Freesurfer October 2008

freesurfer@nmr.mgh.harvard.edu

71 participants
110 discussions

Re: [Freesurfer] convert multiple Analyze to single 4D nifti
by Kara Dyckman 24 Oct '08

24 Oct '08

I'm not sure. When I just tried it, it converted to .nii.gz. Maybe it has to do with the version of fsl being used? I'm posting this to the freesurfer listserv to see if anyone else has ideas. Xu Cui wrote: > Thanks Kara. I tried fslmerge on my images and the result is a single > .img / .hdr pair, not a nii or nii.gz file. Do you have any clue? > The reason to convert to nii is that fsfast seems to require nii file. > > Thanks, > Xu > > On Thu, Oct 23, 2008 at 2:20 PM, Kara Dyckman > <kara(a)nmr.mgh.harvard.edu <mailto:kara@nmr.mgh.harvard.edu>> wrote: > > If I remember correctly, you can use the fslmerge command to merge > all the .hdr files into one nifti file. > > Try this in the directory where your analyze files are: > fslmerge -t outputname *.hdr > > outputname is whatever you want to call your new nifti file > > The result will be outputname.nii.gz > > Hope that helps! > Kara > > > Xu Cui wrote: > > Does anybody know how to convert a series of Analyze files > into a single nii file? Each analyze file is a single 3D > volume at a time point; the nii file would be 4d. > > Thanks, > Xu > > -- > ---------------------------------------------------------------- > Xu Cui > Department of Psychiatry and Behavioral Sciences > Stanford University > ---------------------------------------------------------------- > ------------------------------------------------------------------------ > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > -- > Kara A. Dyckman, Ph.D. > Postdoctoral Fellow, Manoach Lab > Psychiatric Neuroimaging > Massachusetts General Hospital > Charlestown Navy Yard > 149 13th St. > Charlestown, MA 02129 > email: kara(a)nmr.mgh.harvard.edu <mailto:kara@nmr.mgh.harvard.edu> > phone: 617-724-4604 > fax: 617-726-4078 > > http://nmr.mgh.harvard.edu/manoachlab > > > > > -- > ---------------------------------------------------------------- > Xu Cui > Department of Psychiatry and Behavioral Sciences > Stanford University > ---------------------------------------------------------------- -- Kara A. Dyckman, Ph.D. Postdoctoral Fellow, Manoach Lab Psychiatric Neuroimaging Massachusetts General Hospital Charlestown Navy Yard 149 13th St. Charlestown, MA 02129 email: kara(a)nmr.mgh.harvard.edu phone: 617-724-4604 fax: 617-726-4078 http://nmr.mgh.harvard.edu/manoachlab

3 2

deflate compression support
by lan lin 24 Oct '08

24 Oct '08

I'm trying to make a monkey template using mris_make_template. So far, every time I run the mris_make_template, I get this error: monkey.tif: Deflate compression support is not configured. TiffWrite: TIFFWriteScanline returned error

2 1

subcortical masks
by Martin Ystad 24 Oct '08

24 Oct '08

Hi, I'd like to create binary masks in the nifti-format from each of the subcortical segmentations in freesurfer, separately (one for hippocampus, one for thalamus, and so forth..). Is there any way to do this automatically from the command line? Thanks, Martin Ystad Ph.D. candidate, University of Bergen

3 2

Bug with aparcstats2table on aparc.a2005s parcellation - addendum
by Laluz, Victor 23 Oct '08

23 Oct '08

The body of my email was lost because of the attachments: here it is again for those who are curious. Sorry about that, I didn't know a text file attachment would do that. Not sure if this bug has been mentioned before, but there is a bug with using aparcstats2table for the aparc.a2005s parcellation map. If some of the subjects in the group have missing values of a certain type, aparcstats2table fails to designate a 0 for them. So for instance, it's often the case that a subject has no lh_unknown_volume in their aparc.a2005s.stats. Certain other, seemingly random areas will fail to print out as well. This will lead to shifts in the dataset, so that every volume after the missing value for a subject will be incorrect, and will need to be shifted for the blank. The only way I have found to reliably check that the data is valid is to generate seperate stats tables for each subject. Anyway, this is a serious problem for people who collect and analyse data with aparcstats2table using the aparc.a2005s parcellation map. Attached are two examples illustrating the problem. To make it clearer, paste the contents of both into excel, and look at the column mismatch; some of the subjects' data don't make it all the way to the end, and a shift in the values is clear. Victor Laluz : Imaging Coordinator : UCSF Memory and Aging Center 415-476-1680 : 415-476-1816 (fax)

