Freesurfer July 2008

freesurfer@nmr.mgh.harvard.edu

55 participants
74 discussions

deflate compression support
by Jan Kalkus 09 Jul '08

09 Jul '08

Hi everyone, I'm trying to make a monkey template using mris_make_template. So far, every time I run the mris_make_template, I get this error: [jkalkus:~] work% /Volumes/Data/monkey_surface_data/mris_make creating new parameterization... processing subject bu_edited (1 of 1) reading spherical surface /Volumes/Data/monkey_surface_data//bu_edited/ surf/rh.sphere... curvature mean = 0.000, std = 1.000 computing parameterization for surface /Volumes/Data/ monkey_surface_data//bu_edited/surf/rh.inflated.H... curvature mean = 0.000, std = 0.592 computing parameterization for surface /Volumes/Data/ monkey_surface_data//bu_edited/surf/rh.sulc... curvature mean = -0.100, std = 1.787 computing parameterization for surface /Volumes/Data/ monkey_surface_data//bu_edited/surf/rh.smoothwm... writing updated template with 1 subjects to monk_temp0.tif... monk_temp0.tif: Deflate compression support is not configured. TiffWrite: TIFFWriteScanline returned error I am working on an intel MacBook with OS X 10.5.4 and I'm running freesurfer-Darwin-leopard-i686-stable-pub-v4.0.5. Has anyone else encountered this problem? Does anyone have any suggestions? Thanks - Jan Kalkus

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seg edits
by Juranek, Jenifer 09 Jul '08

09 Jul '08

Running Freesurfer v4.0.5 on RHEL5 linux system. General Question: after using the "Edit Segmentation" tool and saving edits by overwriting the aseg.mgz file generated during $recon-all -autorecon-all...which command should I pass to re-enter the analysis pipeline at the most appropriate spot? I understand that after edits to the wm.mgz file, it is fine to re-enter the pipeline with $recon-all -autorecon2-wm -autorecon3. But unable to find much in the Wiki wrt *aseg.mgz* edits and subsequent re-processing (other than "how to" accomplish edits). Specific info: Unusual case with enlarged lateral ventricles (particularly posteriorly). Review of the aseg.mgz after completing $recon-all -autorecon-all indicated that the right lateral ventricle (posterior portion) was partially incorrectly labeled in a range of slices (COR: 86-48) with a "cocktail" of labels, including the following: Right-Lateral-Ventricle; Right-Cerebral-White-Matter; Right-Cerebral-Cortex; None; WM-hypointensities. After editing *wm.mgz* to fill-in missing voxels in the problem areas and re-running $recon-all -autorecon2-wm -autorecon3, segmentation labels of problem areas still required edits. After using the "Edit Segmentation" tool, I have now saved my edits by overwriting *aseg.mgz*. So which command should I pass to re-enter the pipeline? Many Thanks for any advice you can provide. Jenifer

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error message of mris_register
by Deniz KATIRCIOGLU 09 Jul '08

09 Jul '08

Hi, We're getting an error message saying: $FREESURFERHOME/average/rh.average.curvature.filled.buckner40.tif : Not a TIFF file, bad magic number 65535 (0xffff). MRISPread($FREESURFERHOME/average/rh.average.curvature.filled.buckner40.tif): could not open file No such file or directory mris_register: could not open template file $FREESURFERHOME/average/rh.average.curvature.filled.buckner40.tif No such file or directory while running the command: mris_register -curv surf/rh.sphere $FREESURFERHOME/average/rh.average.curvature.filled.buckner40.tif surf/rh.sphere.reg How can we get thru this, or, why is that happening? Thanks in advance... Deniz KATIRCIOGLU METU, Turkey

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Talairach coordinates
by Feng-Xian Yan 08 Jul '08

08 Jul '08

Hi, I have some problems about surface coordinates. After running the qdec and analyzed my data(cortical thickness), I display a plot of the data for a particular vertex by left-clicking on a point while holding down the Ctrl key. It shows a plot and its plot window shows this vertex's *surface coordinates.* 1) Does the surface coordinates differ from Talairach coordinates? 2) If yes, can I translate the surface coordinates to Talairach coordinates? And how do I do? Does Freesurfer have some methods to do that? Thank you in advance. Feng-Xian

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volume of Heschl's gyrus
by Woo-Suk, Tae 08 Jul '08

08 Jul '08

.Bold { font-weight: bold; } .Title { font-weight: bold; font-size: 18px; color: #cc3300; } .Code { border: #8b4513 1px solid; padding-right: 5px; padding-left: 5px;color: #000066; font-family: 'Courier New' , Monospace;background-color: #ff9933; } HiWhat is the exact term of heschl's gyrus in the lists of rh_lt.aparc.a2005s.stats?Woo-Suk, TaeChuncheon, Korea

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"Deflate compression support is not configured"
by Mark A. Pinsk 07 Jul '08

