Freesurfer

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30088 discussions

mri_convert not creating bvecs/bvals
by Matthew Carter 22 Nov '11

22 Nov '11

Hi, I was previously using dcm2nii to convert DWI dicom series to the nifti format. I want to change my process to use mri_convert instead, as I am having a lot of orientation problems using dcm2nii. My problem is that while dcm2nii extracted the bvecs/bvals into files separate from the nifti, mri_convert does not seem to be doing this. I looked on the mailing this for this problem, but it doesn't appear that anyone else is seeing this. Are there any command line switches or options I need to set to accomplish this? Thanks, Matt

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Re: [Freesurfer] Postdoctoral Fellowship
by Emily Rogalski 22 Nov '11

22 Nov '11

*POSTDOCTORAL TRAINEE POSITION AVAILABLE –* *APPLICATION DEADLINE 28 NOVEMBER 2011* Postdoctoral Fellowship Opportunity in the Cognitive Neurology and Alzheimer’s Disease Center at Northwestern University Feinberg School of Medicine. The trainee will work with Drs. Emily Rogalski and Marsel Mesulam on studies of language processing in primary progressive aphasia and investigations of healthy brain aging. Studies are focused on delineating language deficits associated with the progression of neurodegenerative disease as marked by structural and functional neuroimaging as well as event-related potentials. There is also an opportunity to investigate concomitants of healthy brain aging in advanced old age. The training position is competitive and supported by the Mechanisms of Aging and Dementia Training Grant. Applicants should have a PhD degree from an accredited university in cognitive aging, neuropsychology, cognitive neuroscience, or related field with experience in structural neuroimaging. *Applicant must be US citizen or permanent resident*. Experience with PET imaging is also desirable. Start date is negotiable but opportunity is available as early as December 1, 2011. Applicants should submit letters of interest, a CV, and three letters of recommendation to Kristine Zachrich, Northwestern Cognitive Neurology and Alzheimer’s Disease Center, 320 E. Superior St., Searle 11-467, Chicago, Illinois 60611; k-zachrich(a)northwestern.edu; 312-908-9023.

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mask from sig.mgh
by YUMI MAEDA 22 Nov '11

22 Nov '11

Hi, I want to make a mask file from the output file of mri_glmfit, sig.mgh. will you show me how to get it? thank you. YUMI

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question about thickness file
by ZhiLiangLong 21 Nov '11

21 Nov '11

Hi all: After finishing recon-all steps, there are some thickness files generated such as lh.thickness and lh.thickness.fwhm10.fsaverage.mgh which contain cortical thickness values at each vertex. Are the thickness values in lh.thickness file calculated in individual space ,that is , they are absolute values and values in lh.thickness.fwhm10.fsaverage.mgh file computed based on fsaverage template, that is, they represent relative values ? Any suggestions appreciated.

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fs-fast tutorial data
by Verena Gramse 21 Nov '11

21 Nov '11

Hi, I am trying to follow the FS-FAST tutorial but I cant find the required data for it under the links specified on the tutorial site: ftp://surfer.nmr.mgh.harvard.edu/pub/data/fsfast-functional.tar.gz, ftp://surfer.nmr.mgh.harvard.edu/pub/data/fsfast-tutorial.subjects.tar.gz Could you tell me where I find the data? Thanks so much, Verena

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Running 2 versions of Freesurfer on same computer
by Jennifer Addicks 21 Nov '11

21 Nov '11

Hello, I have been successfully running FreeSurfer 4.5 on my MacOSX 10.5.8 with no issues. I recently installed FreeSurfer 5.1 to a separate directory on the same laptop to analyze a new dataset but I am now having various issues using FreeSurfer version 4.5. For Version 4.5, I path the freesurfer directories as follows (identical to before installing version 5.1): setenv FREESURFER_HOME /Applications/freesurfer setenv SUBJECTS_DIR /MRIData/Root/freesurfer/TRDsubjects_dir source $FREESURFER_HOME/SetUpFreeSurfer.csh --------- freesurfer-Darwin-leopard-i686-stable-pub-v4.5.0 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /Applications/freesurfer FSFAST_HOME /Applications/freesurfer/fsfast FSF_OUTPUT_FORMAT nii SUBJECTS_DIR /MRIData/Root/freesurfer/TRDsubjects_dir MNI_DIR /Applications/freesurfer/mni The issue is that now various commands no longer function in version 4.5. For example when typing tkmedit, tksurfer or qdec, I get the following type of error: tkmedit.bin: Command not found. Is it possible that although I installed version 5.1 in a separate directory, that some files were deleted or moved in version 4.5? Is my 4.5 license no longer valid now that I have installed version 5.1 with a new license? It is confusing since some commands appear to function, such as mri_convert and recon-all, but anything involving a GUI seems not to function. Any help would be appreciated. thanks, Jennifer

