Re: [Freesurfer] Fw: Re: error in mri_glmfit-sim when using --bg and doss

2014-02-24 Thread charujing123
Hi doug and others, Thanks doug. Creating the something.y.ocn.dat,I find it can only creating an average thickness for one cluster. When my numbers of clusters in *sig.cluster.summary exceeding 1,then it cannot generate the something.y.ocn.dat,and error will be exported in the window:memory cor

Re: [Freesurfer] Fw: tessellate error in tksurfer

2014-02-24 Thread charujing123
Hi doug, I try "freeview -f $SUBJECTS_DIR/CON_EIU01/surf/rh.orig", and it works. The appearance can be got in the attachment. Is that appropriate? Thanks. All the best. Rujing Zha 2014-02-25 charujing123 发件人:Douglas N Greve 发送时间:2014-02-25 00:32 主题:Re: [Freesurfer] Fw: tessellate error in

Re: [Freesurfer] time course in mri_info lh.gender_age.thickness.10.mgh

2014-02-24 Thread charujing123
Thanks doug All the best. Rujing Zha 2014-02-25 charujing123 发件人:Douglas N Greve 发送时间:2014-02-25 00:31 主题:Re: [Freesurfer] time course in mri_info lh.gender_age.thickness.10.mgh 收件人:"freesurfer" 抄送: On 02/23/2014 08:32 PM, charujing123 wrote: > Hi all, > I have two questions. > 1,If I

Re: [Freesurfer] fsgdf and contrasts

2014-02-24 Thread charujing123
Hi doug and others, Thanks doug. I can understand multiple regression. However there is no obvious relationship between these two variables. So I try to test correlation between thickness and these two variables. If I try to consider all subjects as one group, and test correlation between this o

Re: [Freesurfer] Resolution information

2014-02-24 Thread Douglas N Greve
1mm3 doug On 02/24/2014 06:24 PM, 赵越 wrote: > Hi all, > > I got a few copies of freesurfer data from some data base. Is it > possible to know the resolution of the MRI images, for example, the > brainmask.mgz file, in freesurfer? > > Thanks, > Yue > > > ___

Re: [Freesurfer] FsAverage

2014-02-24 Thread Douglas N Greve
Do you have write permission into that folder? On 02/24/2014 05:28 PM, Boadu, Osei B wrote: > Hello, > > When trying to either create a symbolic link or copy the fsaverage > folder, I am told that permission has been denied. E.g.: > ln -s $FREESURFER_HOME/subjects/fsaverage fsaverage > ln: crea

[Freesurfer] Resolution information

2014-02-24 Thread 赵越
Hi all, I got a few copies of freesurfer data from some data base. Is it possible to know the resolution of the MRI images, for example, the brainmask.mgz file, in freesurfer? Thanks,Yue___ Freesurfer mailing list

[Freesurfer] FsAverage

2014-02-24 Thread Boadu, Osei B
Hello, When trying to either create a symbolic link or copy the fsaverage folder, I am told that permission has been denied. E.g.: ln -s $FREESURFER_HOME/subjects/fsaverage fsaverage ln: creating symbolic link `fsaverage/fsaverage': Permission denied I'm not sure what I should do. Thanks, Osei

Re: [Freesurfer] No labels file in label directory?

2014-02-24 Thread Douglas N Greve
are you sure it did not fail? Can you post the recon-all.log file to the list? On 02/24/2014 04:22 PM, sabin khadka wrote: > Hi all, > I ran recon-all -all and all the subjects finished without any error. > However in few subjects directory, labels sub-directory only have > lh.cortex.label an

Re: [Freesurfer] LGI in Qdec

2014-02-24 Thread Marie Schaer
Hi Krista, Can you be more specific about what is not coming up? If lGI not listed in the menu of qdec, look at the following post: http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg33427.html Otherwise can you describe more precisely the issue? Best, Marie On Feb 24, 2014, a

[Freesurfer] No labels file in label directory?

