Freesurfer August 2006

freesurfer@nmr.mgh.harvard.edu

48 participants
74 discussions

visualizing surfaces
by camilo＠nmr.mgh.harvard.edu 25 Aug '06

25 Aug '06

Hi Freesurfer, Is there a way to visualize 3 surfaces at the same time. I am trying to visualize the BEMs in my flash directory. So far, I can only load 2 of them by loading the main surface and the axiliar surface. Thanks, Camilo

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new feature for glmfir/fsgd
by Doug Greve 25 Aug '06

25 Aug '06

I've added a new feature to the FreeSurfer Group Descriptor (FSGD) file which allows you to easily use the volume subcortical structures as covariates in a mri_glmfit analysis. An example is: GroupDescriptorFile 1 Title test Class main VariableFromASeg Left-Hippocampus Variables Age Input subject1 main 20 Input subject2 main 30 Input subject3 main 40 ... The above fsgdf will have two variables: Age and the volume of the left hippocampus. The volume is obtained from stats/aseg.stats. Within the design matrix, the left hippocampal regressor will appear after that of Age (you'll need to know this to set up your contrast matrices). mri_glmfit will fill in the values. mri_glmfit will write an fsgd as part of it's output, and this will include the volumes. This is formally equivalent to something like: GroupDescriptorFile 1 Title test Class main Variables Age Left-Hippocampus Input subject1 main 20 2000 Input subject2 main 30 3000 Input subject3 main 40 4000 ... You can have more than one VariableFromASeg statement. There are mechanisms to use something other than aseg.stats (eg, if you have your own continuous variables such as age, IQ, etc). I wrote and tested this on a flight from new mexico to boston, so I have not tested it out extensively. Let me know if you experience any turbulence. I'll add some docs to the wiki when I have time. doug -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

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mris_preproc and thickness
by Sasha Wolosin 25 Aug '06

25 Aug '06

Dear all, Does "--meas thickness" as an input for mris_preproc always specify to use the ?h.thickness file in the surf folder? Is there a way to specify a different thickness file as input for mris_preproc? Thanks, Sasha Disclaimer: The materials in this e-mail are private and may contain Protected Health Information. Please note that e-mail is not necessarily confidential or secure. Your use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail.

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Ubuntu linx
by Chacko Cherian 23 Aug '06

23 Aug '06

Hello all, I am using an Ubuntu linux machine to run a few subjects.I ve been having trouble using tksurfer on it but tkmedit seems to be working pretty fine.Could someone please let me know why this problem has occured?Is it something to do with the souce code and the graphics libraries? Thanks in advance Chacko Cherian.

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incompatible vertex number in rh.thickness
by walhovd＠nmr.mgh.harvard.edu 23 Aug '06

23 Aug '06

Hi I just got a a new error message (pasted below this mail) when trying to run a glm I've previously run successfully. It does not get to open/use the rh.thickness file of one of my subjects (MRISreadNewCurvature: incompatible vertex number in file /var/lab-data/barn/recon2//028/surf/rh.thickness). When I delete this particular subject from the fsgd list, the glm runs smoothly, so the error is not in how the glm is set up. The mysterious thing is that I ran glms with this subject in December -05, and none of the files have been changed or saved after this (the rh.thickness file was last saved in September -05). I've tried different versions of Freesurfer, but the same thing happens. I'm grateful for any suggestions on how to solve this problem. Best regards Kristine Error message: nthsubj = 22/28, 028 --------------------------------------- INFO: loading surface /var/lab-data/barn/recon2//028/surf/rh.sphere.reg INFO: Volume /tmp/mritotal_9571/brain_8_dxyz.mnc cannot be found. INFO: Volume /usr/pubsw/packages/mni/current/bin//../share/mni_autoreg/average_3 05_8_dxyz.mnc cannot be found. INFO: The transform was made with average_305.mnc. nvertices = 130773 INFO: loading input thickness as curv Loading surface source data thickness as curv Reading curvature file /var/lab-data/barn/recon2//028/surf/rh.thickness MRISreadNewCurvature: incompatible vertex number in file /var/lab-data/barn/reco n2//028/surf/rh.thickness ERROR: reading curvature ERROR: could not load thickness gdfReadHeader: reading /var/lab-data/barn/recon2//glm_230806/kidsgroups_sex/kids groups_sex.txt INFO: ignoring tag SomeTag WARNING: no variables on 'Variables' line found INFO: gd2mtx_method is doss INFO: Normalized Design Matrix Condition Number is 1 INFO: found 4 elements in group contrast vector 1.000 1.000 -1.000 -1.000; $Id: mris_glm.c,v 1.43 2005/08/17 22:19:35 greve Exp $ Kristine B Walhovd University of Oslo Dept. of Psychology PB 1094 Blindern 0317 Oslo Norway