07 Jul '08

Similar to a thread below, I'm having trouble running mris_make_template. First time I'm trying mris_make_template. On a Mac Pro, running 10.5.4, running FS 4.0.5, installed libtiff from darwinports.... mris_make_template rh sphere monk monk1.tif ..... monk1.tif: Deflate compression support is not configured. TiffWrite: TIFFWriteScanline returned error

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Optseq2 and Mixed ER
by Michelle Umali 07 Jul '08

07 Jul '08

Dear Freesurfer Support, I am using optseq2 to design my experiment and was wondering whether ER or Mixed Block-ER would work best. Here's a brief description of my expt: I am looking at the effects of exposure to emotional stimuli on contrast sensitivity (gabor patches) during Easy and Challenging types of visual search. 2 runs of 3 Emotion Types x 3 Contrast levels during Easy search 2 runs of 3 Emotion Types x 3 Contrast levels during Challenging search All runs are 8 minutes long with 20 trials per condition. Is ER or Mixed Block-ER more appropriate, and if the latter, how would that be entered? Thank you so much, Michelle

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orientation problem when converting from SPM .nii format to bshort
by Leila Reddy 07 Jul '08

07 Jul '08

Hi, I am trying to convert SPM5 .nii files into bshort and I used the following command: mri_concat fkoch-0007*.nii --o bold/007/fspm_000.bshort The command seems to work in that I have a bunch of bshort files in my bold/007 directory but when I try to view the slices (using sliceview-sess for example) the slices are all upside-down (rotated by 180 degrees). Is there an option I can use to get them the right side up? I'm using FS v3 on an IntelMac and my version of mri_concat is stable3. Here is the output of bugr: --------------------------------------------------------------------- FREESURFER_HOME: /Applications/freesurfer Build stamp: freesurfer-Darwin-tiger-i686-stable-pub-v3.0.5 Kernel info: Darwin 8.11.1 i386 --------------------------------------------------------------------- Thanks, Leila

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documentation of the Freesurfer output and directory structure?
by Turner, Jessica 02 Jul '08

02 Jul '08

Hi experts-I have to document for some non-Freesurfer users what is in all the Freesurfer 3.05 subdirectories from an analysis. We have come up with a lot of it from the Wiki pages and tutorials, but there are some things that still aren't clear (what exactly is the bem directory for? What exactly is the mri_nu_correct.mni.log file? Etc.). Is it laid out clearly somewhere? I've seen the pages about which files are created by what process, etc. and it seems like it should say somewhere what these directories and files really are, I'm just missing it. Thanks, Jess ------------------------ Jessica Turner, Ph.D. Project Manager, FBIRN (www.nbirn.net) Department of Psychiatry and Human Behavior University of California, Irvine Phone: (949) 824-3331 Fax: (949) 824-3324

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recon-all fill error
by Bill Monaco 02 Jul '08

02 Jul '08

Hi, I'm running recon-all in the stable4 FreeSurfer environment and am getting an error at the Fill stage I'm unfamiliar with. When I run this command: recon-all -subjid 065036777_nrecon_stable4 -fill I get this error message: INFO: SUBJECTS_DIR is /autofs/space/jabba_003/users/LONI_nrecon Actual FREESURFER_HOME /autofs/space/windu_006/users/freesurfer_stable4_release/stable4 -rwxrwx--- 1 monaco cagn 270977 Jul 2 08:38 /autofs/space/jabba_003/users/LONI_nrecon/065036777_nrecon_stable4/scripts/recon-all.log Linux luke 2.6.18-53.1.14.el5 #1 SMP Wed Mar 5 11:37:38 EST 2008 x86_64 x86_64 x86_64 GNU/Linux #-------------------------------------------- #@# Fill Wed Jul 2 08:41:06 EDT 2008 /autofs/space/jabba_003/users/LONI_nrecon/065036777_nrecon_stable4/mri mri_fill -a ../scripts/ponscc.cut.log -xform transforms/talairach.lta -segmentation aseg.mgz wm.mgz filled.mgz logging cutting plane coordinates to ../scripts/ponscc.cut.log... INFO: Using transforms/talairach.lta and its offset for Talairach volume ... using segmentation aseg.mgz... reading input volume...done. searching for cutting planes...voxel to talairach voxel transform 0.983 -0.086 0.013 -0.725; 0.056 1.018 0.424 -82.711; -0.042 -0.425 0.943 81.256; 0.000 0.000 0.000 1.000; voxel to talairach voxel transform 0.983 -0.086 0.013 -0.725; 0.056 1.018 0.424 -82.712; -0.042 -0.425 0.943 81.256; 0.000 0.000 0.000 1.000; reading segmented volume aseg.mgz... mri_fill: could not find any points where lh and rh wm are nbrs Linux luke 2.6.18-53.1.14.el5 #1 SMP Wed Mar 5 11:37:38 EST 2008 x86_64 x86_64 x86_64 GNU/Linux recon-all exited with ERRORS at Wed Jul 2 08:41:15 EDT 2008 Thanks for your help! -Bill -- Bill Monaco Research Assistant MGH East - CNY 149 149 13th Street - 2271 Charlestown, MA 02129 617-726-9128

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Freesurfer July 2008