Freesurfer

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30088 discussions

Re: [Freesurfer] trac-all -path errors
by Moiyadi, Ammar 01 Aug '11

01 Aug '11

Hi, I am also getting the error where the txt files cannot be opened because they were not created beforehand. Where does the trac-all -prior step take place? Does it appear within the trac-all -prep script? Thank you, Ammar Moiyadi, BS Professional Research Assistant Department of Psychiatry University of Colorado Anschutz Medical Campus 303-724-5490 ________________________________________ From: freesurfer-bounces(a)nmr.mgh.harvard.edu [freesurfer-bounces(a)nmr.mgh.harvard.edu] On Behalf Of freesurfer-request(a)nmr.mgh.harvard.edu [freesurfer-request(a)nmr.mgh.harvard.edu] Sent: Friday, July 29, 2011 10:00 AM To: freesurfer(a)nmr.mgh.harvard.edu Subject: Freesurfer Digest, Vol 89, Issue 99 Send Freesurfer mailing list submissions to freesurfer(a)nmr.mgh.harvard.edu To subscribe or unsubscribe via the World Wide Web, visit https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer or, via email, send a message with subject or body 'help' to freesurfer-request(a)nmr.mgh.harvard.edu You can reach the person managing the list at freesurfer-owner(a)nmr.mgh.harvard.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of Freesurfer digest..." Today's Topics: 1. trac-all -path errors (Ping-Hong Yeh) 2. Re: trac-all -path errors (Priti Srinivasan) ---------------------------------------------------------------------- Message: 1 Date: Fri, 29 Jul 2011 11:09:28 -0400 From: Ping-Hong Yeh <pinghongyeh(a)gmail.com> Subject: [Freesurfer] trac-all -path errors To: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <CAL1NnmP2+KdE5cNMVH4-qhnvSeMeQA7AjQ+cp-qPFtmGv3A+0Q(a)mail.gmail.com> Content-Type: text/plain; charset=ISO-8859-1 Hi, I got the error running "trac-all -path -c configure.txt" ERROR: Could not open ${SUBJECTS_DIR}/$Subject/dlabel/diff/lh.cst_AS_avg33_mni_flt_cpts_5.txt I can only find only image files in the "dlabel/diff" directory, but not text files. Which step(s) create the lh.cst_AS_avg33_mni_flt_cpts_5.txt file? Thanks, Ping ------------------------------ Message: 2 Date: Fri, 29 Jul 2011 11:26:13 -0400 (EDT) From: "Priti Srinivasan" <rspriti(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] trac-all -path errors To: "Ping-Hong Yeh" <pinghongyeh(a)gmail.com> Cc: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <42727.132.183.139.239.1311953173.squirrel(a)mail.nmr.mgh.harvard.edu> Content-Type: text/plain;charset=iso-8859-1 Hi Ping, The text files get created in the trac-all -prior stage. Maybe something went wrong in that step. Is this the case for all the tracts or just for this tract? If you can send us the trac-all.log file under the scripts directory it'll be easier to troubleshoot as to what went wrong. -Priti > Hi, > > I got the error running "trac-all -path -c configure.txt" > > ERROR: Could not open > ${SUBJECTS_DIR}/$Subject/dlabel/diff/lh.cst_AS_avg33_mni_flt_cpts_5.txt > > > I can only find only image files in the "dlabel/diff" directory, but > not text files. > > Which step(s) create the lh.cst_AS_avg33_mni_flt_cpts_5.txt file? > > Thanks, > > Ping > _______________________________________________ > 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 End of Freesurfer Digest, Vol 89, Issue 99 ****************************************** The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

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bbregister
by Michelle Umali 01 Aug '11

01 Aug '11

Hi Bruce, So for the following command: bbregister --s bert --mov func.nii --init-fsl --reg register.dat tkregister2 --mov func.nii --reg register.dat --surf In the case of a retinotopy analysis, which files are register.dat and func.nii? Quoting Bruce Fischl <fischl(a)nmr.mgh.harvard.edu>: [Hide Quoted Text] Hi Michelle Try using bbregister. Cheers Bruce On Jul 31, 2011, at 6:54 PM, Michelle Umali <muu1(a)columbia.edu> wrote: Dear Freesurfers, During my retinotopy analysis, I was getting very strange fieldsign data (blue and red speckles) and my polar and eccentricity data was limited to the occipital pole. It was suggested that I check registration between the functional and anatomical. I was looking up tkregister2 help to figure this out but am still unsure how to register the polar and eccentricity data to the anatomical. Any help would be most appreciated. -Michelle Umali _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