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inter-rater variation in scan workups?
by Glenn Lawyer 22 Aug '06

22 Aug '06

Hi, We are having a small discussion at our lab regarding inter- and intra-rater reliability numbers for our scan workups. We have a number of lab technicians processing the scans, a situation which I suspect is common to many research groups. I can think of a number of steps in the processing stream where operator input could change surface thickness measures. Yet I can't recall ever seeing inter/intra-rater reliability measures in publications. Nor is it mentioned in the FS documentation, and I don't think it is presented at the FS courses. The people I have asked about it (two different labs) have all said something like "ignore it, nobody does it." How are other people handling this issue? -- -------------------------------------- I'm only in it for the glory. > Glenn Lawyer < > +352 061 967 244 < > Instituttgruppe for psykiatri < > Postboks 1130 Blindern < > 0318 Oslo < < http://folk.uio.no/davidgl > <><><><><><><><><><><><><><><><><:)

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Re: Re: [Freesurfer] Parcellation data order
by Bruce Fischl 21 Aug '06

21 Aug '06

Hi Feng, there's an update matlab reader that also extracts the color table, contributed by Thomas Yeo. I've attached it if you're interested. cheers, Bruce On Mon, 21 Aug 2006, fshi wrote: > Hi Dr. Bruce Fischl, > > I subscribe this mailing list form july. I'm glad to answer some questions if I know. > > I think I find the way how color table correspond to the big numbers in annot files. > Just translate the three color values from decimal to binary like 00001111, and put them > together, and then translate the number back to decimal, now you can get the numbers read > form annot files. > > The correspondance between color table and numbers in annot files: > (for example: 1 G_cingularis 25 60 60 3947545) > comments: ~~~index ~~~~~~~~~~RGB color ~~~~~~~numbers computed by color > used in annot files instead of color > > 0 Unknown 0 0 0 0 > 1 G_cingularis 25 60 60 3947545 > 2 G_cuneus 180 20 20 1316020 > 3 G_frontalis_inf-pars_opercularis 220 20 100 6558940 > 4 G_frontalis_inf-pars_orbitalis 140 60 60 3947660 > 5 G_frontalis_inf-pars_triangularis 180 220 140 9231540 > 6 G_frontalis_medius 140 100 180 11822220 > 7 G_frontalis_sup-pars_lateralis 180 20 140 9180340 > 8 G_frontalis_sup-pars_medialis 180 140 100 6589620 > 9 G_frontomarginalis 140 20 140 9180300 > 10 G_hippocampi 25 180 20 1356825 > 11 G_insularis_breves 225 140 140 9211105 > 12 G_occipitalis_inf 140 220 100 6610060 > 13 G_occipitalis_medius-pars_inf 180 60 180 11812020 > 14 G_occipitalis_medius-pars_sup 180 60 180 11812020 > 15 G_occipitalis_sup 20 220 60 3988500 > 16 G_lateralis 60 20 140 9180220 > 17 G_lingualis 220 180 140 9221340 > 18 G_parahippocampi 65 100 20 1336385 > 19 G_orbitalis 220 60 20 1326300 > 20 G_paracentralis 60 100 60 3957820 > 21 G_parietalis_inf-pars_angularis 20 60 220 14433300 > 22 G_parietalis_inf-pars_supramarginalis 100 100 60 3957860 > 23 G_parietalis_sup 220 180 220 14464220 > 24 G_postcentralis 20 180 140 9221140 > 25 G_precentralis 60 140 180 11832380 > 26 G_precuneus 25 20 140 9180185 > 27 G_rectus_and_S_orbitalis_medialis 20 60 100 6568980 > 28 G_rectus_and_S_orbitalis_medialis2 20 60 