Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30088 discussions

create summary images
by McLean John (NHS Greater Glasgow & Clyde) 14 Apr '11

14 Apr '11

I'd like to create some summary images (.tiff, .png ) so that I can quickly inspect subcortical structure segmentation quality on a large number of subjects. I know I can open tkmedit and extract a series of tiff images, I've also been playing with Slicer3 but again I have to load the data for each subject. I'd also like to hone in on particular structures, for example, to extract images only showing the hippocampus (whole segmentation or outline) on the T1 3D backdrop, does anything exist in Freesurfer to do this from the command line? Essentially I'm looking for something similar to the first_roi_slicerdir command in FSL as I found this a really quick way of visually checking segmented data. Any advice around this would be a great help, Thanks John ******************************************************************************************************************** This message may contain confidential information. If you are not the intended recipient please inform the sender that you have received the message in error before deleting it. Please do not disclose, copy or distribute information in this e-mail or take any action in reliance on its contents: to do so is strictly prohibited and may be unlawful. Thank you for your co-operation. NHSmail is the secure email and directory service available for all NHS staff in England and Scotland NHSmail is approved for exchanging patient data and other sensitive information with NHSmail and GSi recipients NHSmail provides an email address for your career in the NHS and can be accessed anywhere For more information and to find out how you can switch, visit www.connectingforhealth.nhs.uk/nhsmail ********************************************************************************************************************

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Visualizing Subcortical Volume Differences
by Jeff Sadino 14 Apr '11

14 Apr '11

Hello, I am interested in a way to visualize the differences in the volume in subcortical structures, preferably in 3D. For example, I would like to view the Thalamus of controls. And then I would like to overlay a color-coded map that shows the difference between the volume of the Control Thalamus and the Study Thalamus. I have seen a couple of different ways to do this, but they all seem rather clunky. Can anyone recommend a method for this? Thank you very much, Jeff Sadino

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bert functional data set
by Palzes, Vanessa 13 Apr '11

13 Apr '11

Hi, I'm trying to go through this tutorial: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/AutomaticRegistratio nSpm I have already downloaded/unpacked the buckner_data-tutorial-subjs.tar.gz, and also set up the correct SUBJECTS_DIR as: setenv TUTORIAL_DATA /Applications/freesurfer/subjects cd $TUTORIAL_DATA/buckner_data/tutorial_subjs setenv SUBJECTS_DIR ${PWD} But, when I try to run the following command, it tells me it cannot find bert-brf... spmregister --s bert-brf --mov f001.img --reg register.dat Any suggestions on how I can locate and use this tutorial data? Vanessa Palzes Research Assistant Brain Imaging & EEG Lab San Francisco VA Medical Center 4150 Clement Street San Francisco, CA 94121 Tel: 415-221-4810 ext. 6155

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Smoothing & ROIs
by pikase＠tin.it 13 Apr '11

13 Apr '11

Dear FS experts, I'm quite sure this is a very trivial question since apparently it hasn't been posed previously. I'm performing a CT analysis with the aim to compare two groups of subjects, which are different regarding the degree of expertise in a given area (experts vs non experts) and using as covariates age and gender. The total number of subjects is 21 for the expert group and 20 for the naive subjects. At first I performed a whole brain analysis both via qdec and command-based, wich reveal substantially no differences between the two groups. Now, I also have some a-priori ROIs I would like to test. I went several times through the steps suggested in the tutorial, but still something is not clear to me. Do I need to apply a smoothing on the ROI I want to draw? I would assume so. How can I do that? Is it possible to extract ROIS from previously smoothed data? (All my datas have been passed through -qcache). Thanks so much for your time and help! Best regards, Laura

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Bug in mri_info?
by Scott Burns 13 Apr '11