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Need help to run MRI data using Freesurfer in Mac OSx
by joanna floria 01 Aug '11

01 Aug '11

Hello Everyone, We just installed Freesurfer on Mac and the software got installed successfully. But when I am running my data, it just gets stuck in between and shows me the error. The command I used was: /Applications/freesurfer/bin/recon-all-s 002 -i /Users/kashou/Desktop/fMRI/Anesthetics/002/SPGR/MR000000 -all -notal-check The error: /Applications/freesurfer/subjects/002/mri \n talairach_avi --i orig.mgz --xfm transforms/talairach.auto.xfm \n ERROR: mpr2mni305 failed, see transforms/talairach_avi.log Darwin Nasser-Kashous-iMac.local 10.4.1 Darwin Kernel Version 10.4.1: Fri Jul 16 23:04:20 PDT 2010; root:xnu-1504.7.51~1/RELEASE_I386 i386 recon-all -s 002 exited with ERRORS Can anyone please help me out with the error? Thanks, Joanna

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mris_flatten problem
by Oya, Hiroyuki (UI Health Care) 01 Aug '11

01 Aug '11

Dear all, A patch created by mris_flatten looked odd (see attached image) . Any suggestion for this problem? Original patch (before flattening) seems good. Thank you. Hiroyuki ________________________________ Notice: This UI Health Care e-mail (including attachments) is covered by the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521, is confidential and may be legally privileged. If you are not the intended recipient, you are hereby notified that any retention, dissemination, distribution, or copying of this communication is strictly prohibited. Please reply to the sender that you have received the message in error, then delete it. Thank you. ________________________________

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Retinotopy Registration to Anatomical
by Michelle Umali 31 Jul '11

31 Jul '11

Dear Freesurfers, During my retinotopy analysis, I was getting very strange fieldsign data (blue and red speckles) and my polar and eccentricity data was limited to the occipital pole. It was suggested that I check registration between the functional and anatomical. I was looking up tkregister2 help to figure this out but am still unsure how to register the polar and eccentricity data to the anatomical. Any help would be most appreciated. -Michelle Umali

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Postdoctoral Fellowship: Multimodal Neuroimaging -MGH/Harvard Medical School
by sheraz＠nmr.mgh.harvard.edu 31 Jul '11

31 Jul '11

Postdoctoral Fellowship: Multimodal Neuroimaging -MGH/Harvard Medical School Job Description A postdoctoral position is available with the TRANSCEND Research Program (www.transcendresearch.org) at the Martinos Center for Biomedical Imaging in Charlestown, MA (www.martinos.org) which is affiliated with the Massachusetts General Hospital, Harvard Medical School and MIT. We are seeking a candidate with a strong basis in magnetic resonance imaging. Emphasis will be on MRI (DTI, spectroscopy, morphometry, ASL as well as resting state fMRI), and on co-registering MEG with MRI. This position will involve analysis of existing multimodal imaging data and collection of new data. The emphasis of the postdoctoral fellowship will be analysis of existing datasets with secondary activity in piloting data for new studies. It will involve working closely with a multidisciplinary team and with children, and will also involve some research oriented analysis of data collected for clinical purposes. After initial phase-in, ample opportunity will also be provided to the candidate to self-explore and lead research. Datasets to be analyzed include: MRI (including DTI and 1H-spectroscopy) and MEG data on 6-12 and teenage matched autism spectrum and control subjects with phenotyping data MRI data ( (morphometry, DTI, spectroscopy) plus laboratory and phenotyping data) on 70 children with autism plus epilepsy and/or mitochondrial dysfunction, along with one or more overnight EEGs on each patient data from children ages 2-10 with and without autism. Overall objectives: To perform multimodal analyses of research and clinical research data, to develop new approaches for performing these analyses, and to design pipelines for data analysis. To write papers and grants which will be high priorities all along the way and will be actively supported by senior faculty. To take advantage of the world class faculty and facilities of the Martinos Center for Biomedical Imaging to perform the above activities to their maximal potential. The programs emphasis is on pathophysiologically grounded brain research and application of advanced imaging acquisition and analysis techniques to neurological and sensory aspects of autism spectrum disorders. Requirements: Candidates must have PhD in neuroscience, physics, biomedical engineering, electrical engineering, computer science or other related fields. Prior experience in MRI analysis is required. Experience with EEG will be an added advantage. Salary will be consistent with Massachusetts General Hospital, Harvard Medical School policies for Postdoctoral trainees and will range between $45,000 to $55,000 depending upon qualifications and experience. Compensation also includes full staff benefits, including health insurance, and vacation time. Contact: Interested applicants may send a CV to Dr. Martha R. Herbert at mherbert1(a)partners.org and cc transcend(a)partners.org.

