Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30057 discussions

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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computing contrast for regression slope comparison
by Marie Schaer 20 Dec '05

20 Dec '05

Hello everybody! I just need a small precision for statistical analysis. I would like to compare the slope of regression between two groups. Therefore I made my fsgdf like that: GroupDescriptorFile 1 Title Thickness comparison Class Control CLASS Patient Variable Age Input subj1 Control 10 Input subj2 Control 15 Input subj3 Control 20 Input subj4 Patient 10 Input subj5 Patient 15 Input subj6 Patient 20 .... And the estimation step with DODS resulted in a design matrix with 4 columns. How do I have to compute the contrast to answer the following question: do cortical thickness decrease more steeply with age in the patient than in the control group? It should be something like 0 0 1 -1 ? (and 1 -1 0 0 will answer to the question: is there any group difference in thickness with age being regressed out?). Thank you very much for your help! Marie Schaer

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re: annotations
by Bruce Fischl 20 Dec '05

20 Dec '05

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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Defining one's own atlas in FreeSurfer
by Greg Harris 19 Dec '05

19 Dec '05

By snooping in the log files in scripts/ and considering the instruction to train and then label with commands such as mris_ca_train -n 2 -t ./iowa_gross_fs_colors.txt rh sphere.reg iowa_gross_hand_parc ${SUBJECT_LIST} ./rh.iowa_gross_cort_parc.gcs which prepares the way for mris_ca_label ${SUBJECT} rh sphere.reg /opt/freesurfer/average/rh.iowa_gross_cort_parc.gcs it becomes evident that the -autorecon3 step applies the MGH standard parcellation atlas from /opt/freesurfer/average/[lr]h.curvature.buckner40.filled.desikan_killiany.gcs and thus, the "standard" atlas is known as "curvature.buckner40.filled.desikan_killiany". When we evaluate our own atlas, we compare hand-traced labels with the labels produced by mris_ca_label. Now my question: Is there a way we could access the training data for "curvature.buckner40.filled.desikan_killiany", so we can compare how mris_ca_label approximates the MGH atlas's gold standard with how it approximates the Iowa atlas's gold standard? We are curious how many subjects went into the standard atlas at mris_ca_train, too. Is there a paper (a pdf?) where this is reported? Greg Harris University of Iowa Psychiatry Brain Imaging Lab

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unpacking multiecho data
by Elizabeth Fenstermacher 19 Dec '05

19 Dec '05

I was wondering if there was a center standard for how multiecho data should be 1) unpacked 2) the individual echo sequences parsed out Thanks! Eliz

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tksurfer: left arrow in dev version
by Dahlia Sharon 16 Dec '05

16 Dec '05

Hi, When working under nmr-dev-env, tksurfer gives me the following error message when I press the left arrow button (and doesn't move the surface): "Error: can't read 'extTransform(translate,dist)': no such variable". Am I doing something wrong? Thanks! Dahlia.

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RE: [Freesurfer]
by Bagnato, Francesca (NIH/NINDS) [F] 16 Dec '05

16 Dec '05

Hi there: I am trying to lunch the stage1 on a set of IR-SPGRs and I keep having an error saying: Mri_fill: could not find valid seed for the cc. I am not sure how to interpret this. 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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saving open lines
by Dahlia Sharon 15 Dec '05

15 Dec '05

Hi, Is there a way to save an open line drawn on a subject's surface to load on the surface in a future tksurfer use? Thanks, Dahlia.

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mris_glm tool
by Alexandre DaSilva 15 Dec '05

15 Dec '05

Hello everybody, I am using the mris_glm tool to the test for the effect of a var2 on thickness (see file and command bellow), and I would like to understand the outcome. First, what is the difference in interpretation of the resulting p-value, and the p-value you'd get from a Pearson's or Spearman's correlation test between thickness and frequency. Second, what does the sign of the resulting significance map mean (red vs blue)? Third, is there a way to account for the effect of a regressor of no interest, for example age? Thanks, Alex X.fsgdf GroupDescriptorFile 1 Class MyTitle Variables Dur Freq Age Input subjid1 Class1 10 15 1000 Input subjid2 Class2 20 20 2000 Input subjid3 Class2 20 20 2000 mris_glm –fsgd X.fsdgf --surfmeas thickness --trgsubj brain –nsmooth 250 –gcv 0010 –sight ./thicknessCORfreq-sight-rh.w paint –hemi rh

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