Freesurfer

freesurfer@nmr.mgh.harvard.edu

16 participants
30084 discussions

R: Re: R: Re: R: Re: average z-score of each subject from a common cluster
by stdp82＠virgilio.it 09 Nov '15

09 Nov '15

Thanks. But what's meaning "colheader"? In my cache.th13.neg.sig.masked.nii.gz I have only a significant ROI. In the summary file there are five column and 5 different value of "mean". Which is the correct, expressing the mean z-score of the cluster? Stefano >----Messaggio originale---- >Da: greve(a)nmr.mgh.harvard.edu >Data: 6-nov-2015 23.07 >A: <freesurfer(a)nmr.mgh.harvard.edu> >Ogg: Re: [Freesurfer] R: Re: R: Re: average z-score of each subject from a common cluster > >under the "Mean" column > >On 11/06/2015 07:46 AM, stdp82(a)virgilio.it wrote: >> I have run >> mri_segstats --seg .../my-glm.wls/group.diff/cache.th13.neg.sig. masked. >> nii.gz rh parc --i subj/fc.seed.surf.rh/R_seed/z.nii.gz --sum >> summaryfile >> >> and I have obtained 9 columns and 5 rows. >> I'm confused on results. Where is the mean z-score for cache.th13. neg. >> sig.masked.nii.gz? >> >> # ColHeaders Index SegId NVoxels Volume_mm3 StructName Mean StdDev >> Min Max Range >> 1 -4 7 7.0 Seg-004 -2.4544 0.5023 >> -3.2164 -1.7619 1.4545 >> 2 -3 153 153.0 Seg-003 -2.6662 1.4724 >> -6.2120 1.7587 7.9707 >> 3 -2 848 848.0 Seg-002 -2.4930 2.0088 >> -6.4504 2.3528 8.8032 >> 4 -1 1518 1518.0 Seg-001 -2.1416 1.6727 >> -6.4227 2.5420 8.9648 >> 5 0 161316 161316.0 Seg0000 1.4152 1.6218 >> -7.0471 14.1452 21.1923 >> >> Because my data are on surface mri_surfcluster should be helpful? >> >> Thanks. >> >> >> Stefano >> >> >>> ----Messaggio originale---- >>> Da: greve(a)nmr.mgh.harvard.edu >>> Data: 3-nov-2015 19.55 >>> A: <freesurfer(a)nmr.mgh.harvard.edu> >>> Ogg: Re: [Freesurfer] R: Re: average z-score of each subject from a >> common cluster >>> look in the summaryfile. Also, don't use --seg z.nii.gz. In the >> command >>> below, it works because you have --annot afterwards, but in general >> it >>> is not correct >>> >>> On 10/30/2015 04:22 PM, stdp82(a)virgilio.it wrote: >>>> Thanks. >>>> I have obtained: >>>> >>>> $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ >>>> >>>> cwd >>>> >>>> cmdline mri_segstats --seg z.nii.gz --annot Control21_FS rh aparc -- >> i >>>> z.nii.gz --sum summaryfile >>>> >>>> sysname Darwin >>>> >>>> hostname iMac-di-Stefano.local >>>> >>>> machine x86_64 >>>> >>>> user Stefano >>>> >>>> UseRobust 0 >>>> >>>> Loading z.nii.gz >>>> >>>> Loading z.nii.gz >>>> >>>> Voxel Volume is 1 mm^3 >>>> >>>> Generating list of segmentation ids >>>> >>>> Found 22 segmentations >>>> >>>> Computing statistics for each segmentation >>>> >>>> 0 -7 2 2.000 >>>> >>>> 1 -6 110 110.000 >>>> >>>> 2 -5 255 255.000 >>>> >>>> 3 -4 518 518.000 >>>> >>>> 4 -3 1190 1190.000 >>>> >>>> 5 -2 1692 1692.000 >>>> >>>> 6 -1 4104 4104.000 >>>> >>>> 7 0 61577 61577.000 >>>> >>>> 8 1 42598 42598.000 >>>> >>>> 9 2 28146 28146.000 >>>> >>>> 10 3 14859 14859.000 >>>> >>>> 11 4 5845 5845.000 >>>> >>>> 12 5 1899 1899.000 >>>> >>>> 13 6 485 485.000 >>>> >>>> 14 7 116 116.000 >>>> >>>> 15 8 75 75.000 >>>> >>>> 16 9 74 74.000 >>>> >>>> 17 10 78 78.000 >>>> >>>> 18 11 65 65.000 >>>> >>>> 19 12 104 104.000 >>>> >>>> 20 13 45 45.000 >>>> >>>> 21 14 5 5.000 >>>> >>>> >>>> How I can know the meaning of this number? Where is z? >>>> >>>> I have tried also with: >>>> >>>> mri_segstats --seg