13 Apr '11

Freesurfers -- This morning, I was trying to convert a 4 frame MPRAGE scan into a 1 frame RMS image. I wrote my own matlab code to do it ... function err = rms_mprage(old,new) %convert 4-frame mprage into 1 frame mprage by taking RMS of voxels old_hdr = load_nifti(old); new_hdr = old_hdr; new_hdr.vol = sqrt((old_hdr.vol(:,:,:,1).^2+old_hdr.vol(:,:,:,2).^2+old_hdr.vol(:,:,:,3).^2+old_hdr.vol(:,:,:,4).^2)/4); err = save_nifti(new_hdr,new); So I ran >>> rms_mprage('MPRAGE1.nii','MPRAGE_new.nii') Also, Bruce said I could do this ... mri_average -noconform -sqr MPRAGE1.nii#0 MPRAGE1.nii#1 MPRAGE1.nii#2 MPRAGE1.nii#3 MPRAGE_rms.nii However... kerryave:002 $ ls -l -rw-rw-r-- 1 sburns lingua 92275040 Dec 21 12:27 MPRAGE1.nii -rw-rw-r-- 1 sburns lingua 24340 Dec 20 15:17 MPRAGE1.nii-infodump.dat -rw-rw-r-- 1 sburns lingua 23069024 Apr 12 13:29 MPRAGE_new.nii -rw-rw-r-- 1 sburns lingua 46137696 Apr 12 13:35 MPRAGE_rms.nii So I was curious why the _rms.nii was twice as big. Probably a datatype issue, right? kerryave:002 $ mri_info MPRAGE_new.nii Volume information for MPRAGE_new.nii type: nii dimensions: 256 x 256 x 176 voxel sizes: 1.0000, 1.0000, 1.0000 type: FLOAT (3) fov: 256.000 dof: 0 xstart: -128.0, xend: 128.0 ystart: -128.0, yend: 128.0 zstart: -88.0, zend: 88.0 TR: 2530.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1 PhEncDir: UNKNOWN ras xform present xform info: x_r = 0.0055, y_r = 0.0068, z_r = -1.0000, c_r = -0.9523 : x_a = -0.9719, y_a = 0.2354, z_a = -0.0037, c_a = 2.8859 : x_s = -0.2354, y_s = -0.9719, z_s = -0.0079, c_s = 0.8822 Orientation : PIL Primary Slice Direction: sagittal voxel to ras transform: 0.0055 0.0068 -1.0000 85.4734 -0.9719 0.2354 -0.0037 97.4806 -0.2354 -0.9719 -0.0079 156.1061 0.0000 0.0000 0.0000 1.0000 voxel-to-ras determinant -1 ras to voxel transform: 0.0055 -0.9719 -0.2354 131.0176 0.0068 0.2354 -0.9719 128.1845 -1.0000 -0.0037 -0.0079 87.0654 0.0000 0.0000 0.0000 1.0000 And... kerryave:002 $ mri_info MPRAGE_rms.nii Volume information for MPRAGE_rms.nii type: nii dimensions: 256 x 256 x 176 voxel sizes: 1.0000, 1.0000, 1.0000 type: FLOAT (3) fov: 256.000 dof: 0 xstart: -128.0, xend: 128.0 ystart: -128.0, yend: 128.0 zstart: -88.0, zend: 88.0 TR: 2530.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1 PhEncDir: UNKNOWN ras xform present xform info: x_r = 0.0055, y_r = 0.0068, z_r = -1.0000, c_r = -0.9523 : x_a = -0.9719, y_a = 0.2354, z_a = -0.0037, c_a = 2.8859 : x_s = -0.2354, y_s = -0.9719, z_s = -0.0079, c_s = 0.8822 Orientation : PIL Primary Slice Direction: sagittal voxel to ras transform: 0.0055 0.0068 -1.0000 85.4734 -0.9719 0.2354 -0.0037 97.4806 -0.2354 -0.9719 -0.0079 156.1061 0.0000 0.0000 0.0000 1.0000 voxel-to-ras determinant -1 ras to voxel transform: 0.0055 -0.9719 -0.2354 131.0176 0.0068 0.2354 -0.9719 128.1845 -1.0000 -0.0037 -0.0079 87.0654 0.0000 0.0000 0.0000 1.0000 Weird that mri_info shows the datatype for both images as float. fslhd shows different things... kerryave:002 $ fslhd MPRAGE_new.nii filename MPRAGE_new.nii sizeof_hdr 348 data_type INT16 dim0 4 dim1 256 dim2 256 dim3 176 dim4 1 dim5 1 dim6 1 dim7 1 vox_units mm time_units ms datatype 4 nbyper 