Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30063 discussions

mri_vol2surf help
by Fornito, Alexander 10 Aug '05

10 Aug '05

Hi, I'm trying to resample a volume (representing a subregion of the subjects T1) onto the surface using mri_vol2surf. When I try to load the output as an overlay in tksurfer, nothing appears. The output is below. Any help would be appreciated (note, I;ve also tried to output in analyze format with no success) Thanks, Alex mri_vol2surf --src 1000027/mri/orig/001/reg_objects/1000027_lh_cog_limbic_surfreg --src_type analyze --srcreg register.dat --fwhm 3 --trgsubject 1000027 --hemi lh --surf white --surfreg 1000027/surf/lh.white --out test/test --out_type cor srcvol = 1000027/mri/orig/001/reg_objects/1000027_lh_cog_limbic_surfreg srctype = analyze srcreg = register.dat srcregold = 0 srcwarp unspecified surf = white hemi = lh trgsubject = 1000027 surfreg = 1000027/surf/lh.white interp = nearest float2int = round INFO: float2int code = 0 INFO: analyzeRead(): found 1 files for 1000027/mri/orig/001/reg_objects/1000027_lh_cog_limbic_surfreg ----------------------------------------------------------------- INFO: could not find 1000027/mri/orig/001/reg_objects/1000027_lh_cog_limbic_surfreg.mat file for direction cosine info. INFO: use Analyze 7.5 hdr->hist.orient value: 0, transverse unflipped (default). INFO: if not valid, please provide the information in 1000027/mri/orig/001/reg_objects/1000027_lh_cog_limbic_surfreg.mat file ----------------------------------------------------------------- INFO: analyzeRead(): min = 0, max = 63 INFO: chaning type to float Done loading volume INFO: smoothing volume at fwhm = 3 mm (std = 1.27398) Reading surface /data/flanders/work/alex/freesurfer/subjects/1000027/surf/lh.white Done reading source surface Mapping Source Volume onto Source Subject Surface vol2surf_linear: nhits = 148018/148018 Done mapping volume to surface Number of source voxels hit = 92960 Reshaping 2 (nvertices = 148018) Writing non-standard value for imnr1 (2, usually 256) in volume structure non-standard value for type (3, usually 0) in volume structure non-standard value for width (74009, usually 256) in volume structure non-standard value for height (1, usually 256) in volume structure

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skull strip
by Sasha Wolosin 10 Aug '05

10 Aug '05

Is it possible to do skull stripping without motion correction or intensity normalization? Disclaimer: The materials in this e-mail are private and may contain Protected Health Information. Please note that e-mail is not necessarily confidential or secure. Your use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail.

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Editing labels
by Fornito, Alexander 10 Aug '05

10 Aug '05

Hi, I've been trying to edit some labels in tkmedit and have noticed that if I save a label in tkmedit and then project it back onto the surface in tksurfer, it appears fragmented (ie., speckled). This happens even if I save a label that was created in tksurfer in tkmedit without even editing it (ie., create label in tksurfer, load it in tkmedit, save it in tkmedit (without editing), and then load it back in tksurfer). I don't understand why this should happen, particulalry in the latter case, as the label should remain unchanged. Can anyone explain why this might happen? Thanks, Alex

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freesurfer for MEG/EEG source imaging
by Zhongming Liu 10 Aug '05

10 Aug '05

I am a new user of Freesurfer. My questions are related to the head modeling and MEG/EEG source modeling. 1. Can freesurfer generate the 3-shell boundary element model (BEM): 3 triangulated interfaces of air-scalp, scalp-skull, skull-brain? 2. Is it possible to generate a closed and folded cortical surface after the segmentation on MR images? Freesurfer seems to output two splitted hemispheres of cortex. I am particularly concerning this, because I will use the cortical surface to constrain the MEG/EEG source location and direction. 3. Is it possible to evenly (or nearly evenly) down-sample the vertices of a fine cortical surface into around 6,000 points, onto which the elementary dipole will be placed? Freesurfer generates the cortical surface with a huge number of triangles, which makes it impossible for MEG-based source imaging. Looking forward to your reply. Best regards, Zhongming Liu

