Freesurfer

freesurfer@nmr.mgh.harvard.edu

16 participants
30084 discussions

running freesurfer after talairach touch-ups...
by Ritobrato Datta 16 Jul '09

16 Jul '09

Hello all, I ran recon-all -autorecon-all -s <subjid> After it ran all the way through, I ran tkregister2 --mgz --s <subjid> --fstal --surf orig and saved everything with the SAVE REG button in the tkregister2 toolbar. Since I initially ran all the steps before the talairach touch-ups, what do I run to re-process the data and re-write with the new talairach modifications ? Do I have to use ' -force ' with the command ? I have a same question for the step, Using Control Points to Fix Intensity Normalization. What command do I run after I am done adding control points ? Thanks Ri

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ideal freesurfer input?
by Stephen Towler 16 Jul '09

16 Jul '09

Hi freesurfers, Are many groups getting good results from single 1mm isovoxel T1 inputs? Anyone experimented with multispectral input? We're acquiring a number of participants on a Philips Achieva 2.5 system with 8-ch SENSE coil. Good scans, very little movement. I realize that the selection of freesurfer inputs and averaging is empirically driven and idiosyncratic to each scanner/sequence/coil combination, but I just want to solicit any thoughts about possible benefit from non-standard sequences. Due to other priorities we are unable to collect two identical T1s in each study, but this is what we do get that might aid automated structural segmentation: - 3D T1 TFE (1 mm3, good contrast among gray, white, and CSF) - 3D T2 FLAIR (1 mm3, high gm/csf contrast but no gm/wm contrast, except for wm hyperintensities) - 3D T1 "FGATIR" (.75 mm3, very high gm/wm contrast but very low gm/ csf contrast) This last sequence is the one I'm most curious about: might the very high gm/wm contrast be used to help freesurfer's segmentation? Image attached, showing a participant's standard 3D T1 TFE on the right and the high g/w contrast T1 on the left. This paper describes the FGATIR sequence: Sudhyadhom, A., Haq, I. U., Foote, K. D., Okun, M. S., & Bova, F. J. (2009). A high resolution and high contrast MRI for differentiation of subcortical structures for DBS targeting: The Fast Gray Matter Acquisition T1 Inversion Recovery (FGATIR). NeuroImage. doi: 10.1016/ j.neuroimage.2009.04.018. Thanks! Stephen -- Stephen Towler Graduate Student, Neuropsychology Dept. Clinical and Health Psychology

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changing image orientation
by Jose Luis Cantero Lorente 16 Jul '09

16 Jul '09

Hi there, I got some mgz files badly reoriented (saggital right - nose bottom, and needed them in saggital left - nose up). Would it be feasible to change the reorientation and save them to mgz from the Freesurfer command line? Thanks in advance. Best, Jose --- Jose Luis Cantero, Ph.D. Laboratory of Functional Neuroscience Department of Physiology, Anatomy, and Cell Biology University Pablo de Olavide Ctra. de Utrera, Km.1 41013 - Sevilla - Spain - Phone: +34 954 977433 Fax: +34 954 349151 Email: jlcanlor(a)upo.es http://www.upo.es/neuroaging/en/

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Freeview for Mac
by jentis＠nmr.mgh.harvard.edu 16 Jul '09

16 Jul '09

Hi, I have a quick question: has freeview been compiled for an intel macbook pro? Thanks, Jon

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window refresh problem with freesurfer v4.4.0
by yzhangd＠artsci.wustl.edu 15 Jul '09

15 Jul '09

Whenever i try to open two windows(ie.' tkmedit bert orig.mgz 'and' tksurfer bert rh pial') the original one will not respond or refresh unless i close the second one,even i turn on the redraw button in the tksurfer. Also,i put the two windows side by side and did not overlay them. i've tried a few combinations, ie. two tkmedit windows, one tkmedit one tksurfer, etc. all of them have the same problem. any idea what's going on? thanks a lot Yuning Zhang 4525 scott ave, medical school,Washington University in St.Louis,63110 Phone:314-362-1219

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averaging mgz files
by Jose Luis Cantero Lorente 15 Jul '09

15 Jul '09

Hi there, is there any FS command to average two .mgz files from the same subject withouth going through the recons steps. I just need to obtain a new mgz file resulting from the average of several mprage of the same patient. Thanks in advance. Best, Jose --- Jose Luis Cantero, Ph.D. Laboratory of Functional Neuroscience Department of Physiology, Anatomy, and Cell Biology University Pablo de Olavide Ctra. de Utrera, Km.1 41013 - Sevilla - Spain - Phone: +34 954 977433 Fax: +34 954 349151 Email: jlcanlor(a)upo.es http://www.upo.es/neuroaging/es/

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Paper for Subcortical Parc
by Vina Goghari 15 Jul '09

15 Jul '09

Hi group, Is there a paper to cite for the subcortical parcellation done by FreeSurfer? Thanks, Vina

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Skip steps for only parcellation and segmentation?
by Renske de Boer 15 Jul '09

15 Jul '09

Hi, I want to run FreeSurfer on a large number of subjects, so I must reduce run time as much as possible. I'm only interested in the parcellation of the cortex and the subcortical segmentation. Are there any (timeconsuming) processing steps I can skip since I'm not interested in e.g. surfaces? Or is every step required to obtain the parcellation and segmentation? And if I only want the cortical parcellation? Thanks! Renske -- _____________________________________ Ms. Renske de Boer, MSc Biomedical Imaging Group Rotterdam Erasmus MC, University Medical Center Rotterdam, the Netherlands www.bigr.nl ______________________________________

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fsaverage flatmap
by Stephan Gerhard 15 Jul '09

15 Jul '09

Hi! I tried to convert the fsaverage rh.cortex.patch.flat to gifti with mris_convert lh.cortex.patch.flat lh.cortex.patch.flat.gii but gives me the error MRISalloc(16711682, 392): could not allocate vertices Cannot allocate memory Same error, when I want to load it in tksurfer with tksurfer fsaverage lh cortex.patch.flat I've got 4GB RAM, this should be enough. In the end, I'd like to display the flat map with an atlas overlayed. So, the number of vertices has to correspond to the number of vertices e.g. in lh.white, correct? Stephen

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making subject directory
by Barnali Basu 15 Jul '09

15 Jul '09

Experts I am stuck up with a real basic issue, which I have done easily manytimes in the older version. I have downloaded and installed the stable v4.4.0 version . I am trying to create a new subject directory, but its throwing the error cd subjects barnali-work:/usr/local/freesurfer/subjects> mksubjdirs ja mkdir: cannot create directory `ja': Permission denied ERROR: creating directory ja I tried doing chmod 755 from root, it says operation not possible. Where am I going wrong Thanks -- Barnali Basu Cell : 425 638 2936 Home: 206 257 0174

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Freesurfer