Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30088 discussions

Retinotopy
by _andreia_＠sapo.pt 01 Feb '12

01 Feb '12

Hello! I'm moving to FS 5.1 and I will be analysing retinotipic data (and the anatomical data bas well). I would like to know if there are any changes or issues while running this analysis in this new version before I move. Thanks, Andreia

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Error with fsaverage/mri.2mm/reg.2mm.dat
by Antonella Kis 01 Feb '12

01 Feb '12

Dear All, Can someone help me to find out what is the equivalent of the fsaverage/mri.2mm/reg.2mm.dat when I use the cvs_avg35 template, I mean I register my FA data over the CVS space? I suppose I will need to repalce the fsaverage/mri.2mm/reg.2mm.dat in the following command: mri_volcluster --in GroupAnalysis_abs.glmdir/contrast/sig.mgh --mask GroupAnalysis_abs.glmdir/mask.mgh --reg /usr/local/freesurfer/subjects/fsaverage/mri.2mm/reg.2mm.dat --no-fixmni --cwsig GroupAnalysis_abs.glmdir/contrast/permcsd.sig.cluster.mgh --sum GroupAnalysis_abs.glmdir/contrast/permcsd.sig.cluster.summary --ocn GroupAnalysis_abs.glmdir/contrast/permcsd.sig.ocn.mgh --cwpvalthresh .05 --seg cvs_avg35 aseg.mgz --csdpdf GroupAnalysis_abs.glmdir/contrast/permcsd.pdf.dat --csd GroupAnalysis_abs.glmdir/csd/permcsd.j001-contrast.csd --vwsig GroupAnalysis_abs.glmdir/contrast/permcsd.sig.voxel.mgh Thank you very much! Antonella

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tabel with labels and name of brain regions for both atlases
by Maria Felber 01 Feb '12

01 Feb '12

Dear all, I am trying to use my freesurfer data for fibertracking. So far it is working and I can even specifically tell the programm, which labels/brain regions to use. However, I haven't found an overview tabel, where all labels stand together with the region's name. It would be painfull, to open for every subject tksurfer and then moving with the mouse over the region of interest to get the correct label. Is there such a table overview for both atlases and where can I find them? Thank you. Sincerely, Maria Felber -- Maria J. Felber, PhD Student Max Planck Institute for Human Cognitive and Brain Sciences Stephanstraße 1A 04103 Leipzig, Germany Phone: +49 341 9940-2465/2522

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Question about .license
by Nooshin Zadeh 01 Feb '12

01 Feb '12

Hi Everyone I have a question about installation of freesurfer, license part. For placing the three lines in a file named ".license" in the directory pointed to by the $FREESURFER_HOME, I used "vi .license" in terminal and it did not work. Also, I can not use "sudo vi .license" because I do not have the password. Can you please guide me on how can I make the .license file? Thanks in advance, Nooshin N. Zadeh Graduate Assistant Departments of Electrical Engineering and Neurology University of Miami ** * * * *

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showedits bug
by Michael Harms 01 Feb '12

01 Feb '12

Hi Nick, I found a small bug in recon-all that prevents the -showedits flag from working in conjunction with expert-options: Line 785 in recon-all of v5.1 currently has an extraneous closing parenthesis: if (-e $XOptsFile)) then but should be: if (-e $XOptsFile) then Also, I'm puzzled how the resulting edits.mgz gets translated when you load it as a segmentation -- e.g., areas with an addition to wm.mgz appear to be assigned the value 2 in edits.mgz, and are labeled as "wm- ON" if you load edits.mgz as a segmentation, but I don't see any entry for "wm-ON" in FreeSurferColorLUT.txt itself. Where is the full "key" for the values in edits.mgz? thanks, -MH

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WG: Save segmentation results as nifi files
by Fellhauer, Iven 01 Feb '12

01 Feb '12

Hi Bruce And thank you for your hint, but where are the files for GM, WM and CFS stored in the Freesurfer output directory structur? Best regards, Iven -----Ursprüngliche Nachricht----- Von: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Gesendet: Montag, 30. Januar 2012 15:20 An: Fellhauer, Iven Cc: freesurfer(a)nmr.mgh.harvard.edu Betreff: Re: [Freesurfer] Save segmentation results as nifi files Hi Ivan you can convert any volume to any supported output type using mri_convert. It will figure out the format from the extension, so: mri_convert aseg.mgz aseg.nii.gz or mri_convert aseg.mgz aseg.nii should do the trick cheers Bruce On Mon, 30 Jan 2012, Fellhauer, Iven wrote: > > Dear all, > > > > I run recon-all with the ?autorecon1 and ?autorecon2 options. Now I > want to store the segmentation results in a spm like way. One nifti > file for each matter. Can I do this with freesurfer? And how can I do > this with freesurfer? > > > > Best regards, > > > > Iven Fellhauer > > > > ---------------------------------------------------------------- > > Universitätsklinikum Heidelberg > > Zentrum für Psychosoziale Medizin > > Klinik für Allgemeine Psychiatrie > > Sektion für Gerontopsychiatrie > > Voßstr. 4 > > 69115 Heidelberg > > Tel.: +49 (0) 6221 - 56 7578 > > Email: iven.fellhauer(a)med.uni-heidelberg.de > > > > > 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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Re: [Freesurfer] Dura too bright/thick: brain extraction
by octavian lie 31 Jan '12

