Freesurfer March 2010

freesurfer@nmr.mgh.harvard.edu

101 participants
153 discussions

clusterwise correction error
by lordowen 04 Mar '10

04 Mar '10

Dear Freesurfer experts: We used QDEC to generate the script for clusterwise correction. After 2 days running, we get error message : ERROR: opening /usr/local/freesurfer/subjects/qdec/group_thickness_age_rh/csd/mc-z.abs.2.69.j001-rh-Avg-Intercept-thickness.csd We checked /csd and find the .csd file already there. But in /contrast, there is no results files (i.e., sig.cluster.summary) exist (by fswiki, they should be there). And a /tmp.mri_glmfit-sim-8708 (I assume this is the temporal folder for simulation, right?) exist in the main folder. We need your advise to point out what's the problem and how to solve it. I attached the log file and script file and hope this can help. Thank you very much. -- Best regards -- 杜政昊 Cheng-Hao Tu, PhD Student Laboratory of Integrated Brain Research Department of Medical Research and Education Taipei Veterans General Hospital No.201, Sect.2, Shih-Pai Rd. Taipei Taiwan Email: lordowen(a)ms10.hinet.net or lordowentu(a)gmail.com Tel: +886-2-28712121 ext 3474 Fax: +886-2-28745182

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mri_watershed and mri_make_bem_surfaces
by Andres Felipe Salazar Gomez 04 Mar '10

04 Mar '10

Hello FreeSurfer users, I am using a set of MNE commands (mne_watershed_bem and mne_flash_bem) that call respectively mri_watershed and mri_make_bem_surfaces to create the BEM surfaces. I am having problems when checking one of them, the inner_skull mesh, since in several subjects, when visualized on tkmedit, it appears to be going not along the edge of the gray matter but inside it, specially at the occipital lobe level. Has anyone had a similar problem? How can the inner_skull file be modified? I found an error log file with the following info but I do not know if it is related to the problem. MRISreadVertexPosition(orig): could not open file $SUBJECTS_DIR/$SUBJECT/bem/flash/lh.orig MRISreadVertexPosition(pial): could not open file SUBJECTS_DIR/$SUBJECT/bem/flash/lh.pial I appreciate any help in this matter. Thank you, -- Andrés -- Andres F. Salazar Research Technologist Neuroscience Statistics Research Laboratory asalazar(a)nmr.mgh.harvard.edu 149 13th Street, Room 4005 Charlestown, MA 02129

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Cerebellum volume analysis
by Cindy Eckart 04 Mar '10

04 Mar '10

Dear FreeSurfers, I plan to do a cerebellar volume analysis in a rather large clinical sample and thereto originally aimed to follow the instructions of Makris and colleaugues (2003, 2005). Unfortunatly I was not able to get access to all the necessary software and accordingly I am forced to improvise and find another solution. Thus I have a lot of questions: 1. I learned from the mailing list archive that there already have been several requests concerning that topic and that there also have been some plans for labeling parts of the cerebellum (according to an email from David Salat, 07/09/2008)... have any of this plans been completed yet? Because I certainly do not want to reinvent the wheel ;-) ..... 2. If not.... to keep as close as possible to the procedures described in Makris and colleaugues (2003, 2005), I originally planned to inflate the surface of the cerebellum (they quote in their papers that there might be a way to do that with Freesurfer, when the cerebellum is segmented in its grey and white matter as it is meanwhile implemented in the conventional aseg procedure??); then I wanted to create a cerebellar parcellation atlas according to its gyral and sulcal pattern in a subset of subject and finally hoped to be able to process the rest of my population largely automatically with the help of this new atlas... does this seem reasonable? And do anyone have experience with tasks like that? 3. But then, I learned again from the mailing list archive that surface extraction of the cerebellum is that hampered (due to the comprehensible resolution issues), that it is completely disadvised. Instead it was recommended (if any) to include respective volume labels in the aseg procedure and to do a volumetric analysis. Is this right? And are there any instructions how I could do that? 4.As I do not have any experience in tasks like that and sometimes tend to overrate myself (;-)) do you think that it might in principal be feasible to do a automatic cerebellar volume analysis or would I generally be better of in trying to do it manually? Thank you (again :-)) very much for your advise!! Kind regards Cindy ___________________________________________________________ WEB.DE DSL: Internet, Telefon und Entertainment für nur 19,99 EUR/mtl.! http://produkte.web.de/go/02/

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How to verify cerebellum segmentation
by Gergely Orsi 04 Mar '10

04 Mar '10

Hi all! We have processed 100 subjects with autorecon. I'd like to know how to check the cerebellum segmentation on the subjects. It would be crucial, because the images are a bit dimmer at the lower areas (it's far from the isocenter) and despite the intensity normalisation it still has lower intensity compared to the dorsal part of the cerebellum. After the skull-strip the cerebellum is still intact (the whole cerebellum exists on the images), but I'd like to know wether freesurfer recognised the lower intensity parts or not. Unfortunatly BET in FSL simply cut off these areas, thus our VBM results (showing significan changes at the ventral cerebellum) are compromised. We have measured significant group differences in total cerebellar volume using freesurfer, but we should check the segmentation first, and believe the results later. Could anyone help us in this? And if the segmentation failed, is there any manual method to correct it (by hand), because the whole cerebellum is on the images (despite of the different intensity). And one last question, is it possible to carry out VBM in freesurfer (after checking/correcting the cerebellum if needed, although the intensity difference will still be a big problem in VBM ). Thank you very much. Gergely Orsi

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Re: [Freesurfer] How to verify cerebellum segmentation
by Gergely Orsi 04 Mar '10

