Freesurfer

freesurfer@nmr.mgh.harvard.edu

30132 discussions

Mean Curvature
by Kasper Jessen 09 Mar '18

09 Mar '18

Hej FreeSurfer, Question regarding the meancurv extracted from the Desikan atlas using aparcstats2table. Is the meancurv the absolute mean curvature? Thus all the values are positive? Best regards Kasper Sent from [ProtonMail](https://protonmail.com), Swiss-based encrypted email. Sent with [ProtonMail](https://protonmail.com) Secure Email.

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Brainstem registration
by Chungmin Han 08 Mar '18

08 Mar '18

Dear whomever it may concern, I'm Chungmin, a graduate research assistant in University of Texas at Austin, I'm fairly new to using freesurfer, I'd appreciate to get some advice on what I'm facing, I have fMRI limited FOV collected on brainstem + little cerebellum/visual area, I've tried SPM manual registration to MNI space, falls in 1-2mm (1-2 voxels) away from accurate registering brainstem correctly, is there a way to create transformation matrix optimized to fit brainstem in MNI space? Registering cortical region slightly bit wrong is okay to me at this moment, https://surfer.nmr.mgh.harvard.edu/fswiki/BrainstemSubstructures I've noticed this has been posted pretty recently, but would like to figure out how to align in standard space for comparison. I've also thought of inverse registering from MNI to each native space, however, if the transformation focuses on maximizing registration on the cortical level (T1) I don't think inverse registration solves the issue, Thank you in advance :) Best Chungmin Chungmin Han Graduate Research Assistant The University of Texas at Austin 204 E. Dean Keeton St Austin TX 78712 Mobile: 512-717-1671

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Question regarding recon-all
by Levitas, Daniel 08 Mar '18

08 Mar '18

Hello, I am running recon-all for the first time, and I am wondering when it is proper to use the -i option. My current recon-all command includes the -i option: recon-all -i T1.nii.gz -s 1020 -all, where T1.nii.gz is a nifti file of all 160 anatomical dicoms. I've seen some commands like this however: recon-all -s subjid -all?. My question is, is it safer to specify the input, and if I choose not to, do I need to create an mri/orig/001.mgz file from mri_convert? Thank you for the help, Dan

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FreeSurfer Edit Sequence Inquiry
by David S Lee 08 Mar '18

08 Mar '18

Hello FreeSurfer Group, I am writing to inquire about Editing Sequence. The "Troubleshooting your output" page (https://surfer.nmr.mgh. harvard.edu/fswiki/FsTutorial/TroubleshootingData) explains the edits sequence as brain mask --> wm volume --> white surface --> control points. Do you suggest people to absolutely stick to this particular sequence? Thanks for your time, David

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Eliminate variable which is the same for all patients from FreeSurfer's Design Matrix
by k.ohmstedt＠stud.uni-heidelberg.de 08 Mar '18

08 Mar '18

Dear all, I am trying to correlate psychometric measurements and the local Gyrification Index. To do so, I use the FreeSurfer pipeline to calculate the lGI and then PALM, following the advice in this thread (https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2017-March/050703.ht…) All my subjects are part of the same group, so I used a FSGD with the group "main" to create the design matrix and mask for my data that are required by PALM. Having a closer look at the design matrix that was created, I found that there was a variable for the group that was the same for all my patients. As it is the same for all patients, I thought eliminating it would not be a problem. But after re-running PALM without it, there were huge differences in my results and effects were notably larger and more significant. Do any of you have any experience which option is best in this case? Is it a valid choice to eliminate the variable for the group, as it is the same for each patient anyway? Furthermore, would you recommend centering for the design matrix? I found that this can have an impact, but I am lost on in which cases it should be done and in which it shouldn't. Thank you for your help! Best regards Kai Ohmstedt

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[Freesurfer/Freeview cutting]
by Dave Yas 08 Mar '18

