Freesurfer April 2013

freesurfer@nmr.mgh.harvard.edu

131 participants
220 discussions

qdec - design interaction
by Klara Mareckova 02 Apr '13

02 Apr '13

Hi, I'm new to freesurfer and I'm trying to use qdec to run a 2-way anova (sex, age, sex*age). How do I set up the design to get results for the interaction? Do I do that withing the qdec design tab? Or how else do I do it? (e.g. do I need to create a FSGD file? But where in qdec would I upload it?) Thanks a lot for your advice, Klara

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RAS coordinates of adjacent vertices on surface
by Cesar Echavarria 02 Apr '13

02 Apr '13

Hi freesurfers, I'm looking at the flattened fsaverage surface and trying to figure out how to select a number of vertices that all lie on the same line. I would like to make this an automatic process so I'm trying to figure out how the RAS coordinates of these vertices relate to each other. I plan to then make a label file in which these vertices are listed. Please let me know if you have any insight into how this might be done. Thanks, Cesar Echavarria

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R: R: Re: R: Re: perirhinal analysis
by stdp82＠virgilio.it 02 Apr '13

02 Apr '13

Dear Doug, I'm trying to follow your indication but, please, could you explicate what's meaning "subjet with" and where I should put it?Could you show me the correct command line, please? The wrong command line is mri_label2label --srcsubject fsaverage --srclabel rh.perirhinal.label --trgsubject Con01 --trglabel Con01/label/rh.perirhinal.label --hemi rh --regmethod surface Many thanks, Stefano ----Messaggio originale---- Da: greve(a)nmr.mgh.harvard.edu Data: 28-mar-2013 18.32 A: <stdp82(a)virgilio.it> Cc: <freesurfer(a)nmr.mgh.harvard.edu> Ogg: Re: R: Re: [Freesurfer] perirhinal analysis If the source subject is subject_prova then you need to spec that subjet 2with --srcsubject (instead of fsaverage) doug On 03/28/2013 01:11 PM, stdp82(a)virgilio.it wrote: > Yes, it is located in > /Applications/freesurfer/subjects/subject_prova/Con01/label/rh.perirhinal.label. > > > > Stefano > > > > > ----Messaggio originale---- > Da: greve(a)nmr.mgh.harvard.edu > Data: 28-mar-2013 17.46 > A: <freesurfer(a)nmr.mgh.harvard.edu> > Ogg: Re: [Freesurfer] perirhinal analysis > > It says "no such file or directory" > does rh.perifhyinal.label exist? > > > On 03/28/2013 11:55 AM, stdp82(a)virgilio.it wrote: > > Hi list, > > > > I'm running perirhinal analysis with this error: > > > > mri_label2label --srcsubject fsaverage --srclabel rh.perirhinal.label > > --trgsubject Con01 --trglabel Con01/label/rh.perirhinal.label --hemi > > rh --regmethod surface > > > > srclabel = rh.perirhinal.label > > srcsubject = fsaverage > > trgsubject = Con01 > > trglabel = Con01/label/rh.perirhinal.label > > regmethod = surface > > > > srchemi = rh > > trghemi = rh > > trgsurface = white > > srcsurfreg = sphere.reg > > trgsurfreg = sphere.reg > > usehash = 1 > > Use ProjAbs = 0, 0 > > Use ProjFrac = 0, 0 > > DoPaint 0 > > > > SUBJECTS_DIR/Applications/freesurfer/subjects/subject_prova > > FREESURFER_HOME /Applications/freesurfer > > Loading source label. > > No such file or directory > > mri_label2label: could not open label file rh.perirhinal.label > > No such file or directory > > ERROR reading rh.perirhinal.label > > > > My $SUBJECTS_DIR=/Applications/freesurfer/subjects/subject_prova and > > rh.perirhinal.label exist and it is located > > in /Applications/freesurfer/subjects/subject_prova/Con01/label > > > > > > Thanks, > > > > > > Stefano > > > > > > > > _______________________________________________ > > 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > _______________________________________________ > 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. > > > -- 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 Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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Projection of markers from the scalp to cortical surfaces
by Eleonora Maggioni 02 Apr '13

