Freesurfer

freesurfer@nmr.mgh.harvard.edu

17 participants
30129 discussions

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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freesurfer-Linux-rh9-dev20050627.tar.gz
by Massimiliano Calabrese 06 Aug '05

06 Aug '05

Hi everybody I have seen this new dev release on freesurfer site. Do you think it is good for me to update my old version ( feb 2004) ? The old version works properly but I don't know if there are new functions in this new release that are important for freesurfer. Thank you very much for your help Max _________________________________________________________________ Personalizza MSN Messenger con sfondi e fotografie! http://www.ilovemessenger.msn.it/

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Multiple simultaneous overlays
by Jane Aspell 05 Aug '05

05 Aug '05

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Multiple simultaneous overlays
by Jane Aspell 05 Aug '05

05 Aug '05

1 0

Multiple simultaneous overlays
by Jane Aspell 05 Aug '05

05 Aug '05

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