Freesurfer July 2005

freesurfer@nmr.mgh.harvard.edu

39 participants
68 discussions

Question
by Wan Park 26 Sep '06

26 Sep '06

Hello, my name is Wan Park and I am working at Columbia University. After converting General Electric DIACOM files into COR, I go to the Setup Structural Scans. There I set the Structural Scan Dir and then Convert/Average. After that, Start the Process Volume, but it seems that there is a problem when it tries to strip the skull. i receive this message: Images (brain): /Users/../Volumes/ste/freesurfer/subjects/scott/mri/brain/COR-001.. not found ... strip skull first So I go to see the logs and I find this: /Users/wanpark/Desktop/FreeSurfer/freesurfer/bin/Darwin/mri_normalize /Users/../Volumes/stem/freesurfer/subjects/scott/mri/orig /Users/../Volumes/stem/freesurfer/subjects/scott/mri/T1 reading from /Users/../Volumes/stem/freesurfer/subjects/scott/mri/orig... normalizing image... 3d normalization pass 1 of 2 building Voronoi diagram... performing soap bubble smoothing... 3d normalization pass 2 of 2 building Voronoi diagram... performing soap bubble smoothing... writing output to /Users/../Volumes/stem/freesurfer/subjects/scott/mri/T1 3D bias adjustment took 3 minutes and 23 seconds. Command Finished /Users/wanpark/Desktop/FreeSurfer/freesurfer/bin/Darwin/mri_watershed /Users/../Volumes/stem/freesurfer/subjects/scott/mri/T1 /Users/../Volumes/stem/freesurfer/subjects/scott/mri/brain ************************************************************ The input file is /Users/../Volumes/stem/freesurfer/subjects/scott/mri/T1 The output file is /Users/../Volumes/stem/freesurfer/subjects/scott/mri/brain If this is incorrect, please exit quickly the program (Ctl-C) *************************WATERSHED************************** preflooding height equal to 25 percent Sorting... first estimation of the COG coord: x=125 y=148 z=132 r=54 first estimation of the main basin volume: 693155 voxels ******************************************************** ******************************************************** ******************************************************** White matter intensity 0 is lower than CSF intensity 26. Please examine input images. Will terminate ... ******************************************************** ******************************************************** ******************************************************** ************************************************************** MRIstipSkull failed. ************************************************************** Command Finished Could you tell me what's wrong? Thanks, Wan Park

4 3

Overlay on cortical surface
by Arvind Gururajan 01 Aug '05

01 Aug '05

� Hello all, I was wondering if it possible to overlay functional data on to (pre-generated)cortical surface? Does freesurfer provide an option to functional/surface registration( I dont have any .cor data instead only .orig)? Could anyone please point out how this could be done? Thanks, Arvind Gururajan

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anatomical_stats
by Fornito, Alexander 30 Jul '05

30 Jul '05

Hi, Is there anyway to print the output of mri_anatomical_stats to a text file? Thanks, Alex

2 1

problem with make_average_surfaces script
by Glenn Lawyer 29 Jul '05

29 Jul '05

Hi, When I run make_average_surface, the script fails on line 117. The line in the script is cp ${FREESURFER_HOME}/average/surf/${hemi}.sphere.reg . The error is "file not found" Should the line read cp ${FREESURFER_HOME}/subjects/average7/surf/${hemi}.sphere.reg . instead? It seems obvious to me, but thought it better to double-check I am using the 20040218 version of freesurfer, which has the following in the ${FREESURFER_HOME}/average directory: [shell] ls /usr/local/freesurfer/average/ lh.atlas2002_simple.gcs rh.atlas2002_simple.gcs rigidly_aligned_brain_template.tif lh.average.tif rh.average.tif talairach_mixed.gca lh_trans_toSulc.gcs rh_trans_toSulc.gcs tissue_parms.txt Thanks, +glenn -- I want to go farther, farther! A. E. L. > Glenn Lawyer < > +352 061 967 244 < > Instituttgruppe for psykiatri < > Postboks 1130 Blindern < > 0318 Oslo < < http://folk.uio.no/davidgl > <><><><><><><><><><><><><><><><><:)

2 1

difficultly generating talairach.m3z
by Elizabeth Fenstermacher 29 Jul '05

29 Jul '05

Hello All, One of our collaborators is trying to generate the talairach.m3z and is running into great difficulties doing so. It seems like the only necessary input is the talairach.xfm, but even after running stage2 independently a second time it did not generate? Has anyone every encountered this difficulty? They are trying to actually generate it by today in order to get some eTIV volumes for a paper that is being submitted, so please let me know soon! Thanks Eliz

