Freesurfer

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19 participants
30088 discussions

MP-RAGE protocol
by mustafa amin 20 May '19

20 May '19

External Email - Use Caution Dear Freesurfer experts, I need advice, the MRI operator need to confirm whether she had done the right protocol of MP-RAGE. I have attached the picture that has been taken by her. Please share some thoughts. Thank you in advance. Yours faithfully, Mustafa M. Amin Consultant Psychiatrist in Biological Psychiatry Department of Psychiatry Faculty of Medicine Universitas Sumatera Utara

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Postdoctoral position in multimodal neuroimaging on frontotemporal dementia
by Erik Lindberg 20 May '19

20 May '19

External Email - Use Caution Dear all, We are looking for a post-doc student for our lab at Karolinska institute in Stockholm. We are doing structural and functional MRI research on dementia. In current project we are acquiring multimodal MRI on frontotemporal dementia patients. We are also running an experimental fMRI paradigm on these patients. We are looking for a person that is well familiar with doing analysis of multimodal MRIs, to relate findings to other variables such as CSF-data, neuropsychology etc. See further: https://ki.mynetworkglobal.com/what:job/jobID:254449/

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mri_convert segmentation fault (core dumped) in v5.3 on centos6
by Caspar M. Schwiedrzik 20 May '19

20 May '19

External Email - Use Caution Hi! We are getting segmentation fault (core dumped) error when trying to run mri_convert on NIFTI files. This is running Freesurfer v5.3 on Centos6, specifically v1.179.2.7 of mri_convert. I suspect that this has to do with libcrypt incompatibilities described for other operating systems , e.g., here: https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2014-September/04052… and in the known issues list of v5.3. here https://surfer.nmr.mgh.harvard.edu/fswiki/PreviousReleaseNotes. We have libcrypt version 2.17 installed and do not have access to libcrypt-2.14.1.so. Is there a way to get libcrypt-2.14.1.so from you or is there another known workaround (other then updating to Freesurfer 6)? Thank you very much! Caspar

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statistical map in matlab
by Worker, Amanda 19 May '19

19 May '19

External Email - Use Caution Hi, I am working with cortical thickness data in matlab and I have a t-statistic map that I'd like to firstly write to .mgh/mgz format so that I can overlay it in freeview. And secondly, convert it to MNI space and write it out as a volume (preferably nifti). I think that save_mgh might be what I need but I don't understand what M is and how I would get that info for a statistical map in fsaverage space. Any ideas would be much appreciated. Thanks in advance, Amanda

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PetSurfer gtmpvc
by Boris Rauchmann 17 May '19

17 May '19

External Email - Use Caution Hi all, is there a way to easily get the volume stats for all regions after pvc correction using mri_gtmpvc ? I think its not included in gtm.stats.dat. Thanks, Boris

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Postdoctoral position in object and face recognition at NYU Abu Dhabi
by Olivia Cheung 17 May '19

17 May '19

External Email - Use Caution *Postdoctoral position in object and face recognition at NYU Abu Dhabi* A postdoctoral research position is open at the Objects and Knowledge Laboratory, headed by Dr. Olivia Cheung, at New York University Abu Dhabi ( http://www.oliviacheunglab.org/) The postdoctoral researcher will carry out behavioral and fMRI experiments on human object, face, letter, and/or scene recognition. Potential research projects include, but are not limited to, investigations of the influences of experience and conceptual knowledge on recognition processes. Applicants must have a Ph.D. in Psychology, Cognitive Neuroscience, or a related field, and should possess strong programming skills (e.g., Matlab). Prior experience with neuroimaging and psychophysical techniques is highly preferred. Initial appointment is for up to two years. Starting date is flexible, preferably between August/September 2019. The Objects and Knowledge Laboratory is part of the rapidly growing Psychology division at New York University Abu Dhabi. The lab is located in the campus on Saadiyat Island (Abu Dhabi’s cultural hub), and has access to the state-of-the-art neuroimaging and behavioral facilities (including MRI, MEG, eyetracking). Apart from a generous salary, the postdoctoral researcher will receive housing and other benefits. More information about living in Abu Dhabi can be found here: http://nyuad.nyu.edu/en/campus-life/residential-education-and-housing/livin… New York University has established itself as a Global Network University, a multi-site, organically connected network encompassing key global cities and idea capitals. The network has three foundational degree-granting campuses: New York, Abu Dhabi, and Shanghai, complimented by a network of eleven research and study-away sites across five continents. Faculty and students circulate within this global network in pursuit of common research interests and the promotion of cross-cultural and interdisciplinary solutions for problems both local and global. Informal inquiries regarding the position, university, or area, are encouraged. To apply, individuals should email a curriculum vita, a brief statement of research interests, the expected date of availability, and contact information of two referees. All correspondence should be sent to Olivia Cheung (olivia.cheung(a)nyu.edu) **Olivia Cheung is at the Vision Sciences Society (VSS) conference this week and will be happy to meet with any individuals who are interested in learning more about the position.**

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(no subject)
by Boris Rauchmann 17 May '19

17 May '19

External Email - Use Caution Dear Freesurfer community, I am trying to extract SUV values from sub-cortical segmentation or gtmseg I don t want to use any PVC. I used the following commands: gtmseg --s xyz then mri_coreg --s xyz --mov abetapet.nii.gz --reg abetapet.reg.lta following mri_vol2vol --mov abetapet.nii --reg abetapet.reg.lta --targ orig.mgz --o abetapet.sm00.nii.gz and mri_segstats --annot xyz lh gtmseg --i abetapet.sm00.nii.gz --sum xyz_abeta.stats resulting in this dimension mismatch error: input 256 256 256 seg 416 450 476 Is that the correct way for doing this analysis? any suggestions how to solve the mismatch error? Thanks, Boris

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Generating cortical correspondence vectors
by K. Wagstyl 17 May '19

17 May '19

External Email - Use Caution Hello FreeSurfer Developers, I'm interested in regenerating cortical correspondence vectors between pial and white surfaces as described in "Microstructural parcellation of the human brain." Is this currently the default way that freesurfer extracts the vectors/surfaces? Or is there flag/separate code to generate these vectors? Thanks! Konrad

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brainstem - partial volume effect
by Dusan Hirjak 16 May '19

16 May '19

External Email - Use Caution Dear Freesurfer experts, I have one question regarding the partial volume effects on brainstem volume when using Freesurfer 6.0 brainstem tool: Could partial volume effects in a comparatively small sample (n=92) have an influence on the results (group difference in SCP volumes)? How should I deal with this effect? Any suggestions are welcome. best regards Dusan

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Re: [Freesurfer] brainstem - partial volume effects
by Iglesias Gonzalez, Eugenio 16 May '19

16 May '19

External Email - Use Caution Hi Dusan, Volumes are computed from soft segmentations, which ameliorates the problems with partial voluming with the surrounding CSF. Kind regards, /Eugenio -- Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.com From: <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of Dusan Hirjak <dusanhirjak(a)hotmail.com> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Date: Thursday, 16 May 2019 at 16:21 To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu>, "freesurfer-request(a)nmr.mgh.harvard.edu" <freesurfer-request(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] brainstem - partial volume effects External Email - Use Caution Dear Freesurfer experts, I have one question regarding the partial volume effects on brainstem volume when using Freesurfer 6.0 brainstem tool: Could partial volume effects in a comparatively small sample (n=92) have an influence on the results (group difference in SCP volumes)? How should I deal with this effect? Any suggestions are welcome. best regards Dusan

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