Freesurfer

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30088 discussions

Voxel Displacement When Loading DICOM Images
by Sullivan, Patrick M. 27 Jul '11

27 Jul '11

Hi All, I'm a new Freesurfer user, and I'm trying my best to pick it up on my own with the wealth of documentation available. Unfortunately, I can't seem to find any mention of this particular problem in the wiki or in the archives of this newsletter, so I hope someone can help. Please forgive me, I'm still learning, and I may not know the correct terminology for some items; I will try to describe the problem as best I can. I'm attempting to simply view a set of DICOM images (T1 format) with TkMedit before I convert and/or process them at all, just to make sure they are loading properly. The 120 slices load fine using the Philips proprietary DICOM viewer, but for some reason when I load the image in TkMedit, a strange series of displacements occur. In each plane at least 1 or 2 "lines" appear, dividing the brain so that the entire image has been shifted (by perhaps a voxel or half a voxel) beyond this line. This shift can happen in any direction (anterior/posterior, lateral/medial, superior/inferior). For instance, when viewing the image in the sagittal plane, one of these lines appears at approximately the pre-central gyrus, traveling straight "up and down" so that everything in front of the line is shifted as though I had scrolled 1 additional slice sagitally through the brain. (In the lateral/medial direction, the temporary "z" axis when viewing the image sagitally, not the true superior/inferior z axis). This was immediately visually obvious because some slices of the brain have starkly different contrast, so when different parts of the brain were being shown at different slices, it really popped out. However, other similar lines are simply shifted "up/down" or "forward/back" one voxel, making them less obvious but still problematic. All of these lines are constant, in the same location for each slice. I am really not sure what is causing this, although my first tentative guess is to wonder whether the images were perhaps acquired at an oblique angle and TkMedit is trying to compensate for that in some way. Beyond that though, I really do not have any guesses. Does anyone have any ideas about what might be going on, and how I might fix it? I apologize if I have stated any of this poorly. Any help or pointers in the right direction would be appreciated tremendously. Thank You, -Patrick

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WM and ASEG edition... recon-all continue command...
by Gonzalo Rojas Costa 27 Jul '11

27 Jul '11

Hi I editted the wm.mgz and aseg.mgz files... Which recon-all command must I use to continue the processing ?... Sincerely, Gonzalo Rojas Costa

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Loading atlases
by Antonella Kis 26 Jul '11

26 Jul '11

Hi, I would like to check if my subcortical segmentation is correct so I was running: tkmedit SUBJECT1 brainmask.mgz \ -aux T1.mgz -surfs \ -segmentation aseg.mgz $FREESURFER_HOME/FreeSurferColorLUT.txt 1). Pial (red line), and white (yellow line) surfaces are shown and I wonder how I can add a green lie for my orig surface? 2). After I load the aparc+aseg.mgz is theer a way to load and overlay the original/correct atlas so I can see if my segmentation is correct? Thank you very much. Antonella

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Reproducible Qdec error color bar not updated when clicking reverse value.
by Knut J Bjuland 26 Jul '11

26 Jul '11

Hi When I click on reverse values in Qdec the color on the hemisphere will change, but the color bar at the bottom on the screen will stay the same. Is there anything I can do to force Qdec to change the color bar at the bottom of the screen? I am send along to attachment one with reverse values and one without reversing the values. To reproduce this error I have sent a picture of the same correlation with one exception I have clicked on reverse value on the file named error.jpg. Best regards Knut J

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Unknown label
by Antonella Kis 26 Jul '11

26 Jul '11

Hi Bruce, I forgot to ask why my data does not include an unknown region in my aparc.stats file? My stats data starts with bankssts region and continue with caudalanteriorcingulate, etc. Do I need to have the unknown region if I use the new version of the FS 5.1.0? Thank you. Antonella

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Pre-processing issues
by Antonella Kis 26 Jul '11

26 Jul '11

Dear Bruce, I have two more questions for today, please: 1). Just to be sure that I understood correct: for my cortical thickness studies and also for a group studies analysis I will use only the data from the 3DAx_T1series which was converted to a .nii.gz file. Is this right? 2). If I want to shortness the pre-processing time while running the recon-all for my subjects, can I run recon-all for three subjects by opening three terminals in the same time? Running more subjects in the same time will induce more errors for a manual correction or the results will be the same with the one while running each subject individual/only one terminal at the time. Thank you and have a great weekend. Antonella

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Postdoctoral Fellowship: Multimodal Neuroimaging -MGH/Harvard Medical School
by sheraz＠nmr.mgh.harvard.edu 26 Jul '11

26 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 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.

