Freesurfer

freesurfer@nmr.mgh.harvard.edu

4 participants
30090 discussions

Conversion
by Anna Josefson 15 Jun '13

15 Jun '13

Dear FreeSurfer users! I am new to Freesurfer, and I have succesfully managed to run recon-all on my data, for every subject. Now I plan to use the output - some of the different cortical and subcortical brain structures as ROI's in my SPM analyses. Then I would have to convert from freesurfer space to SPM space via the coordinates. And - I would also have to convert from .mgz to .nii data format. Does any have any tips on how to do this? Or a script? Kind Regards, Anna B. Josefson

3 4

Group Analysis Error
by Nooshin Zadeh 15 Jun '13

15 Jun '13

Dear FreeSurfer Group I wanted to Group Analysis with qdec. I have MRIs of one patient in two different dates and I wanted to do group analysis on them to see the changes. I have "gender", "age", and "diagnosis". In qdec deme, when I make the analysis based on "thickness", I receive the attached error. I do not know what is the reason. Any help and advice would be appreciated. Thanks, Nooshin

2 1

2013年6月15日 20:37:34 自动保存草稿
by xiangbo_2010 15 Jun '13

15 Jun '13

Dear experts, I was wondering if anyone can advise on the best way to use an ROI mask created in SPM (XjView) to extract cortical thickness values in freesurfer. Though which was pointed out by reseachers, but I still can not know it. I hope some experts help me, Thanks! Bo Thank you in advance for your help!

1 0

Installation Conflict
by Mark Plantz 14 Jun '13

14 Jun '13

Hello, I recently installed FreeSurfer on an OS x machine. After finishing the process, I received the following output: *Setting up environment for FreeSurfer/FS-FAST (and FSL)* *FREESURFER_HOME /Applications/freesurfer* *FSFAST_HOME /Applications/freesurfer/fsfast* *FSF_OUTPUT_FORMAT nii.gz* *SUBJECTS_DIR /Applications/freesurfer/subjects* *grep: Command not found.* *wc: Command not found.* *grep: Command not found.* *wc: Command not found.* *grep: Command not found.* *wc: Command not found.* *MNI_DIR /Applications/freesurfer/mni* */usr/local/fsl/etc/fslconf/fslmachtype.sh: line 14: uname: command not found* *FSL_DIR /usr/local/fsl* */usr/local/Applications/freesurfer: No such file or directory.* Why can the grep, wc, of MNI commands not be found? Also, when I type the command: *$FREESURFER_HOME/subjects* I receive the following error: /Applications/freesurfer/subjects: Permission denied. Any ideas on how to solve this problem? Is it a licensing issue? I have already created the .license file. Best, Mark Plantz

2 1

methods Q
by Joshua Lee 14 Jun '13

14 Jun '13

Hi Experts, I just wanted confirm my understanding that Freesurfer does not employ multi-atlas label fusion methods. Is this correct? Thanks, Best, Joshua - Joshua Lee Graduate Student Center for Mind and Brain & Department of Psychology University of California, Davis 530.747.3805

2 2

Overlapping perirhinal and entorhinal ex-vivo labels
by Sasa Kivisaari 14 Jun '13

14 Jun '13

Dear FS experts, first I would like to thank you for the very nice perirhinal cortex ex-vivo label you provide in your latest releases! My question concerns the relationship between the ?h.perirhinal.label and the ?h.entorhinal_exvivo.label. Going over some brains in our data set, it looks to me that these two labels have some degree of overlap which often occupies the lateralmost ~1-2 mm of the parahippocampal gyrus crown and ~1-2 mm of the collateral sulcus medial wall, depending on the y-level and the brain. As I understand, these labels (unlike e.g. the labels in the aparc.annot) were created independently from one another thus allowing such overlap. I appreciate that given the transitional nature of the BA35, one would not expect to see a clear border between the two cytoarchitectonic areas. Still, I would like to inquire whether you have any information on which label is 'more reliable' and whether you have any insights as to how to best go about resolving this ambiguity? Thank you for your help in advance! Best, Sasa

2 3

Errors during test of Freesurfer installation
by Rando, Kenneth 14 Jun '13

14 Jun '13

I recently installed Freesurfer on a computer running Red Hat Enterprise 6 for which the updates are current. The first tests, involving freeview, tkmedit, and qdec all produce the error: libGL error: failed to load driver: nouveau. free view produces no other error messages, but tkmedit adds: Reading /usr/local/freesurfer/tktools/tkm_common.tcl Reading /usr/local/freesurfer/tktools/tkm_wrappers.tcl Reading /usr/local/freesurfer/lib/tcl/fsgdfPlot.tcl Reading /usr/local/freesurfer/tktools/tkUtils.tcl qdec repeats the error followed by: Reading /usr/local/freesurfer/tktools/tkUtils.tcl Using /usr/local/freesurfer/lib/tcl/fsgdfPlot.tcl >From what I have discovered "nouveau" is the open source nvidia driver used now by RHEL6. Is the problem with nouveau, or with my Freesurfer installation? Thanks. Ken Kenneth Rando Research Assistant 2 203-974-7731 Yale OCD Research Clinic Yale University School of Medicine Connecticut Mental Health Center 34 Park Street, Room W309 New Haven, CT 06519