2014-02-24 Thread sabin khadka
Hi all, I ran recon-all -all and all the subjects finished without any error. However in few subjects directory, labels sub-directory only have lh.cortex.label and rh.cortex.label and not other label files like *.label and *.annot. Could anyone help me on how to fix this. -Sabin

[Freesurfer] LGI in Qdec

2014-02-24 Thread krista kelly
Hello, I followed instructions on how to incorporate the lgi_pial measure into QDec, however, it's not coming up when I go to choose this as a measure. I ran recon-all -s my_subject_id -qcache -measure pial_lgi and created a Qdecrc file in my $SUBJECTS_DIR directory. Does anyone have any insight a

[Freesurfer] (no subject)

2014-02-24 Thread Joshua Lee
Hello, I noticed that Freesurfer's latest release offers an expert option "added -first_wm_peak flag to mris_make_surfaces, which may aid accurate more white matter surfaces especially in heavily myelinated areas like visual cortex on data that is higher res than 1mm. enable the flag via an expert

Re: [Freesurfer] Tracula: from anatomical to diffusion space and FSL probtracx

2014-02-24 Thread Anastasia Yendiki
Hi Gari - The authors of probtrackx would be able to give you more information on how to normalize probtrackx outputs, but I'd suggest taking a look at the methods section of this paper as an example: S. B. Eickhoff, S. Jbabdi, S. Caspers, A. R. Laird, P. T. Fox, K. Zilles, and T. E. J. Beh

Re: [Freesurfer] recon-all subject folder size

2014-02-24 Thread Pedro Paulo de Magalhães Oliveira Junior
300mb is fine. - Pedro Paulo de Magalhães Oliveira Junior Netfilter & SpeedComm Telecom -- www.netfilter.com.br -- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441 On Mon, Feb 24, 2014 at 3:01 PM, Durai Arasa

Re: [Freesurfer] stats from a volume ROI (in diffusion space)

2014-02-24 Thread Garikoitz Lerma-Usabiaga
Thanks Doug! On Mon, Feb 24, 2014 at 7:12 PM, Douglas N Greve wrote: > > Use --seg instead of --mask. Also, use --id 1 to get only the ROI in the > mask (otherwise it will give you the mask as one ROI and everything > outside of the mask as a 2nd ROI) > > doug > > > On 02/24/2014 12:51 PM, Gari

Re: [Freesurfer] stats from a volume ROI (in diffusion space)

2014-02-24 Thread Douglas N Greve
Use --seg instead of --mask. Also, use --id 1 to get only the ROI in the mask (otherwise it will give you the mask as one ROI and everything outside of the mask as a 2nd ROI) doug On 02/24/2014 12:51 PM, Garikoitz Lerma-Usabiaga wrote: > Hi, > I have some volume ROIs in diffusion space (1-s a

[Freesurfer] recon-all subject folder size

2014-02-24 Thread Durai Arasan
Hi Freesurfer experts, I am successfully running recon-all on my cluster. However I find that the subject folders have sizes ranging from 300mb to 900mb. I grepped all recon-all.log files for "finished without error" and that seemed fine for all subjects. But I would like to know what is the exp

[Freesurfer] stats from a volume ROI (in diffusion space)

2014-02-24 Thread Garikoitz Lerma-Usabiaga
Hi, I have some volume ROIs in diffusion space (1-s and 0-s). I would like to obtain, for example, the average FA values in that ROI. I tried using mri_segstats, but it gives me an error, it needs a segmentation volume. mri_segstats --i dmri/dtifit_FA.nii.gz --mask FSL_waypoint2Hipplh.unc_AS_avg33

Re: [Freesurfer] Contrast Vectors

2014-02-24 Thread Douglas N Greve
When you design an analysis, you postulate certain effects (eg, diagnosis, age). Each of these effects gets a column in the design matrix (eg, normal, AD, age or young/old). Each column has a regression coefficient that gets fit in the analysis that indicates the size of each of the effects. T

Re: [Freesurfer] Brodmann atlas

2014-02-24 Thread Douglas N Greve
We don't have coverage for all BAs yet. Note that the BAs we do supply are based on actual histology, as opposed to other atlases which just give a "best guess". Getting histology-based BAs is very difficult. "Best guesses" are free :-) doug On 02/24/2014 08:35 AM, Brahim Belaoucha wrote: >

Re: [Freesurfer] fwhm31+ ?