04 Mar '10

Dear Bruce, Sorry, the data did not fit to the clipboard. Find it attached. Best regards, Gergely Orsi

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average V1 gm thickness values
by ridatta＠mail.med.upenn.edu 03 Mar '10

03 Mar '10

Hello All, I piped around 70 subjects through freesurfer and the created V1 labels using Hinds and Fischl method. I used these labels to calculate average gm thickness in V1. I am getting around 1.6 mm thickness values with 0.6 standard deviation. Has anyone looked at the values in V1 ? Is that in the range or below ? Please let me know. Thanks Rito

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Error with Talairach Transform and tkregister?
by Janani Dhinakaran 03 Mar '10

03 Mar '10

Hello, I'm running recon-all on a second set of data. It ran smoothly until mpr2mni305 success and then it gave the following: -------------------------------------------- tkregister2_cmdl --mov nu.mgz --targ /usr/local/freesurfer/average/mni305.cor.mgz --xfmout transforms/talairach.auto.xfm --vox2vox talsrcimg_to_711-2C_as_mni_average_305_t4_vox2vox.txt --noedit --reg talsrcimg.reg.tmp.dat tkregister_tcl /usr/local/freesurfer/lib/tcl/tkregister2.tcl Vox2Vox Matrix -0.003 -0.077 0.242 71.612; 0.001 0.055 -0.022 129.085; -0.004 -0.904 1.028 97.306; 0.000 0.000 0.000 1.000; target volume /usr/local/freesurfer/average/mni305.cor.mgz movable volume nu.mgz reg file talsrcimg.reg.tmp.dat LoadVol 0 ZeroCRAS 0 $Id: tkregister2.c,v 1.86.2.12 2009/03/19 22:04:20 greve Exp $ Diagnostic Level -1 INFO: loading target /usr/local/freesurfer/average/mni305.cor.mgz Ttarg: -------------------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; INFO: loading movable nu.mgz Tmov: -------------------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; mkheaderreg = 1, float2int = 0 Computing reg from header (and possibly input matrix) ---- Input registration matrix (computed) -------- -0.003 -0.242 -0.077 35.722; 0.004 1.028 0.904 -15.429; 0.001 0.022 0.055 -5.367; 0.000 0.000 0.000 1.000; --------------------------------------- ---- Input registration matrix -------- -0.003 -0.242 -0.077 35.722; 0.004 1.028 0.904 -15.429; 0.001 0.022 0.055 -5.367; 0.000 0.000 0.000 1.000; Determinant -0.000168945 subject = subject-unknown RegMat --------------------------- -0.003 -0.242 -0.077 35.722; 0.004 1.028 0.904 -15.429; 0.001 0.022 0.055 -5.367; 0.000 0.000 0.000 1.000; register: file talsrcimg.reg.tmp.dat written `talsrcimg_to_711-2C_as_mni_average_305_t4_vox2vox.txt' -> `transforms/talsrcimg_to_711-2C_as_mni_average_305_t4_vox2vox.txt' removed `talsrcimg.4dfp.hdr' removed `talsrcimg.4dfp.ifh' removed `talsrcimg.4dfp.img' removed `talsrcimg.4dfp.img.rec' removed `talsrcimg.hdr' removed `talsrcimg.img' removed `talsrcimg.mat' removed `talsrcimg.reg.tmp.dat' removed `talsrcimg_g11.4dfp.hdr' removed `talsrcimg_g11.4dfp.ifh' removed `talsrcimg_g11.4dfp.img' removed `talsrcimg_g11.4dfp.img.rec' removed `talsrcimg_to_711-2C_as_mni_average_305_t4' -------------------------------------------- Wed Mar 3 13:43:27 GMT 2010 talairach_avi done cp transforms/talairach.auto.xfm transforms/talairach.xfm #-------------------------------------------- #@# Talairach Failure Detection Wed Mar 3 13:43:28 GMT 2010 /home/s0964091/Desktop/Newdata/JS/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0000, pval=0.0000 < threshold=0.0050) Linux CRIC-0012 2.6.31-19-generic #56-Ubuntu SMP Thu Jan 28 02:39:34 UTC 2010 x86_64 GNU/Linux recon-all exited with ERRORS at Wed Mar 3 13:43:28 GMT 2010 I don't understand this error. Please let me know what I can do to fix this. Thank you Jan -- I am the Sun, I know no darkness.

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Volumes of four major cortical lobes
by caoaize 03 Mar '10

03 Mar '10

Hi, Bruce, We want calculate the four major cortical lobe volumes, i.e. frontal, parietal, temporal, and occipital, to see the relationship between them and some ROIs. I did fully run recon-all, but not clear which file should be used and what cortical areas should be included in these four lobes seperatively. May you please give me some instruction? Thanks. Aize _________________________________________________________________ MSN十年回馈，每位用户可免费获得价值25元的卡巴斯基反病毒软件2010激活码，快来领取！ http://kaba.msn.com.cn/?k=1

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autorecon with one image
by ayumi＠haskins.yale.edu 02 Mar '10

02 Mar '10

Hi, I am analyzing structural data (analyze format). How can I run autorecon with one image? A similar question was already asked on 14 Jun 2008, but I couldnt find how to run it. Thanks, Amy

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Application of Default Surface Based Registration to Surfaces Other than the Sphere
by Matt Glasser 02 Mar '10

02 Mar '10

Hi, I am wondering if there is a way to apply the default surface based registration that is done during recon-all to surfaces other than the sphere so that the nodes are all lined up? I am wanting to have registered white matter surfaces that I can map data from the volume to the surface to and then average across subjects. Thanks, Matt.

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Freesurfer March 2010