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.
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
Hi all,
I humbly ask for an explanation of contrast vectors, specifically what do 0, 1,
-1 indicate, exactly?
best,
Jon
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The inform
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
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
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)
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
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
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
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
> --
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
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
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
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:
>
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
>
>
> ___
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
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
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
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
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
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