Freesurfer

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30070 discussions

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

2 3

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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thickness maps
by Sasha Wolosin 18 Aug '06

18 Aug '06

Dear all, When I load ?h.thick files as an overlay in tksurfer I notice that values at the thickest points are all listed as having a thickness of exactly 5. Is this a max cutoff in the actual values, or is it just that tksurfer won't display larger values? Is there a better way to visualize thickness files? 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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RE: [Freesurfer] problem with mris_anatomical_stats
by A. Douiri 18 Aug '06

18 Aug '06

that s works! Cheers! At 01:51 18/08/2006, Nick Schmansky wrote: >Abdel, > >I don't think there is a matlab alternative to mris_anatomical_stats. > >However, there is a suspicious line of code in mris_anatomical_stats that >I have fixed, and I'm wondering if you can give a new binary a try. It is >found here: > > http://surfer.nmr.mgh.harvard.edu/pub/dist/ > >and named: > > mris_anatomical_stats.gz > >To install, after downloading: > > gunzip mris_anatomical_stats.gz > chmod o+x mris_anatomical_stats > mv mris_anatomical_stats $FREESURFER_HOME/bin > >While I cannot recreate the error you see, I do not have a Slackware >installation, and I am wondering if its core libs are revealing a bug in >our code. > >Let me know if it works. > >Thanks, > >Nick > > > > Hi Nick, > > Thanks in advance for your help and i would like to ask is there an > > alternative in matlab for example to do mris_anatomical_stats? > > The detail of the outjkputs is: > > > > the output of: > > $ mris_anatomical_stats --all-info > > ProgramName: mris_anatomical_stats ProgramArguments: --all-info > > ProgramVersion: $Name: stable3 $ TimeStamp: 06/08/17-10:28:55-GMT CVS: > > $Id: > > mris_anatomical_stats.c,v 1.35.2.1 2006/04/21 19:45:19 nicks Exp $ User: > > douiri Machine: img-179 Platform: Linux PlatformVersion: 2.6.16.22 > > CompilerName: GCC CompilerVersion: 30400 > > > > I tried with other subjects and also bert and i get the same problem: > > > > $ mris_anatomical_stats -mgz -f ../stats/lh.aparc.stats -b -a > > ../label/lh.aparc.annot -c ../stats/aparc.annot.ctab bert lh > > INFO: assuming MGZ format for volumes. > > computing statistics for each annotation in ../label/lh.aparc.annot. > > reading volume .mgz... > > zcat: /home/samba/user/douiri/freesurfer/subjects/01_00/scripts/.mgz.gz: > > No > > such file or directory > > mghRead(/home/samba/user/douiri/freesurfer/subjects/01_00/scripts/.mgz, > > -1): > > read error > > mris_anatomical_stats: could not read input volume .mgz > > > > > > the freesurfer version > > $ cat $FREESURFER_HOME/build-stamp.txt > > freesurfer-Linux-centos4-stable-pub-v3.0.3 > > > > > > and the linux version is: > > $ cat /etc/slackware-version > > Slackware 10.2.0 > > > > > > > > > > > > -----Original Message----- > > From: freesurfer-bounces(a)nmr.mgh.harvard.edu > > [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Nick > > Schmansky > > Sent: 17 August 2006 00:06 > > To: Abdel Douiri > > Cc: Freesurfer Mailing List > > Subject: RE: [Freesurfer] problem with mris_anatomical_stats > > > > Abdel, > > > > This problem is truly strange. The filename seems to just disappear. > > > > Can you send me the output of: > > > > mris_anatomical_stats --all-info > > > > Also, does this error repeat? That is, if you try: > > > > cd $SUBJECTS_DIR/01_00/scripts > > mris_anatomical_stats -mgz -f ../stats/lh.aparc.stats \ > > -b -a ../label/lh.aparc.annot \ > > -c ../stats/aparc.annot.ctab 01_00 lh > > > > does it fail again? And does this happen for other subjects? > > > > Also, which freesurfer version is being used? To find out, type: > > > > cat $FREESURFER_HOME/build-stamp.txt > > > > And which Linux OS is it installed upon? > > > > Nick > > > > > > On Wed, 2006-08-16 at 17:16 +0100, Abdel Douiri wrote: > >> Thanks Bruce > >> I have put the subject and that is "01_00" and the first and second > >> autorecon was OK only the autorecon3 where it was the problem. Attached > > the > >> log file. > >> Thanks a lot for your help > >> Abdel > >> -----Original Message----- > >> From: freesurfer-bounces(a)nmr.mgh.harvard.edu > >> [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Bruce > >> Fischl > >> Sent: 16 August 2006 14:01 > >> To: Abdel Douiri > >> Cc: freesurfer(a)nmr.mgh.harvard.edu > >> Subject: Re: [Freesurfer] problem with mris_anatomical_stats > >> > >> Hi Abdel, > >> > >> is that the full command line? If so, you need to specify a subject with > >> -subjid. If not, could you send us the full command line and > > recon-all.log? > >> > >> cheers, > >> Bruce > >> > >> > >> On Wed, 16 Aug 2006, Abdel Douiri wrote: > >> > >> > Hi all, > >> > > >> > > >> > > >> > I will be grateful if someone can tell me what going wrong in the > >> following > >> > problem: > >> > > >> > When running "recon-all -autorecon3" the program stop with error > >> exactly > >> in > >> > the "mris_anatomical_stats" cmd stage and I have the following error: > >> > > >> > > >> > > >> > mris_anatomical_stats -mgz -f ../stats/lh.aparc.stats -b -a > >> > ../label/lh.aparc.annot -c ../stats/aparc.annot.ctab 01_00 lh > >> > > >> > > >> > > >> > computing statistics for each annotation in ../label/lh.aparc.annot. > >> > > >> > reading volume .mgz... > >> > > >> > zcat: > >> /home/samba/user/douiri/freesurfer/subjects/01_00/scripts/.mgz.gz: > >> No > >> > such file or directory > >> > > >> > mghRead(/home/samba/user/douiri/freesurfer/subjects/01_00/scripts/.mgz, > >> -1): > >> > read error > >> > > >> > mris_anatomical_stats: could not read input volume .mgz > >> > > >> > INFO: assuming MGZ format for volumes. > >> > > >> > Linux img-179 2.6.16.22 #2 SMP Mon Jun 26 15:49:31 BST 2006 i686 > >> unknown > >> > unknown GNU/Linux > >> > > >> > > >> > > >> > recon-all exited with ERRORS at Tue Aug 15 20:52:49 BST 2006 > >> > > >> > > >> > > >> > > >> > > >> > Thanks > >> > > >> > A > >> > > >> > > >> _______________________________________________ > >> 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 > > > > > >

