vous acceptez l'invitation de Max Gunther, vous pourrez voir qui vous connaissez dans son réseau et demander à Max Gunther de vous présenter. Appartenir à un réseau est toujours un plus pour votre carrière. -- (c) 2012, LinkedIn Corporation

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Re: [Freesurfer] white-gray contrast algorithm
by Douglas N Greve 02 Apr '12

02 Apr '12

why don't you use the gray/white contrast map that freesurfer produces? On 04/02/2012 04:24 PM, John Fredy wrote: > Dear Douglas and David, > > I am trying to know the gray-white contrast in images from epileptic > patients. In know that I can use the freesurfer surface to obtain the > coordinates for the interface between gray-white substance, but some > help is welcome because the paper that I read introduce elements like > use the data 0.5 before and 0.5 after the interface > > How I can convert the surface to voxel coordinates? > > How I can obtain the data (0.5 mm) out of the resolution of my images > (that is 1 mm)? > > Any interpolation suggestion? > > Exists some code that I can use > > Thanks in advance > > John Ochoa > Bioingeniería > Universidad de Antioquia > > On Mon, Apr 2, 2012 at 12:12 PM, Bruce Fischl > <fischl(a)nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> wrote: > > Hi John > > Doug and David (ccd) can point you in the right direction once you > are done with your surface recons > > cheers > Bruce > > > On Mon, 2 Apr 2012, John Fredy wrote: > > Dear Bruce, > I have interest in the tools that you mentioned > > Best > > John Ochoa > > On Sat, Mar 31, 2012 at 5:31 PM, Bruce Fischl > <fischl(a)nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> > wrote: > Hi John > > we can provide that for you if you download and install > FreeSurfer, then run recon-all on your data. We also provide > tools for computing gray/white contrast once recon-all > has been > run. > > cheers > Bruce > > On Sat, 31 Mar 2012, John Fredy wrote: > > Hello all, I am looking for a white-gray matter contrast > algorithm > > I see the publication: Individual Differences in Verbal > Abilities Associated > with Regional Blurring of the Left Gray and White Matter > Boundary > > http://www.ncbi.nlm.nih.gov/pubmed/22031871 > > But,how I can obtain the coordinates of the interface > between gray and white > matter? > > Thanks in advance > > > > > > > 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. > > > > -- 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

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Re: [Freesurfer] TRACULA exited with errors
by Anastasia Yendiki 02 Apr '12

02 Apr '12

Hi Carolina - The bvecs file that you're attaching has commas as the decimal separator. See this suggestion: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg18395.html The input DWIs can be in a format other than dicom, but then some additional inputs must be specified, see: http://surfer.nmr.mgh.harvard.edu/fswiki/dmrirc Also, from http://surfer.nmr.mgh.harvard.edu/fswiki/Tracula: Note that, because TRACULA relies on the underlying anatomy as derived from the FreeSurfer cortical parcellation and subcortical segmentation, these need to be generated before running trac-all. This means that before you run trac-all you will have to analyze your subjects' anatomical images with recon-all and make sure that they have a good-quality mri/aparc+aseg.mgz. Hope this helps, a.y On Mon, 2 Apr 2012, Carolina Valencia wrote: > I have under dmri folder of Diff001 2 files bvals and bvecs without an order of columns, in the same folder I found files called > dwi_orig.mghdti.bvals andbvecs which have the rows and columns you said. I attached the files (I rename them to old in order to save > the correct ones) Regarding the question to process my own data. I have to recon-all my structural data and to have the orig DWI > dicoms in order to use trac-all, right? > > Thanks for the help! > > 2012/4/2 Anastasia Yendiki <ayendiki(a)nmr.mgh.harvard.edu> > > Hi Carolina - The bvecs and bvals in the tutorial data should have 3 lines and 1 line, respectively, with 70 entries in > each line. Is that not what you have? > > For different possibilities for inputs, please see the tracula wiki page, and particularly the link to the example dmrirc > file: > http://surfer.nmr.mgh.harvard.edu/fswiki/Tracula > > a.y > > On Mon, 2 Apr 2012, Carolina Valencia wrote: > > > Hi FS users > I'm trying to run TRACULA tutorial without sucess. After setting the dmrirc_single_subject and run the first > command step trac-all > -prep -c $TUTORIAL_DATA/diffusion_tutorial/scripts/dmrirc_single_subject > It exited with ERRORS, related to bvecs and bvals which is weird because I downloaded the data via wget and > chech the size. > > #@# Tensor fit lun abr 2 13:23:46 COT 2012 > dtifit -k /home/cvalencia/freesurfer/subjects/tracula_tutorial//diffusion_tutorial/Diff001/dmri/dwi.nii.gz -m > /home/cvalencia/freesurfer/subjects/tracula_tutorial//diffusion_tutorial/Diff001/dlabel/diff/aparc+aseg_mask.bbr.nii.gz > -r > /home/cvalencia/freesurfer/subjects/tracula_tutorial//diffusion_tutorial/Diff001/dmri/bvecs -b > /home/cvalencia/freesurfer/subjects/tracula_tutorial//diffusion_tutorial/Diff001/dmri/bvals -o > /home/cvalencia/freesurfer/subjects/tracula_tutorial//diffusion_tutorial/Diff001/dmri/dtifit > Error: bvecs and bvals don't have the same number of entries > Linux cvalencia-Precision-WorkStation-T3400 2.6.35-32-generic-pae #67-Ubuntu SMP Mon Mar 5 21:23:19 UTC 2012 > i686 GNU/Linux > > trac-preproc exited with ERRORS at lun abr 2 13:23:49 COT 2012 > > Another question is related to process my own data. I have to recon-all my structural data and to have the > orig DWI dicoms in order to > use trac-all, right? > > Many thanks, > > Best regards > -- > -- > Carolina Valencia M > > > > > 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. > > > > > -- > -- > Carolina Valencia M > >

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fsgd contrast question
by McGwier, Meghan (NIH/NIMH) [F] 02 Apr '12

02 Apr '12

Dear experts, I've been reading through the tutorial for group analysis, but I am still a little confused about the contrasts and want to make sure that my contrast is set properly for what I'm interested in looking for. I've made my fsgd file, which contains three groups: ADdiagnosisGroup1, ADdiagnosisGroup2, ADdiagnosisGroup3, and one continuous variable: symptom duration. I want to test if thickness differs between groups controlling for symptom duration. I set my contrasts to: [1 0 -1 0 0 0], [1 -1 0 0 0 0], [0 1 -1 0 0 0]. Since there isn't an fsgd example for 3 groups (1 factor, 3 levels), and one covariate, I wasn't sure if this is correct. Thanks in advance, Meghan Meghan McGwier Postbaccalaureate IRTA Fellow Molecular Imaging Branch National Institute of Mental Health Phone: 301-451-2038 Fax: 301-480-3610

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Freesurfer April 2012