02 Apr '13

Hi Freesurfer experts, I am new to FreeSurfer and I have a question. I have markers of EEG electrodes on the T1 image of a subject and I want to project them from the scalp to his pial surface (that I reconstructed using the standard procedure). To do so, I manually selected the central point of each marker in tkmedit and I defined a control point. Then I red that control point with tksurfer on the corresponding pial surface. This should be the projection to the pial surface: is this procedure correct? If yes, in which coordinate system is the projection made? Thank you in advance, Kind regards, -- Eleonora Maggioni BioEngineering PhD student Politecnico di Milano Istituto E.Medea, Bosisio Parini (LC)

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Advertisement for a post-doc position
by Katell Mevel 02 Apr '13

02 Apr '13

Hi, I would be grateful if the following could be spread through the Freesurfer list. Thank you for your help, Best Katell Dear list, One post-doc position in multimodal brain imaging is available in our group, the deadline is 6th of May 2013. Please find the details below: *** Department Center of Neurodevelopmental Disorders at Karolinska Institutet (KIND)(www.ki.se/kind<http://www.ki.se/kind>) KIND is a competence center for research, development and education within the area of developmental psychopathology. The center is established in collaboration between Karolinska Institutet and Stockholm County Council, and aims at improving clinical practice, generating basic research, and spreading new knowledge to stakeholders. The Roots of Autism Twin Study Sweden (RATSS) is a research project within KIND, focusing on monozygotic twins being discordant for autism spectrum disorder and other neurodevelopmental disorders, e.g. ADHD. Twins are examined on multiple levels, among them functional and structural neuroimaging using MRI. Scanning is performed in the Karolinska Institutet MR Research Center, using a 3 Tesla MR scanner (GE MR750). The project is running since the late Summer 2011 and more than 40 pairs have been included. *** Duties As a post-doc, you will be mainly responsible for the acquisition and analyses of the multimodal neuroimaging data. This includes DTI, resting-state fMRI and structural T1, to be combined according to a brain connectome approach. This work will be done in close collaboration with the department of Clinical Neuroscience. The position also includes several other responsibilities, e.g. coordination of the neuroimaging works at KIND, involvement in international collaborations, administrative tasks, grant application and article writing. All the details about this position can be found here: https://ki.netrecruiter.se/what:job/jobID:18940/where:4/ Applications should be submitted here: https://ki.netrecruiter.se/en/what:login/jobID:18940/where:4/ Please note that we DO NOT ACCEPT applications being submitted by email. To be considered, your application must be submitted through the application system. Best Regards, Katell MEVEL for KIND ________________________________ Katell Mevel | PhD Karolinska Institutet Center of Neurodevelopmental Disorders (KIND) Gävlegatan 22B, floor 8 | 113 30 Stockholm +46 (0)8 51452706 | +46 (0)721 980 350 katell.mevel(a)ki.se<mailto:katell.mevel@ki.se> | ki.se/kind<http://ki.se/ki/jsp/polopoly.jsp;jsessionid=aMdk8ad4iRL6OYOdFn?l=en&d=130> ___________________________________________________________________________________ Karolinska Institutet - a medical university

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tracula bvecs
by stdp82＠virgilio.it 02 Apr '13

02 Apr '13

Hi Anastasia, my subjects have gradient=0 only in first or last line. I'm noting that the subjects having 0.000 0.000 0.000 in the first line of bvecs.txt (0 in vals.txt) show correct tracts. The subjects that having 0.000 0.000 0.000 as last line of bvecs.txt show wrong or lacking tracts. For these subjects, I have already checked registration and gradients. Is possible that this issue depends from setting of nb0. In both cases (first or last line with 0.000) I have used set nb0 = 1. Is this correct? Thank you very much, Stefano

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qdec - 3 timepoints
by Harry Hallock [hhal5293＠uni.sydney.edu.au] 02 Apr '13

02 Apr '13

Hi, I'm currently doing a long analysis of a data set that contains two groups (training and control) and 3 timepoints (baseline -BL, follow up1- FU1 follow up2-FU2) I've put it through qdec. But for the analysis qdec only gives me one measure for long.thickness-avg, rate, pc1 and spc. How do i know which timepoints are being analyzed? i.e. is it simply FU2-BL? Or is it FU2-FU1 or FU1-BL? Is there a way i can test for each of these changes over time? Cheers, Harry

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How to get surface-based AAL template
by ZhiLiangLong 01 Apr '13

01 Apr '13

Hi all; I need a suface-based aal template which is compatible with FS surface file. Is there a way i can get the surface-based aal template? I have an idea, that is to just transform the AAL template (.nii file) in MNI space onto the surface template (e.g. fsaverage template) in FS. Is it correct? if in this case, how can i do the transformation? Any suggestions appreciated. Besh wishes.