1 0

recon-all errors
by Linda Zhang 14 Jun '13

14 Jun '13

Dear all, I've been running recon-all (subj) -all for a group of subjects on Freesurfer v5.1.0 on Virtualbox. Three of them exited with errors, each one having a different error. I've attached the recon-all.logs. For napo0195, the problem may be with the wm.mgz as someone mentioned before, but I don't know what the issue might be for the other two subjects. Thanks for your help! Cheers, Linda

2 1

mprage flag in recon-all
by Caspar M. Schwiedrzik 14 Jun '13

14 Jun '13

Hi! Is there more documentation on what settings the mprage flag enables in recon-all? Specifically, I would be interested which individual steps it affects and what the parameters are for each of the steps. Thanks! Caspar

5 12

Re: [Freesurfer] Hippocampal subfields intensity
by Juan Eugenio Iglesias 13 Jun '13

13 Jun '13

Hi Marcos, 1. your fix of MRIread.m is great. I forgot of this bug; we should totally take care of it. 2. a problem is that nu.mgz (or norm.mgz) and the posteriors are in difference voxel space. So, you need to resample norm.mgz to the space of the subfields. To do so, you can use mri_convert with the option -rl ("reslice like"): mri_convert norm.mgz norm_resampled.mgz -rl posterior_subiculum.mgz 3. Now you can do: A=MRIread('norm.mgz'); data=A.vol(:); B=MRIread('posterior_subiculum.mgz'); post=double(B.vol(:)); mean=sum(data.*post)/sum(post); variance=sum((data-mean).^2.*post)/sum(post); Cheers, /Eugenio On Mon, 2013-06-10 at 17:17 -0300, Marcos Martins da Silva wrote: > Hi, Eugenio > TY for your fast help. I understood you were suggesting to compute > that on MatLab and I tried this: > > NU=MRIread('nu.mgz') ### that runs ok > Ps=MRIread('posterior_left_subiculum.mgz') ### it fails with the > following message > WARNING: error reading MR params > Attempted to access mr_parms(1); index out of bounds because > numel(mr_parms)=0. > > Error in MRIread (line 100) > tr = mr_parms(1); > > I solved creating a little customized nMRIread.m with the following > changes: > > if numel(mr_parms) > 0 > tr = mr_parms(1); > flip_angle = mr_parms(2); > te = mr_parms(3); > ti = mr_parms(4); > else > mr_parms(1) = 0; > mr_parms(2) = 0; > mr_parms(3) = 0; > mr_parms(4) = 0; > tr = mr_parms(1); > flip_angle = mr_parms(2); > te = mr_parms(3); > ti = mr_parms(4); > end > > With those changes I assigned 0 to mr-parms elements so it runs > without errors > But whe I tried the following line I copy and pasted from your > message: > mean=sum(Ps.*NU)/sum(Ps); ### I got the following error > Undefined function 'times' for input arguments of type 'struct'. > > Any help? > Cheers, Marcos > > PS: I promised I will post the final solution to list. But I guess it > is more didactic if these little problems are solved before. > TY, again. > Em Seg, 2013-06-10 às 14:19 -0400, Juan Eugenio Iglesias escreveu: > > Hi Marcos, > > the right way of doing this is using the soft posteriors to compute the > > mean and variance, rather than thresholding at p=0.5. For instance, if > > you wanted to compute the mean and variance of the intensitites of the > > subiculum, you would do something like this: > > mean=sum(Ps.*NU)/sum(Ps); > > variance=sum(Ps.*(NU-mean).^2)/sum(Ps); > > (where Ps is the posterior of the subiculum) > > Cheers, > > /Eugenio > > > > > > > > On Mon, 2013-06-10 at 15:12 -0300, Marcos Martins da Silva wrote: > > > Hi, Freesurfer Experts > > > > > > After usual processing with recon-all -all we get the aseg.stats file > > > with several data including intensity values like: > > > normMean normStdDev > > > normMin normMax normRange > > > Left-Hippocampus 77.8939 7.5748 46.0000 > > > 105.0000 59.0000 > > > > > > How could I get similar results for each hippocampal subfield, > > > assuming I also generated all posterior*.mgz files corresponding to > > > each subfield? > > > I guess I should first binarize each of the subfields file with a > > > threshold=127 to map all the pertinent voxels, and then use these > > > files as masks over nu.mgz and calculate the intensities values. But I > > > do not know the best way to accomplish this after the binarize step. > > > > > > Thank you in advance for any help. > > > > > > Marcos > > > _______________________________________________ > > > Freesurfer mailing list > > > Freesurfer(a)nmr.mgh.harvard.edu > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > -- Juan Eugenio Iglesias, PhD http://www.jeiglesias.com iglesias(a)nmr.mgh.harvard.edu Athinoula A. Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, Massachusetts 2129 U.S.A.

2 4

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