Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30084 discussions

writing thickness of ROI to tabel (fwd)
by Bruce Fischl 18 Jul '09

18 Jul '09

---------- Forwarded message ---------- Date: Sat, 18 Jul 2009 13:44:22 +0200 From: Rosa Steimke <rosasteimke(a)gmx.de> To: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> Subject: writing thickness of ROI to tabel Hi freesurfer experts, iam trying to get the thichness of a Roi i specified in qdec into a table. i used the mris_anatmical stats command to generate stats for this roi for all participants. I tried the aparc2tabel command with different flags, but the roi i specified was never inside the table. wish flag do i have to use to get the roi that i drew in qdec? thanks in advance! rosa -------- Original-Nachricht -------- > Datum: Fri, 17 Jul 2009 14:35:55 -0400 (EDT) > Von: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > An: Rosa Steimke <rosasteimke(a)gmx.de> > CC: freesurfer(a)nmr.mgh.harvard.edu > Betreff: Re: [Freesurfer] mris_anatomical_stats > why is there a \ in your command line? > On Fri, 17 Jul 2009, Rosa Steimke > wrote: > >> >> Hi freesurfer experts, >> I have a problem using the mris_anatomical_stats command to generate > stats for a region of interest that i drew in qdec. >> It gives me the following error: >> >> >> >> >> [admins-imac:~/Rosa_MRTs] steimke% mris_anatomical_stats -l > rh.FUSIFORM.label \ -t rh.thickness -b -f 1/stats/rh.FUSIFORM.label 1 rh >> limiting computations to label rh.FUSIFORM.label. >> >> Flagged-options must go first in argument list. >> >> usage: mris_anatomical_stats [options] <subject name> <hemi> [<surface > name>] >> >> This program measures a variety of anatomical properties. >> >> Valid options are: >> >> -i <low thresh> <hi thresh> - only consider thicknesses in >> the specified range >> -l <.label file> - limit calculations to specified label >> -t <thickness file> - use specified file for computing >> thickness statistics >> -a <.annot file> - compute properties for each label >> in the annotation file separately >> -b - tabular output >> -f <tablefile> - table output to a file named tablefile >> (different format than -b) must specify >> an annotation file with -a or label >> file with -l >> -log <log> - will write the stats into a file >> named <log> >> -nsmooth <#> - will smooth the thicknessmap # of >> iterations before using it >> -c <.ctab file> - output the colortable for this annotation >> [admins-imac:~/Rosa_MRTs] steimke% mris_anatomical_stats -l > rh.FUSIFORM.label \ -t rh.thickness -b -f 1/stats/rh.FUSIFORM.label 1 rh >> >> >> >> >> do you know what i did wrong? >> thanks in advance! >> rosa >> >> > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- GRATIS für alle GMX-Mitglieder: Die maxdome Movie-FLAT! Jetzt freischalten unter http://portal.gmx.net/de/go/maxdome01

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mris_anatomical_stats
by Rosa Steimke 17 Jul '09

17 Jul '09

Hi freesurfer experts, I have a problem using the mris_anatomical_stats command to generate stats for a region of interest that i drew in qdec. It gives me the following error: [admins-imac:~/Rosa_MRTs] steimke% mris_anatomical_stats -l rh.FUSIFORM.label \ -t rh.thickness -b -f 1/stats/rh.FUSIFORM.label 1 rh limiting computations to label rh.FUSIFORM.label. Flagged-options must go first in argument list. usage: mris_anatomical_stats [options] <subject name> <hemi> [<surface name>] This program measures a variety of anatomical properties. Valid options are: -i <low thresh> <hi thresh> - only consider thicknesses in the specified range -l <.label file> - limit calculations to specified label -t <thickness file> - use specified file for computing thickness statistics -a <.annot file> - compute properties for each label in the annotation file separately -b - tabular output -f <tablefile> - table output to a file named tablefile (different format than -b) must specify an annotation file with -a or label file with -l -log <log> - will write the stats into a file named <log> -nsmooth <#> - will smooth the thicknessmap # of iterations before using it -c <.ctab file> - output the colortable for this annotation [admins-imac:~/Rosa_MRTs] steimke% mris_anatomical_stats -l rh.FUSIFORM.label \ -t rh.thickness -b -f 1/stats/rh.FUSIFORM.label 1 rh do you know what i did wrong? thanks in advance! rosa -- GRATIS für alle GMX-Mitglieder: Die maxdome Movie-FLAT! Jetzt freischalten unter http://portal.gmx.net/de/go/maxdome01

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ANOVA and co-variable
by Zhang, Xiaochu (NIH/NIDA) [F] 17 Jul '09

17 Jul '09

Hi Freesurfer experts, I want to do a group ANOVA analysis with one co-variable. I have read the corresponding wiki but still have some problems. I need your help. I have 4 group subjects (A1B1, A1B2, A2B1, A2B2) and one co-vaiable (C). I want to get the interaction between A and B. However, because C is different in different groups, I need to rule out the influence from C in my ANOVA analysis. So the model is A*B+C. The fsgd file is GroupDescriptorFile 1 Title SK-SZ Class A1B1 Class A1B2 Class A2B1 Class A2B2 Variable C Input S1 A1B1 0.0 Input S2 A1B2 2.0 Input S3 A2B1 3.0 Input S4 A2B2 0.0 The mtx file is 0.5 -0.5 -0.5 0.5 0 0 0 0 Is it correct? Thanks a lot! Xiaochu Zhang PhD Visiting Research Fellow Neuroimaging Research Branch National Institute on Drug Abuse - IRP Biomedical Research Center 251 Bayview Blvd. Suite 200 (NIDA) Baltimore MD 21224 Tel: 443-740-2619

