Freesurfer October 2013

freesurfer@nmr.mgh.harvard.edu

136 participants
244 discussions

FSL masks applied to Freesurfer surfaces?
by Ruth Carper 04 Oct '13

04 Oct '13

Hi, I'd like to take some masks that I have in MNI standard space in FSL and map them to Freesurfer surface space. The goal is to extract measures of average cortical thickness (or area or etc) for those regions for each subject. Is there a standard way to do this?

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Half_brain when converting into mgz
by Erik Lindberg 04 Oct '13

04 Oct '13

Dear Freesurfer experts! I am running a number of images in Freesurfer and for some reason there are a few that gets cut when they are converted into mgz. If I am looking at the orignal dicom the image it is ok but as soon as it is converted into MGZ something goes wrong (see attached image). What can the be the reason for this? I have around 60 images and 4 gets cut on the top of the brain. Thanks Olof

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Patch x y z
by Oya, Hiroyuki 03 Oct '13

03 Oct '13

Hello, read_patch (patch_name) gives x,y and z values. Are these vertex RAS? Thank you. Hiroyuki

3 2

Re: [Freesurfer] Why don't no-mask flag work?
by shahin＠nmr.mgh.harvard.edu 03 Oct '13

03 Oct '13

preproc-sess -s <SbjName> -fwhm 2 -per-run -fsd bold -mni305-1mm -nomask -no-subcort-mask I also tried per-session and mni305-2mm but still did not help. I even tried doing it in native space (by not mentioning mni305/fsaverage) but did not work either. > What was your preproc-sess command? > > > On 10/03/2013 10:29 AM, SHAHIN NASR wrote: >> Hi Doug, >> Did you have a chance to find the reason for this problem? >> >> >> On Wed, Oct 2, 2013 at 3:20 PM, <shahin(a)nmr.mgh.harvard.edu >> <mailto:shahin@nmr.mgh.harvard.edu>> wrote: >> >> I still receive the same error message (1mm is now 2mm in the >> message). >> >> outanadir = >> /autofs/cluster/tootell/pitcairn/1/shahin/Retina_Prj/Sbj_53/abir/bold/RetinaPrj_nomask2 >> Error using MRIread (line 76) >> ERROR: cannot determine format of >> /autofs/cluster/tootell/pitcairn/1/shahin/Retina_Prj/Sbj_53/abir/bold/008/masks/.mni305.2mm >> (MRIread) >> >> >> Error in fast_selxavg3 (line 146) >> runmask = MRIread(flac.maskfspec); >> >> >> >> > Does the same thing happen if you use the 2mm instead of the 1mm? >> > >> > On 10/02/2013 02:21 PM, SHAHIN NASR wrote: >> >> Hi, >> >> I want to test activity outside the brain (around >> eyes/retina) but >> >> when I use "-no-mask" flag in my mkanalysis-sess (to be able to >> see >> >> activity outside brain) as below: >> >> >> >> mkanalysis-sess -analysis RetinaPrj_nomask -fwhm 2 -paradigm >> >> Conds.par -mni305 1 -event-related -polyfit 2 -gammafit 2.25 1.25 >> >> -mcextreg -TR 2.000 -nconditions 3 -refeventdur 14 -force >> -runlistfile >> >> RunList -per-run -fsd bold -no-mask >> >> >> >> I get this error: >> >> >> >> outanadir = >> >> >> /autofs/cluster/tootell/pitcairn/1/shahin/Retina_Prj/Sbj_53/abir/bold/RetinaPrj_nomask >> >> Error using MRIread (line 76) >> >> ERROR: cannot determine format of >> >> >> /autofs/cluster/tootell/pitcairn/1/shahin/Retina_Prj/Sbj_53/abir/bold/008/masks/.mni305.1mm >> >> (MRIread) >> >> >> >> >> >> Error in fast_selxavg3 (line 146) >> >> runmask = MRIread(flac.maskfspec); >> >> >> ------------------------------------------ >> >> ERROR: fast_selxavg3() failed\n >> >> >> >> Note: >> >> ** I have already used -nomask and -no-subcort-mask in the >> preproc-sess >> >> *** If I remove this flag, everything looks fine except for the >> fact >> >> that all activity outside brain is masked! >> >> >> >> >> >> -- >> >> Shahin Nasr >> >> >> >> PhD in Cognitive Neuroscience >> >> Martinos Imaging Center, MGH >> >> Harvard Medical School >> >> >> > >> > -- >> > Douglas N. Greve, Ph.D. >> > MGH-NMR Center >> > greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> >> > Phone Number: 617-724-2358 <tel:617-724-2358> >> > Fax: 617-726-7422 <tel:617-726-7422> >> > >> > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >> > www.nmr.mgh.harvard.edu/facility/filedrop/index.html >> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >> > Outgoing: >> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >> > >> > >> > >> >> >> >> >> >> -- >> Shahin Nasr >> >> PhD in Cognitive Neuroscience >> Martinos Imaging Center, MGH >> Harvard Medical School > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > >

3 2

bias field segmentation issue
by David Lahna 03 Oct '13

03 Oct '13

Hello all, I'm trying to run Freesurfer recon-all on a series of T1 images with pretty extreme bias field intensity inhomogeneities. Signal dropoff in the inferior-most and superior-most slices results in temporal lobe and superior cortical volume underestimation. It's related to the coil and is stereotypically present in every one of the scans so there should be a way to correct them all for bulk processing. I tried N4 bias field correction which resulted in a modest improvement but was far from perfect. I also tried adding control points and rerunning a subset of 20 of them as suggested elsewhere in the forum. Adding the control points improved the subset slightly, but estimating bias field from those subjects and applying the correction to everyone else resulted in worse segmentation overall. Can anyone suggest a method for correcting this? Thanks in advance for any advice. -David

1 0

aparcstats2table for manually drawn ROIs
by Jackie Lam 03 Oct '13

03 Oct '13

Hi there, So I've run recon-all on my group of subjects, ran them in QDEC, manually drawn my ROIs, used mris_anatomical_stats to create a .stats files for each subject from my hand drawn ROIs and now I want to use aparcstats2table to gather the thicknesses from all my subjects.... Is there an option to gather stats from a particular .stats file rather than from just the two parcellation atlases? I think there is something similar in asegstats2table (--stats=lh.xxx.stats), but is there something like that for aparcstats2table? Many thanks, Jack

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LGi computation on computer cluster
by Jon Wieser 03 Oct '13

03 Oct '13

Hio We want to compute the LGI index, using our local computing cluster. the cluster does not have matlab or it's image processing toolbox on the computing nodes. Which matlab .m files does the LGI computation use? Thanks -- Jon Wieser Research Specialist UW-Milwaukee Psychology Department, Pearse Hall Rm 366 2441 East Hartford Ave Milwaukee, WI 53211 Phone: 414-229-7145 Fax: 414-229-5219

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Re: [Freesurfer] missing eTIV in asegstats2table
by Daniel Ferreira 03 Oct '13

03 Oct '13

Hi, Thanks Marcos for your reply. My problem is that asegstats2table does not output values for eTIV. I do not manage to figure out why. But maybe your script could work. Anyone knows what is the corresponding FieldName Index for eTIV?? I checked a aseg.stats file and did not find it. Thanks a lot Dani Message: 7 Date: Wed, 02 Oct 2013 10:32:51 -0300 From: Marcos Martins da Silva <marcosm(a)hucff.ufrj.br> Subject: Re: [Freesurfer] missing eTIV in asegstats2table To: Daniel Ferreira <danifer(a)ull.es> Cc: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <1380720771.1845.9.camel@alien> Content-Type: text/plain; charset="utf-8" You can use in a loop with your subjects. It extracts the fields I want and some others including the etiv to a table named AsegVol. You may change the number of the fields to get what you need. The code I am sending you addresses hippocampus, putamen and caudate (both sides). ________________________________________________________________________ for i in $(ls -d suj*) do asegstats2table --segno 11 12 17 50 51 53 -s $i --tablefile AsegVol done ________________________________________________________________________ Notice that suj is the prefix of all my subjects in freesurfer/subjects folder I hope it helps you. Em Qua, 2013-10-02

2 1

Hippocampal subfield segmentation paused
by Irene Lee 03 Oct '13

03 Oct '13

Hi, there, I am running the hippocampal subfield segmentation on a high resolution T2 data that only covers the bilateral hippocampus and nearby temporal lobe areas. Following the instruction on this webpage: http://ftp.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldSegmentation I used the command recon-all -s my subject -all -hippo-subfields It was running well, however, it halted/paused after it displayed the following information:"final transformation (x=..,yr=..,zr=..) and a 4x4 matrix". For a week it is not going anywhere and not producing any output. The computer I was running it on had sufficient computational resources and a Fedora linux system. It does not seem to be related to the configuration of the computer. Has anyone ever encountered this problem?? Any diagnostic advice will be appreciated!! -Irene

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Re: [Freesurfer] Effects of age on different parameters (thickness, lGI...)
by Daniel Klein 03 Oct '13

03 Oct '13

Hi Doug, I´m a bit unsure about polynomial fitting with qdec. So I want to demonstrate linear, quadratic and cubic effects of age on lGI. You wrote: If you need to test all 3, then you'll have to use mri_glmfit with and FSGD file. I want to be sure if it is correct to demonstrate: 1. age linear effects: age linear (for example 12 Years) as continous (covariate)? 2. age quadratic effects: age square (144 Years) as continous (covariate) and age linear (12 Years) as nuisance variable? 3. age cubic effects: age cubic (1728 Years) as continous (covariate) and age linear (12 years) as nuisance variable? Is it neccesary to include age square (144 years) in the model to show only the cubic effects? And if it is neccesary do I need mri_glmfit with a FSGD file or can I add age square (144 Years) as a seocond nuisance variable in qdec? Best wishes and thanks a lot Daniel

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Freesurfer October 2013