2 3

can't seem to source dev env
by Tamara Knutsen 29 Jul '05

29 Jul '05

/usr/local/freesurfer/nmr-dev-env: No such file or directory. is anyone else getting this error this morning? i already rebooted my computer...not sure what else it could be. thanks, tamara

2 1

recon-all error
by Colleen Kristen Tuffy 28 Jul '05

28 Jul '05

Hi FreeSurfer Gurus, I recently moved from using a linux-based FreeSurfer to one of the newer Darwin distributions. I've been following the tutorial at http://surfer.nmr.mgh.harvard.edu/docs/ftp/pub/docs/fsTutorial/morphAndReco…, but my cortical reconstruction was failing on -autorecon2 with the following error: --------------------------------------------- Intensity Normalization2 Thu Jul 14 23:51:48 PDT 2005 /Volumes/Storage/data/freesurfer/subjects/clda/mri mri_normalize -mask brain nu.mgz T1.mgz reading from nu.mgz... corRead(): can't open file /Volumes/Storage/data/freesurfer/subjects/clda/mri/brain/COR-.info mri_normalize: could not open mask volume brain. using MR volume brain to mask input volume... ERROR: mri_normalize exited with non-zero status recon-all exited with errors at Thu Jul 14 23:51:54 PDT 2005 ============================================= So I installed a newer recon-all from Doug's outgoing ftp directory (timestamp 7/26/05) that Russ Poldrack recommended. This one crashed (seg fault) after initial inflation, during topology correction, I think. I have attached a copy of the most recent log file. I am running panther on a G5 with two 2.5 GHz CPUs and 4 GB of memory. Please let me know what other information you might need. Thanks for any advice, Colleen Tuffy Human Neuroimaging Lab University of Oregon

1 0

tkregister2 help
by Tracy Wang 28 Jul '05

28 Jul '05

Hi all, I'm trying to run tkregister2 and I have the following questions: 1. It seems to look for a talairach directory in the main subject directory. Does this mean I have to make/modify this directory each time i want the tkregister2 to manually correct the talairach transform? 2. when tkregister tries to initialize, it tries to read the talairach.xfm file, but it's not finding the talairach.xform. What does this mean? Here is the error output: tkregister2 --mgz --s 000112_vc1552_test --fstal --surf orig surfname set to orig INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume (null) reg file (null) LoadVol 1 $Id: tkregister2.c,v 1.35 2005/07/12 19:50:28 greve Exp $ Diagnostic Level -1 talairach.xfm --------------------- 0.874 -0.173 -0.004 -3.334; 0.188 0.957 -0.284 -10.880; 0.046 0.217 0.760 31.928; 0.000 0.000 0.000 1.000; WARNING: can't find the talairach xform '/Users/Shared/freesurfer/subjects/00112_vc1552_test/mri/transforms/ talairach.xfm' WARNING: transform is not loaded into mri corRead(): can't open file /Users/Shared/freesurfer/subjects/talairach/mri/orig/COR-.info ERROR: could not read /Users/Shared/freesurfer/subjects/talairach/mri/orig as 0 Thanks for any assistance! Tracy Wang Research Assistant Cognitive Neuroscience Laboratory Washington University Department of Psychology, Campus Box 1125 One Brookings Drive St. Louis MO 63130-4899 314-935-5019 twang(a)artsci.wustl.edu

3 5

more on make_average_surface
by Glenn Lawyer 28 Jul '05

28 Jul '05

Hi, Sorry, another question on make_average_surface. after averaging the curvatures and the surfaces, the script moves to the surf directory: cd ${SUBJECTS_DIR}/${average_subject}/surf However, it does not return to the top directory before the second iteration of the foreach hemi (lh rh) loop. This gives me the following output when processing the rh: MRISwriteCurvature: could not open ../average/surf/rh.avg_sulc This suggests that MRISwriteCurvature expects to be one directory below the subjects directory. Finally, my question: Would it be better to modifiy the script so that the first command in the foreach hemi (lh rh) loop is cd ${SUBJECTS_DIR}/${average_subject} ? +glenn -- I want to go farther, farther! A. E. L. > Glenn Lawyer < > +352 061 967 244 < > Instituttgruppe for psykiatri < > Postboks 1130 Blindern < > 0318 Oslo < < http://folk.uio.no/davidgl > <><><><><><><><><><><><><><><><><:)

1 0

Average Brain atlas
by Tracy Wang 27 Jul '05

27 Jul '05

Hi all, I was just wondering what the difference is between the talairach_mixed.gca, talairach_mixed_a1_new_b.gca and talairach_mixed_new_b.gca Thanks! Tracy Wang Cognitive Neuroscience Laboratory Washington University Department of Psychology, Campus Box 1125 One Brookings Drive St. Louis MO 63130-4899 314-935-5019 twang(a)artsci.wustl.edu

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Freesurfer July 2005