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ROI analysis with label in both hemispheres -still looking for an answer
by Katie Bettencourt 26 Jul '11

26 Jul '11

I'm still looking for an answer on this. If the answer is you can't do it, I'm ok with that, I just would like to know! Thanks! Hi all, > > I was wondering if anyone had any idea if it was possible to combine > together ROIs from the separate hemispheres into one ROI (for example LH V1 > and RH V1) and then perform a functional ROI analysis on it. I know how to > combine ROIs (through labels_union) and how to do a functional ROI analysis > (using func2roi-sess and roisummary-sess), but I don't know if it is > possible to do it with a label that runs across both hemispheres. Thoughts? > > Thanks, > Katie >

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mri_surfcluster coordinates
by Chris Hyatt 26 Jul '11

26 Jul '11

Dear Freesurfers, I know that Qdec outputs coordinates in a "Freesurfer specific space", rather than in Talairach space, per this old thread https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2008-November/008878.… However, I found that mri_surfcluster (Freesurfer v5.0) in its summary output also outputs coordinates in this same "Freesurfer specific space", even though the columns indicate TalX, TalY and TalZ. I was going to use this summary info to list the location of the statistical maxima of each cluster in a cortical thickness p-map. Is this a bug in mri_surfcluster? Any suggestions on how to get the coordinate data? Here is the summary info for the left hemisphere (note the positive TalX values, when all X values should be negative): # Cluster Growing Summary (mri_surfcluster) # $Id: mri_surfcluster.c,v 1.51.2.1 2011/03/28 15:32:36 greve Exp $ # $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ # CreationTime 2011/07/23-17:08:39-GMT # cmdline mri_surfcluster --in ./lh.CvsA.glmdir/group.diff/sig.mgh --subject fsaverage --hemi lh --surf inflated --thmin 1.301 --sum lh.CvsA.thickness.summary --oannot ./lh.CvsA.thickness.annot # cwd /prod4/other/freesurfer/glm_cth/age_of_onset # sysname Linux # hostname everest # machine x86_64 # FixVertexAreaFlag 1 # FixSurfClusterArea 1 # # Input ./lh.CvsA.glmdir/group.diff/sig.mgh # Frame Number 0 # srcsubj fsaverage # hemi lh # surface inflated # SUBJECTS_DIR /prod4/other/freesurfer/subjects # SearchSpace_mm2 62822.2 # SearchSpace_vtx 163842 # Bonferroni 0 # Minimum Threshold 1.301 # Maximum Threshold infinity # Threshold Sign abs # AdjustThreshWhenOneTail 1 # Area Threshold 0 mm^2 # Overall max 2.53286 at vertex 81529 # Overall min -2.67513 at vertex 24566 # NClusters 36 # Total Cortical Surface Area 62822.2 (mm^2) # FixMNI = 1 # # ClusterNo Max VtxMax Size(mm^2) TalX TalY TalZ NVtxs 1 -2.675 24566 287.98 7.6 95.9 0.5 533 2 2.533 81529 83.49 -7.4 -28.4 50.2 199 3 2.530 6795 386.88 -15.4 -86.6 -9.4 677 4 -2.496 129236 79.10 -27.0 27.1 22.6 166 5 -2.483 138360 227.18 -5.7 84.6 2.6 343 6 2.481 18891 211.45 3.4 -96.6 -26.2 373 7 2.460 33958 277.19 37.6 5.5 15.4 354

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Qdec does not change the color bar though the color scare is reversed on the brain.
by Knut J Bjuland 26 Jul '11

26 Jul '11

Hi I have a problem when using qdec. When I check the option reverse values there color on the brain switch color, but the color bar stays the same. Is there anything that might be wrongs in my files? Is there anything that I might edit in Qdec configuration file? I do not know what kind of log that are required and I would be happy to send them. Cheers Knut J Bjuland figure attachment http://vedlegg.uib.no/?id=73435c1da0c1f0c1ba792601c4fa1199 http://vedlegg.uib.no/?id=20e06d09dcc450ff4abcd85e1e5ab1c5

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