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Re: [Freesurfer] read in .vtk files ? (fwd)
by Ruopeng Wang 17 Jul '09

17 Jul '09

I'm not quite sure but I think freesurfer surface has some strict format that may be difficult to covert to from an external mesh. (Someone correct me if I'm wrong). As to freeview, the stable release is not the latest version. Ruopeng Ritobrato Datta wrote: > Hello Dr. Wang, > > Thanks for your kind reply. Can freesurfer convert .vtk files to freesurfer format ? I need to take a .vtk mesh and work it backward to volumetric data using freesurfer. Do you think thats possible ? > > Please let me know. > > Is freeviewer in the latest version of freesurfer ?? > > Thanks a lot for the help > > Sincerely > > Ri > > Ritobrato Datta, Ph.D. > Post Doctoral Fellow > Department of Neurology > University of Pennsylvania School of Medicine > 3rd Floor Gates Building > 3400 Spruce St. > Philadelphia > Pa 19104 > > > > ----- Original Message ----- > From: "Ruopeng Wang" <rpwang(a)nmr.mgh.harvard.edu> > To: "Ritobrato Datta" <ridatta(a)mail.med.upenn.edu> > Cc: freesurfer(a)nmr.mgh.harvard.edu > Sent: Friday, July 17, 2009 12:20:30 PM GMT -05:00 US/Canada Eastern > Subject: Re: [Freesurfer] read in .vtk files ? (fwd) > > Hi, > > What program in freesurfer do you want to load .vtk surface with? I can > potentially add .vtk file support for freeview. It will only be pure > visualization, though. Do you need to do anything with the surface? > > Ruopeng > > >> ---------- Forwarded message ---------- >> Date: Fri, 17 Jul 2009 00:10:19 -0400 (EDT) >> From: Ritobrato Datta <ridatta(a)mail.med.upenn.edu> >> To: freesurfer(a)nmr.mgh.harvard.edu >> Subject: [Freesurfer] read in .vtk files ? >> >> Hello All, >> >> Can freesurfer read in .vtk surface files ? >> >> Please let me know. >> >> Thanks >> >> Ri >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> >> > > >

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Confusion about mri_label2label
by Stephen Tyree 17 Jul '09

17 Jul '09

Hello, I'm attempting to convert labels from one subject's cortical surface to locations or nodes on another's cortical surface via spherical registration. My thought was to use mri_label2label, e.g. mri_label2label --srcsubject Bob --srclabel Bob/label/lh.cortex.label --trgsubject bert --trglabel Bob/label/bobToBert.lh.cortex.label --regmethod surface --hemi lh My understanding is that this should translate the labels for the nodes on Bob's lh surface to labels/nodes/locations (I'm not really sure which) on bert's lh surface. However, each label file seems to end up with a different number of labels. Bob/label/lh.cortex.label: 146415 Bob/label/bobToBert.lh.cortex.label: 122917 bert/label/lh.cortex.label: 122108 bert/label/bertToBob.lh.cortex.label: 145629 Can someone explain more precisely what mri_label2label does and what output it produces? Thanks. -- Stephen Tyree Neuroimaging Computer Scientist Laureate Institute for Brain Research Tulsa, OK, USA

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Hausdorff distance
by Jared Price 17 Jul '09

17 Jul '09

Hi gurus, I am evaluating two segmentation routines relative to a gold standard and would like to calculate the Hausdorff distance for each routine relative to the gold standard in the left and right Amygdala, Caudate, Putamen, and Hippocampus. I know that there are 3 main options to the mri_hausdorff_dist binary, namely -b <thresh> (binarize input volumes with threshold <thresh>), -g <sigma> (blur the input image with Gaussian <sigma>) and -max (compute the max of the min distances instead of the mean) but I am not quite sure how to use them to get the desired result. Does anyone know how best to use this tool to get structure-specific Hausdorff distances from 2 aseg.mgz volumes?

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from dicom to mgz
by Jose Luis Cantero Lorente 17 Jul '09

17 Jul '09

Hi, I am trying to convert from dicom to mgz (or nii) in Freesurfer by using dicom files as the one attached to this message. However, Freesurfer reports that this file is not a dicom. It seems weird to me since it can be opened with MRIcro, SPM as dicom, but not with Freesurfer. Could anyone tell me if there is another Freesurfer command to covert these dicoms to mgz from the command line? Thanks in advance. Best, Jose --- Jose Luis Cantero, Ph.D. Laboratory of Functional Neuroscience Department of Physiology, Anatomy, and Cell Biology University Pablo de Olavide Ctra. de Utrera, Km.1 41013 - Sevilla - Spain - Phone: +34 954 977433 Fax: +34 954 349151 Email: jlcanlor(a)upo.es http://www.upo.es/neuroaging/en/

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read in .vtk files ?
by Ritobrato Datta 17 Jul '09

17 Jul '09

Hello All, Can freesurfer read in .vtk surface files ? Please let me know. Thanks Ri

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follow-up to Hausdorff distance question
by Jared Price 16 Jul '09

16 Jul '09

Hi all, I asked an earlier question about Hausdorff distance and was told there was a binary "mri_hausdorff_dist" that could calculate it, but I don't see it in the /Applications/freesurfer/bin directory. Is it elsewhere? Is it included with 4.4.0?

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mean symmetric surface distance, Hausdorff distance etc..
by Jared Price 16 Jul '09

16 Jul '09

Hi freesurfer masters, I was wondering if freesurfer had a way of comparing two segmentations for surface differences, something along the lines of a Hausdorff distance or the symmetric mean absolute surface distance Cheers, Jared

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