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Re: [Freesurfer] use of --a2009s flag
by Douglas N Greve 21 Nov '11

21 Nov '11

does that file exist? LAOUCHEDI MAKHLOUF wrote: > hi doug > i am using the v5.0.0 version, the massage i have when > running "mri_aparc2aseg --s ctr12 --a2009s" is : > ( SUBJECTS_DIR makh_free > subject ctr12 > outvol makh_free/ctr12/mri/aparc.a2009s+aseg.mgz > useribbon 0 > baseoffset 10100 > RipUnknown 0 > > Reading lh white surface > makh_free/ctr12/surf/lh.white > > Reading lh pial surface > makh_free/ctr12/surf/lh.pial > > Loading lh annotations from makh_free/ctr12/label/lh.aparc.a2009s.annot > could not read annot file makh_free/ctr12/label/lh.aparc.a2009s.annot > No such file or directory > ERROR: MRISreadAnnotation() failed > makh_free/ctr12/label/lh.aparc.a2009s.annot) > > same thing when using : --annot aparc.a2009s > > thanks for your help > > > --- En date de : *Lun 21.11.11, Douglas N Greve > /<greve(a)nmr.mgh.harvard.edu>/* a écrit : > > > De: Douglas N Greve <greve(a)nmr.mgh.harvard.edu> > Objet: Re: [Freesurfer] use of --a2009s flag > À: "LAOUCHEDI MAKHLOUF" <laoumakhl(a)yahoo.fr> > Cc: Freesurfer(a)nmr.mgh.harvard.edu > Date: Lundi 21 novembre 2011, 18h18 > > What version are you using? You can accomplish the same thing with > --annot aparc.a2009s > doug > > LAOUCHEDI MAKHLOUF wrote: > > hi everyone > > > > i am trying to use the mri_aparc2aseg command with > the > > --a2009s flag to have the aparc.a2009s labels and i have the > following > > message " Option --a2009s unknown" > > > > thanks > > > > > ------------------------------------------------------------------------ > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > </mc/compose?to=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 </mc/compose?to=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 > </mc/compose?to=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. > -- 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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reg-feat2anat
by Michelle Umali 21 Nov '11

21 Nov '11

Dear Freesurfers, I've previoiusly run reg-feat2anat on some fsl feat data, but now my advisor things i should re-preprocess my fsl data with a larger kernel size. Since it's the same dataset , do I have to re-run reg-feat2anat on this or can I just copy the registration folder from the old analysis? Thanks. Michelle

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control points didn't work
by Tetiana Dadakova 21 Nov '11

21 Nov '11

Dear FreeSurfer list, I was trying to edit wm surface by adding control points. After saving them and re-running recon-all -autorecon2-cp -autorecon3, the control points are still there, but wm is not edited (although cp worked in other places for the same brain). The intensity there is around 95-98 depending on slice. Could you please suggest what could go wrong? Thank you, Tanja.

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T1 mapping, mri_ms_fitparms and flip angle map
by Dr.med. Johannes C. Klein 21 Nov '11

21 Nov '11

Dear all, For a structural study, I would like to determine cortical T1 values. T1 map generation from two FLASH images works like a charm, and I would like to add B1 correction now. I have acquired flip angle maps for my subjects (using the Yarnykh method with interleaved FLASH and two TRs), and would like to correct my T1 maps accordingly. Looking at the online help of mri_ms_fitparms, I think the parameter -afi should do the trick. However, I'm not sure about the properties of the flip angle map that I need to supply to mri_ms_fitparms. Does that programme expect absolute flip angle values? Or can I feed in my two AFI FLASH volumes in some way? If anyone can point me in the right direction, that would be great! Thanks for you help, Johannes

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