08 Mar '18

Hello, Can we cut the surface (for flatting later) in freeview? if yes, how? I cant find a tutorial online for that. tksurfer is not working, it crashes by it self. If i cant use freeview to cut, do you suggest another alternative? thank you

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Brain microstructure MRI postdoc (Italy)
by Jovicich, Jorge 08 Mar '18

08 Mar '18

Hello, We will soon advertise a 2-year postdoctoral fellowship at the MRI Group <http://r.unitn.it/en/cimec/mri> of the Center for Mind/Brain Sciences (CIMeC <http://www.cimec.unitn.it/en>), University of Trento <http://www.unitn.it/en/>, Italy. The focus of this position will involve the development, testing and validation of MRI techniques that allow quantification of tissue microstructure properties. The successful candidate will be part of an international multidisciplinary team developing and applying MRI techniques to study brain structure and function supporting normal higher cognitive function as well as the study of cognitive dysfunction in various neurological and neuropsychiatric conditions (including pre-surgical planning, plasticity in deaf and blind, novel markers sensitive to the progression of neurodegenerative diseases). Facilities: The CIMeC MRI neuroimaging lab will house a Siemens Prisma 3T scanner (tentatively May 2018) designed for research and clinical studies. The position will allow for training opportunities in pulse sequence development, brain anatomy, and translational clinical research. The fellow is expected to be able to work independently as well as part of a multidisciplinary team with supervisory responsibilities of graduate student research. The fellow will support research MRI users, will have opportunities to develop new ideas and advance their own research interests in an international academic environment. Requirements: Minimum qualifications are a doctoral degree in cognitive neurosciences, physics, engineering, computer sciences or related area, strong scientific publication record, and demonstrated expertise in MRI methods development and applications. The ideal candidates should be proficient in programming, such as C++, Matlab. Experience in pulse sequence design, particularly on Siemens platform, and/or image reconstruction will be a plus. Additional requirements include high self-motivation, ability of solving research problems independently, and excellent communication skills. Contact: Interested candidates please contact Jorge Jovicich, Ph.D, MSc., Assistant Professor (jorge.jovicich(a)unitn.it) -- Jorge Jovicich, Ph.D. MR Lab Head Center for Mind/Brain Sciences University of Trento, Via delle Regole, 101 38100 Mattarello (TN) Italy Telephone: +39-0461-28 3064 Fax: +39-0461-28-3066 Email: jorge.jovicich(a)unitn.it MRI Methods Group: http://r.unitn.it/en/cimec/mri CIMEC: http://www.cimec.unitn.it/

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Jin, David S. wants to share the file alreadyexists_recon-all.log with you
by Jin, David S. 07 Mar '18

07 Mar '18

To view alreadyexists_recon-all.log, sign in<https://partnershealthcare-my.sharepoint.com/personal/david_jin_mgh_harvard…> or create an account.

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Collecting 2 T1s Best?
by Alessandra Macbeth 07 Mar '18

07 Mar '18

Hi there, I know in the past, it was recommended to acquire 2 T1 scans so that they could be averaged for better SNR, etc. in order to improve cortical thickness and surface area measurements. Is this still the recommendation? We have a few extra minutes in our scanning protocol and are debating whether to include a 2nd T1. Our parameters are: MPRAGE with .8mm^3 voxel size, slice thickness of .8, FA = 8 degrees, TR = 2400ms, TE = 2.72ms, TI = 1060ms. Best, Alessandra -- Alessandra Macbeth, M.A. Doctoral Candidate - Department of Psychology University of California, Riverside

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lh.BA_exvivo.annot Already Exists Error
by Jin, David S. 07 Mar '18

07 Mar '18

Hi, On our machine, with FS6, when we try to run recon-all, FS throws an error of "lh.BA_exvivo.annot already exists" . However, upon deleting lh.BA_exvivo.annot, it still gives the same error. Has anybody else encountered this? Many thanks, David

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