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Re: [Freesurfer] wmfill
by Arvind Gururajan 08 Aug '05

08 Aug '05

I get the following error message, when I do the 'create surface'. Images (filled): /subjectsdir/mri/filled/COR-001 not found. wmfill first. Log file says, could not find a valid seed for the CC. Seed point not in structure. So I think the problem is with cutting planes. Does CC position changed to (_,_,_) mean, it is already transformed? Thanks, Arvind Gururajan On 7 Aug 2005, Bruce Fischl wrote: > Hi Arvind, > > is your problem with the talairach or the cutting planes? You can alsways > use tkregister2 to manually talairach. > > Bruce > > > On Fri, 5 Aug > 2005, Arvind Gururajan wrote: > > > > > Hello all, > > > > This is a follow up question on this mail. > > http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg00565.html > > > > I have exactly the same problem as Margaret had mentioned, tried all the > > suggestion by Tosa. My talairach fails when I do the mri_convert nu nu.mnc. > > How do I generate nu in my mri directory? > > > > Thanks, > > > > Arvind Gururajan > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > >

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Re: [Freesurfer] wmfill
by Arvind Gururajan 07 Aug '05

07 Aug '05

Hello all, This is a follow up question on this mail. http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg00565.html I have exactly the same problem as Margaret had mentioned, tried all the suggestion by Tosa. My talairach fails when I do the mri_convert nu nu.mnc. How do I generate nu in my mri directory? Thanks, Arvind Gururajan

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Multiple simultaneous overlays
by Jane Aspell 07 Aug '05

07 Aug '05

hi i need to view several overlays simultaneously (to see where my activation lies relative to retinotopic map overlays) on a surface. is there no way of doing this with freesurfer? its seems like a function that a lot of users would need. in one posting regarding this you suggested loading the overlays into matlab using load_wfile, combine them, then write them out using write_wfile...are these actual programs? where would i get them from and do i need any additional matlab programs for this to work? and how does the combining stage work - are there any further instructions on this? many thanks! Jane

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thickness map
by Goldman, Aaron (NIH/NIMH) 07 Aug '05

07 Aug '05

Hi, I've been doing thickness analyses with mris_glm, and was wondering how I could create a map simply showing the average thickness of my entire sample (just as a quality check). Thanks, -Aaron- Aaron L. Goldman Post-Bacc IRTA Genes, Cognition and Psychosis Program, NIMH Building 10, Room 3C108 Phone: (301) 435-0944 Email: aarong(a)mail.nih.gov <mailto:aarong@mail.nih.gov>

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RE: [Freesurfer] anatomical_stats
by Fornito, Alexander 07 Aug '05

07 Aug '05

Hi Brian, I tried the -f flag and got the following. Is there a newer version of anatomical_stats that runs the -f option? mris_anatomical_stats -f ./lh_aff_limbic.txt -l 1000027/label/1000027_lh_aff_limbic.label 1000027 lh pial unknown option -f -----Original Message----- From: Brian T. Quinn [mailto:btquinn@nmr.mgh.harvard.edu] Sent: Sat 7/30/2005 4:27 PM To: Fornito, Alexander Cc: freesurfer(a)nmr.mgh.harvard.edu Subject: Re: [Freesurfer] anatomical_stats sure: cd $SUBJECTS_DIR mris_anatomical_stats -f file.txt -b -a subjid/label/hemi.aparc.annot subjid hemi On Sat, 30 Jul 2005, Fornito, Alexander wrote: > Hi, > Is there anyway to print the output of mri_anatomical_stats to a text file? > Thanks, > Alex > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > -- brian t. quinn

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unload segmentation?
by walhovd＠nmr.mgh.harvard.edu 06 Aug '05

06 Aug '05

Hi when I've loaded the aseg in tkmedit, is it possible to unload it, or do I have to close tkmedit to view a volume without it again? Thanks, Kristine

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