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mni_paths
by bdragans＠uke.uni-hamburg.de 18 Aug '06

18 Aug '06

Dear Nick and colleagues, after solving the first problem with nu_correct (fix_mni_paths ... the way you suggested, thanks) we face the fact that the mni paths have to be fixed again after every 2nd, 3rd subject if we try to preprocess a number of subjects data. We run freesurfer with a CentOS 4 version (v3.0.3) on a Windows XP system with VMware and Fedora Core 4. Any suggestions are greatly appreciated... Many thanks Stefan & Bogdan Your last suggestion regarding those issues was: nu_correct is a script which assumes that perl is installed in /usr/bin/perl. If it is not instaled there (and it is by default on centos), then the script fixup_mni_paths will correct the mni scripts to point to your perl path. Also confirm that the environment variables MNI_DATAPATH and MNI_PERL5LIB point into the $FREESURFER_HOME/mni path. You should try running the MNI tools, like nu_correct, and others (see $FREESURFER_HOME/mni/bin) to confirm they work, since there may be some funny interaction with VMWare (but I obviously don't know this just yet). Nick The error is as follows: #@# Nu Intensity Correction Sat Aug 12 09:24:33 BST 2006 mri_nu_correct.mni --i orig.mgz --o nu.mgz --n 2 /mnt/d/freesurfer/subjects/sub18/mri /mnt/d/freesurfer//bin/mri_nu_correct.mni --i orig.mgz --o nu.mgz --n 2 nIters 2 $Id: mri_nu_correct.mni,v 1.3 2005/12/08 01:27:21 greve Exp $ Linux localhost.localdomain 2.6.15-1.1830_FC4 #1 Thu Feb 2 17:23:41 EST 2006 i686 athlon i386 GNU/Linux Sat Aug 12 09:24:33 BST 2006 Setuid/gid script is writable by world. tmpdir is ./tmp.mri_nu_correct.mni.27966 /mnt/d/freesurfer/subjects/sub18/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.27966/nu0.mnc mri_convert orig.mgz ./tmp.mri_nu_correct.mni.27966/nu0.mnc Can't find the talairach xform '/mnt/d/freesurfer/subjects/sub18/mri/transforms/talairach.xfm' Transform is not loaded into mri reading from orig.mgz... Talairach transform /mnt/d/freesurfer/subjects/sub18/mri/transforms/talairach.xfm does not exist ... Cannot load tal xfm file /mnt/d/freesurfer/subjects/sub18/mri/transforms/talairach.xfm TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, -1.46282e-09) j_ras = (7.41336e-09, 0, -1) k_ras = (0, 1, 0) writing to ./tmp.mri_nu_correct.mni.27966/nu0.mnc... -------------------------------------------------------- Iteration 1 Sat Aug 12 09:24:42 BST 2006 nu_correct - clobber ./tmp.mri_nu_correct.mni.27966/nu0.mnc ./tmp.mri_nu_correct.mni.27 966/nu1.mnc Setuid/gid script is writable by world. ERROR: nu_correct Linux localhost.localdomain 2.6.15-1.1830_FC4 #1 Thu Feb 2 17:23:41 EST 2006 i686 athlon i386 GNU/Linux recon-all exited with ERRORS at Sat Aug 12 09:24:42 BST 2006

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problem with mris_anatomical_stats
by Abdel Douiri 17 Aug '06

17 Aug '06

Hi all, I will be grateful if someone can tell me what going wrong in the following problem: When running "recon-all -autorecon3" the program stop with error exactly in the "mris_anatomical_stats" cmd stage and I have the following error: mris_anatomical_stats -mgz -f ../stats/lh.aparc.stats -b -a ../label/lh.aparc.annot -c ../stats/aparc.annot.ctab 01_00 lh computing statistics for each annotation in ../label/lh.aparc.annot. reading volume .mgz... zcat: /home/samba/user/douiri/freesurfer/subjects/01_00/scripts/.mgz.gz: No such file or directory mghRead(/home/samba/user/douiri/freesurfer/subjects/01_00/scripts/.mgz, -1): read error mris_anatomical_stats: could not read input volume .mgz INFO: assuming MGZ format for volumes. Linux img-179 2.6.16.22 #2 SMP Mon Jun 26 15:49:31 BST 2006 i686 unknown unknown GNU/Linux recon-all exited with ERRORS at Tue Aug 15 20:52:49 BST 2006 Thanks A

3 5

error message regarding mri_ca_register_
by Chacko Cherian 17 Aug '06

17 Aug '06

Hello all, I got this error message while running one of my subjects: ERROR: mri_ca_register with non-zero status Linux ernie 2.6.17.1 #4 PREEMPT Sat Aug 5 09:35:33 MST 2006 i686 pentium4 i386 GNU/Linux recon-all exited with ERRORS at Mon Aug 14 09:35:29 MST 2006 Does anyone knw wat this could possibly mean? THanks in advance. Chacko Cherian.

2 3

wm and pial edits
by Dziobek, Isabel 17 Aug '06

17 Aug '06

Dear All, I have two short questions concerning edits to the wm and pial surface. 1. if I make edits to both wm and pial surface, can I rerun autorecon2 adding the -wm and -pial flags in one command (i.e. recon-all -autorecon2-wm -autorecon2-pial -s subjname)? 2. I did save as a jpg the inflated surfaces before making edits to the wm and pial surfaces. After rerunning autorecon2 the new inflated surfaces look the same as the old ones (although I see with "tkmedit brainmask.mgz lh.white that my edits were accepted and used to construct differnt wm and pial surfaces). Should I have erased the old inflated surfaces before editing and rerunning? Thanks a lot and regards from Berlin, Isabel

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