Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30132 discussions

creating a binary mask volume
by Mehul Sampat 12 Apr '10

12 Apr '10

Hi Folks, I would like to create a binary mask volume for the Right-Thalamus (all voxels of right-thalamus as 1 and 0 otherwise). I looked at this help page http://surfer.nmr.mgh.harvard.edu/fswiki/mri_vol2roi and i think I should use the following command described on this page: mri_vol2roi --label your.label --srcvol f --srcreg register.dat --finalmskvol labelbinmask --roiavg /tmp/not.wanted.dat is this correct ? also could someone give me an example? i am not sure what all of the parameters are. thanks Mehul

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Gabriel Castrillón wants to stay in touch on LinkedIn
by Gabriel Castrillón 12 Apr '10

12 Apr '10

LinkedIn ------------Gabriel Castrillón souhaite se connecter à vous sur LinkedIn : ------------------------------------------ Freesurfer, I'd like to add you to my professional network on LinkedIn. - Gabriel Castrillón Accepter l'invitation de Gabriel Castrillón http://www.linkedin.com/e/qaAr-Z_86TRZ5lXG-dA9kZQ49qSe59qYFaT9QmQ47Ub3yw/bl… Voir l'invitation de Gabriel Castrillón http://www.linkedin.com/e/qaAr-Z_86TRZ5lXG-dA9kZQ49qSe59qYFaT9QmQ47Ub3yw/bl… ------------------------------------------ SAVEZ-VOUS que vous pouvez valider le parcours des candidats grâce à LinkedIn, lorsque vous recrutez ? Tapez le nom de l'entreprise et les années concernées, ou le nom du candidat, pour identifier des référents dans votre réseau. Cela vous permet de mieux appréhender le parcours professionnel d'un candidat. http://www.linkedin.com/e/rsr/inv-27/ ------ (c) 2010, LinkedIn Corporation

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Postdoctoral Fellowship: Multimodal Imaging at MGH
by sheraz＠nmr.mgh.harvard.edu 12 Apr '10

12 Apr '10

Postdoctoral Fellowship: Multimodal Imaging Description: A two year 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. 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) and on co-registering EEG and MEG with MRI. 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, electrical engineering, computer science or other related fields. 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.

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problems on converting images from the GE scanner
by Chun-Hsien Hsu 12 Apr '10

12 Apr '10

Hi FreeSurfer users, I have the anatomical MR images from the GE scanner, and want to convert the images into the mgz file. These images's file name looks as follows: IM1 IM2 . . IM176 I use the function "mri_convert" to converting the file: % mri_convert -it dicom IM1 $SUBJECTS_DIR/15/mri/orig/001.mgz The problem is that the image in the output file (001.mgz) looks like "white noise". I have posted the logs regarding to this function at the end. I have tried several ways, such as converting the files into *.ima files or a nii file before running "mri_convert", and still have the same problem. Would someone have ideas about what to do? Thanks! Chun-Hsien Hsu mri_convert -it dicom IM1 /Users/kevin/Subjects/15/mri/orig/001.mgz $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ reading from IM1... Starting DICOMRead2() dcmfile = /Users/kevin/Subjects/15/mri/IM1 dcmdir = /Users/kevin/Subjects/15/mri Ref Series No = 3 Found 179 files, checking for dicoms Found 176 dicom files in series. First Sorting Computing Slice Direction Vs: 0.007 -0.168 0.9856 Vs: 0.00700112 -0.168027 0.985758 Second Sorting Counting frames nframes = 1 nslices = 176 ndcmfiles = 176 PE Dir = ROW (dicom read) TransferSyntaxUID: --1.2.840.10008.1.2.1-- jpegUID: --1.2.840.10008.1.2.4-- Loading pixel data TR=3.06, TE=0.82, TI=1100.00, flip angle=7.00 i_ras = (-0.999935, -0.00973536, -0.00592059) j_ras = (0.00860625, -0.985602, 0.16886) k_ras = (-0.00700112, 0.168027, 0.985758) writing to /Users/kevin/Subjects/15/mri/orig/001.mgz...

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Miao Wen wants to stay in touch on LinkedIn
by Miao Wen 12 Apr '10

12 Apr '10

LinkedIn ------------Miao Wen souhaite se connecter à vous sur LinkedIn : ------------------------------------------ Freesurfer, I'd like to add you to my professional network on LinkedIn. - Miao Wen Accepter l'invitation de Miao Wen http://www.linkedin.com/e/qaAr-Z_86TRZ5lXG-dA9kZQ49qSe59qYFaT9QmQ47Ub3yw/bl… Voir l'invitation de Miao Wen http://www.linkedin.com/e/qaAr-Z_86TRZ5lXG-dA9kZQ49qSe59qYFaT9QmQ47Ub3yw/bl… ------------------------------------------ SAVEZ-VOUS que LinkedIn peut trouver une réponse aux questions les plus complexes ? Publiez ces questions dans la rubrique Réponses de LinkedIn pour profiter de l'expertise des plus grands experts internationaux : http://www.linkedin.com/e/ask/inv-23/ ------ (c) 2010, LinkedIn Corporation

