Freesurfer

freesurfer@nmr.mgh.harvard.edu

30132 discussions

Qdec/Tksurfer keyboard input error
by Victor Montal Blancafort 31 May '17

31 May '17

Dear Freesurfer experts: Recently, I have update my OS to Ubutnu 16.04. Afterwards, I tried to re-run some analysis using Qdec 1.4 (stable 5.1) and Qdec 1.5 (stable 6.0). However, I am not able to input any threshold via my keyboard (neither the Subjects or Display tab). This issue also happens when I try to use tksurfer. I have seen several posts regarding this issue in the mail-list, but none of them received any answer. Any insight would be really appreciated. Thank you in advance, Victor M.

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mri_annotation2label No such file or directory
by Duy Nguyen 30 May '17

30 May '17

Dear FreeSurfer experts I am trying to extract the label using standard aparc.annot and will be using mri_mergelabels to create my own lobes to do GLM fit later on for ROI analysis. However, it shows me the error like this when I check there are the files aparc.annot and the file from surf folder. [toibigi2007@localhost OASIS_Data]$ mri_annotation2label --subject OASIS_0002_MR1 --hemi lh --outdir $SUBJECTS_DIR/OASIS_0002_MR1/label subject = OASIS_0002_MR1 annotation = aparc hemi = lh outdir = /media/3B110EAE3B9DE8E0/OASIS_Data/OASIS_0002_MR1/label surface = white ERROR: creating directory /media/3B110EAE3B9DE8E0/OASIS_Data/OASIS_0002_MR1/label No such file or directory One more question is that it says default is "white" surface, but I want to measure the cortical thickness. Can I leave white in like this or do I change into --surf to gray for this? Thank you and best regards, *--v-- Peace --v--* *Duy Nguyễn * *Biomedical Engineering Department- IU HCMC* *Cell: (+84)909999056* *Email: duy.nguyenbme(a)gmail.com <duy.nguyenbme(a)gmail.com>*

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Problem with Recon-All for Volmetric
by Becker, Valerie 30 May '17

30 May '17

Hi all, Forgive me, as I' new at this, but I cant seem to quite make heads or tails of the Recon-all page with instructions on how to divide it the commands. We're just trying to run individual volumetric analyses at the moment. Is there a way to do that with a recon- proc? So as to shorten processing time? Thanks, Valerie UT Dallas

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FDR implementations
by Mihaela Stefan 30 May '17

30 May '17

Dear FreeSurfers, I have a ROI that I want to correct with FDR. I found that FreeSurfer has different implementations of FDR correction and all of them give different results. My ROI has 4205 vertices with p values between -5.0366 and 1.1673. When I set FDR in tksurfer (MRISfdr2vwth), I get p threshold 3.8765. According to a post in the mail archive ( https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=subj… ) I should get the same results using fast_fdrthresh matlab function in the fsfast toolbox. However, I get 4.0911. If I use lme_mass_FDR, I get 5.0911, while lme_mass_FDR2 gives 1.9501. Where can I find MRISfdr2vwth and why MRISfdr2vwth and fast_fdrthresh don't give me the same results? Could it be that MRISfdr2vwth seems to use all the vertices in sig.map? MRISfdr2vwth(): np = 163842, nv = 163842, fdr = 0.05, vwth=3.8765 MRISfdr2vwth(rate=0.050000, sign=0, 1, only_marked=0) = 3.876498 surfer: MRISfdr2vwth with rate 0.05 and sign 0 returned threshold 3.876498 I used this command in matlab: pthreshFS=fast_fdrthresh(p(maskvtx),0.05), where maskvtx=4205. Which FDR implementation should I use? Based on other posts, lme_mass_FDR2 seems to be preferred. I am just trying to understand these functions and use them appropriately. Thank you! Mihaela

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Project volumes in MNI to lrsym_fsaverage6
by Meiling Li 30 May '17

30 May '17

Dear freesurfer experts I have processed resting state fMRI data in MNI space , for example: Data: 91*109*91*240, 240 was the time frames number. How could i project the data in MNI space to the symmetric surface(eg lrsym_fsaverage6) ? Thanks in advance! Meiling