z.nii.gz --annot Control_21 rh aparc --i z. nii. >> gz >>>> --sum summaryfile --mask >>>> .../fc.ramgseed.surf.rh/R_Amygdala/my-glm.wls/group.diff/cache. th13. >> neg.sig.masked.nii.gz >>>> --avgwfvol mrivol >>>> >>>> >>>> but I have problem with interpretation. >>>> >>>> >>>> >>>> Stefano >>>> >>>> >>>> ----Messaggio originale---- >>>> Da: greve(a)nmr.mgh.harvard.edu >>>> Data: 30-ott-2015 16.17 >>>> A: <freesurfer(a)nmr.mgh.harvard.edu> >>>> Ogg: Re: [Freesurfer] average z-score of each subject from a >>>> common cluster >>>> >>>> >>>> >>>> On 10/30/15 7:16 AM, stdp82(a)virgilio.it wrote: >>>>> Hi list, >>>>> I have two queries, please. >>>>> >>>>> I'd like to have the z-score from my rsfMRI data (seed- >> analyis). >>>>> 1) I have extract the z-score from the Vtx Max >>>>> >>>>> In details, after groups comparison analysis, I have opened >>>>> the cache.th13.pos.sig.cluster.summary contained in group. diff >>>>> folder and I have read the Vtx Max coordinates. >>>>> Next, I have open the z.nii.gz of each subject and I have >>>>> expected the z-score from the vertex which have the Vtx Max >>>>> coordinates. >>>>> >>>>> Is this procedure corrected? >>>> Yes >>>>> 2) z-score of each subject from a common cluster >>>>> >>>>> I would like to use the cluster which shows the group >> difference >>>>> (cache.th13.pos.sig.cluster.nii.gz) as ROI mask. Thus, I would >>>>> extract from it the average of the z-score which is contained >> in >>>>> each subject. >>>>> How should I do? >>>> Use mri_segstats passing the z map as the input (--i) and the >>>> cluster map as the seg. The output will be --sum. Run with -- >> help >>>> for more info >>>>> Thanks. >>>>> >>>>> >>>>> Stefano >>>>> >>>>> >>>>> >>>>> _______________________________________________ >>>>> Freesurfer mailing list >>>>> Freesurfer(a)nmr.mgh.harvard.edu >>>>> https://mail.nmr.mgh.harvard. edu/mailman/listinfo/freesurfer >>>> >>>> >>>> >>>> >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer(a)nmr.mgh.harvard.edu >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> -- >>> Douglas N. Greve, Ph.D. >>> MGH-NMR Center >>> greve(a)nmr.mgh.harvard.edu >>> Phone Number: 617-724-2358 >>> Fax: 617-726-7422 >>> >>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>> Outgoing: ftp://surfer.nmr.mgh.harvard. >> edu/transfer/outgoing/flat/greve/ >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer(a)nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >>> 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. >>> >>> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> > >-- >Douglas N. Greve, Ph.D. >MGH-NMR Center >greve(a)nmr.mgh.harvard.edu >Phone Number: 617-724-2358 >Fax: 617-726-7422 > >Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >www.nmr.mgh.harvard.edu/facility/filedrop/index.html >Outgoing: ftp://surfer.nmr.mgh.harvard. edu/transfer/outgoing/flat/greve/ > >_______________________________________________ >Freesurfer mailing list >Freesurfer(a)nmr.mgh.harvard.edu >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >

2 1

ROI
by UQAM 09 Nov '15

09 Nov '15

Hi I have created and saved labels for 2 regions in the anterior cingulate and corpus callosum in the left hemisphere and I would like to know if there is a way I can convert my .label files from the lh->rh without drawing them by hand in the other hemisphere. Thanks in advance, Best regards, Geneviève

