Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30132 discussions

tksurfer inflated
by africa millan 25 Sep '09

25 Sep '09

Hello everybody, The image I enclose you in this mail (jpeg and gif format) represents 3 images ( the same region but different orientation) of a subject, corresponding to the inflated (tksurfer lh inflated) obtained after 4 times of recon 2 running. As you can see, there are several soft peaks that I couldn't remove although I repeated and corrected the segmentation three times. Do you think it is necessary to repeat the segmentation again? Thanks Africa. _________________________________________________________________ Nuevo Windows Live, un mundo lleno de posibilidades. Descúbrelo. http://www.microsoft.com/windows/windowslive/default.aspx

2 1

Labels for the auditory cortex
by Nasim Maleki 25 Sep '09

25 Sep '09

Dear developers, I was wondering if you would have labels for the Broadman areas corresponding to the auditory cortex for the fsaverage subject. Thank you, Nasim

2 1

how to use mri_surf2surf
by Guang Zeng 24 Sep '09

24 Sep '09

Hi, there, mri_surf2surf resamples one CorticalSurface onto another. If I have two subjects from different time points (tp1 and tp2), I'd like to compare the FreeSurfer analyzed surface data. For example, could I use mri_surf2surf to resample the white matter surface of tp1 onto tp2, so I can overlay the white matter surface of tp2 to tp1 using tkmedit? Thanks! guang _________________________________________________________________ Hotmail® has ever-growing storage! Don’t worry about storage limits. http://windowslive.com/Tutorial/Hotmail/Storage?ocid=TXT_TAGLM_WL_HM_Tutori…

3 2

Re: [Freesurfer] FSL to FreeSurfer registration
by Estephan Moana 24 Sep '09

24 Sep '09

Thanks for you input Michael. For some reason, I only saw your answer after Dougla's response. Assuming that I do not want to do volume-based analysis and just want "nice pics" of my blobs over a 3D brain, would Michael's suggestion work? If so, what is the next step after using fslroi, as the input for reg-feat2anat is a feat directory (an not a single example_func file)? An unrelated question: is there a way to get the FreeSurfer mailing list via a RSS feed? This would be help decrease the amount of emails in my inbox... Thanks again. Estephan

3 4

hippocampus volume difference
by Guang Zeng 24 Sep '09

24 Sep '09

Hi, there, I use the following matlab code to find right and left hippocampus in aseg.mgz %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% filename = 'case_1/mri/aseg.mgz'; [vol, M, mr_parms, volsz] = load_mgh(filename); hippo_left = find( (vol > 16.99) & (vol < 17.01) ); hippo_right = find( (vol > 52.99) & (vol < 53.01) ); %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% I found size(hippo_left, 1) = 3075; size(hippo_right, 1) = 3237; However, the value I found in aseg.mgz is 3162 3162.0 Left-Hippocampus 3390 3390.0 Right-Hippocampus Why these values are different (3075 < 3162, 3237 < 3390)? Thanks a lot! Guang _________________________________________________________________ Hotmail® has ever-growing storage! Don’t worry about storage limits. http://windowslive.com/Tutorial/Hotmail/Storage?ocid=TXT_TAGLM_WL_HM_Tutori…

2 1

cortex.label stats
by Dankner, Nathan (NIH/NIMH) [F] 24 Sep '09

24 Sep '09

Hi all, In past versions, I have been using this command to generate average cortical thickness across the cortex: Mris_anatomical_stats -l (hemi).cortex.label -f (id)/stats/(hemi).cortex.stats (id) (hemi) However, I have noticed that in version 4.5 the cortex.stats files are no longer in the stats folder. Are they somewhere else, or is there a different method which I should now use to compute these statistics?

2 1

fsgd and contrast matrix
by Martin Kavec 24 Sep '09

24 Sep '09

Hi, I would like to study cortical thickness in a cohort of patient with respect to MMSE and CDR. I prepared a fsgd file where I have both MMSE and CDR listed: GroupDescriptorFile 1 Title Mytitle Class Male Class Female Variable Age Variable MMSE Variable CDR Class Ctrl Class MCI Input subject1 Male 70 27 0.5 MCI Input subject2 Female 65 28 0 Ctrl My design matrix should thus have 4*(3+1)=16 columns/regressors. I am puzzeled a bit, how would I set the contrast matrix to study only correlation of thickness with MMSE, while ignoring CDR. Or should I have a separate fsgd file? Thanks, Martin