31 Jan '12

Thank you. Unfortunately, we use a Phillips scanner for 3T scans: MPRAGE T1 TR 9.89; TE 4.60. If you have any suggestions, including which of the protocols comes closest, let mw know. Best, Octavian On 1/31/12, Andre van der Kouwe <andre(a)nmr.mgh.harvard.edu> wrote: > Do you have a Siemens scanner? > > You can compare your protocols with the examples at > www.nmr.mgh.harvard.edu/~andre. > > On Tue, 31 Jan 2012, Bruce Fischl wrote: > >> Hi Octavian >> >> what kind of scanner are you using? Andre van der Kouwe and Dylan Tisdall >> (ccd) have developed a multi-echo mprage that allows one to identify dura >> by >> it's short T2*. They might be able to give it to you depending on your >> scanner and relationship with Siemens. Otherwise it can be difficult, as >> lenghtening your TE to reduce the dura signal also reduced gray/white >> contrast. >> >> cheers >> Bruce >> On Tue, 31 Jan 2012, octavian lie wrote: >> >>> Dear All, >>> >>> I am trying to perform brain extraction on T1 3D images, however the >>> dura appears too bright and thick compared to the underlying gray >>> matter. It seems that I have a hard time stripping the dura away. Do >>> you have any suggestions in terms of optimizing freesurfer parameters >>> to help with this problem, or alternatively, do you suggest a specific >>> T1 protocol (TE/TR) to dim the dura a bit? >>> Thank you, >>> >>> >>> Octavian Lie. >>> _______________________________________________ >>> 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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Dura too bright/thick: brain extraction
by octavian lie 31 Jan '12

31 Jan '12

Dear All, I am trying to perform brain extraction on T1 3D images, however the dura appears too bright and thick compared to the underlying gray matter. It seems that I have a hard time stripping the dura away. Do you have any suggestions in terms of optimizing freesurfer parameters to help with this problem, or alternatively, do you suggest a specific T1 protocol (TE/TR) to dim the dura a bit? Thank you, Octavian Lie.

3 2

Installation
by Nooshin Zadeh 31 Jan '12

31 Jan '12

Hi, I am trying to install FS on the mini Mac. I downloaded the darwin leopard version of FS and it went to "Application". For setup configuration step, in tcsh terminal I wrote "setenv FREESURFER_HOME /Application/freesurfer " and then "source $FREESURFER_HOME/SetUpFreeSurfer.csh". It says no such file or directory, but I see SetUpFreeSurfer.csh in the FS folder on the "Application". Once I copied the FS on the desktop and then wrote "setenv" and "source" again. It worked temporarily but when I was done with all installation steps, it did not recognize tkmedit and tksurfer. Can you please guide me how can I fix the problem. Thanks, -- Best Regards --------------------------------------------------- Nooshin N. Zadeh Graduate Assistant Departments of Electrical Engineering and Neurology University of Miami ** * * * *

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Re: [Freesurfer] re-running mri_glmfit-sim
by Douglas N Greve 31 Jan '12

31 Jan '12

That is a slight bug in that there is no default (you have to specify). Below is the text from running it with --help. If you have an apriori hypothesis that group1 > group2, then choose positive. If you don't know the sign, then use abs. Choosing a sign will yield stronger results (ie, smaller p-values), but you will lose the other sign. doug This is the sign of the threshold used to create the clusters for cluster-wise correction of multiple comparisons. Antonella Kis wrote: > Dear Doug, > > Thank you so much for your help. I still have one more question > please: WHEN i WAS TRYING TO RUN THE: > > mri_glmfit-sim \ > --glmdir Group_Analysis.glmdir \ > --sim neg perm 10000 3 permcsd\ > --cwpvalthresh .05 > > > as you recommended me so withouth --sim-sign I got the error that I > must specify the sign so I choose neg. I believe the default should be > abs but can you please shortly explain what exactly the --sim-sign means? > > Thank you very much. > Antonella > > ------------------------------------------------------------------------ > *From:* Douglas N Greve <greve(a)nmr.mgh.harvard.edu> > *To:* Antonella Kis <atorok9(a)yahoo.com> > *Cc:* "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> > *Sent:* Tuesday, January 31, 2012 12:39 PM > *Subject:* Re: [Freesurfer] re-running mri_glmfit-sim > > You have to re-run > doug > > Antonella Kis wrote: > > dear All, > > > > I would like to know if I am running the > > mri_glmfit-sim \ > > --glmdir Group_Analysis.glmdir \ > > --sim perm 10000 3 permcsd \ > > --sim-sign neg \ > > --cwpvalthresh .05 > > > > and I want to change the --sim-sign from neg to positive if I need > to run again the whole simulation or I can just run: > > > > mri_glmfit-sim --glmdir Group_Analysis.glmdir \ --no-sim --sim-sign > pos or how exactly to edit the mri_glmfit in this case? > > > > Also if I need to add one more subject do I need to re-run the whole > simulation or for multiple comparison I can just use the --no-sim option? > > > > Thank you very much! > > Antonella > > ------------------------------------------------------------------------ > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu <mailto:Freesurfer@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 <mailto:greve@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > > > 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

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