Freesurfer

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30065 discussions

overlay thickness maps
by Kirk, Gregory 24 Dec '05

24 Dec '05

I would like to overlay lh.thickness, rh.thickness on inflated for single subject, not the glm results, how to do that is well documented from the tutorial/tutorial group study tried tksurfer subject lh inflated - got the gray surface next file->load overlay -> $SUBJECTS_DIR/subject/surf choose lh.thickness * calculate identity map it redraws the surface but there is no colormap of the thickness can I do what I am trying ? Happy Holidays Greg.

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Paracingulate Gyri Parcellating
by Faden, Eric (NIH/NIMH) [F] 23 Dec '05

23 Dec '05

After reading the paper I am still a little confused about how the Subcortical Parcellation labels the parasingulate gyri when some people have one and others have two? Can anyone shed a little light on this issue? -Eric

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wmfill problem
by Sven Panis 22 Dec '05

22 Dec '05

Hi surfers, I experience a problem during the first step of the create surface routine : fill white matter. Specifically, the ponscall.dat file in mri/tmp is empty and at the start of step two (tessellate RH white matter) I'm asked to confirm that "the images in .../mri/filled/COR-0 cannot be found .... wmfill first." I have already tried to enter the coordinates of the corpus callosum and the pons manually (paying attention to the fact that xTal = coronal, yTal = horizontal, zTal = saggital + to make sure the cc is disconnected), without result... (I use the values in the Volume Index, no Talairachs). Do I have to pay attention to other things when entering coordinates manually? Or does anyone of you have an idea about what's going wrong? Any help appreciated! Thanks and enjoy the holidays, Sven Panis University of Leuven Department of Psychology Tiensestraat 102 3000 Leuven BELGIUM tel: +32-16-32.60.94 Mailto: sven.panis(a)psy.kuleuven.be Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm

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RE: [Freesurfer] Sulcal depth
by Bagnato, Francesca (NIH/NINDS) [F] 22 Dec '05

22 Dec '05

Yes, this is what I mean. Thanks, -francesca Francesca Bagnato, MD NIB-NINDS-NIH 10 Center Drive Building 10, Room 5B16 Bethesda, MD, 20892 USA ph #: 001-301-402.6391 fax #: 001-301-402.0373 -----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Thursday, December 22, 2005 5:37 PM To: Bagnato, Francesca (NIH/NINDS) [F] Cc: Fornito, Alexander; freesurfer(a)nmr.mgh.harvard.edu Subject: RE: [Freesurfer] Sulcal depth you mean in a parcellation unit? It's whatever the parcellation unit is defined to be. On Thu, 22 Dec 2005, Bagnato, Francesca (NIH/NINDS) [F] wrote: > As far as the cortical thickness of sulci is concerned, the program > refers to the cortex in between two giry, right? > Thanks, > -francesca > > Francesca Bagnato, MD > NIB-NINDS-NIH > 10 Center Drive > Building 10, Room 5B16 > Bethesda, MD, 20892 > USA > ph #: 001-301-402.6391 > fax #: 001-301-402.0373 > > > -----Original Message----- > From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] > Sent: Thursday, December 22, 2005 5:30 PM > To: Fornito, Alexander > Cc: freesurfer(a)nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] Sulcal depth > > not all that easily, although I guess we could write out something from > mris_inflate that has the units of mm. > > On Fri, 23 Dec 2005, Fornito, Alexander wrote: > >> Hi all, >>> From my understanding, ?h.sulc can be used to measure sulcal depth. >> I'm wandering if it is possible to use this to get the depth of a > sulcus within an ROI, and if so, how you would extract the relevant > measures, i.e.., would it be obtainable through mris_anatomical_stats? >> Thanks, >> Alex >> >> Alex Fornito >> M.Psych/PhD (clin. neuro.) candidate >> Melbourne Neuropsychiatry Centre and Department of Psychology >> The University of Melbourne >> alexander.fornito(a)wh.org.au >> >> ________________________________ >> >> >> _______________________________________________ >> 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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RE: [Freesurfer] Sulcal depth
by Bagnato, Francesca (NIH/NINDS) [F] 22 Dec '05