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generating WM parcellation using Destrieux atlas
by Mehul Sampat 11 Apr '10

11 Apr '10

Hi Folks, I was trying to help a colleague generate a wmparc for the Destrieux atlas. That is I am trying to create "wmparc.a2009s.mgz" and "wmparc.a2009s.stats" I used the following two commands: mri_aparc2aseg --s subject_id --labelwm --hypo-as-wm --rip-unknown --new-ribbon --wmparc-dmax 4 --o mri/wmparc.a2009s.mgz --ctxseg aparc.a2009s+aseg.mgz mri_segstats --seg mri/wmparc.a2009s.mgz --sum stats/wmparc.a2009s.stats --pv mri/norm.mgz --excludeid 0 --brain-vol-from-seg --brainmask mri/brainmask.mgz --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --subject subject_id --surf-wm-vol --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt I was able to run this and I noticed that a number of labels in "wmparc.a2009s.stats" do not have any voxels assigned to them. for examples: 762 4174 0 0.0 wm-rh-S_subcentral_ant 0.0000 0.0000 0.0000 0.0000 0.0000 763 4175 0 0.0 wm-rh-S_subcentral_post 0.0000 0.0000 0.0000 0.0000 0.0000 764 4176 0 0.0 wm-rh-S_suborbital 0.0000 0.0000 0.0000 0.0000 0.0000 765 4177 0 0.0 wm-rh-S_subparietal 0.0000 0.0000 0.0000 0.0000 0.0000 766 4178 0 0.0 wm-rh-S_supracingulate 0.0000 0.0000 0.0000 0.0000 0.0000 768 4180 0 0.0 wm-rh-S_temporal_superior 0.0000 0.0000 0.0000 0.0000 0.0000 769 4181 0 0.0 wm-rh-S_temporal_transverse 0.0000 0.0000 0.0000 0.0000 0.0000 It seems like only labels corresponding to the Desikan atlas have voxels assigned to them in "wmparc.a2009s.stats" ? do you think I made an error while generating "wmparc.a2009s.stats" ? thanks Mehul

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Missing usage for mris_distance_map
by Michael Waskom 11 Apr '10

11 Apr '10

Hi All, I'd like to use mris_distance_map, but it looks like the usage/help info is missing or broken (At least in 4.4.0/4.5.0). When I try it with just the command or -help, it looks like this: mwaskom@ba2:~$ mris_distance_map --help usage: mris_distance_map [options] <input surface file> <output scalar field (.mgz)> This program will compute a distance map of each point on the surface to a reference point (vertex 0 by default) valid options are: mwaskom@ba2:~$ Can someone help me out with these mysterious options? Also, how is it calculating distance? Thanks! Mike

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Analysis of Cortical dysplasia
by Bhavani shankara 10 Apr '10

10 Apr '10

Dear freesurefer experts, I am a freesurfer beginner , e have a MPRAGE image of cortical dysplasia. Is their any way of analysing that single image and to compare with the standard (talairchie or other) template and note the involvement of the cortex. I tried doing recon-all but in autorecon1 command itself it is stopping in the middle and saying that on comparing with the template it is not fitting with the template. Please let me know any methods Thank you in advance expecting a answere. -- Dr. BHAVANI SHANKARA BAGEPALLY PHD STUDENT (CLINICAL NEUROSCIENCES) NIMHANS, BANGALORE, bshankara(a)ymail.com

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Processing of brains with malformations of cortical development
by Diego Herrera 09 Apr '10

09 Apr '10

Hello Do you know how would theorically behave Freesurfer with pathologic brains with malformations like polymicrogiria, schizencephaly, etc. Also, do you have experience with subtle malformations like Focal Cortical Dysplasia (FCD)? Recently, we tried recon-all in a polimicrogiric brain obtaining a very acceptable segmentation. Thanks -- Diego Herrera, M.D. Neuroradiologist Medellin, Colombia

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CEPHES ERROR: fdtrc domain error
by Lars M. Rimol 09 Apr '10

09 Apr '10

Hi, I get this error message when running glm_fit (v.3.02): CEPHES ERROR: fdtrc domain error (I see you've handled this error message before, but there was no solution there: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg11602.html) I'm using a model with two groups, and age and ICV as continuous regressors. The error message comes when estimating the 0 0 0 1 contrast, i.e. ICV. Matrix condition = 494.18. The beta for this covariate shows very small numbers, i.e. 0-6*10^-1. And the sig.mgh file for it shows all vertices = 1e+10. yours, Dr. Lars M. Rimol

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