Freesurfer

freesurfer@nmr.mgh.harvard.edu

15 participants
30064 discussions

RE: [Freesurfer] Edit label
by Goradia, Dhruman D 27 Jul '06

27 Jul '06

Hello Rahul, Thank you for your reply. I tried to combine the different regions to create one label for each lobe but could not figure it out. Can you suggest how I can combine different regions using tksurfer? Is there a wiki page where the steps are explained? Thank you -Dhruman -----Original Message----- From: Rahul Desikan [mailto:rahul@nmr.mgh.harvard.edu] Sent: Thursday 27 July 2006 15:15 To: Goradia, Dhruman D Cc: freesurfer(a)nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Edit label Hi Dhruman, If you are interested in lobe-wise comparisons, you can indeed add up the individual regions of a specific lobe, create one massive label for that lobe, and get statistics on those. For example, if you were interested in the temporal lobe, you could combine: lateral occipital cuneus lingual pericalcarine and generate an *h.occiptal.label (you can use tksurfer to combine the regions). You could do the same for the other labels and thus create a 'lobe based' parcellation. Once you are done, you can use mris_anatomical_stats to generate stats on the new labels you have generated. best, Rahul On Thu, 27 Jul 2006, Goradia, Dhruman D wrote: > Hi all, > > I am interested in lobe wise surface measurement. I read Desikan et al. > paper to understand that their atlas divides the lobes into different > region and freesurfer uses that atlas to gets measurement for each > region. Is it possible to load the Desikan label and edit it to fuse all > the region belonging to each lobe and create a new label, which I could > use to get surface measurement? Thanks in advance. > > Dhruman > > --

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Edit label
by Goradia, Dhruman D 27 Jul '06

27 Jul '06

Hi all, I am interested in lobe wise surface measurement. I read Desikan et al. paper to understand that their atlas divides the lobes into different region and freesurfer uses that atlas to gets measurement for each region. Is it possible to load the Desikan label and edit it to fuse all the region belonging to each lobe and create a new label, which I could use to get surface measurement? Thanks in advance. Dhruman

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About FreeSurfer
by M SAMANTA 27 Jul '06

27 Jul '06

Hello, I am interested in using FreeSurfer for my task. I have read the site about getting started. I would like to know if FreeSurfer is supported by SGI IRIX and if it is raster based imaging or understands it? I need to know specifically if TIFF images can be supported by FreeSurfer. Thanks, Ruma

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recon-all exited with errors
by Chacko Cherian 27 Jul '06

27 Jul '06

Hello all, I was running recon-all for one of my images and this happened to be the error that i got.Could someone please clarify, Thanks in advance Chacko. "mri_watershed: error while loading shared libraries: libstdc++.so.6: cannot open shared object file: No such file or directory Linux elmo 2.6.12.1 #2 Thu Jul 14 11:14:31 MST 2005 i686 unknown unknown GNU/Linux recon-all exited with ERRORS at Wed Jul 26 13:09:41 MST 2006" __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com

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output from single subject sphere morph to atlas
by Lars M. Rimol 27 Jul '06

27 Jul '06

Hi, Is the determinant of the Jacobian matrix for the sphere morph to atlas space saved vertex by vertex? If so, where is it saved? -- yours, LMR

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recon-all exited with ERRORS
by Chacko Cherian 26 Jul '06

26 Jul '06

Hello all, I was running recon-all for one of my images and this happened to be the error that i got.what is libstdc++?? Could someone please clarify, Thanks in advance Chacko. "mri_watershed: error while loading shared libraries: libstdc++.so.6: cannot open shared object file: No such file or directory Linux elmo 2.6.12.1 #2 Thu Jul 14 11:14:31 MST 2005 i686 unknown unknown GNU/Linux recon-all exited with ERRORS at Wed Jul 26 13:09:41 MST 2006" __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com

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display SPM group results
by Thomas Stephan 26 Jul '06

26 Jul '06

Dear FSL list, I would like to use freesurfer to render fMRI results obtained by SPM group analysis onto inflated surfaces of the template brain. I succeeded to do so by inflating the template provided with SPM and using tkregister2 with the functional data. Are there any recommendations for this procedure with regard to the template to use, or should I use the fsaverage surfaces provided with freesurfer? Best regards Thomas -- ====================================================================== Dr. Thomas Stephan Email: tstephan(a)nefo.med.uni-muenchen.de Klinikum Grosshadern Neurologisches Forschungshaus Marchioninistr. 23 Fon: +49 089 / 7095-4819 81377 Muenchen Fax: +49 089 / 7095-4801 ======================================================================

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Queue tasks?
by Jake Freimer 25 Jul '06

25 Jul '06

I was wondering if it is possible to queue up various subjects like if the computers were going to be left for several days to run autorecon1 and 2 on a subject, and when that finishes move on to the next subject etc. If it is not possible in freesurfer has anyone written a script that I could use to do this kind of thing? Thanks -- -Jake

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parcellate_subject error
by Darren Weber 25 Jul '06

25 Jul '06

-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 What is this error: endorphin.16> parcellate_subject ucsf_wa could not open translation file /home/dweber/freesurfer/home/Simple_surface_labels2002.txt mris_ca_label: could not read annotation file /home/dweber/freesurfer/home/Simple_surface_labels2002.txt... No such file or directory - -- Darren L. Weber, Ph.D. Postdoctoral Scholar Dynamic Neuroimaging Laboratory, UCSF Department of Radiology, 185 Berry Street, Suite 350, Box 0946, San Francisco, CA 94107, USA. Tel: +1 415 353-9444 Fax: +1 415 353-9421 www: http://dnl.ucsf.edu/users/dweber "To explicate the uses of the brain seems as difficult a task as to paint the soul, of which it is commonly said, that it understands all things but itself." Thomas Willis (The Anatomy of the Brain and Nerves, 1664) -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.3 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org iD8DBQFExVw6xaCYN7qs0v4RAkLUAJ9BNVQgy/oyu9I0BXu3oAdnce5kVACglRYJ F6VQxAqkmFwhRheo9pnztGc= =RANa -----END PGP SIGNATURE-----

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Re: [Freesurfer] mri_em_register args, ICV, etc
by Graham Wideman 24 Jul '06

24 Jul '06

(...and now to the list, for closure...) Jenni: Ah-ha, got it -- "hidden" in the comments :-) Thanks, Graham At 7/24/2006 02:44 PM, Jenni Pacheco wrote: >The ICV is calculated during the -segstats step with all of the other >volume measures that use the aseg. They are all found within the >aseg.stats file in the stats subdir. > >Jenni

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