2 bitpix 16 pixdim0 0.0000000000 pixdim1 1.0000000000 pixdim2 1.0000000000 pixdim3 1.0000000000 pixdim4 2530.0000000000 pixdim5 1.0000000000 pixdim6 1.0000000000 pixdim7 1.0000000000 vox_offset 352 cal_max 0.0000 cal_min 0.0000 scl_slope 1.000000 scl_inter 0.000000 phase_dim 0 freq_dim 0 slice_dim 0 slice_name Unknown slice_code 0 slice_start 0 slice_end 0 slice_duration 0.000000 time_offset 0.000000 intent Unknown intent_code 0 intent_name intent_p1 0.000000 intent_p2 0.000000 intent_p3 0.000000 qform_name Scanner Anat qform_code 1 qto_xyz:1 0.000000 0.000000 -1.000000 87.473366 qto_xyz:2 -0.976296 0.216439 -0.000000 100.261627 qto_xyz:3 -0.216439 -0.976296 -0.000000 153.275482 qto_xyz:4 0.000000 0.000000 0.000000 1.000000 qform_xorient Anterior-to-Posterior qform_yorient Superior-to-Inferior qform_zorient Right-to-Left sform_name Aligned Anat sform_code 2 sto_xyz:1 0.005469 0.006804 -0.999962 85.473358 sto_xyz:2 -0.971887 0.235419 -0.003714 97.480621 sto_xyz:3 -0.235385 -0.971870 -0.007900 156.106079 sto_xyz:4 0.000000 0.000000 0.000000 1.000000 sform_xorient Anterior-to-Posterior sform_yorient Superior-to-Inferior sform_zorient Right-to-Left file_type NIFTI-1+ file_code 1 descrip FreeSurfer Dec 18 2010 aux_file kerryave:002 $ fslhd MPRAGE_rms.nii filename MPRAGE_rms.nii sizeof_hdr 348 data_type FLOAT32 dim0 3 dim1 256 dim2 256 dim3 176 dim4 1 dim5 1 dim6 1 dim7 1 vox_units mm time_units s datatype 16 nbyper 4 bitpix 32 pixdim0 0.0000000000 pixdim1 1.0000000000 pixdim2 1.0000000000 pixdim3 1.0000000000 pixdim4 2.5299999714 pixdim5 1.0000000000 pixdim6 1.0000000000 pixdim7 1.0000000000 vox_offset 352 cal_max 0.0000 cal_min 0.0000 scl_slope 0.000000 scl_inter 0.000000 phase_dim 0 freq_dim 0 slice_dim 0 slice_name Unknown slice_code 0 slice_start 0 slice_end 0 slice_duration 0.000000 time_offset 0.000000 intent Unknown intent_code 0 intent_name intent_p1 0.000000 intent_p2 0.000000 intent_p3 0.000000 qform_name Scanner Anat qform_code 1 qto_xyz:1 0.005469 0.006804 -0.999962 85.473358 qto_xyz:2 -0.971887 0.235419 -0.003714 97.480621 qto_xyz:3 -0.235385 -0.971870 -0.007900 156.106079 qto_xyz:4 0.000000 0.000000 0.000000 1.000000 qform_xorient Anterior-to-Posterior qform_yorient Superior-to-Inferior qform_zorient Right-to-Left sform_name Scanner Anat sform_code 1 sto_xyz:1 0.005469 0.006804 -0.999962 85.473358 sto_xyz:2 -0.971887 0.235419 -0.003714 97.480621 sto_xyz:3 -0.235385 -0.971870 -0.007900 156.106079 sto_xyz:4 0.000000 0.000000 0.000000 1.000000 sform_xorient Anterior-to-Posterior sform_yorient Superior-to-Inferior sform_zorient Right-to-Left file_type NIFTI-1+ file_code 1 descrip FreeSurfer Mar 19 2011 aux_file fslhd shows different data types, which explains the difference in size. I think there's a bug in mri_info that is incorrectly reading MPRAGE_new.nii as float data. Not an earth shattering bug by any means, but I thought I'd let you know anyways. Scott Burns Kuperberg Lab Martinos Center for Biomedical Imaging sburns(a)nmr.mgh.harvard.edu 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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Checking correct hemisphere in tksurfer
by Ed Gronenschild 13 Apr '11