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Thickness from ROI_mask.label
by stdp82＠virgilio.it 30 May '17

30 May '17

Hi list,is possible to calculate the thickness of a ROI_mask.label which I have drawn using tksurf?Please could you suggest a command line?ThanksStefano

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Regarding: Comparing hippocampal volume from different scanners for two different population
by Dr Sampada Sinha 30 May '17

30 May '17

Dear freesurfer experts, I am presently trying to calculate hippocampal volume for two different study groups. One study group images (MDD) was acquired on 1.5T and the other age-matched study group (Healthy controls) on 3T MRI. On doing the statistics I have significant differences in the hippocampal volume correlating with their cognitive scores between the two study groups. Do I need to take into consideration different scanner parameters when doing the statistics? How do I go about it? Thanks for your help. Kind regards, Sam -- Dr Sampada Sinha Research medical scientist (B) Department of Geriatric Mental Health (DGMH) King George Medical University Lucknow-226003 , Uttar Pradesh India

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Postdoctoral Fellow at Emory University
by Junjie Wu 30 May '17

30 May '17

The Emory University School of Medicine is seeking two postdoctoral fellows to join the research team of the Emory Healthy Brain Study (EHBS), a $25 million project, and to work on the development, application, and analysis of novel magnetic resonance imaging (MRI) techniques focusing primarily on the brains of healthy 50-70 year-old adults as well as patients with mild cognitive impairments (http://healthyaging.emory.edu) Applicants must have a doctoral degree in physics, engineering, neuroscience or a related field. Experience in one or more of the advanced MR techniques are desirable such as arterial spin labeling, spectroscopy, diffusion imaging, functional connectivity, vascular reactivity and quantitative susceptibility imaging as well machine-learning methods for developing predictive models. Experience with MR pulse sequence design and programming is a plus but not necessary. Above all, we are looking for bright candidates with a passion in research. The size and scope of the project provide an outstanding platform for position holders to grow and prepare for next step of their careers, with close interactions with MR physicists, radiologists, neuroscientists, etc. A Siemens 3T PRISMA scanner is dedicated to the study and access to other state-of-the-art research resources on Emory campus is also available including additional two research-dedicated Siemens 3T PRISMA Siemens (two PRISMA and the other Tim-Trio) scanners, one human PET scanner, one 9.4T animal MR scanner, and a powerful GPU-equipped computer cluster. Position is available immediately. To apply please visit http://hr.emory.edu/careers and then search within the Staff Positions for job requisition 63047BR in the search field. If you have questions about this position please email: Deqiang Qiu, PhD (dqiu3(a)emory.edu) and Bruce Crosson, PhD (bruce.crosson(a)emory.edu) Emory University is an EEO/AA/Disability/Veteran Employer

1 0

Gray matter volume calculation
by Josue Luiz Dalboni Da Rocha 30 May '17

30 May '17

Dear Freesurfer team, We are analyzing the gray matter volume of some customized labels, using mris_anatomical_stats. We are wondering about some characteristics of the obtained volume. Is the volume of a label (as calculated by mris_anatomical_stats) the sum of the volume elements of each vertex contained in that label (considering the volume elements per vertices stored in the file '?h.volume' inside the 'surf' folder)? Is the 'volume element per vertex' (?h.volume) calculated from the 'white surface area element per vertex' (?h.white), 'pial surface area element per vertex' (?h.pial) and 'thickness element per vertex' (?h.thickness) ? What would be the formula to calculate 'volume element per vertex'? Bests, Josue

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PETSURFER - smooth question
by Eduard Vilaplana Martinez 30 May '17

30 May '17

Dear FS experts, I've been working with the proposed pipeline, but I still have a doubt regarding the degree of smooth to be applied to the final surfaces prior to the analyses. The first question is that, given a "standard" PET scanner, with a PSF between 5-8mm, what size smooth would you apply? Would 10mm or 15mm be reasonable (as for MRI)? The second question is if it is correct, in your opinion, to use the same size of smooth kernel for a multimodal PET and MRI analysis (i.e., local intermodality correlations, for example FDG and MRI)? Or, given the more smooth nature of the PET signal, would you apply a lower degree of smooth to the final PET surface? Thanks in advance for your advices, Edu V.

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