Freesurfer December 2015

freesurfer@nmr.mgh.harvard.edu

115 participants
187 discussions

Help importing files from a previous SPM analysis
by Luis Fernado Silva Castro de Araújo 20 Dec '15

20 Dec '15

Hi all, I am just starting to learn to analyse neuroimaging data. So these are my first steps with FreeSurfer. I apologize if the question is too basic to the mail list. I set myself the goal of finding volumes for several areas in a dataset from the lab I am working on, but I got stuck very early on the exercise. As far as I understood by reading the Tutorials, all the magic happens with the recon-all command, right? But it seems that it requires a specific directory structure to run properly (the FSFAST structure <http://freesurfer.net/fswiki/FsFastTutorialV5.1/FsFastDirStruct>). The problem is that the dataset for my exercise is organized in a different structure. It was previously analysed in SPM. The structure is as follows. For patients: /experiment/patients/A.o/ and for controls: /experiment/controls/A.o/ Within each directory there are .hdr, .img, .mat and .mask files for each observation, which was obtained in two different times. So the naming of the files have the following order: experiment_subjectnumber_time1.img and for the second acquisition reads: experiment_subjectnumber_time2.img The same with all the before mentioned extensions (hdr, mat, mask). It seems that in the FreeSurfer workflow the command unpacksdcmdir <https://surfer.nmr.mgh.harvard.edu/fswiki/FsFastUnpackData> is used to extract data from the nii and dicon types and organize them in the FSFAST structure. Can it be used on directory structures like the one I have? Or is there anyway of automating the conversion from this structure into the FSFAST’s? Thank you, luis

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Meaning of resample type in mri_convert - Repost
by Gronenschild Ed (NP) 20 Dec '15

20 Dec '15

Hi FreeSurfer developers, Can you please provide information on the resample types "interpolate" and "weighted" which can be specified with option -rt in mri_convert? Cheers, Ed

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Masks on tksurfer
by stdp82＠virgilio.it 18 Dec '15

18 Dec '15

Hi list, I would like to make a mask of a significant cluster after FDR correction on sig.mgz (FS-FAST analysis). I'm using tksurfer and its options (custom fill, new label from marked) but I have some difficulties to save the mask. Could you suggest me a reference/guide page, please? Thanks Stefano

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move annotations across hemispheres
by Peggy Skelly 18 Dec '15

18 Dec '15

Hi, I am attempting to move an annotation file from the right to left hemisphere. I have run xhemi registration with: surfreg —s $subj —t fsaverage_sym —lhrh surfreg —s $subj —t fsaverage_sym —lhrh —xhemi The annotation file is rh.myclusters.annot in the $subj/xhemi/label subdirectory. I've tried using both mri_surf2surf and mris_apply_reg: mri_surf2surf --srcsubject s1315_base/xhemi --sval-annot $SUBJECTS_DIR/s1315_base/xhemi/label/rh.myclusters.annot --tval $SUBJECTS_DIR/s1315_base/label/lh.myclusters.annot --trgsubject s1315_base --srchemi rh --trghemi lh --srcsurfreg fsaverage_sym.sphere.reg --trgsurfreg fsaverage_sym.sphere.reg mris_apply_reg --src-annot $SUBJECTS_DIR/s1315_base/xhemi/label/rh.myclusters.annot --trg $SUBJECTS_DIR/s1315_base/label/lh.myclusters.annot --streg $SUBJECTS_DIR/s1315_base/xhemi/surf/rh.fsaverage_sym.sphere.reg $SUBJECTS_DIR/s1315_base/surf/lh.fsaverage_sym.sphere.reg --no-rev I've tried mris_apply_reg with and without the '--no-rev' flag. The output from each of these commands is the same: the clusters are on the medial aspect of the LH. They were clusters in the supramarginal and temporal regions on the RH, so I was expecting them to be in the same regions on the LH. Thanks, Peggy

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Re: [Freesurfer] Tracula: trac-all prep badly formed if error
by Anastasia Yendiki 18 Dec '15

18 Dec '15

Hi Katherine - I believe that it's because you define bvecfile and bvalfile as lists of 2 file names each. Both bvecfile and bvalfile accept a single file name. In bveclist you can enter as many gradient tables as input volumes. Best, a.y On Thu, 17 Dec 2015, Katherine Damme wrote: > Here is all of the output to the terminal. > > On Thu, Dec 17, 2015 at 5:12 AM, Anastasia Yendiki > <ayendiki(a)nmr.mgh.harvard.edu> wrote: > > Hi Katherine - I don't see this error in the log file, but the > last > command that it ran before it stopped was this: > > mri_probedicom --i > /media/Data/Temple/Temple_Tracula/31313422_2998/dti_dicom/31313422_2998.MR. > Temple.9.1.20140521.105357.1f9ykdm.dcm > > > /media/Data/Temple/Temple_Tracula/31313422_2998/dmri/dcminfo.dat > > Does this .dat file exist? If so the error probably happened > after this > command. Can you send the exact error message that you see on > your > terminal? > > Thanks! > > a.y > > On Tue, 15 Dec 2015, Katherine Damme wrote: > > > Hello Everyone! > > > > I am getting a badly formed number error in my trac-all any > ideas? > > > > > > > > > _______________________________________________ > 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. > > > > > -- > > Kate Damme | Affective and Clinical Neuroscience Lab | Northwestern > University > > (847) 491-4069 | 2029 Sheridan Rd. | 226 Swift Hall | > email | LinkedIn | Academic > > > >

