Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30088 discussions

Myelinated cortical thickness ratio map
by Damien MARIE 22 Oct '18

22 Oct '18

External Email - Use Caution Dear experts, I am working with R1 maps that I project on the surface. The goal is to look at intra-cortical myelin. I detect interesting effects between two groups. Now I would like to compute myelinated cortical thickness ratio maps, in order to control for the effect of cortical thickness variations occurring with gyrification. Here is a paper where they describe a way to compute those myelinated cortical thickness ratio map with MIPAV and the MPI-CBS toolbox : https://www.ncbi.nlm.nih.gov/pubmed/29321232 <https://www.ncbi.nlm.nih.gov/pubmed/29321232> « The proportional thickness of the myelinated part of the cortex in relation to its overall thickness (myelinated cortical thickness) was computed with a fuzzy classification technique combining information about radial and tangential fibers. « 1- Is it possible to do the same in FreeSurfer? 2- What about dividing my individual myelin maps by the individual cortical thickness maps? Is it possible to do that in FreeSurfer? SPM ImCalc would do the job in the volume but I don’t know how I could do that in FreeSurfer. Any comments / other suggestions are welcome. Thank you and best, Damien

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postdoctoral research opportunity
by Bruce Fischl 22 Oct '18

22 Oct '18

FYI ---------- Forwarded message ---------- Date: Mon, 22 Oct 2018 12:16:59 -0700 From: Rahul Desikan <rahuldesikan(a)gmail.com> To: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> Subject: one more favor External Email - Use Caution One more favor Bruce. If possible could you please post this on the FS/FSL lists? Many thanks! Best, Rahul UCSF, Dept. of Radiology & Biomedical Imaging is seeking a Postdoctoral Scholar for The Laboratory for Precision Neuroimaging We are seeking a postdoctoral candidate with a strong background in genetics human imaging and a desire to use a multi-disciplinary approach to pursue neurodegenerative and neurodevelopment research. The candidate should have a strong statistical/computational background with experience with data analytic tools such as Matlab, R, and PLINK and potentially, MRI image analysis tools such as Freesurfer, FSL, and SPM. Applicants should have a Ph.D. or M.D. degree with less than five years of postdoctoral experience. Highly motivated individuals with a record of productive research are encouraged to apply. The position is available starting immediately. Salary is commensurate with qualifications and experience. Job Requirements: 1. CV/NIH biosketch (must contain previous research experience) 2. Cover Letter - Short statement on why you are interested in this position and how this position will help you achieve your career goals 3. Three references If interested please contact Dr. Leo Sugrue at leo.sugrue(a)ucsf.edu

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GE data issue
by Pan Yunzhi 22 Oct '18

22 Oct '18

External Email - Use Caution Dear sir/madam, I try to use TRACULSR to analysis DTI data of GE machine. But when I transfer origin data to nii, I found 2 nii file producted per sample. Can I use these data to run TRACULAR、 If yes, how can I combine 2 nii file? I hope someone can help me. Thank you so much Pan Yunzhi University of Western Ontario

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(no subject)
by Pan Yunzhi 22 Oct '18

22 Oct '18

External Email - Use Caution Dear freesurfer, I have some question about GE date (have 2 run) to run TRACULAR. How can I get some answers? Sent from Mail for Windows 10

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Which command generates the lh.area.pial.fsaverage.mgh file?
by ts+ml＠rcmd.org 22 Oct '18

22 Oct '18

External Email - Use Caution Dear FreeSurfer experts, I would like to know how to (re-)generate the files 'lh.area.pial.fsaverage.mgh' and 'rh.area.pial.fsaverage.mgh' for a subject (in the surf/ dir). I have tried the following: 1.) ensured that the source files, lh.area.pial and rh.area.pial, exist (under surf/). 2.) run: 'recon-all -s <subject> -qcache -measure area' But this does not generate the expected files (only those for the white surface). Any clues? Tim -- Dr. Tim Schäfer Postdoc Computational Neuroimaging Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany

