Freesurfer

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30076 discussions

RE: [Freesurfer] major lobes - frontal, parietal occipital and temporal
by lfriedman10＠comcast.net 14 Apr '07

14 Apr '07

Burce and Rahul, thanks so much for your help. So I am a little new to freesurfer. I have been using lh.ribbon and rh.ribbon as neocortical masks and aseg.mgz for subcortical gray structures, with labels from FreeSurferColorLUT.txt. What I want to do now is to further subdivide the *h.ribbon masks into frontal, temporal, occipital and parietal lobes. How would one go about this? Lee -------------- Original message ---------------------- From: rahul(a)nmr.mgh.harvard.edu > Hi Lee, > > Bruce is correct in that some ROIs cross two or more lobar boundaries > (i.e. fusiform) while others (i.e. cingulate subdivisions) can be > considered separately or can be included to follow the 4 lobes. To the > best of my ability, if you are using the *h.aparc.annot, you can add up > the individual ROIs as such to get the lobes: > > Frontal: > Superior Frontal > Rostral and Caudal Middle Frontal > Pars Opercularis, Pars Triangularis, and Pars Orbitalis > Lateral and Medial Orbitofrontal > Precentral > Paracentral > Frontal Pole > > Parietal: > Superior Parietal > Inferior Parietal > Supramarginal > Postcentral > Precuneus > > Temporal > Superior, Middle, and Inferior Temporal > Fusiform > Transverse Temporal > Entorhinal > Temporal Pole > Parahippocampal > > Occipital: > Lateral Occipital > Lingual > Cuneus > > Cingulate (if want to include in a lobe): > Rostral Anterior (Frontal) > Caudal Anterior (Frontal) > Posterior (Parietal) > Isthmus (Parietal) > > Best, > > rahul > > > Hi Bruce, > > > > Are you saying that you don't think I even could build these lobar groups > > using the existing codes in the LUT.txt file? > > > > Lee > > > > -----Original Message----- > > From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] > > Sent: Saturday, April 14, 2007 2:21 PM > > To: lfriedman10(a)comcast.net > > Cc: freesurfer(a)nmr.mgh.harvard.edu > > Subject: Re: [Freesurfer] major lobes - frontal, parietal occipital and > > temporal > > > > Hi Lee, > > > > sorry, not really - we've never done a lobar parcellation, and I don't > > think the existing units break down that way. > > > > Bruce > > On Sat, 14 Apr 2007 > > lfriedman10(a)comcast.net wrote: > > > >> I know that I could go thru the > >> FreeSurferColorLUT.txt > >> file to get codes for different cortical structures. > >> Is there an easier way to get the major lobes: > >> frontal, parietal occipital and temporal. > >> > >> Lee > >> _______________________________________________ > >> Freesurfer mailing list > >> Freesurfer(a)nmr.mgh.harvard.edu > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >> > >> > >> > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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major lobes - frontal, parietal occipital and temporal
by lfriedman10＠comcast.net 14 Apr '07

14 Apr '07

I know that I could go thru the FreeSurferColorLUT.txt file to get codes for different cortical structures. Is there an easier way to get the major lobes: frontal, parietal occipital and temporal. Lee

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bad white surface
by Derin Cobia 13 Apr '07

13 Apr '07

I have two subjects where the white surface does not follow the gray-white gradient (see attached pic for example). Is there any way to fix this? I'm assuming it has to do with the limitations of my scan too (it's FLASH data). I'm running 3.0.4, thanks. -Derin

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Insula: Why no label in parcellation?
by Graham Wideman 12 Apr '07

12 Apr '07

Folks: We see that parcellation has insula labelled as "unknown". Is this by design and if so is there a discussion of the rationale? Thanks, Graham

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Volumes for labels
by Alex Fornito 11 Apr '07

11 Apr '07

Hi, I was just wandering exactly how the grey matter volume for a given label is calculated in mris_anatomical_stats. Multiplying the average thickness by the area estimate I get in the output file does not give me exactly the same estimate of grey matter volume as what mris_anatomical_stats returns. Is the mris_anatomical_stats volume estimate calculated on a vertex-by-vertex basis? Thanks, Alex Alex Fornito JN Peters Research Fellow Melbourne Neuropsychiatry Centre National Neuroscience Facility The University of Melbourne Levels 2 & 3, 161 Barry St Carlton South 3053 Vic Australia Ph: +61 3 8344 1861 Fax: +61 3 9348 0469 Email: fornitoa(a)unimelb.edu.au

