Freesurfer

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30086 discussions

volumetric version of fsaverage brain
by Ritobrato Datta 13 Apr '10

13 Apr '10

Hello All, Which is the volumetric version of the fsaverage brain in freesurfer ? Can you tell me what is it called ? Thanks Ri

2 1

mri_surf2vol
by Jerald Zhao 13 Apr '10

13 Apr '10

Hi all, I'm a new user of freesurfer. It's a simple question. I want to convert ?h.smoothwm and ?h.smoothwm.nofix to .mgz as binary volume (foreground/background = 1/0). So I found mri_surf2vol command, but the command I used could be problem. > mri_surf2vol --template ./orig/001.mgz --volreg reg.dat --surface ../surf/lh.white --hemi lh error message is below. --- gdiagno = -1 ERROR: cannot recognize the type of ../surf/lh.white --- If mri_surf2vol cannot be used for what I want, is there any method to convert ?h.white? Thanks,

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Re: [Freesurfer] changing watershed threshold has no effect
by Andreas Berger 13 Apr '10

13 Apr '10

on one group of subjects i ran "recon-all -all -clean -wsthresh n", which according to http://surfer.nmr.mgh.harvard.edu/fswiki/OtherUsefulFlags includes what "-clean-bm" does. on the other group i ran "recon-all -all -wshthresh n" after deleting everything and converting them from raw invol data to freesurfer format again. as i understand it, "-clean" is not required because no previous data is there to be overwritten/cleaned. to prevent confusion, i am not comparing these two groups, it's just that we have a separate group of subjects of which whe don't have the raw data, so i had to use -clean. i compared using "-wsthresh" against not using it in a few subjects from both groups. as far as the "-clean" flags are concerned, there is no bug: they do change the result, so i assume the previous volume is overwritten as it should, however the results are no improvement (see screenshots). On Mon, 12 Apr 2010 15:54:47 -0400 (EDT) Allison Stevens <astevens(a)nmr.mgh.harvard.edu> wrote: > Andreas, > I'm not very clear on your response. Did using -clean-bm on the subjects > you had used -clean on when running with -wsthresh, change the skull strip > for the better? > > when you ran it on the already clean data set, you said using -wsthresh 0 > still did not get a good skull strip? > Allison > > -- > > On Fri, 9 Apr 2010, Andreas Berger wrote: > > > Sorry for the slow response, > > > > yes, the "-clean" flag should imply "-clean-bm" (among others) > > > > besides, on one group of the subjects i ran "recon-all -all -wsthresh n" after converting them from invol data again, everything from scratch (no cleaning required), with the same result. also, the fact that the surfaces did change (however not as i hoped) indicates that it's not a problem with the flags. > > > > > > > > > > On Wed, 31 Mar 2010 13:01:32 -0400 (EDT) > > Allison Stevens <astevens(a)nmr.mgh.harvard.edu> wrote: > > > >> Andreas, > >> Did using -clean-bm work? > >> Allison > >> > >> -- > >> > >> On Mon, 29 Mar 2010, Allison Stevens wrote: > >> > >>> Andreas, > >>> Let me know how this turns out. The response you got about the command (using > >>> -clean-bm) is correct but since you used -clean, that should have worked just > >>> as well. Can you please let me know if using -clean-bm does anything > >>> differently from -clean? If so, we'll have to investigate this as a potential > >>> bug. > >>> Thanks, > >>> Allison > >>> > >>> > >> > >> > >> 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. > >> > > > > > > -- Andreas Berger <andreas.berger.01(a)gmail.com>

2 4

Extracting time series from aparc.a2009s+aseg.mgz
by liang wang 12 Apr '10

12 Apr '10

Hi FSusers, Is there a way to extract averaged BOLD signal from the identified cortical regions in aparc.a2009s+aseg.mgz. Thanks Liang -- Liang Wang, PhD Postdoctoral Fellow Woodward Lab Department of Psychiatry University of British Columbia BC Mental Health & Addiction Services 938 West 28th Avenue Vancouver BC V5Z 4H4 Telephone: 1-604-875-2000 (ext. 4735) Fax: 1-604-875-3871 Email: wanglbit(a)gmail.com

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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

3 4

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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