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Re: [Freesurfer] question BrainMap
by Thomas Yeo 18 Dec '15

18 Dec '15

Hi Joost, This is a good question and something I should have anticipated. I am cc-ing the freesurfer list (since it might be helpful for others). I am attaching a zip file. If you unzip the zip file, the folder YeoBrainmapFreeSurfer/Specialization/ contains 10 csv files corresponding to 10 to 14 components, left and right hemispheres, i.e., 5 x 2 = 10 files. Each csv file consists of two columns. First column corresponds to ROI number and second column corresponds to top component. For example, for 12 components, the ROI in the superior temporal lobe corresponds to ROI #2 and is specialized for component 3 (auditory). So the csv file (rh.YeoSpecialization_12comp_top.csv) has a row with first column corresponding to 2 and second column corresponding to 3. Let me know if this makes sense. Regards, Thomas On Thu, Dec 17, 2015 at 8:49 PM, Joost Janssen <joost.janssen76(a)gmail.com> wrote: > Dear Prof. Yeo, > > Frame 2 of lh.Yeo_Brainmap_10to14Comp_SpecializationROI.mgz > > contains all the numbered ROIs of the 12-component specialization map, but > the ROIs are not categorized in each of the 12 components - i think. Goal: I > have results on fsaverage and want to quantify the overlap (# vertices) with > each of the 12 components and for this i need the ROIs to be categorized > into components (e.g. ROI #1 - component X, ROI #2 - component Y, etc.), i > think. > > advice? > > thanks! > -joost

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WM Hyperintensities
by Junjie Wu 17 Dec '15

17 Dec '15

Hello all, I have a quick question. As we know, T2 FLAIR can be used in Freesurfer to refine the pial surfaces. I am wondering if T2 FLAIR can also be used to improve the detection of white matter hyperintensities? Thanks, Junjie

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annot file to volume mask in the subject folders
by Woo, Jonghye 17 Dec '15

17 Dec '15

Hi Freesurfers, What would be the best way to convert annot to volume mask (like nifty format) from fsaverage atlas? Thanks,

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average cortical thickness measure?
by Maria Kharitonova 17 Dec '15

17 Dec '15

Hi, in response to the average thickness measure (see below). In ?h.aparc.stats, I see a variable ThickAvg, is that it? And then to get the average thickness across the *entire* cortex, I average across the couple of dozen regions that it provides? Thanks! Maria > > >Message: 7 >Date: Fri, 11 Dec 2015 13:49:23 -0500 >From: Douglas N Greve <greve(a)nmr.mgh.harvard.edu> >Subject: Re: [Freesurfer] average cortical thickness measure? >To: freesurfer(a)nmr.mgh.harvard.edu >Message-ID: <566B1AB3.9090309(a)nmr.mgh.harvard.edu> >Content-Type: text/plain; charset=windows-1252; format=flowed > >In ?h.aparc.stats, you'll find a line like > ># Measure Cortex, MeanThickness, Mean Thickness, 2.40617, mm > >You'll have to get the value for each hemi and compute the mean > > >On 12/11/2015 01:38 PM, Maria Kharitonova wrote: >> I know that the aseg atlas provides a number of voume measures >> (e.g. EstimatedTotalIntraCranialVol, TotalGrayVol), but is there a >> variable for an average cortical thickness? I?d like to see if >> thickness in some of the regions is associated with a variable of >> interest over and above an overall main effect, so would like to >> control for the average thickness, but can?t figure out a good way to >> do that. >> >> Thanks! >> Maria >> >> ? >> Maria Kharitonova, PhD >> Research Assistant Professor >> Department of Medical Social Sciences >> Northwestern University Feinberg School of Medicine >> 625 N. Michigan Ave, Suite 2700 >> Chicago, IL 60611 >> Phone: (312) 503-6503 >> Email: maria.kharitonova(a)northwestern.edu >> <mailto:maria.kharitonova@northwestern.edu> >> >> >> >> _______________________________________________ >> 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 > >Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >www.nmr.mgh.harvard.edu/facility/filedrop/index.html >Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > > >------------------------------

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gyrification and longitudinal processing
by Bernardoni, Fabio 17 Dec '15

17 Dec '15

dear freesurfer enthusiasts, does it makes sense to compute the local Gyrification Index (lGI) on longitudinally preprocessed subjects? thanks fabio Dr. Fabio Bernardoni wiss. Mitarbeiter Klinik und Poliklinik für Kinder- und Jugendpsychiatrie und -psychotherapie Tel. +49 (0)351 458-5245 Fax +49 (0)351 458-7206 Universitätsklinikum Carl Gustav Carus an der Technischen Universität Dresden Anstalt des öffentlichen Rechts des Freistaates Sachsen Fetscherstraße 74, 01307 Dresden http://www.uniklinikum-dresden.de Vorstand: Prof. Dr. med. D. M. Albrecht (Sprecher), Wilfried E. B. Winzer Vorsitzender des Aufsichtsrates: Prof. Dr. med. Peter C. Scriba USt.-IDNr.: DE 140 135 217, St.-Nr.: 203 145 03113

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Freesurfer December 2015