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Problem with CVS server?
by Akio Yamamoto 01 Apr '13

01 Apr '13

Hi, I'm trying to download the source code from the cvs but it failed due to the following error: cvs [checkout aborted]: Could not map memory to RCS archive /usr/fscvsroot/dev/distribution/average/fsaverage.tar.gz,v: Cannot allocate memory Any problems with the cvs server? Your help will be very much appreciated. Akio

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Re: [Freesurfer] Problem with longitudinal edits
by Vy Dinh 01 Apr '13

01 Apr '13

Hi Bruce, I just noticed this reply. Looks like you came to save the day! I am using a Mac OSX - Snow Leopard 10.6.8 (2 x 3 GHz Quad-Core Intel Xeon) Thanks, Vy On Mon, Apr 1, 2013 at 4:17 PM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu>wrote: > Hi Vy and Martin > > there was a bug in mri_mask that I just fixed that caused the > brain.finalsurfs.mgz to be empty when the brain.finalsurfs.manedit.mgz > existed. Vy: if you tell us what hardware/software platform you are using > we can get you an updated version. Not sure if this will fix your problem, > but it might. I also modified mris_make_surfaces in a way that could help > and you can try a new version of that if mri_mask doesn't fix things for > you > > cheers > Bruce > On Mon, 1 Apr 2013, Martin Reuter wrote: > > > > > Also: brain.finalsurfs.manedit is mainly for correcting situations where > the > > pial surface extends into the cerebellum. Did that happen in your case > > without editing? For other edits (e.g. pial including dura) you should > fix > > the brainmask.mgz . > > > > Best, Martin > > > > > > > > On 04/01/2013 04:39 PM, Martin Reuter wrote: > > Hi Vy, > > > > not sure what it going on in your data. Surfaces are copied from > > the base and if they are not accurate there you need to fix it > > there. It seems you did that and you worked the edits in the > > right order. > > > > What exactly happened? You fixed cross and base and everything > > look fine. When you run long it looks fine, but when you edit > > long and run it again it messes up? > > > > Did you edit only the brain.finalsurfs or also other things at > > the same time? Also, if you edited long, these edits will be > > kept and not replaced with new edits from base or cross. So if > > cross or base get edited it may be good to rename or remove the > > edit file in the long and run long without edits again. This way > > the cross and base edits get transferred to long automatically. > > Only if that is not sufficient you need to do edits in the long. > > > > Sorry I cannot say more right now without knowing what you did. > > > > Best, Martin > > > > > > > > On Fri, Mar 29, 2013 at 10:13 AM, Vy Dinh > > <vy_dinh(a)rush.edu> wrote: > > BTW, we are using Freesurfer 5.1: > > freesurfer-i686-apple-darwin9.8.0-stable5-20110525 > > > > On Fri, Mar 29, 2013 at 10:08 AM, Vy > > Dinh <vy_dinh(a)rush.edu> wrote: > > Dear Developers, > > I have a significant problem when rerunning the pial > > edits for the longitudinal data. Our dataset > > consists of subjects & a followup scan (for each > > sub). To be thorough, we edited > > brain.finalsurfs.manedit.mgz (as it was further in > > the processing stream) for the cross-sectional > > scans, the base scans, and the longitudinal scans. > > The longitudinal data were created only after the > > base has been edited and rerun. Likewise, the base > > was only created and rerun after the > > cross-sectionals were finalized. > > > > We work with a clinical population so minor edits do > > show up on the longitudinal scans. However, after > > editing and recreating the surfaces from these > > longitudinal scans, the pial surfaces has extended > > to include dura & other voxels that were not > > previously included within the pial surface (during > > the initial creation of the longitudinal data). We > > tried both commands (listed below) and get this same > > problem: > > > > recon-all -autorecon2-pial -autorecon3 -long tpN > > tp_base > > (http://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalEdits) > > or recon-all -autorecon3-pial -long tpN tp_base ( > http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/LongitudinalTutorial) > > > > Could you please help us figure out why the pial > > surface extends to include nonbrain regions when > > recreating the surfaces? > > > > What solutions would you suggest in resolving this > > problem? > > > > Thank you, > > > > Vy Dinh > > Research Associate > > Department of Neurological Sciences > > Rush University Medical Center > > > > > > > > > > > > _______________________________________________ > > 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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Freesurfer April 2013