22 Dec '05

As far as the cortical thickness of sulci is concerned, the program refers to the cortex in between two giry, right? Thanks, -francesca Francesca Bagnato, MD NIB-NINDS-NIH 10 Center Drive Building 10, Room 5B16 Bethesda, MD, 20892 USA ph #: 001-301-402.6391 fax #: 001-301-402.0373 -----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Thursday, December 22, 2005 5:30 PM To: Fornito, Alexander Cc: freesurfer(a)nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Sulcal depth not all that easily, although I guess we could write out something from mris_inflate that has the units of mm. On Fri, 23 Dec 2005, Fornito, Alexander wrote: > Hi all, >> From my understanding, ?h.sulc can be used to measure sulcal depth. > I'm wandering if it is possible to use this to get the depth of a sulcus within an ROI, and if so, how you would extract the relevant measures, i.e.., would it be obtainable through mris_anatomical_stats? > Thanks, > Alex > > Alex Fornito > M.Psych/PhD (clin. neuro.) candidate > Melbourne Neuropsychiatry Centre and Department of Psychology > The University of Melbourne > alexander.fornito(a)wh.org.au > > ________________________________ > > > _______________________________________________ > 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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mri_ca_normalize
by Margo McKenna Benoit 22 Dec '05

22 Dec '05

Hello, I am having a problem with the mri_ca_normalize step in autorecon2. When I run autorecon2 (in the dev version: recon-all-nmr -subjid avm004 -autorecon2 -nosubcortseg -hemi lh), it gives me a message that norm.mgz is missing, and it seems that the files are not being created (either in the <subjid>/mri /norm folder or in norm.mgz format). I tried running mri_ca_normalize alone with the following command: "mri_ca_normalize -mask avm004/mri/brain.mgz avm004/mri/nu.mgz ${FREESURFER_HOME}/average/RB40_talairach_2005-07-20.gca avm004/mri/transforms/talairach.xfm avm004/mri/norm.mgz" and I get the following output, still with no norm.mgz or norm files: reading atlas from '/usr/local/freesurfer/dev/average/RB40_talairach_2005-07-20.gca'... setting gca type = Normal gca type reading transform from 'avm004/mri/transforms/talairach.xfm'... reading input volume from avm004/mri/nu.mgz... Note: program considers input volume #1 as the most T1-like using real data threshold=53.0 using (111, 120, 127) as brain centroid... mean wm in atlas = 110, using box (97,105,108) --> (125, 135,146) to find MRI wm before smoothing, mri peak at 184 after smoothing, mri peak at 184, scaling input intensities by 0.596 scaling channel 0 by 0.596172 using 269906 sample points... INFO: transform used GCApriorToSourceVoxelFloat: needs vox-to-vox transform Is there some way to get the normalize step to run during autorecon2? Thanks for your help, Margo

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Re: Estimating Quality of Automatic Parcellation
by hwier＠uchicago.edu 21 Dec '05

21 Dec '05

Hello All, We'll try to clarify our question. We would like to obtain a measure that reflects the degree to which the parcellation algorithm thinks the parcellation is successful on a brain-by-brain basis. Is there any log file, or verbose mode we could use to extract this sort of parameter? Intuitively, we would think that for some brains there would be a large "error term" reflecting uncertainty of the parcellation quality, whereas for other brains this term would be smaller, so we were assuming that there was probably some way to quantify this. Thanks and Happy Holidays, Helen

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mris
by Bagnato, Francesca (NIH/NINDS) [F] 21 Dec '05

21 Dec '05

Dear All: I am having an error saying: "couldn't determine type of file ..../mri/wm" when I lunch the mris_anatomical_stats. I am not sure how to deal with that. THANKS! -francesca Francesca Bagnato, MD NIB-NINDS-NIH 10 Center Drive Building 10, Room 5B16 Bethesda, MD, 20892 USA ph #: 001-301-402.6391 fax #: 001-301-402.0373

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RE: annotations
by Bruce Fischl 20 Dec '05

