Freesurfer February 2010

freesurfer@nmr.mgh.harvard.edu

96 participants
153 discussions

subject to fsaverage
by Mishkin Derakhshan 11 Feb '10

11 Feb '10

Hi, I am looking for the transformation matrix that takes my input volume (orig.mgh) and maps it into the same space as fsaverage (or the inverse of this transformation if it already exists). I've already run recon-all -all, and -qcache, so I'm pretty sure this information exists somewhere, but after searching through the data, the wiki and the mailing list, I'm embarrassed to say that I still can't find it. If this information hasn't been stored, I imagine mri_surf2surf can calculate it for me. Would this be the best way? thanks, mishkin

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GM exclusion
by johanna feiler 11 Feb '10

11 Feb '10

Dear freesurfer experts, After running the autorecon2 process the pial surface fails to catch up pieces of gm in the medial region. I gained no improvement with setting control points. The problem lasts about twelve slices. As an illustration, I attached a screenshot with three of the problematic slices. How can I solve this problem? Any help would be appreciated! Johanna Feiler ______________________________________________________ GRATIS für alle WEB.DE-Nutzer: Die maxdome Movie-FLAT! Jetzt freischalten unter http://movieflat.web.de

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question about effect of juxta-cortical lesion
by Mehul Sampat 11 Feb '10

11 Feb '10

Hi Folks, We have a patient with a large juxta-cortical lesion (top right hand side in figure 1) Overall Freesurfer does a great job in defining the white and pial surfaces (figure 2 and 3) (It is actually amazing how well it does in this difficult case.) However, I think that due to the lesion some of the cortical gray matter is not included. Could someone advice what is the recommended procedure in such cases. Should I add control points to correct for this issue ? Also we have 3 MRI exams for this subject (each a year apart) and the lesion is present on every scan and I have the same issue on the other time-points. Thanks Mehul

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Paula Diniz wants to stay in touch on LinkedIn
by Paula Diniz 11 Feb '10

11 Feb '10

LinkedIn ------------Paula Diniz souhaite se connecter à vous sur LinkedIn : ------------------------------------------ Freesurfer, I'd like to add you to my professional network on LinkedIn. - Paula Diniz Accepter l'invitation de Paula Diniz http://www.linkedin.com/e/vLfSn8bYH8_5DFBPLmfTK84Tj6M6DmxAKLgTCa4LI_82zo/bl… Voir l'invitation de Paula Diniz http://www.linkedin.com/e/vLfSn8bYH8_5DFBPLmfTK84Tj6M6DmxAKLgTCa4LI_82zo/bl… ------ (c) 2010, LinkedIn Corporation

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Re: [Freesurfer] Skull Stripping extra dura & vasculature
by Sherri Novis 10 Feb '10

10 Feb '10

Thanks Bruce. Is there anyway to address it in the intensity normalization phase? -----Original Message----- >From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> >Sent: Feb 9, 2010 12:29 PM >To: Sherri Novis <echotalk(a)earthlink.net> >Cc: freesurfer(a)nmr.mgh.harvard.edu >Subject: Re: [Freesurfer] Skull Stripping extra dura & vasculature > >Hi Sherry, > >that's pretty tough. The dura is very bright and quite close to the gm. >You may need to erase more of the dura > >Bruce > >On Tue, 9 Feb 2010, Sherri Novis >wrote: > >> Hello, >> >> I have a series of datasets with skull stripping issues - namely left over dura/vasculature in the occipital cortex, and some in frontal areas.(Attached is a jpeg of the type of issue. It's pervasive throughout the slices, across a handful of subject data.) >> >> I have rerun skull stripping changing the watershed value, however it's not making the distinction between dura and gray matter. (recon-all -skullstrip -wsthresh [tried 0..35] -clean-bm -no-wsgcaatlas -subjid [subject_id] - FS version: freesurfer-Linux-centos4-stable-pub-v4.3.0) >> >> I also attempted to edit 50% of the slices by erasing voxels to make a clear boundary between the dura and cortex and then re-ran autorecon2 to see if it would at least adjust the pial surfaces - however that did not work (pial surfaces still crossed the one pixel boundary I made into the dura). >> >> Can you recommend any other flags or things to try before I edit/erase the excess by hand? >> >> Thanks for your time - >> Sherri

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DICOM Multiframe support
by J. Gabriel Castrillón G. 10 Feb '10

10 Feb '10

Hi! Is Freesurfer compatible with the DICOM MR multiframe files? Thanks in advance, -- Gabriel Castrillón Instituto de Alta Tecnología Médica de Antioquia - IATM http://www.iatm.com.co

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Fw: manually specifying design matrix
by raka maitra 10 Feb '10