2 2

Re: [Freesurfer] FSL to FreeSurfer registration
by Douglas N Greve 24 Sep '09

24 Sep '09

Hi Michael, while fslmaths has an option to do "2D" smoothing, this is still only smoothing in a slice of the volume and has the same problems as 3D smoothing (ie, smoothing across tissue types and sulci). The "2D" that FS implements with mris_volsmooth is along the cortical surface, which is unrelated to the volume axes. So, unfortunately, you do still have to do two analyses if you want a volume-based analysis with smoothing. doug Michael Scheel wrote: > Hi Estephan, > > you don't necessarily have to rerun the full 1st level Analysis in total. > What you have to find out is which of your volumes is the one that > example_func is created from. > Normally this should be the middle timepoint fmri image of your > functional run (e.g. if you have 99 volumes then number 45 > will be taken as example_func) that's the default if you haven't > specified it otherwise. > You can use fslroi as a command to extract this volume for the above > example e.g.: > fslroi input_fmri.nii.gz middle_volume.nii.gz 44 1 > (fslroi starts counting from 0 thats why it is 44 instead of 45) > > 2D and 3D smoothing can also be done with > fslmaths see the -s and the -kernel option > > Best, Michael > On 23-Sep-09, at 6:52 PM, Douglas N Greve wrote: > >> >> >> Estephan Moana wrote: >>> So what I need to do is to run the 1st level FEAT as usual for the FSL >>> pipeline, and repeat this analysis for FS with the only difference >>> been to set the "Spatial smoothing FWHM" to zero on the pre-stats tab >>> of the FEAT GUI? >> yes >>> >>> Also, can you explain if this smoothing on the FEAT GUI is the 3D you >>> refer to? And how 2D smoothing is accomplished? >> Yes, this the 3D smoothing. 2D smoothing on the raw data is more >> difficult inside of feat. You'd have to use MC and then run >> mris_volsmooth (FS program) outside of FEAT, then pass FEAT the >> preprocessed data and tell it not to do MC or smoothing. >>> >>> Thank you. >>> >>> Estephan >>> >>> Douglas N Greve wrote: >>>> The example_func does not actually get smoothed, so smoothing itself >>>> will not affect the registration. 3D smoothing will smooth values >>>> from WM and CSF into gray and from across sulci into functionally >>>> distinct regions. For this reason we recommend not using 3D smoothing >>>> (or doing 2D smoothing on the surface). Unfortunately, this requires >>>> two different analyses. >>>> >>>> doug >>>> >>>> Estephan Moana wrote: >>>>> Hello all, I took the FS course last June at the OHBM in San >>>>> Francisco, and am now playing with it to get to know it better. One >>>>> of the slides on the talk about FSL-FS integration mentioned that >>>>> the input data (from FEAT) for the reg-feat2anat command should have >>>>> not been smoothed prior to registering to FS. >>>>> >>>>> Considering that FEAT 1st level analysis has a default of 5mm >>>>> spatial smoothing (and that's what I used on my data), it seems >>>>> counterintuitive to need to run a 1st level analysis again so the >>>>> output files are not spatially smoothed. >>>>> >>>>> So my questions are: 1) having the example_func file spatially >>>>> smoothed will necessarily hinder a proper registration to the FS >>>>> anatomical?; 2) if so, should I re-run all my FEAT 1st level >>>>> analysis without smoothing or is there any other way? >>>>> >>>>> I know this is quite a beginners question, but I could not find the >>>>> answers on the FS FAQ or the mailing list archives. I appreciate any >>>>> light on this. >>>>> >>>>> Regards, >>>>> >>>>> Estephan Moana, DDS >>>>> Graduate Student >>>>> Oral Biology PhD Program - Neurobiology track >>>>> School of Dentistry, UNC- Chapel Hill >>>>> 2140 Old Dental Building, CB# 7455 >>>>> Chapel Hill, NC 27599 >>>>> Phone: (919) 966-5680 Fax: (919) 966-5339 Cell: (612) 702-3295 >>>>> moana(a)email.unc.edu <mailto:moana@email.unc.edu> >>>>> ------------------------------------------------------------------------ >>>>> >>>>> >>>>> >>>>> _______________________________________________ >>>>> Freesurfer mailing list >>>>> Freesurfer(a)nmr.mgh.harvard.edu >>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> >> >> -- >> Douglas N. Greve, Ph.D. >> MGH-NMR Center >> greve(a)nmr.mgh.harvard.edu >> Phone Number: 617-724-2358 >> Fax: 617-726-7422 >> >> In order to help us help you, please follow the steps in: >> surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

1 0

problem saving in tkmedit
by Stacey M Schaefer 23 Sep '09

23 Sep '09

Hello freesurfer gurus, We are running into the following error when trying to save edits to the brainmask volume in tkmedit: % ERROR: opening pipe gzip -f -c > /study/midus/data/mri/processed/freesurfer/subject006/mri/brainmask.mgz, errno = 12 Cannot allocate memory mghWrite(/study/midus/data/mri/processed/freesurfer/subject006/mri/brainmask.mgz, -1): could not open file There is also a popup error window that reads; Error: Saving Volume Couldn't save volume The files could not be written. Check to make sure the destination directory exists, that you have permission to write to it, and that there is sufficient disk space. ***However, please note that sometimes it DOES save. When only a few changes are made, it seems to save, but once we start getting about 1/5 to 1/4 of the way through an image, the above errors occur.**** Any suggestions? Thanks very much, Stacey --------------------------------------------------- Stacey M. Schaefer, Ph.D. Waisman Laboratory for Brain Imaging and Behavior University of Wisconsin - Madison 1500 Highland Ave Rm A127 Madison, WI 53705 Waisman Phone: 608-263-9321 Laboratory for Affective Neuroscience UW Psychology Dept, Brogden 1202 W Johnson St Rm 392 Madison, WI 53706 Brogden Phone: 608-262-9937

1 0

GLOBAL region of the brain empty! error due to error in intensity normalization?
by Ana Catarino 23 Sep '09

23 Sep '09

Hello, I was just running autorecon1 on a subject and I got the mri_watershed Error: GLOBAL region of the brain empty! I am aware that there was a bug in previous versions but I'm using v4.3.1, which I think it's not supposed to have that bug any longer. I tried running -skullstrip with the -no-wsgcaatlas flag, which caused the whole brain and part of the head to be striped out instead of just the skull. Next I tried to compare the output images step by step with images at the same stage for another subject with no error. Regarding the 001.mgz, rawavg.mgz and orig.mgz there were no obvious differences between both subjects, except that the images looked a little darker for the subject that got the error later. However, the nu.mgz image was quite different. The subject with error presented a very dark image, with signal intensities around 40, whereas the subject without error presented normal intensities around 110. The quality of the original images was the same, same sequence, everything. I already ran 20 subjects and this was the first one to show this error. Any help provided with be very much appreciated! Thank you, Ana Catarino

2 1

Jump to page:

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

Freesurfer