2014-02-24 Thread Douglas N Greve
The files in the mult-comp-cor folder are generated from a simulation, so the simulation has to be run with larger FWHMs. In the end, I think that 25 is probably too much smoothing. You can start to see low spatial frequency artifacts when you smooth too much. I usually use 10-15 doug On 0

Re: [Freesurfer] error in mri_glmfit-sim when using --bg and doss

2014-02-24 Thread Douglas N Greve
sorry, you are right, the csd files are in the csd folder. The csf file will have a name with the contrast name in it. Copy it to a file with a name where you substitute the old contrast name for another contrast name. doug On 02/21/2014 09:18 PM, charujing123 wrote: > Hi doug and others, > Th

Re: [Freesurfer] Fw: Re: extracting mean thickness from specific cluster

2014-02-24 Thread Douglas N Greve
Sorry, the summary file is not what you want. Can you send a list of the files in the folder? doug On 02/24/2014 11:26 AM, Douglas N Greve wrote: > > what version of FS are you using? there should be a file with > "summary" in the name. Also, try looking at the help with > mri_glmfit-sim --he

Re: [Freesurfer] Fw: tessellate error in tksurfer

2014-02-24 Thread Douglas N Greve
Looks like it could be a video driver problem. Can you see it in freeview? doug On 02/23/2014 11:38 PM, charujing123 wrote: > sorry,this e-mail has the attachment. > Rujing Zha > 2014-02-24 > > charujing123 > --

Re: [Freesurfer] Fw: Re: error in mri_glmfit-sim when using --bg and doss

2014-02-24 Thread Douglas N Greve
Try setting the cwpvalthresh to .9 or so. I think this is a numerical error that occurs when the cwpthreshold is close to 1 doug On 02/22/2014 04:53 AM, charujing123 wrote: > Hi doug and others, > I tried to perform it by this command "mri_glmfit-sim --glmdir my_dir > --no-sim mc-z.neg.3 --cwpv

Re: [Freesurfer] time course in mri_info lh.gender_age.thickness.10.mgh

2014-02-24 Thread Douglas N Greve
On 02/23/2014 08:32 PM, charujing123 wrote: > Hi all, > I have two questions. > 1,If I want to get the value of specific voxel from the > lh.gender_age.thickness.10.mgh, which code can I use to perform it? You can go to that vertex when you have it loaded into FreeView, otherwise you can load it

Re: [Freesurfer] Fw: Re: extracting mean thickness from specific cluster

2014-02-24 Thread Douglas N Greve
what version of FS are you using? there should be a file with "summary" in the name. Also, try looking at the help with mri_glmfit-sim --help doug On 02/21/2014 11:39 PM, charujing123 wrote: > Hi doug, > I tried to generate the mean thickness of the cluster in uncorrected p > value<0.005 for e

Re: [Freesurfer] testing a quadratic effect of age

2014-02-24 Thread Douglas N Greve
yes, that works too On 02/24/2014 11:20 AM, Yang, Daniel wrote: > Thanks, Doug. I will standardize the age first. > > I can also think of another way of doing this: divide the sample into > 4 age bins and treat age as a Discrete Factor with 4 levels. > > Best, > Daniel > > -- > Daniel (Yung-Jui)

Re: [Freesurfer] fsgdf and contrasts

2014-02-24 Thread Douglas N Greve
if you have multiple variables then you have to do multiple regression before testing the correlation doug On 02/21/2014 09:35 PM, charujing123 wrote: > Hi doug and others, > I want to perform correlation analysis,just one dependent variable and > one independent variable. Previously I think the

Re: [Freesurfer] testing a quadratic effect of age

2014-02-24 Thread Douglas N Greve
Yes, though you might want to demean age before computing the quadratic. doug On 02/24/2014 10:13 AM, Yang, Daniel wrote: > Hi FreeSurfer Experts, > > With age as a continuous variable, qdec can test the linear effect of > age. To test the quadratic effect of age, do I just create a > curviline

[Freesurfer] Contrast Vectors

2014-02-24 Thread Jonathan Holt
Hi all, I humbly ask for an explanation of contrast vectors, specifically what do 0, 1, -1 indicate, exactly? best, Jon ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The inform

Re: [Freesurfer] Fw: Re: extracting mean thickness from specific cluster

2014-02-24 Thread charujing123
Hi doug and others, Creating the something.y.ocn.dat,I find it can only creating an average thickness for one cluster. When my numbers of clusters in *sig.cluster.summary exceeding 1,then it cannot generate the something.y.ocn.dat,and error will be exported in the window:memory corruption. I kno

[Freesurfer] Sub cortical volumes and CVS

2014-02-24 Thread Jennifer Eastman
Hello, I am interested in comparing sub-cortical volumes across subjects in my data set. I am wondering if using the CVS registration step is useful in improving the accuracy of the sub-cortical volume measurements independently. I will not be examining the cortical thickness just sub-cortical.