2 1

node coordinates
by André Schmidt 09 Nov '15

09 Nov '15

Dear experts, I defined 84 regions obtained from the aparc+aseg.mgz file as my nodes for later graph analysis. For visualization purposes, I want to assign each node the corresponding MNI coordinates. Can you please help me how I can do this? Is this documented somewhere? Many thanks for your help André

3 5

MNI coordinates for regions in aparc+aseg.mgz file
by André Schmidt 09 Nov '15

09 Nov '15

Dear FS experts, I would like to know the MNI coordinates of my ROIs obtained from recon-all (aparc+aseg.mgz file). For example what for coordinates has number 10 (left thalamus)? Are the coordinates of each region listed somewhere? Many thanks for your help Best wishes André

2 1

R: Re: R: Re: R: Re: error MRS voxel as seed in FS-FAST
by stdp82＠virgilio.it 09 Nov '15

09 Nov '15

I hope that this information are fine fslinfo $SUBJECTS_DIR/Control22/MRS_MASK.nii.gz data_type FLOAT32 dim1 256 dim2 256 dim3 256 dim4 1 datatype 16 pixdim1 1.000000 pixdim2 1.000000 pixdim3 1.000000 pixdim4 0.000000 cal_max 0.0000 cal_min 0.0000 file_type NIFTI-1+ fslstats $SUBJECTS_DIR/Control22/MRS_MASK.nii.gz -V 22926 22926.000000 Thanks, Stefano >----Messaggio originale---- >Da: greve(a)nmr.mgh.harvard.edu >Data: 5-nov-2015 23.43 >A: <freesurfer(a)nmr.mgh.harvard.edu> >Ogg: Re: [Freesurfer] R: Re: R: Re: error MRS voxel as seed in FS- FAST > >How many non-zero voxels are in MRS_MASK.mgz? Is MRS_MASK.mgz 256^3, 1mm3 ? > >On 11/05/2015 04:47 PM, stdp82(a)virgilio.it wrote: >> Please see the file attached. >> Thanks >> >> Stefanofile >> >> ----Messaggio originale---- >> Da: greve(a)nmr.mgh.harvard.edu >> Data: 5-nov-2015 15.43 >> A: <freesurfer(a)nmr.mgh.harvard.edu> >> Ogg: Re: [Freesurfer] R: Re: error MRS voxel as seed in FS-FAST >> >> sorry, should have been >> >> fcseed-sess -debug -s Control22_FS -cfg MRS_MASK.config |& tee doug.log >> >> >> >> On 11/4/15 6:05 PM, stdp82(a)virgilio.it wrote: >>> Hi Dough, >>> in summary: >>> I have the MRS_MASK.mgz within $SUBJECTS_DIR/Control22/mri >>> thus, I have copy this file in fMRI directory (fMRI/Control22_FS) the >>> MRS_MASK.mgz >>> and run: >>> fcseed-config -segid 1 -seg Control22_FS/MRS_MASK.mgz -fsd rest -mean - >>> cfg MRS_MASK.config >>> fcseed-sess -s Control22_FS -cfg MRS_MASK.config >>> >>> ...Writing to >>> /Applications/freesurfer/subjects/fMRI/Control22_FS/rest/001/tmp. fcseed- >>> sess.12305/avgwf.mgh >>> Segmentation fault >>> >>> Therefore, according with your suggestion, I have now run: >>> fcseed-sess -debug -s -cfg MRS_MASK.config | & tee doug.log >>> ERROR: cound not find session -cfg >>> >>> The doug.log is attached. >>> >>> Thanks, >>> >>> >>> Stefano >>> >>> >>> >>> >>>> ----Messaggio originale---- >>>> Da:greve@nmr.mgh.harvard.edu >>>> Data: 4-nov-2015 16.58 >>>> A:<freesurfer(a)nmr.mgh.harvard.edu> >>>> Ogg: Re: [Freesurfer] error MRS voxel as seed in FS-FAST >>>> >>>> First, when running fcseed-config, don't give it the full path, just >>> the >>>> path relative to subject/mri (in this case only