Freesurfer

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30086 discussions

Postdoc Opportunity in Montréal
by Lussier,Desiree 31 Aug '20

31 Aug '20

External Email - Use Caution Seeking Postdoctoral Fellow for Multiomics Investigations in Neurodegenerative Diseases The Multiomics Investigation of Neurodegenerative Diseases Lab, directed by Dr. AmanPreet Badhwar, is looking for a postdoctoral fellow. The successful candidate will leverage extensive datasets (neuroimaging, molecular ‘omics’ and clinical/neuropsychological data) to test hypotheses linking multiomics changes to age-related dementias, with an initial focus on Alzheimer’s disease and Vascular Cognitive Impairment and Dementia (VCID). The desired candidate is a motivated individual willing to work in a highly collaborative and multidisciplinary environment. The candidate is also expected to work closely with research teams with expertise in machine learning and AI, and she/he will have opportunities to build on, and/or develop these skills. Education and experience requirements * Prior training in Neuroscience (age-related dementias a plus) or Biomedical Engineering * Experience in structural MRI, resting-state functional MRI, brain connectivity * Knowledge of Matlab and/or Python programing * Expertise in statistics (SPSS, R, Nilearn/Nistats, or other) * Team-oriented; excellent organizational, interpersonal and communication skills * Experience in multivariate pattern analysis, computational modeling, and/or machine learning are all assets Start duration and salary The position is available beginning 2021 in the laboratory of Dr. AmanPreet Badhwar, located at the Centre de Recherche de l’Institut Universitaire de Gériatrie de Montréal (CRIUGM), University of Montreal, Montreal, Canada. Funding is available for 1 year, renewable, but selected candidates are expected to apply for external fellowships. Candidates must be a Canadian citizen/permanent resident or be eligible to work in Canada (after obtaining an appropriate visa). Contact Applicants should submit a cover letter stating their research interests and experience, together with a CV, transcripts, and contact information for two reference writers. Please send as a single PDF via email with the subject heading “ApplicantName_Postdoctoral_Applicant” to Dr. AmanPreet Badhwar at amanpreet.badhwar(a)criugm.qc.ca<mailto:amanpreet.badhwar@criugm.qc.ca>. Applications will be accepted until the position is filled.

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How to re-run recon-all
by Camargo, Aldo 29 Aug '20

29 Aug '20

External Email - Use Caution Hi Freeserufer experts: By mistake I cancel the recon-all when it was about 3 hours of processing. There is a way to re-run the recon-all and that continues where it was stopped ? Thanks a lot, Aldo

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How can I get only aparc+aseg.mgz
by Camargo, Aldo 28 Aug '20

28 Aug '20

External Email - Use Caution Hi Freesurfer experts: I would like to get the aparc+aseg.mgz file, which options of recon-all should I use to get only that file. Because recon-all takes several hours. Have a nice day, Aldo

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Question about LGI stats file
by Lab of Autism and Developmental Neuroscience, Lab of Autism and Developmental Neuroscience 28 Aug '20

28 Aug '20

External Email - Use Caution Dear FreeSurfer experts, Hope this email finds you well. I was wondering if someone could please help clarify some components of the LGI pipeline. So the wiki tells us the following command needs to be done to obtain a stats file with the LGI info for one subject: mri_segstats --annot my_subject_id lh aparc --i $SUBJECTS_DIR/my_subject_id/surf/lh.pial_lgi --sum lh.aparc.pial_lgi.stats Should I perform this for each subject and then join them all into one file? I was hoping that you guys could direct me to some stats2table command that could do all of this automatically and thus be less time consuming. Thank you and stay safe All the best, Alex

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Covariates vs sample size
by Sunil Khokhar 28 Aug '20

28 Aug '20

External Email - Use Caution Dear Experts, With a sample size of 45, can I perform GLM analysis with one primary independent variable and 6 covariates? Dependent variable is cortical thickness. Thanks in advance! Sunil.

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missing one tract but differently for a few subjects
by Zeng, Qi 27 Aug '20

27 Aug '20

External Email - Use Caution Hi, When I examined the 18 tracts of /dpath results, a few subjects were found missing one tract but differently, for example, fmajor were missing for one subject and the other one was missing lh.slfp and rh.slfp. I was thinking could it be that AP-PA was flipped. Attached screenshots of dtifit_FA.nii, aparc+seg_mask.nii, and bvec. Can you provide some information about the flip so that I can examine it for the rest of the subjects? Best, Qi

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Visualizing significant clusters, monte-carlo and permutation
by Avi Gharehgazlou 27 Aug '20