100 6568980 > 29 G_subcentralis 60 20 220 14423100 > 30 G_supracingularis 145 220 220 14474385 > 31 G_temporalis_transversalis 225 60 60 3947745 > 32 G_temporalis_inf 220 220 100 6610140 > 33 G_temporalis_medius 180 60 60 3947700 > 34 G_temporalis_sup-pars_lateralis 220 60 220 14433500 > 35 G_temporalis_sup-planum_polare 60 220 60 3988540 > 36 G_temporalis_sup-planum_temporale 20 140 20 1346580 > 37 Plica_falciformis 141 220 100 6610061 > 38 Polus_occipitalis 140 20 60 3937420 > 39 Polus_temporalis 220 180 20 1357020 > 40 S_temporalis_transversalis 221 60 60 3947741 > 42 S_angularis 181 20 20 1316021 > 43 S_calcarinus 61 180 180 11842621 > 44 S_centralis_insulae_&_G_insularis_longus 21 220 20 1367061 > 46 S_centralis 221 20 20 1316061 > 47 S_cingularis 181 100 20 1336501 > 48 S_cingularis-pars_marginalis 221 20 100 6558941 > 49 S_circularis_insulae_ant 221 60 140 9190621 > 50 S_circularis_insulae_inf 221 20 220 14423261 > 51 S_circularis_insulae_sup 61 220 220 14474301 > 52 S_corpori_callosi 181 220 20 1367221 > 53 S_diagonalis 21 60 20 1326101 > 54 S_frontalis_inf 221 220 20 1367261 > 55 S_frontalis_medialis 141 60 60 3947661 > 56 S_frontalis_medius 141 20 100 6558861 > 57 S_frontalis_sup 61 220 100 6609981 > 58 S_frontomarginalis 21 220 60 3988501 > 59 S_intermedius_primus 141 60 20 1326221 > 60 S_intermedius_secundus 141 100 100 6579341 > 61 S_intracingularis 181 60 20 1326261 > 62 S_intraoccipitalis_medius 141 140 20 1346701 > 63 S_intraoccipitotemporalis_lateralis 221 180 180 11842781 > 64 S_intraparietalis 141 20 220 14423181 > 65 S_lateralis-pars_ant-ramus_horizontalis 61 20 220 14423101 > 66 S_lateralis-pars_ant-ramus_verticalis 61 20 60 3937341 > 67 S_lateralis-pars_horizontalis 101 100 220 14443621 > 68 S_lateralis-pars_post 61 60 100 6569021 > 69 S_lunatus 141 180 100 6599821 > 70 S_occipitalis_ant 61 20 180 11801661 > 71 S_occipitalis_inf 21 60 180 11811861 > 72 S_occipitalis_medius 101 60 220 14433381 > 73 S_occipitalis_sup 21 20 140 9180181 > 74 S_occipitalis_transversalis 61 20 20 1315901 > 75 S_occipitopolaris 201 240 60 3993801 > 76 S_occipitotemporalis_lateralis 221 140 20 1346781 > 77 S_occipitotemporalis_medialis 141 100 220 14443661 > 78 S_orbitales 101 20 20 1315941 > 79 S_orbitalis_lateralis 221 100 20 1336541 > 80 S_paracalcarinus 221 140 100 6589661 > 81 S_paracentralis 21 180 140 9221141 > 82 S_parietalis_transversalis 181 100 60 3957941 > 83 S_parieto_occipitalis 101 100 180 11822181 > 84 S_postcentralis 21 140 220 14453781 > 85 S_precentralis 21 20 220 14423061 > 86 S_retrocalcarinus 21 100 20 1336341 > 87 S_rhinalis 221 100 100 6579421 > 88 S_subcentralis_ant_&_post_ 61 180 60 3978301 > 89 S_suborbitalis 21 20 60 3937301 > 90 S_subparietalis 101 60 60 3947621 > 91 S_supracingularis 21 220 220 14474261 > 92 S_temporalis_inf 21 180 180 11842581 > 93 S_temporalis_sup 221 220 60 3988701 > 94 S_triangularis 181 140 140 9211061 > > > The way read annot files with matlab (taken from archives of this maillist) > ------------------- > function [annots] = read_annotation(fname) > % > % [annots] = read_annotation(fname) > % reads a binary annotation file into a vector > % > % open it as a big-endian file > fid = fopen(fname, 'rb', 'b') ; > if (fid < 0) > str = sprintf('could not open annotation file %s.', fname) ; > error(str) ; > end > vnum = fread(fid, 1, 