Freesurfer

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6 participants
30091 discussions

Extract surface from volume
by Valtina Pouegue 02 Apr '13

02 Apr '13

I have a volume in mnc and nii format. I would like to extract the outer surface from those volumes to be able to use in Freesurfer. I tried 'mri_vol2surf' but I didn't have the registration file. So I try make_register to create a registration file and the system give me an error as it couldn't open the header file to configure the fctstem...Does anyone know another way for extract the surface ( even with Matlab) ? Thanks, VP

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Re: [Freesurfer] Error with .license after upgrading to 5.2
by Nicola Toschi 02 Apr '13

02 Apr '13

Hi - no luck unfortunately (I had already tried changing permissions).... On 03/22/2013 04:09 PM, Varghese Chikku wrote: > Hi Nicola, > Can you try this command,and echo the license.It may ask for > password.I have similar issues with 5.2 and this how i sorted. > sudo chmod -R a+rwX /Applications/freesurfer > then > echo each line of the licence. > Let me know > In thanks > chikku

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advice for subcortical Freesurfer processing of 2 year old brains
by Joshua Lee 02 Apr '13

02 Apr '13

The aseg has shown poor performance in my sample. Are there settings, atlases, etc, available that might improve performance? - Josh

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recon-all with multiple spgr's per subject
by Salil Soman 02 Apr '13

02 Apr '13

Dear Freesurfer experts, Could someone point me to the syntax for having recon-all use multiple T1 volumes for the same subject (which I believe it is supposed to motion correct and average). Thanks, Salil Soman, MD, MS

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preproc-sess erros
by Mario Ortega 02 Apr '13

02 Apr '13

Hi freesurfer team, I have been having intermittent problems ( Im assuming bbregister problems.) the register.dof6.dat file is not being written, and I find an error in the dat.log error is here: flirt.fsl -ref bold/011/tmp.bbregister.10308/fslregister/refvol.fslregister.nii -in bold/011/tmp.bbregister.10308/fslregister/movvol.fslregister.nii -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -verbose 0 -omat bold/011/tmp.bbregister.10308/fslregister/fslma t0.trans.mat -schedule /usr/local/fsl/etc/flirtsch/xyztrans.sch -init bold/011/tmp.bbregister.10308/reg.init.dat.fsl.mat0 ** ERROR (nifti_image_read): failed to find header file for 'bold/011/tmp.bbregister.10308/fslregister/refvol.fslregister' ** ERROR: nifti_image_open(bold/011/tmp.bbregister.10308/fslregister/refvol.fslregister): bad header info Error: failed to open file bold/011/tmp.bbregister.10308/fslregister/refvol.fslregister ERROR: Could not open image bold/011/tmp.bbregister.10308/fslregister/refvol.fslregister Image Exception : #22 :: Failed to read volume bold/011/tmp.bbregister.10308/fslregister/refvol.fslregister.nii terminate called after throwing an instance of 'RBD_COMMON::BaseException' Abort (core dumped) I do have disk space. the command that I use is preproc-sess -s FCBA05_MR1 -fsd bold -per-run -stc siemens -force -surface fsaverage rhlh -fwhm 6 Any help is appreciated as I continue tracing the error. Thanks, Mario

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

02 Apr '13

Now is ok. Thank you very much!! Stefano ----Messaggio originale---- Da: greve(a)nmr.mgh.harvard.edu Data: 2-apr-2013 20.09 A: <stdp82(a)virgilio.it> Cc: <freesurfer(a)nmr.mgh.harvard.edu> Ogg: Re: [Freesurfer] R: R: Re: R: Re: perirhinal analysis Try mri_label2label --srcsubjectsubject_prova --srclabel rh.perirhinal.label --trgsubject Con01 --trglabel Con01/label/rh.perirhinal.label --hemi rh --regmethod surface also note that if you run mri_label2label with only the --help argument, it will print out help as to what each flag means as well as examples. Reading the help is a good approach when you cannot get immediate assistant from the list. You'll also learn about how the command is supposed to work. Pretty soon, you'll be the one helping others! doug On 04/02/2013 04:37 AM, stdp82(a)virgilio.it wrote: > 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/ > > > > > -- 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

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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/

2 1

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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