2 1

convert multiple Analyze to single 4D nifti
by Xu Cui 23 Oct '08

23 Oct '08

Does anybody know how to convert a series of Analyze files into a single nii file? Each analyze file is a single 3D volume at a time point; the nii file would be 4d. Thanks, Xu -- ---------------------------------------------------------------- Xu Cui Department of Psychiatry and Behavioral Sciences Stanford University ----------------------------------------------------------------

1 0

Bug with aparcstats2table on aparc.a2005s parcellation
by Laluz, Victor 23 Oct '08

23 Oct '08

Hello, Not sure if this bug has been mentioned before, but there is a bug with using aparcstats2table for the aparc.a2005s parcellation map. If some of the subjects in the group have missing values of a certain type, aparcstats2table fails to designate a 0 for them. So for instance, it's often the case that a subject has no lh_unknown_volume in their aparc.a2005s.stats. Certain other, seemingly random areas will fail to print out as well. This will lead to shifts in the dataset, so that every volume after the missing value for a subject will be incorrect, and will need to be shifted for the blank. The only way I have found to reliably check that the data is valid is to generate seperate stats tables for each subject. Anyway, this is a serious problem for people who collect and analyse data with aparcstats2table using the aparc.a2005s parcellation map. Attached are two examples illustrating the problem. To make it clearer, paste the contents of both into excel, and look at the column mismatch; some of the subjects' data don't make it all the way to the end, and a shift in the values is clear. Victor Laluz : Imaging Coordinator : UCSF Memory and Aging Center 415-476-1680 : 415-476-1816 (fax)

1 0

creating "intermediate" surfaces
by Rudolph Pienaar 23 Oct '08

23 Oct '08

Hi all - Is there a way to create "intermediate" surfaces in FreeSurfer? By intermediate I mean "some fraction" between gray/white and pial. Cheers -=R -- Rudolph Pienaar, M.Eng, D.Eng / email: rudolph(a)nmr.mgh.harvard.edu MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging 149 (2301) 13th Street, Charlestown, MA 02129 USA

2 1

mri_convert
by sameer kumar 23 Oct '08

23 Oct '08

Hi all, I am new to FS and I would like to know the usage of mri_convert to convert the results of FreeSurfer into the analyze format. Thanks, Regards, Sameer Kumar Gottipati

3 7

FreeSurferColorLUT & aparc
by Juranek, Jenifer 23 Oct '08

23 Oct '08

Hi, Running fsv405 on RHEL5. I've encountered some unexpected numerical values wrt FreeSurferColorLUT.txt. Are my expectations off? 1) In the aparc+aseg.mgz file, intensity values for the cortical labels range from -32768 to 654, with negative values falling in some regions in the left hemisphere. 2) Identical results are obtained if mri_aparc2aseg is used to generate an output file: mri_aparc2aseg --s mysubject --o ./aparc2aseg.mgz 3) Values of aseg.mgz map perfectly well to FreeSurferColorLUT.txt Example values obtained from aparc+aseg.mgz are listed below: lh.superiortemporal=484 (expecting 1030 from FreeSurferColorLUT.txt) rh.superiortemporal=32767 (expecting 2030) Although these numerical values do not match the LUT, they are consistent across subjects. Many Thanks for any insights... Jenifer

2 5

questions about longitudinal analysis
by Wang, Xin 23 Oct '08

23 Oct '08

Hi, groups, I noticed the updates of longitudinal analysis in the new version of Freesurfer. However, I still have a couple of questions about the goal of longitudinal analysis. 1. The goal of longitudinal analysis is to detect the atrophy (thinning), but the transformation in the registration step will minimize any atrophy. An example of outcomes of FLIRT and FNIRT on FSL website exactly demonstrates that the atrophy disappears in the 'best' transformation (FNIRT) http://www.fmrib.ox.ac.uk/fsl/fnirt/index.html. In our experience, the number of vertex of post-transformed tp2 is very close to tp1. It is not clear to me how the difference in the original thickness between tp2 and tp1 is preserved in this transformation. One may argue that processing tp1 and tp2 independently does not solve this problem because the registration is also used in the routine recon. Is it true? 2. The new longitudinal process is still using volume-based registration if I read it correctly. Why not switch to surface-based since people have argued the advantage of surface-based over volume-based? Thank you for any clarification, Wang

2 1

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

Freesurfer October 2008