'int32') ; > tmp = fread(fid, vnum*2, 'int') ; > annots = tmp(2:2:vnum*2) ; > > fclose(fid) ; > ------------------- > > Hope it useful. > > ----------- > Feng Shi, > Automation Institute,Chinese Academy of Sciences,Beijing,China > ======= 2006-07-25 09:13:28 ======= > >> Hi Neel, >> >> the .annot files should have the color table embedded in them precisely >> to avoid this type of confusion. I think Doug has a tool for extracting the >> color table from the .annot file, don't you Doug? >> >> cheers, >> Bruce >> >> >> On Mon, 24 Jul 2006, Neel Kishan wrote: >> >>> surface_labels.txt has 94 ROIs in contrast to the 81 in >>> Simple_surface_labels2005.txt, and it does not seem to match the numbering >>> system I find in SUMA. Does this file indicate that there is another >>> parcellating method to identify 94 ROIs? >>> >>> Nick Schmansky wrote: >>>> Simple_surface_labels2005.txt was the older name. It is now called: >>>> >>>> surface_labels.txt >>>> >>>> and is found in $FREESURFER_HOME. Sorry! >>>> >>>> On Mon, 2006-07-24 at 15:47 -0500, Neel Kishan wrote: >>>> >>>>> Thanks for the information. Please note that >>>>> Simple_surface_labels2005.txt was not distributed in v3.0.3 for Mac OS X >>>>> Tiger. >>>>> >>>>> To convert an annot file to roi file for SUMA the following lines can be >>>>> used for each hemisphere: >>>>> >>>>> FSread_annot -input $SUBJECTS_DIR/subject/label/rh.aparc.a2005s.annot >>>>> -roi_1D rh.aparc.a2005s.1D.roi >>>>> FSread_annot -input $SUBJECTS_DIR/subject/label/rh.aparc.annot -roi_1D >>>>> rh.aparc.1D.roi >>>>> >>>>> The following list corresponds with SUMA's labeling of the first roi file: >>>>> 3 G_cingulate-Isthmus >>>>> 4 G_cingulate-Main_part >>>>> 5 G_cuneus >>>>> 6 G_frontal_inf-Opercular_part >>>>> 7 G_frontal_inf-Orbital_part >>>>> 8 G_frontal_inf-Triangular_part >>>>> 9 G_frontal_middle >>>>> 10 G_frontal_superior >>>>> 11 G_frontomarginal >>>>> 12 G_insular_long >>>>> 13 G_insular_short >>>>> 14 G_and_S_occipital_inferior >>>>> 15 G_occipital_middle >>>>> 16 G_occipital_superior >>>>> 17 G_occipit-temp_lat-Or_fusiform >>>>> 18 G_occipit-temp_med-Lingual_part >>>>> 19 G_occipit-temp_med-Parahippocampal_part >>>>> 20 G_orbital >>>>> 21 G_paracentral >>>>> 22 G_parietal_inferior-Angular_part >>>>> 23 G_parietal_inferior-Supramarginal_part >>>>> 24 G_parietal_superior >>>>> 25 G_postcentral >>>>> 26 G_precentral >>>>> 27 G_precuneus >>>>> 28 G_rectus >>>>> 29 G_subcallosal >>>>> 30 G_subcentral >>>>> 31 G_temporal_inferior >>>>> 32 G_temporal_middle >>>>> 33 G_temp_sup-G_temp_transv_and_interm_S >>>>> 34 G_temp_sup-Lateral_aspect >>>>> 35 G_temp_sup-Planum_polare >>>>> 36 G_temp_sup-Planum_tempolare >>>>> 37 G_and_S_transverse_frontopolar >>>>> 38 Lat_Fissure-ant_sgt-ramus_horizontal >>>>> 39 Lat_Fissure-ant_sgt-ramus_vertical >>>>> 40 Lat_Fissure-post_sgt >>>>> 41 Medial_wall >>>>> 42 Pole_occipital >>>>> 43 Pole_temporal >>>>> 44 S_calcarine >>>>> 45 S_central >>>>> 46 S_central_insula >>>>> 47 S_cingulate-Main_part_and_Intracingulate >>>>> 48 S_cingulate-Marginalis_part >>>>> 49 S_circular_insula_anterior >>>>> 50 S_circular_insula_inferior >>>>> 51 S_circular_insula_superior >>>>> 52 S_collateral_transverse_ant >>>>> 53 S_collateral_transverse_post >>>>> 54 S_frontal_inferior >>>>> 55 S_frontal_middle >>>>> 56 S_frontal_superior >>>>> 57 S_frontomarginal >>>>> 58 S_intermedius_primus-Jensen >>>>> 59 S_intraparietal-and_Parietal_transverse >>>>> 60 S_occipital_anterior >>>>> 61 S_occipital_middle_and_Lunatus >>>>> 62 S_occipital_superior_and_transversalis >>>>> 63 S_occipito-temporal_lateral >>>>> 64 S_occipito-temporal_medial_and_S_Lingual >>>>> 65 S_orbital-H_shapped >>>>> 66 S_orbital_lateral >>>>> 67 S_orbital_medial-Or_olfactory >>>>> 68 S_paracentral >>>>> 69 S_parieto_occipital >>>>> 70 S_pericallosal >>>>> 71 S_postcentral >>>>> 72 S_precentral-Inferior-part >>>>> 73 S_precentral-Superior-part >>>>> 74 S_subcentral_ant >>>>> 75 S_subcentral_post >>>>> 76 S_suborbital >>>>> 77 S_subparietal >>>>> 78 S_supracingulate >>>>> 79 S_temporal_inferior >>>>> 80 S_temporal_superior >>>>> 81 S_temporal_transverse >>>>> >>>>> The second file corresponds with the following list: >>>>> 0 unknown/unlabeled >>>>> 1 bankssts >>>>> 2 caudalanteriorcingulate >>>>> 3 caudalmiddlefrontal >>>>> 4 corpuscallosum >>>>> 5 cuneus >>>>> 6 entorhinal >>>>> 7 fusiform >>>>> 8 inferiorparietal >>>>> 9 inferiortemporal >>>>> 10 isthmuscingulate >>>>> 11 lateraloccipital >>>>> 12 lateralorbitofrontal >>>>> 13 lingual >>>>> 14 medialorbitofrontal >>>>> 15 middletemporal >>>>> 16 parahippocampal >>>>> 17 paracentral >>>>> 18 parsopercularis >>>>> 19 parsorbitalis >>>>> 20 parstriangularis >>>>> 21 pericalcarine >>>>> 22 postcentral >>>>> 23 posteriorcingulate >>>>> 24 precentral >>>>> 25 precuneus >>>>> 26 rostralanteriorcingulate >>>>> 27 rostralmiddlefrontal >>>>> 28 superiorfrontal >>>>> 29 superiorparietal >>>>> 30 superiortemporal >>>>> 31 supramarginal >>>>> 32 frontalpole >>>>> 33 temporalpole >>>>> 34 transversetemporal >>>>> >>>>> Jenni Pacheco wrote: >>>>> >>>>>> Hi Neel, >>>>>> >>>>>> You could refer to the surface label files that should be in your >>>>>> $FREESURFER_HOME directory. I believe that the >>>>>> $FREESURFER_HOME/Simple_surface_labels2005.txt corresponds with >>>>>> aparc.a2005s.annot parcellations and the >>>>>> $FREESURFER_HOME/average/colortable_desikan_killiany.txt corresponds with >>>>>> the aparc.annot parcellations. >>>>>> >>>>>> Jenni >>>>>> >>>>>> >>>>>> On Mon, 24 Jul 2006, Neel Kishan wrote: >>>>>> >>>>>> >>>>>>> Hi List, >>>>>>> >>>>>>> Thanks for providing the mris_ca_label program and the two papers from >>>>>>> 2004 and 2006. I'm using AFNI's FSread_annot to read the aparc.annot and >>>>>>> aparc.a2005s.annot files into SUMA. The ROIs are imported numbered 0 to >>>>>>> 34 for the aparc.annot files and 0 to 81 for the aparc.a2005s.annot >>>>>>> files. I can see that the aparc.annot files correspond to the 2006 >>>>>>> Desikan et al. paper, but I'm not sure how they were ordered in the >>>>>>> annot file. I'm also wondering how the aparc.a2005s.annot files >>>>>>> identified and ordered the ROIs. >>>>>>> >>>>>>> Thanks for your help, >>>>>>> Neel Kishan >>>>>>> _______________________________________________ >>>>>>> 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 >>>>> >>>>> >>>>> >>> >>> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> > > = = = = = = = = = = = = = = = = = = = = > Feng Shi, Ph.D. Candidate > Medical Imaging and Computing Group > National Laboratory of Pattern Rcognition > Automation Institute,Chinese Academy of Sciences > Beijing, 100080 > +86-10-62659278(Office) > fshi(a)nlpr.ia.ac.cn > > > >