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label value 0 in annot file
by Forrest Sheng Bao 31 Jul '11

31 Jul '11

hi, I noticed an interesting thing today. I used read_annotation function in matlab to load an .annot file, i.e., [Vertexes,Label,Colortable]=read_annotation(AnnotFile); But some labels in Labels were 0's. They did not appear in the 5th column of Colortable.table. And 0 was the only label that i couldn't find in the 5th column of Colortable.table. All other labels were fine. Any idea what the cause of 0's as labels might be? Cheers, Forrest

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mri_robust_register registration file
by Kami Koldewyn 29 Jul '11

29 Jul '11

Hi All, I was trying to use the registration file that is created by mri_robust_register with mri_vol2vol - but it is in a different format than registration files created by bbregister or tkregister. Is it fsl format? Is there an easy way to use this registration file with other freesurfer functions (like mri_vol2vol)? Thanks very much, -kami --------------------------------------------------------------- Kami Koldewyn, PhD. McGovern Institute for Brain Research MIT, Building 46 Room 4141 (Kanwisher Lab) Cambridge, MA 02139 kamik(a)mit.edu

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Intensity Normalization error
by Antonella Kis 29 Jul '11

29 Jul '11

Dear Bruce, 1). What is the minimum value/the range for the intensity in order to be considered acceptable? I know the value in wm should be very close to 110 but what is the accepted value closed to this? If is not exactly 110 (foe example if is 101) do I need to add control points in order to normalize the intensity and get the value 110? 2). I was trying to create a table with my statistical results (the cortical thickness and the number of vertices) and I was running: aparcstats2table --hemi lh --subjects bert NPI001 --meas thickness -t lh.aparcstas.THICKNESS.txt When I tried to also get the number of vertices a table by running: aparcstats2table --hemi lh --subjects bert NPI001 --meas vertices -t lh.aparcstas.VERTICES.txt I got the following error: aparcstats2table: error: option --measure: invalid choice: 'Voxels' (choose from 'area', 'volume', 'thickness', 'thicknessstd', 'meancurv') I Why I don't have an option for the no. of vertices? Can I get a table with both data: cortical thickness and no. of vertices? Many thanks, Antonella

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Problems at mri_em_register
by Tali Swisher 29 Jul '11

29 Jul '11

Hi all, I'm running FreeSurfer v4.0.5 and keep getting the following error: ####################################### #------------------------------------- #@# EM Registration Thu Jul 28 16:09:51 EDT 2011 /home/pnlstaff/freesurfer/subjects/ucsd_20110726/mri mri_em_register -mask brainmask.mgz nu.mgz /share/apps/freesurfer4.0.5/average/RB_all_2008-03-26.gca transforms/talairach.lta using MR volume brainmask.mgz to mask input volume... reading 1 input volumes... logging results to talairach.log reading '/share/apps/freesurfer4.0.5/average/RB_all_2008-03-26.gca'... average std = 6.9 using min determinant for regularization = 4.7 0 singular and 1812 ill-conditioned covariance matrices regularized reading 'nu.mgz'... freeing gibbs priors...done. bounding unknown intensity as < 14.9 or > 790.2 total sample mean = 84.0 (478 zeros) ************************************************ spacing=8, using 2185 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 2185, passno 0, spacing 8 GCAhistoScaleImageIntensities: could not find wm peak resetting wm mean[0]: 102 --> 107 resetting gm mean[0]: 64 --> 64 input volume #1 is the most T1-like using real data threshold=29.0 using (130, 118, 99) as brain centroid... mean wm in atlas = 107, using box (130,93,92) --> (129, 143,105) to find MRI wm before smoothing, mri peak at 0 after smoothing, mri peak at 0, scaling input intensities by inf Linux compute-4-7.local 2.6.9-34.ELsmp #1 SMP Fri Feb 24 16:56:28 EST 2006 x86_64 x86_64 x86_64 GNU/Linux recon-all exited with ERRORS at Thu Jul 28 16:11:08 EDT 2011 Any ideas? Thanks! -- Talis M. Swisher, BA Research Assistant Psychiatry Neuroimaging Laboratory Harvard Medical School, Brigham and Women's Hospital 1249 Boylston St, 3rd Floor Boston, MA 02215 Office: (617) 525-6119 Cell: (336) 577-5071 Fax: (617) 525-6150

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