Freesurfer

freesurfer@nmr.mgh.harvard.edu

17 participants
30130 discussions

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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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

1 0

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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