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Manuals and Scuba
by Sharon Ruso 11 Apr '07

11 Apr '07

Dear FreeSurfer Team I'm a new user of freesurfer and I would like to ask you few questions. 1.Where can I find more information regarding SCUBA? 2.I read very carefully through the freesurfer website, (all the work flow and tutorials) however, I was wondering weather every time I do any kind of changes, do I have to run recon all again,, or there are any single commands that repair/edit my own revisions? 3. What is the newest version of the FreeSurfer Manual and where can I find it Thank You in advance Sharon

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cortical thickness problem
by burak ozkalayci 11 Apr '07

11 Apr '07

Dear surfers, I ran the recon-all -s bert -autorecon1 recon-all -s bert -autorecon2 recon-all -s bert -autorecon3 commands and all of them finished without any error. The log files of the commands and the file list of the resultant bert folder are attached to the mail. I can see the surface of the pial and the white with the tksurfer and try to load the ?h.thickness files as curvature files to the surfaces. But I only get fully red colored surface. What may be wrong? Also how can I read the ?h.thickness files manually to check is there any meaningful information there. The curvature maps are working but the thickness is not working. The snapshots of the the thickness and curvature are also attached. For the next step I want to ask one more question. In a previous mail in the list it is said that "we compute the closest vertex on the pial from each vertex on the white, and visa-versa, then set the thickness to the average of the two." for the thickness calculation. I understand from this statement that the thickness is just measured for the surface vertices but not for the voxels in the original volume. For voxel based morphometry do you have any advice to get thickness values for the voxels of the grey matter? Thanks in advance for any advice and reply. Burak

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mri_surfcluster error
by Kirk, Gregory 11 Apr '07

11 Apr '07

running freesurfer-v3.0 SUBJECTS_DIR=/home/gkirk/freesurfer-v3.0/freesurfer/subjects/sickle_cell glm is at /home/gkirk/freesurfer-v3.0/freesurfer/subjects/sickle_cell and contains age.mat lh.sickle.glmdir mris_preproc.surface.lh.log rh.sickle.thickness.10.mgh FSGDstudy.txt lh.sickle.thickness.10.mgh mris_preproc.surface.rh.log rh.sickle.thickness.mgh FSGDstudy.txt~ lh.sickle.thickness.mgh rh.sickle.glmdir surfer.log lh.sickle.glmdir contains age ar1.mgh beta.mgh eres.mgh fsgd.X.mat mri_glmfit.log rstd.mgh rvar.mgh Xg.dat y.fsgd age/ contains C.dat F.mgh gamma.mgh maxvox.dat sig.mgh SUBJECTS_DIR has average directory with the group av surf & vol stuff I run mri_surfcluster --src lh.sickle.glmdir/age/sig.mgh --sum lh.sickle.glmdir/age/sig.cluster.sum --ocp lh.sickle.glmdir/age/ sig.cluster.mgh ( on same line of course ) and get ERROR: hemi must be supplied I add --hemi lh and get ERROR: srcsubjid must be supplied etc. can't seem to make it happy. thanks Greg.

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System requirements.
by Goradia, Dhruman D 11 Apr '07

11 Apr '07

Hello All, I have a P4 1.5 GHZ, 1GB ram, 65GB hard disk running redhat fedora core release 5. I am planning to install the latest version of freesurfer on it. It will be a dedicated system for a small study with the only task of processing the data on freesurfer. Will this work? I understand that it will be slow, but are there any chances of installation not working just because of hardware qualifications? Thank you, Dhruman D. Goradia (M.S.) Research Specialist. Western Psychiatric Institute and Clinic. 3811 O'Hara St. Suite 431 Pittsburgh, PA 15213

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func2tal
by Alessandro Gagliardi 11 Apr '07

11 Apr '07

I'm trying to regester my BOLD images to a common space. I tried func2tal but I got ERROR: only selxavg, selavg, and sfa functypes are currently supported. When I try to run mri_vol2vol --fstal, it expects talmni305 in my subjects directory which I don't have. Did I miss a step in the installation? Should I have talmni305 and if so, where can I get it? Otherwise, is there a new version of func2tal that accepts bshort (or other) volumes as input? Or perhaps there is another way to get my 4D data into talairach space altogether? Thanks, -- Alessandro Gagliardi Integrative Neuroscience Program Rutgers University Mind Brain Analysis alessandro(a)gagliardi.name

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