10 Feb '10

Hello Sorry for reposting again. Would really appreciate a feedback on the following mail. Thanks in advance for your time Raka ----- Forwarded Message ---- From: raka maitra <rakamaitra(a)yahoo.com> To: Douglas N Greve <greve(a)nmr.mgh.harvard.edu> Sent: Fri, January 15, 2010 9:34:02 PM Subject: Re: [Freesurfer] manually specifying design matrix Thank you Doug. I am trying to create a design matrix for repeated measures anova. Lets say subjects A and B have been measured at sitting and standing positions. As the same subjects have been measured at the same positions, hence both the factors i.e subjects and positions are fixed factors. Hence a design matrix exploring the within subject effects of positions would be 1 0 1 0 0 1 1 0 1 0 0 1 0 1 0 1 The first two columns are position and the last two are the subjects. But mri_glmfit does not accept this design and I get the following error message: 'Matrix condition is 1e+08 ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08 Possible problem with experimental design: Check for duplicate entries and/or lack of range of continuous variables within a class.' Looking forward to your suggestion Thanks in advance Raka ________________________________ From: Douglas N Greve <greve(a)nmr.mgh.harvard.edu> To: raka maitra <rakamaitra(a)yahoo.com> Cc: freesurfer(a)nmr.mgh.harvard.edu Sent: Thu, January 14, 2010 7:05:28 PM Subject: Re: [Freesurfer] manually specifying design matrix If you specify it manually, you don't specify groups, etc, or pass an fsgd file. You just create your design matrix pass it to mri_glmfit directly with the --X flag. doug raka maitra wrote: > > Hi all > > I want to specify a design matrix manually. > > In the usual pipeline for analysis in freesurfer, one specifies the > groups, regressors in the fsgd and then when mri_glmfit is run, it > creates the design matrix. > For eg if I have two classes with 3 subjects each, in my fsgd, > mri_glmfit would create the following design matrix > 1 0 > 1 0 > 1 0 > 0 1 > 0 1 > 0 1 > > If I want to specify the above design matrix manually, how and where > do I specify the groups, regressors ? > > > Thanks in advance > Raka > > ------------------------------------------------------------------------ > > _______________________________________________ > 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 _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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tksurfer error
by Daniel Ferreira Padilla 10 Feb '10

10 Feb '10

Dear Freesurfer users, I hope you could help me with that problem. I do the recon-all preprocessing step and then I try tksurfer. But the following error comes up. Moreover tksurfer window open up but it looks like 'empty'. Please find it attached. Thank you very much! Daniel Ferreira -------- freesurfer-Linux-centos4-stable-pub-v4.5.0 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /home/Neuropsicologia/freesurfer FSFAST_HOME /home/Neuropsicologia/freesurfer/fsfast FSF_OUTPUT_FORMAT nii SUBJECTS_DIR /home/Neuropsicologia/DANI/subjects MNI_DIR /home/Neuropsicologia/freesurfer/mni FSL_DIR /home/Neuropsicologia/fsl Neuropsicologia@linux-tand:~> cd DANI/subjects Neuropsicologia@linux-tand:~/DANI/subjects> tksurfer GJ25_3D lh inflated -aparc -gray surfer: current subjects dir: /home/Neuropsicologia/DANI/subjects surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /home/Neuropsicologia/DANI/subjects surfer: Reading header info from /home/Neuropsicologia/DANI/subjects/GJ25_3D/mri/T1.mgz surfer: vertices=123902, faces=247800 surfer: curvature read: min=-1.349975 max=2.259740 reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/amaebi_026/users/buckner_cortical_atlas/scripts/colortable_fin al.txt) Found embedded color table in annotation. surfer: single buffered window surfer: tkoInitWindow(GJ25_3D) surfer: using interface /home/Neuropsicologia/freesurfer/lib/tcl/tksurfer.tcl Reading /home/Neuropsicologia/freesurfer/lib/tcl/tkm_common.tcl Reading /home/Neuropsicologia/freesurfer/lib/tcl/tkm_wrappers.tcl Reading /home/Neuropsicologia/freesurfer/lib/tcl/fsgdfPlot.tcl Reading /home/Neuropsicologia/freesurfer/lib/tcl/tkUtils.tcl Successfully parsed tksurfer.tcl reading white matter vertex locations... %

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Re: [Freesurfer] Freesurfer Digest, Vol 72, Issue 25
by Sebastian Moeller 10 Feb '10

10 Feb '10

Hi Tamara, neuroecon is not ia64 but x86_64, that is you binaries will probanbly never run on this cluster no matter the permissions. You can just ask the neuroecon support people (help-hpc(a)caltech.edu) to install 4.5.0 under /share/apps. In addition to actually use freesurfer on this system (say with NX remote control) you will need some adjustement to the calls to tkregister2 and /or tksurfer/tkmedit. I can simp[ly copy you the version of FS 4.5.0 we got working on that machine... best Sebastian On Feb 10, 2010, at 6:30 AM, freesurfer-request(a)nmr.mgh.harvard.edu wrote: > Message: 3 > Date: Tue, 9 Feb 2010 20:41:13 -0500 (EST) > From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] Trouble installing freesurfer to a cluster > To: Tamara Knutsen <knutsen(a)gmail.com> > Cc: freesurfer(a)nmr.mgh.harvard.edu > Message-ID: > <Pine.LNX.4.62.1002092040520.20105(a)gate.nmr.mgh.harvard.edu> > Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed > > hmmm, have you tried: > > chmod a+x /home/knutsen/freesurfer/bin/* > > not sure why they wouldn't be executable though. > Bruce > On Tue, 9 Feb 2010, Tamara > Knutsen > wrote:

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question abt mri_vol2surf - projfrac
by ridatta＠mail.med.upenn.edu 10 Feb '10

10 Feb '10

Hello, I also had a question abt projfrac I have 3 x 3 x 3 mm voxel functional data - BOLD and ASL that I am trying to resample to fsaverage. Is the projfrac label applicable here at all ? In the help page it specifies only for thickness. If it is applicable, what value ? Thanks Ri

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Freesurfer February 2010