Freesurfer

freesurfer@nmr.mgh.harvard.edu

17 participants
30086 discussions

Freesurfer Color LUT & Saving ROIs
by Vy Dinh 03 Jan '11

03 Jan '11

Dear Freesurfer experts, Is there a way to save out ROIs for all the regions listed in the Freesurfer LUT? I've found posts and tutorials for saving multiple labels from an annotation file, saving an annotation file from multiple labels, and saving rois via the GUI. However, I don't quite understand how Freesurfer comes up with the labels from the LUT. To come up with the annotation file from the LUT, I tried: (while in Freesurfer/subjects/) >>mris_label2annot --subject SUBID/ --hemi lh --ctab ../../FreeSurferColorLUT.txt --a test --ldir annot_test but get the error message: subject 00303226_1/ hemi lh SUBJECTS_DIR /Applications/fmri_progs/freesurfer/subjects ColorTable annot_test/lh.ctx-lh-unknown.label AnnotName annot_test/lh.ctx-lh-bankssts.label nlables 5003 Loading /Applications/fmri_progs/freesurfer/subjects/00303226_1//surf/lh.orig No such file or directory mris_label2annot: could not open label file annot_test/lh.Unknown.label No such file or directory ERROR: reading annot_test/lh.Unknown.label Any suggestions would be much appreciated. Thanks, Vy T.U. Dinh Research Assistant, Neurological Sciences Rush University Medical Center Phone: (312) 563-3853 Fax: (312) 563-4660 Email: Vy_dinh(a)rush.edu<mailto:Vy_dinh@rush.edu>

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Small bug in mri_probedicom
by Inge Amlien 03 Jan '11

03 Jan '11

Hi, trying to chuck together a script to do consistency checking for when our scans get off the scanner using mri_probedicom with the --compare flag. There is a small bug with the tag for software version, the program reports the tag for model twice. The tag for software version I believe should be (18,1020). eg. 0 Manufacturer (8,70) SIEMENS SIEMENS 1 Model (8,1090) Avanto Avanto 2 Software Version (8,1090) Avanto Avanto Merry xmas! Inge Amlien University of Oslo --------------------------------------------------------------------- Build stamp: freesurfer-Linux-centos5_x86_64-stable-pub-v5.0.0 RedHat release: Red Hat Enterprise Linux Client release 5.5 (Tikanga) Kernel info: Linux 2.6.18-194.26.1.el5 x86_64 cmdline: mri_probedicom --compare 1.IMA 2.IMA

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mri_vol2surf --cortex and --mask flags appear ineffective
by Michael Waskom 03 Jan '11

03 Jan '11

Hey developers, It seems as if the --cortex and --mask flags for mri_vol2surf are not doing anything. E.g., if I use the exact same command line: mri_vol2surf --hemi rh --o rh.w-cortex.nii.gz --out_type niigz --reg register.dat --reshape --projfrac-avg 0 1 .1 --mov cope2.nii.gz --cortex With and without "--cortex" and then diff the output, they are identical. When you load the overlay in tksurfer, the medial wall has values that are not 0. Here's my bugr data: FREESURFER_HOME: /software/Freesurfer/5.0.0 Build stamp: freesurfer-Linux-centos5_x86_64-stable-pub-v5.0.0 Debian version: squeeze/sid Kernel info: Linux 2.6.31-22-generic x86_64 Best, Mike

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Whole Surface SNR Calculation for Individual Functional Runs
by Adam Nitenson 03 Jan '11

03 Jan '11

Hello Freesurfers, We are beginning to perform QC on our subjects and want to look at signal to noise ratio. I've taken a look at the fsnr.nii overlay files, but we would like to be able to calculate a whole surface value for SNR for each functional run of each subject, so that we can exclude runs if that SNR values falls below our designated threshold. Is there a way to accomplish this? Thanks, Adam Nitenson, B.S. Brain Genomics Lab Massachusetts General Hospital

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spikedet-sess buglet & solution
by Sebastian Moeller 03 Jan '11

03 Jan '11

Dear All I just noticed that spikedet-sess (for both FS 4.5 and 5.0) will error out if the mystudy/log directory does not yet exist. I think that would be easy to fix by including the following after line 72: if !(-e ./log) then mkdir -p ./log endif Best Sebastian -- Sebastian Moeller telephone: 626-807-5242 / 626-395-6523 / 626-395-6616 fax: 626-395-8826 German GSM: 0 15 77 - 1 90 31 41 US CDMA: + 1 - 626 - 807 - 5242 moeller(a)caltech.edu Division of Biology MC 114-96 California Institute of Technology 1200 East California Boulevard CA 91125, Pasadena USA