MRS_MASK.mgz) >>>> >>>> However, I don't think that is the problem. Please run >>>> >>>> fcseed-sess -debug -s -cfg MRS_MASK.config |& tee doug.log >>>> >>>> and send me doug.log >>>> >>>> >>>> >>>> >>>> >>>> On 11/04/2015 04:14 AM,stdp82(a)virgilio.it wrote: >>>>> Hi list, this error is still occurring: >>>>> >>>>> mri_convert $SUBJECTS_DIR/subj/mri/MRS_MASK.nii.gz >>>>> $SUBJECTS_DIR//subj/mri/MRS_MASK.mgz >>>>> fcseed-config -segid 1 -seg $SUBJECTS_DIR//subj/mri/MRS_MASK. mgz - >>> fsd >>>>> rest -mean -cfg MRS_MASK.config >>>>> fcseed-sess -s -cfg MRS_MASK.config >>>>> >>>>> During >>>>> >>>>> fcseed-sess -s subj -cfg MRS_MASK.config >>>>> >>>>> Voxel Volume is 64.5752 mm^3 >>>>> Generating list of segmentation ids >>>>> Found 1 segmentations >>>>> Computing statistics for each segmentation >>>>> 0 1 0 0.000 >>>>> MRIalloc(0, 1, 1): bad parm >>>>> Reporting on 0 segmentations >>>>> Computing spatial average of each frame >>>>> >>>>> Writing to /Applications/freesurfer/subjects/fMRI/sub/rest/001/tmp. >>>>> fcseed-sess.97908/avgwf.mgh >>>>> Segmentation fault >>>>> >>>>> I have read your previous message and you can check the MRS voxel >>>>> features. >>>>> MRS voxel mask is in subj directory where I have run recon all - >>> all. >>>>> data_type FLOAT32 >>>>> dim1 256 >>>>> dim2 256 >>>>> dim3 256 >>>>> dim4 1 >>>>> datatype 16 >>>>> pixdim1 1.000000 >>>>> pixdim2 1.000000 >>>>> pixdim3 1.000000 >>>>> pixdim4 0.010747 >>>>> cal_max 0.0000 >>>>> cal_min 0.0000 >>>>> file_type NIFTI-1+ >>>>> >>>>> >>>>> The features are same of other subject that runs fine. >>>>> data_type FLOAT32 >>>>> dim1 256 >>>>> dim2 256 >>>>> dim3 256 >>>>> dim4 1 >>>>> datatype 16 >>>>> pixdim1 1.000000 >>>>> pixdim2 1.000000 >>>>> pixdim3 1.000000 >>>>> pixdim4 0.010747 >>>>> cal_max 0.0000 >>>>> cal_min 0.0000 >>>>> file_type NIFTI-1+ >>>>> >>>>> Thank you very much. >>>>> >>>>> >>>>> Stefano >>>>> >>>>> >>>>>> ----Messaggio originale---- >>>>>> Da:stdp82@virgilio.it >>>>>> Data: 16-ott-2015 23.15 >>>>>> A:<freesurfer(a)nmr.mgh.harvard.edu> >>>>>> Ogg: [Freesurfer] R: Re: R: import FS-FAST results in FSL >>>>>> >>>>>> I'd like to open with FSLview the sig.nii.gz which is produced by >>>>>> selxavg3-sess. >>>>>> If I use mri_surf2vol, which is the template to added in -- >>> template? >>>>>> It should be in Tailairach space? Where can I find the template >>> that >>>>> I >>>>>> should added? >>>>>> Thanks, >>>>>> >>>>>> Stefano >>>>>> >>>>>> subj/rest/fc.seed.surf.lh/L_seed/sig.nii.gz >>>>>> data_type FLOAT32 >>>>>> dim1 27307 >>>>>> dim2 1 >>>>>> dim3 6 >>>>>> dim4 1 >>>>>> datatype 16 >>>>>> pixdim1 1.000000 >>>>>> pixdim2 1.000000 >>>>>> pixdim3 1.000000 >>>>>> pixdim4 1100.000000 >>>>>> cal_max 49.1815 >>>>>> cal_min -12.3855 >>>>>> file_type NIFTI-1+ >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> Thanks, >>>>>> >>>>>> Stefano >>>>>> >>>>>> >>>>>>> ----Messaggio originale---- >>>>>>> Da:greve@nmr.mgh.harvard.edu >>>>>>> Data: 29-set-2015 22.09 >>>>>>> A:<freesurfer(a)nmr.mgh.harvard.edu> >>>>>>> Ogg: Re: [Freesurfer] R: import FS-FAST results in FSL >>>>>>> >>>>>>> Do you mean surface-based analysis? You'd have to put them back >>>>> into >>>>>> the >>>>>>> volume using mri_surf2vol, write them out as nifti and then run >>>>>> fslview >>>>>>> on them >>>>>>> >>>>>>> On 09/29/2015 11:17 AM,stdp82(a)virgilio.it wrote: >>>>>>>> Hi list, >>>>>>>> >>>>>>>> I would like to import FS-FAST results (conjunction maps) >>> in >>>>>> FSL, >>>>>>>> opening them by fslview. >>>>>>>> Could you provide me any suggestion? >>>>>>>> >>>>>>>> Thank you very much >>>>>>>> Best regards, >>>>>>>> >>>>>>>> >>>>>>>> Stefano >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> _______________________________________________ >>>>>>>> Freesurfer mailing list >>>>>>>> Freesurfer(a)nmr.mgh.harvard.edu >>>>>>>> https://mail.nmr.mgh.harvard. edu/mailman/listinfo/freesurfer >>>>>>> -- >>>>>>> Douglas N. Greve, Ph.D. >>>>>>> MGH-NMR Center >>>>>>> greve(a)nmr.mgh.harvard.edu >>>>>>> Phone Number: 617-724-2358 >>>>>>> Fax: 617-726-7422 >>>>>>> >>>>>>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>>>>>> FileDrop:https://gate.nmr.mgh.harvard.edu/filedrop2 >>>>>>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>>>>>> Outgoing:ftp://surfer.nmr.mgh.harvard. >>>>>> edu/transfer/outgoing/flat/greve/ >>>>>>> _______________________________________________ >>>>>>> Freesurfer mailing list >>>>>>> Freesurfer(a)nmr.mgh.harvard.edu >>>>>>> https://mail.nmr.mgh.harvard. edu/mailman/listinfo/freesurfer >>>>>>> >>>>>>> >>>>>>> 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. >>>>>>> >>>>>>> >>>>>> _______________________________________________ >>>>>> Freesurfer mailing list >>>>>> Freesurfer(a)nmr.mgh.harvard.edu >>>>>> https://mail.nmr.mgh.harvard. edu/mailman/listinfo/freesurfer >>>>>> >>>>> _______________________________________________ >>>>> Freesurfer mailing list >>>>> Freesurfer(a)nmr.mgh.harvard.edu >>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>> >>>>> >>>> -- >>>> Douglas N. Greve, Ph.D. >>>> MGH-NMR Center >>>> greve(a)nmr.mgh.harvard.edu >>>> Phone Number: 617-724-2358 >>>> Fax: 617-726-7422 >>>> >>>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>>> FileDrop:https://gate.nmr.mgh.harvard.edu/filedrop2 >>>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>>> Outgoing:ftp://surfer.nmr.mgh.harvard. >>> edu/transfer/outgoing/flat/greve/ >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer(a)nmr.mgh.harvard.edu >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> >>>> >>>> >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer(a)nmr.mgh.harvard.edu >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >-- >Douglas N. Greve, Ph.D. >MGH-NMR Center >greve(a)nmr.mgh.harvard.edu >Phone Number: 617-724-2358 >Fax: 617-726-7422 > >Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >www.nmr.mgh.harvard.edu/facility/filedrop/index.html >Outgoing: ftp://surfer.nmr.mgh.harvard. edu/transfer/outgoing/flat/greve/ > >_______________________________________________ >Freesurfer mailing list >Freesurfer(a)nmr.mgh.harvard.edu >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >

2 1

Drawing a circle around a vertex on a surface
by Reza Rajimehr 09 Nov '15

09 Nov '15

Hi, I want to draw a circle around a vertex on the smoothwm or pial surface, with a particular radius (e.g. 10 mm), fill the circular region and save it as a label file, then repeat this for all the vertices on the surface. I need this for doing a searchlight analysis. Does anyone have a script/code for it? I know that mris_pmake (using Dijkstra's algorithm) can be used for this purpose, but I don't know exactly how to make it to work in a script for drawing circular ROIs. Thanks for any help! Reza

3 4

convert label to mgh
by Yang, Daniel 09 Nov '15

09 Nov '15

Dear FreeSurfer Experts, Is it possible to convert a label file to a surface-based mgh file? Could you please provide an example (e.g., on a white surface)? Best, Daniel -- Daniel Yang, Ph.D. Yale Child Study Center E-mail: daniel.yj.yang(a)yale.edu

2 2

Research Scientist job in fMRI data analysis
by Pablo Velasco 09 Nov '15

09 Nov '15

New York University is looking for an Assistant Research Scientist who will work with faculty in the Center for Brain Imaging (CBI) to help implement analysis techniques, establish data analysis streams, and to make state-of-the-art MR techniques such as multi-echo/multi-plexed BOLD fMRI, diffusion imaging, and advanced anatomical measurements available to the broader research community. Responsibilities include: - Assisting in training graduate students, postdocs, and new researchers in neuroimaging data collection and analysis, including use of FSL, SPM, Freesurfer, AFNI and Matlab-based toolboxes. - Consulting with researchers to select appropriate tools and methods for data analysis, including modern statistical techniques for multiple-comparisons correction, denoising, multivariate analyses, functional connectivity analyses, and surface-based analyses. - Technical support and training for faculty, staff, and students acquiring MRI data, primarily on Siemens Prisma scanner. - Organizing training workshops and seminars to expose researchers to new developments in imaging methods and analysis techniques. - Expertise in EEG and TMS a plus. Qualified applicants should have: - A PhD or equivalent experience in Psychology, Neuroscience, Mathematics, or Statistics. - Two years relevant experience or equivalent combination, which must include experience with MR imaging principles, research training, data acquisition and analysis, statistics, and/or signal processing. - Excellent interpersonal, organizational and writing skills. - Ability to effectively communicate with individuals of all levels. - Strong analytical skills. - Ability to multitask and work independently. Salary to be commensurate with experience. Interested individuals should contact Pablo Velasco, Ph.D. at pablo dot velasco at nyu dot edu New York University is an Equal Opportunity Employer. New York University is committed to a policy of equal treatment and opportunity in every aspect of its hiring and promotion process without regard to race, color, creed, religion, sex, pregnancy or childbirth (or related medical condition), sexual orientation, partnership status, gender and/or gender identity or expression, marital or parental status, national origin, ethnicity, alienage or citizenship status, veteran or military status, age, disability, predisposing genetic characteristics, domestic violence victim status, unemployment status, or any other legally protected basis. Women, racial and ethnic minorities, persons of minority sexual orientation or gender identity, individuals with disabilities, and veterans are encouraged to apply for vacant positions at all levels.

1 0

How to compute area of subcortical structures
by anirudh nihalani 09 Nov '15

09 Nov '15

Hi, I am trying to find how to compute the area of subcortical structures like amygdala, hippocampus, thalamus etc. I have checked stats/aseg.stats file but it doesn't have areas. I looked at mri_asegstats and mris_anatomicalstats commands. Using mris_anatomicalstats I am able to compute surface area of cortical structures. But I am unable to figure out how to compute area of subcortical structures. Please suggest or give some pointers on how to achieve this. Thank you. Regards, Anirudh

2 1

recon-all error message
by Nicole Zurcher 09 Nov '15

09 Nov '15

Dear all, One of my freesurfer recons is failing and I am not sure how to troubleshoot. This is the error message that I get at the end of the recon-all log file: mris_calc -o lh.area.mid lh.area add lh.area.pial WARNING: # of slices=-106 in header - assuming 124... read_signa([path]/surf/I.001): could not open file No such file or directory mris_calc: could not establish read access to 'lh.area'. No such file or directory and this is the command that appears in the recon-all.error CMD mris_calc -o lh.area.mid lh.area add lh.area.pial See attachment for entire recon-all log file. Any help is greatly appreciated. Thanks a lot Nicole

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