27 Aug '20

External Email - Use Caution Hi experts, I am a bit confused with visualizing my significant clusters after having corrected my results for multiple comparisons. after running mri_glmfit, I corrected with monte carlo and permutation as explained below, will you please confirm my understanding below is correct ? 1. I ran monte carlo simulation (1.3 sig level). My understanding is that "cache.th13.abs.sig.cluster.summary" shows the clusters that are significant after correction for multiple comparisons. I have 1 cluster listed in this file. Thus, I am interpreting this as having 1 significant cluster after correction at p<0.05, is this correct? When I want to visualize my corrected results I use the command line below. I am assuming this command line displays only the significant clusters that survived multiple comparison correction because only the cluster that is listed in my "cache.th13.abs.sig.cluster.summary" file appears on the brain here, and because I have put " cache.th13.abs.sig.cluster.mgh" and as overlay " cache.th13.abs.sig.ocn.annot" and set the threshold to 1.3 in my command line. Is it correct that the cluster that appears when running the below command line is my significant cluster surviving multiple comparisons correction at p<0.05? vglrun freeview -f $SUBJECTS_DIR/fsaverage/surf/lh.inflated :overlay=lh.lgi.TD_PTSD_age_SA_IQ_FWHM0.glmdir/group.diff/cache.th13.abs.sig.cluster.mgh:overlay_ threshold=1.3,5:annot=lh.lgi.TD_PTSD_age_SA_IQ_FWHM0.glmdir/group.diff/cache.th13.abs.sig.ocn.annot -viewport 3d also, how can I get the clusters to look their appropriate colours when I am vieweing them with the command line above? all my clusters appear gray (regardless of whether they have positive or negative max values, in which case they should be yellow and blue, respectively) 2. I then ran permutation testing. My "perm.th13.abs.sig.cluster.summary" file is blank. I interpret this as no clusters having survived multiple comparison correction with permutation testing. Am I correct? When I use the below command line to visualize my result I see a blank brain (with no clusters coloured). Which makes sense to me because my "perm.th13.abs.sig.cluster.summary" also showed no significant clusters. is this interpretation and the command line I am using below correct? vglrun freeview -f $SUBJECTS_DIR/fsaverage/surf/lh.inflated:overlay=lh.lgi.TD_PTSD_age_SA_IQ_FWHM0.glmdir/group.diff/perm.th13.abs.sig.cluster.mgh:overlay_threshold=1.3,5:annot=lh.lgi.TD_PTSD_age_SA_IQ_FWHM0.glmdir/group.diff/perm.th13.abs.sig.ocn.annot -viewport 3d -layout 1 I think my understanding is correct, but I am confused because the FreeSurfer instructions state that the above command lines will display "all clusters, regardless of significance"... but using the above command lines seems to only display my significant clusters. I am assuming this is because I set my threshold to 1.3 (the same threshold I used to correct for multiple comparisons in 1 and 2 above). But wanted to make sure I am correct before proceeding. Thank you so much for your support, Avi

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FW: RBV PVC
by Nathalie Mertens 27 Aug '20

27 Aug '20

External Email - Use Caution Dear, Many thanks for these explanations! Further, I do have 4 additional questions linked to the mask option when applying RBV PVC in Freesurfer. (1) Could you please tell me how the brainmask is generated when using the –auto-mask option, eg –-auto-mask 5 0.01. From which image is the generation of the mask started? (brain.mgz, brainmask.auto.mgz, brainmask.mgz, or something else?) (2) I noticed that the amount of segments (used in RBV PVC) is reduced (compared to amount of roi’s in gtmseg) after using the mask. Can you explain this? (3) Could you please tell me when in the RBV PVC calculations this mask is applied? (4) I guess this mask has nothing to do with the ‘masking rbv to brain’, which is applied in the end when running the RBV PVC? Can you elaborate on this final step? Many thanks for your help. Kind regards, Nathalie Mertens On 8/19/2020 2:42 AM, Nathalie Mertens wrote: External Email - Use Caution Dear, I am not sure if the questions below were sent correctly to you, since I did not receive any copy of it. Please find my message below. Many thanks, looking forward to your reply. Kind regards, Nathalie Mertens sorry, did not see the original posting *Van: *Nathalie Mertens <nathalie.mert...(a)kuleuven.be> *Datum: *dinsdag 18 augustus 2020 om 09:33 *Aan: *"freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> *Onderwerp: *RBV PVC Dear, I do have some questions linked to RBV PVC implemented in Freesurfer: 1. Could you please tell me how the RBV PVC is acquired? Is the RBV PVC acquired based on Muller-Gartner (on a region-level, and based on only using gray- versus white matter), or when and how are the different regions from gtm_seg applied to obtain GTM? See the RBV paper. Thomas, B.A., Erlandsson, K., Modat, M., Thurfjell, L., Vandenberghe, R., Ourselin, S., Hutton, B.F., 2011. The importance of appropriate partial volume correction for PET quantification in Alzheimer's disease. Eur. J. Nucl. Med. Mol. Imaging 38, 1104\u20131119. 1. 2. What would be the advantage of using your technique compared to for instance sGTM? sGTM is ROI-only, RBV is voxelwise. 1. 2. Could you please tell me the difference in region-definition between aparc+aseg and the gtm_seg? (I saw that the latter contains less regions compared to aparc+aseg.) What is the reason to use the latter compared to the aparc+aseg, based on the definitions of the regions? (I know that gtm_seg is used which has a high resolution, but not quite sure, apart from the resolution, why you are not using aparc+aseg for the RBV PVC.) gtmseg.mgz is higher resolution (using the subvoxel surfaces). It also has pons and vermis defined. It has a few regions merged with others. It also has extracerebral structures. 1. 2. Is there a mask applied to the gtm_seg to exclude regions that are located outside the brain? No, it is a full head model. 1. Many thanks for your answers. Kind regards, Nathalie _______________________________________________ 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

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Segmentation of CT Scans
by mudassar liaq 27 Aug '20

27 Aug '20

External Email - Use Caution Hi, As far as I searched, Freesurfer does not segment CT Scans. Can anybody guide me to how I can segment Brain CT Scans in an automated way. (Any pointer or guiders are welcome). I have searched but couldn't find something similar to freesurfer (MRI). Thanks and Regards, Liaq.

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How to only include frontal and temporal lobes in surface based group analyses and multiple comparison correction
by Paul 27 Aug '20

27 Aug '20

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