13 Apr '11

Dear FreeSurfer developers, With tksurfer you have to watch out to select the correct hemisphere when loading an overlay or annotation. My suggestion to the developers is to implement an easy check since it is known to which hemisphere the displayed surface belongs. As far as I know, the only file for which such a check would fail is sig.mgz, the result of a statistical analysis. Kind regards, Ed

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Shifting hdr information in .nii?
by Joakim Vinberg 12 Apr '11

12 Apr '11

A little off-topic maybe, but: I am working to load external data into analysis programs using .nii format files. I have inplanes acquired at an ACPC orientation, as well as data collected and specially pre-processed through a MATLAB pathway that unfortunately strips away all orientation information. I have been trying to find a way to use the header information from the inplanes to orient the data (unfortunately, automated alignment algorithms fail due to the nature of the data). Does anybody have any suggestions, or information on exactly which fields in the .nii header to shift? Thanks in advance for all of the help on a thorny problem! Joakim

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Postdoctoral Fellowship: Multimodal Neuroimaging -MGH/Harvard Medical School
by sheraz＠nmr.mgh.harvard.edu 12 Apr '11

12 Apr '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 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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fill problem in properly normalized volume
by Fred Dick 12 Apr '11

12 Apr '11

Dear all we have had some odd behavior in 4 fairly high quality datasets that have been very nicely normalized and deskulled with a good Talairach but then only half filled in wm.mgz and all surfs (to various semi-planes). Orientation seems correct in tkmedit as well. We were thinking that it might be a cutting plane problem but weren't sure how this would happen since all else is OK. Anyone else have this issue (and a solution?) Thanks, Fred

2 3

Segmentation Fault
by Allie Rosen 12 Apr '11

12 Apr '11

Hi All, Upon trying to assembly my subjects into a single surface space, I got the following error: *ERROR: number of vertices in /media/AMMONIS/fsSubjects/AR_normals/C42/surf/lh.thickness does not match surface (142271,140585) ERROR: reading curvature file * I then tried to perform recon-all -make all, but got this error: *ERROR: mpr2mni305 failed, see transforms/talairach_avi.log* In the .log, I got this: *-7.5000 22.5000 15.0000 2793.2134 1Segmentation fault ERROR: 'imgreg_4dfp /usr/rapps/freesurfer/average/711-2C_as_mni_average_305 /usr/rapps/freesurfer/average/711-2B_as_mni_average_305_mask talsrcimg_g11 none talsrcimg_to_711-2C_as_mni_average_305_t4 4355' failed! status=139 ERROR: mpr2mni305 execution aborted* Which is a segmentation fault. Can anyone help me fix this? Thanks, Allie Rosen, MSc Candidate Graduate Student, Department of Neurosurgery Toronto Western Hospital 14-327 399 Bathurst St. University of Toronto

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Freesurfer