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Postdoctoral Fellowship: Multimodal Neuroimaging -MGH/Harvard Medical School
by sheraz＠nmr.mgh.harvard.edu 03 Jan '11

03 Jan '11

Postdoctoral Fellowship: Multimodal Neuroimaging Description: A postdoctoral position pursuing multimodal imaging 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 and MIT. There is a second location at a clinical site, the MGH-affiliated Lurie Family Center for Autism, where we have a 128 lead EGI EEG in a shielded room as well as a photogrammetry machine and autonomic monitoring equipment, and will shortly have a near-infrared tissue spectrometer (NIRS) machine. The programs emphasis is on pathophysiologically oriented brain research and application of advanced imaging acquisition and analysis techniques to neurological and sensory aspects of autism spectrum disorders. Emphasis will be on MRI (DTI, spectroscopy, morphometry, ASL), on co-registering EEG and MEG with MRI, and on studying neurovascular coupling with EEG and NIRS. This position will involve analysis of existing multimodal imaging data and collection of new data. 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. The age range of our subjects is primarily from early infancy to mid-adolescence, with some additional studies including young adults. An ample opportunity will also be provided to the candidate to self-explore and lead research. Requirements: Candidates must have PhD in neuroscience, physics, biomedical engineering, electrical engineering, computer science or other related fields. Candidates without this training and experience need not apply. Prior experience in MRI analysis and EEG signal processing is required. 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 and statement of interest addressing background and specific pertinence of the candidates interest to Dr. Martha R. Herbert at mherbert1(a)partners.org and cc transcend(a)partners.org. Applications will be considered until the position is filled.

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(no subject)
by FIDEL ALFARO ALMAGRO 02 Jan '11

02 Jan '11

Happy holidays for those who celebrate it today, Hi. Is there any documentation on how to use mri_mark_temporal_lobe application and what is its output? I cannot find any. Thanks in advance.

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cortical thickness of a ROI
by angela.favaro＠unipd.it 02 Jan '11

02 Jan '11

Dear all, I have not received any advice about this point. Can somebody help me? thank you! I followed the instructions found in Freesurfer tutorials ('cortical thickness of a volume-defined ROI'). However, in the point 4 of the procedure I am not able to change the --reshape default. My run is: mri_surf2surf --s subj001 --trgsubject fsaverage --hemi rh --sval rh.thickness --tval rh.thickness.fsaverage.mgh --reshape-factor 7 but it continues to create (like default) a reshape with 6. For this reason, I think, the following command: mri_segstats --seg $SUBJECTS_DIR/rh.fsaverage.mask21.mgh --in rh.thickness.fsaverage.mgh --sum segstats-mask21.txt give: ERROR: dimension mismatch between input volume and seg input 27307 1 6 seg 23406 1 7 What can I do to solve this problem? Thank you for your help! Angela Angela Favaro, MD, PhD, MSc Psychiatric Clinic Department of Neurosciences via Giustiniani 3 35128 Padova Italy

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Interpreting results from Qdec
by Gallen, Courtney (NIH/NIDA) [F] 02 Jan '11

02 Jan '11

Hi, I'm currently running analyses in Qdec and have identified areas that show significant effects in my contrasts. I have two questions related to interpreting these results. 1. How can you interpret the effect in each "blob?" (i.e., which group has a greater cortical surface area, etc.). Right now, all I know is that there is an effect in certain areas. Can you export this data to get means and standard errors? 2. Is there a way to localize where these effects are? E.g., a tool that tells you this effect is located in __ area of the brain? Thanks in advance Courtney Courtney Gallen Post-baccalaureate IRTA Neuroimaging Research Branch National Institute on Drug Abuse (IRP) 251 Bayview Blvd Suite 200 Baltimore, MD 21224 Tel: (443) 740-2631

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Smoothing fwhm.dat
by Joana Braga Pereira 02 Jan '11

02 Jan '11

Dear all, I have a question regarding smoothing in qdec. >From what i've understood from previous emails, for monte carlo simulations qdec calculates the best smoothing for your data set, saving it in the file fwhm.dat. How does it calculate this smoothing? Many thanks, Joana

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