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BEMs
by camilo＠nmr.mgh.harvard.edu 19 Aug '06

19 Aug '06

Hi, I am doing EEG source localization, and I am trying to understand the resulting differences between the watershed algorithm and the command mri_make_bem_surfaces. I know that the watershed gives me 4 surfaces (brain, inner skull, outer skull, outer skin) and the mri_make_bem_surfaces gives me 3 surfaces (inner skull, outer skull, outer skin). But, which of those two will give me at the end of the day the most accurate source estimates in EEG? And also, do I need some special MRI sequences to obtain those BEMs (i know that in the case of mri_make_bem_surfaces i will need to process the flash 5 synthesized sequence, but is this the same case for the watershed? Any comments and advice are strongly appreciated. Thanks, Camilo

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Intel Mac
by Ray Fix 19 Aug '06

19 Aug '06

Hello, Any plans for a Mac OS X Tiger Intel release? Ray

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Converting .dcm to COR files
by camilo＠nmr.mgh.harvard.edu 18 Aug '06

18 Aug '06

Hi Freesurfer help, I am trying to convert my .dcm files to COR format. I use: mri_convert -ot cor 003DCM 003 I get the following error: mri_convert -ot cor 003DCM 003 reading from 003DCM... corRead(): can't open file /autofs/space/rao_001/users/patrickp/eeg_propofol/control_01... /bourget/control_01/mri/orig/003DCM/COR-.info I am running the standar enviroment in the nmr, and the location of my files is: /autofs/space/rao_001/users/patrickp/eeg_propofol/control_01/... bourget/control_01/mri/orig Can someone give me some advise in this issue? Thanks, Camilo

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Freesurfer August 2006