20 Dec '05

no problem. Not the most informative of error messages :) On Wed, 21 Dec 2005, Fornito, Alexander wrote: > That worked. So sorry! > > Alex Fornito > M.Psych/PhD (clin. neuro.) candidate > Melbourne Neuropsychiatry Centre and Department of Psychology > The University of Melbourne > alexander.fornito(a)wh.org.au > > > > -----Original Message----- > From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] > Sent: Wed 21/12/2005 10:36 AM > To: Fornito, Alexander > Cc: freesurfer(a)surfer.nmr.mgh.harvard.edu > Subject: RE: annotations > > Hi Alex, > > try a space between lh and sphere.reg > > Bruce > > On Wed, 21 Dec 2005, Fornito, > Alexander wrote: > >> That worked - thank you so much!! >> I tried to run mris_ca_train on 4 subjects as an intial test and it seems to want a ?h.sphere.reg.smoothwm file, that I've never come across before. The output is below. Thanks again for your help. >> >> mris_ca_train -n 2 -t >> /usr/local/freesurfer-dev20050905/alex_ACC_colour_LUT.txt lh.sphere.reg >> lh_acc.annot 1000040 1000054 1000001 1000050 lh_acc_template.gcs >> computing means for 3 subject processing subject 1000054, 1 of 3... >> MRISread(/data/flanders/work/alex/freesurfer/subjects_fe/1000054/surf/lh.sphere.reg.smoothwm): >> could not open file No such file or directory mris_ca_train: could not >> read surface file >> /data/flanders/work/alex/freesurfer/subjects_fe/1000054/surf/lh.sphere.reg.smoothwm >> for 1000054 No such file or directory >> >> Alex Fornito >> M.Psych/PhD (clin. neuro.) candidate >> Melbourne Neuropsychiatry Centre and Department of Psychology >> The University of Melbourne >> alexander.fornito(a)wh.org.au >> >> >> >> -----Original Message----- >> From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] >> Sent: Wed 21/12/2005 1:38 AM >> To: Fornito, Alexander; freesurfer(a)surfer.nmr.mgh.harvard.edu >> Subject: re: annotations >> >> Hi Alex, >> >> sorry, this was our fault - we gave you an incomplete description of how to >> create a .annot file. When you export an annotation, it exports all labels >> *that have been assigned to a structure* into the .annot file. The way you >> do the assignment is you bring up the labels window (window->view->labels), >> and assign each label to a structure and it's associated color. If you want >> to modify the set of available structures (and their colors), then you >> should create a new file in the same format as >> $FREESURFER_HOME/FreeSurferColorLUT.txt >> >> and do file->load color table in tksurfer I think. >> >> Kevin: anything to add to this? >> >> sorry for the confusion. >> >> Bruce >> >> >> >> >> > > > >

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RE: annotations
by Bruce Fischl 20 Dec '05

20 Dec '05

Hi Alex, try a space between lh and sphere.reg Bruce On Wed, 21 Dec 2005, Fornito, Alexander wrote: > That worked - thank you so much!! > I tried to run mris_ca_train on 4 subjects as an intial test and it seems to want a ?h.sphere.reg.smoothwm file, that I've never come across before. The output is below. Thanks again for your help. > > mris_ca_train -n 2 -t > /usr/local/freesurfer-dev20050905/alex_ACC_colour_LUT.txt lh.sphere.reg > lh_acc.annot 1000040 1000054 1000001 1000050 lh_acc_template.gcs > computing means for 3 subject processing subject 1000054, 1 of 3... > MRISread(/data/flanders/work/alex/freesurfer/subjects_fe/1000054/surf/lh.sphere.reg.smoothwm): > could not open file No such file or directory mris_ca_train: could not > read surface file > /data/flanders/work/alex/freesurfer/subjects_fe/1000054/surf/lh.sphere.reg.smoothwm > for 1000054 No such file or directory > > Alex Fornito > M.Psych/PhD (clin. neuro.) candidate > Melbourne Neuropsychiatry Centre and Department of Psychology > The University of Melbourne > alexander.fornito(a)wh.org.au > > > > -----Original Message----- > From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] > Sent: Wed 21/12/2005 1:38 AM > To: Fornito, Alexander; freesurfer(a)surfer.nmr.mgh.harvard.edu > Subject: re: annotations > > Hi Alex, > > sorry, this was our fault - we gave you an incomplete description of how to > create a .annot file. When you export an annotation, it exports all labels > *that have been assigned to a structure* into the .annot file. The way you > do the assignment is you bring up the labels window (window->view->labels), > and assign each label to a structure and it's associated color. If you want > to modify the set of available structures (and their colors), then you > should create a new file in the same format as > $FREESURFER_HOME/FreeSurferColorLUT.txt > > and do file->load color table in tksurfer I think. > > Kevin: anything to add to this? > > sorry for the confusion. > > Bruce > > > > >

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