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Re: [Freesurfer] leak of white surface into ventricles
by Antonin Skoch 21 Oct '18

21 Oct '18

External Email - Use Caution Hi Bruce, thanks for the feedback. Orig surface is NOT crossing the ventricle (screenshot: red - white surface, yellow - orig.nofix surface, blue - orig surface). In fact, there appears a topological defect in orig.nofix, which seems to be correctly fixed. It seems that the issue lies in recon-all -white step. I am using v6.0.0 version for this. Antonin Hi Antonin what does the orig surface look like? If it is crossing the ventricle and the orig.nofix is not, then there is a topogical defect that is causing the leakage cheers Bruce On Sat, 20 Oct 2018, Antonin Skoch wrote: External Email - Use Caution Dear experts, in several subjects I am encountering "leak" of white surface into ventricles (see screenshot with enlarged cursor indicating the problematic area). According to my experience, editing of aseg.presurf.mgz or wm.mgz does not help. orig.nofix surface seems OK (without leak into ventricle). Could you please advise how to correct this type of error? I have also uploaded example subject (named white_surface_in_ventricles.tar.gz) to your FTP server so that you can have a look. Regards, Antonin Skoch

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leak of white surface into ventricles
by Antonin Skoch 20 Oct '18

20 Oct '18

External Email - Use Caution Dear experts, in several subjects I am encountering "leak" of white surface into ventricles (see screenshot with enlarged cursor indicating the problematic area). According to my experience, editing of aseg.presurf.mgz or wm.mgz does not help. orig.nofix surface seems OK (without leak into ventricle). Could you please advise how to correct this type of error? I have also uploaded example subject (named white_surface_in_ventricles.tar.gz) to your FTP server so that you can have a look. Regards, Antonin Skoch

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Ask for your help about freesurfer submillimeter reconstruction!
by Nian Rui 20 Oct '18

20 Oct '18

External Email - Use Caution Dear FreeSurfer Developers, I am now working on the analysis of MRI images with the voxel resolution less than 0.2mm3. I read your webpage about submillimeter reconstruction, https://urldefense.proofpoint.com/v2/url?u=https-3A__surfer.nmr.mgh.harvard…, which said Freesurfer 6.0 works well for voxel sizes 0.75 mm3, and inputs with 0.5 mm3 voxels or below will have a brainmask failure (we are working on it!). So I am writing to ask for your help about the reconstruction with freesurfer. I would like to know, have you solved the higher resolution problem in the new version v6.0? Could I use it to analyze the cortical thickness of these MRI images now? If not, is there any other way to help processing these MRI images and we could run freesurfer step by step for evaluation? Look forward to your timely help! Thanks a lot in advance! yours sincerely, Rui

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acquisition protocols 3T Prisma
by Ammons, Carla 19 Oct '18

19 Oct '18

External Email - Use Caution Hello. Could you point me to any recommended acquisition protocols specific to longitudinal studies on a 3T Prisma (morphometry and fMRI)? Thanks! Carla Ammons, M.S. Doctoral Candidate | Medical Clinical Psychology University of Alabama at Birmingham

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Problems to run -autorecon2
by Rosalia Dacosta Aguayo 19 Oct '18

19 Oct '18

External Email - Use Caution Dear FreeSurfer team, I am trying to run recon -all -autorecon2 using the following command line: *recon-all -sd ~/Desktop/MS_STUDY/subjects -s 001 -i /home/rosalia/Desktop/MS_STUDY/subjects/001 -autorecon2* It is the same command I used yesterday to run -autorecon1 without problems. However, maybe now it is different. Should I point to another sub folder? I do not know which -i I should point out now. My directory for this subject is as follows: rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop/MS_STUDY/subjects/001/mri $ ls brainmask.auto.mgz nu.mgz rawavg.mgz brainmask.mgz orig T1.mgz mri_nu_correct.mni.log orig.mgz talairach_with_skull.log mri_nu_correct.mni.log.bak orig_nu.mgz transforms rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop/MS_STUDY/subjects/001/mri $ Best regards, Rosalia

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