Hi all,
I learned the tutorial in the website
"http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis";. At the
beginning of the manu, it told me to run command in tcsh. Can I just run
commands in bash shell. If so, what is the function of tcsh?
Thanks.
All the best.
2013-12-18
Ru
Hi Ruth - If you apply the same mask to all the volumes in the DWI series,
it's not a problem. The important thing is not to have applied any
operation that would change the intensities of the images inside the
brain. So these should NOT be the DWIs after the eddy_correct step, they
should be
Hi all,
I try to run mri_glmfit, but it export
"ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08
Possible problem with experimental design:
Check for duplicate entries and/or lack of range of
continuous variables within a class.".
I upload the data
Good morning,
I have a group of subjects reconed with v5.1 and a group reconed with v5.3.
In order to get the same aseg structures for all subjects in the stats file:
Is there an option to update the aseg file only (like flags -cortparc &
-parcstats for cortical measures)?
Best,
Jesus
The i
Dear FreeSurfers,
I have a question regarding the installation of xhemi (I am using FreeSurfer
5.1)
I tried to follow the guide on: https://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi
to install the necessary files, however the following files do not seem to be
present on the ftpserver:
ftp://sur
Ciao Francesco - The problem is that the pre-processing encountered an
error, so parts of it didn't actually complete:
Image Exception : #22 :: ERROR: Could not open image /path/to/mni_template
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
You can comment out that
Dear Freesurfer experts
When I ran: mris_anatomical_stats -i 0 0.002 -l label/lh.roi.label -t /
surf/lh.MD.mgh -b -f stats/lh.roi.stats subid lh to get the DTI value for a
particular label, the function does not really take the thresholds I set into
account as it displayed:
only considering
Hi,
I've been using QDEC to run my GLM analyses. I want to obtain the exact p
values and can't seem to locate them. I'm wondering if you can help me find a
solution to this issue.
Thanks so much.
Kind regards,
Catherine
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yes
On 12/17/2013 10:06 PM, Rujing Zha wrote:
> Dear Doug,
> Thanks for your precious help.
> Considering the 2nd example, I just want to know whether some brain
> surface thickness correlate the score without subjects coming from
> control or patient group. I think my aim is the same as want you
I don't know what you mean. Can you elaborate?
doug
On 12/17/2013 10:12 PM, Rujing Zha wrote:
> Dear Doug,
> Thanks Doug.
> In my server, I cannot visualize the file but seeing the time courese
> window. I want to know whether there is a limit in graphics card for
> visualing the inflated data.
You do not, but you will need to source the proper env file (
SetUpFreeSurfer.sh instead of SetUpFreeSurfer.csh)
doug
On 12/18/2013 09:57 AM, Rujing Zha wrote:
> Hi all,
> I learned the tutorial in the website
> "http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis";.
> At the be
There are lots of warnings in the log file. Have you anonymized this
data or done anything to the DICOM files since they came from the scanner?
On 12/18/2013 03:44 AM, Rujing Zha wrote:
> Dear Doug,
> Thanks for your kindhearted help, Doug.
> I upload the standard output and error message file
freesurfers,
we've acquired fMRI data from [slightly different] slice prescriptions, all
partial brain slices. we want to analyze this data all together, but we
also want to have the best registration possible [i.e., use bbregister].
what's the best way to do this? here are the ideas we have:
1
Could be several things. You only have two IA_female and and only 3
con_female. Also, the age and edu are highly correlated. I would try
creating a single IA group with males and females and a single con group
doug
On 12/18/2013 11:21 AM, Rujing Zha wrote:
> Hi all,
> I try to run mri_glmfit,
Try here instead
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.1.0/xhemi/
On 12/18/2013 11:37 AM, Sofie Valk wrote:
> Dear FreeSurfers,
>
> I have a question regarding the installation of xhemi (I am using FreeSurfer
> 5.1)
>
> I tried to follow the guide on:
> https://surfer.nmr.mgh.ha
The pvalues for what? Each voxel or cluster? When you click on a vertex,
QDEC will show you the pvalue in the form of -log10(p) signed by the
contrast. So 2 is p=.01 with a positive contrast.
doug
On 12/18/2013 01:21 PM, Hubbard, Catherine S. wrote:
> Hi,
> I've been using QDEC to run my GLM a
Hi Douglas,
I would go to the annotation drop down menu in freeview, select
l/rh.aparc.a2009s.annot and then it would freeze. I can't seem to
reproduce that problem today, but for every subject that I load an
annotation for now, the rh annotation loads properly, but the lh annotation
loads onto t
On 12/18/2013 12:08 PM, Hamza Alshuft wrote:
>
> Dear Freesurfer experts
>
>
> When I ran: mris_anatomical_stats -i 0 0.002 -l label/lh.roi.label -t
> / surf/lh.MD.mgh -b -f stats/lh.roi.stats subid lh to get the DTI
> value for a particular label, the function does not really take the
> thre
oh, if the lh annot is being loaded onto the rh surface, then that will
definitely create the tye-died appearance. Maybe Ruopeng can weigh in on
the freeview issue.
doug
On 12/18/2013 04:53 PM, Laura Taylor wrote:
> Hi Douglas,
>
> I would go to the annotation drop down menu in freeview, selec
Hi Rosa, let me see if I have this straight. For a single subject (in a
single session?) you have multiple runs. Each run only covers a part of
the brain (do the different runs overlap?). In the end, you want to have
a full brain analysis by combining the different parts. Is that right?
doug
Make sure you have a carriage return after your "end" statement (I'd add
a few)
doug
On 12/16/2013 04:24 PM, Emad Ahmadi wrote:
> Hello,
>
> I am having a tcsh scripting problem for generating a text file containing
> the list of subjects, and I would appreciate any help. I've explained my
> pro
Hi Doug,
I collected all the runs in the same subject in one session for the same
brain region (roughly the same slice window) but I collected a field map
for each run and undistorted each run independently. I also motion
corrected each run independently. Each run covers roughly the same part of
t
Hi Doug,
OK, I see. Thanks Doug.
All the best.
2013-12-19
Rujing Zha
发件人：Douglas N Greve
发送时间：2013-12-19 04:38
主题：Re: [Freesurfer] design matrix and contrast in fsgdf
收件人："Rujing Zha"
抄送："freesurfer"
yes
On 12/17/2013 10:06 PM, Rujing Zha wrote:
> Dear Doug,
> Thanks for your precious h
Hi Doug,
I see. Thanks Doug.
All the best.
2013-12-19
Rujing Zha
发件人：Douglas N Greve
发送时间：2013-12-19 04:49
主题：Re: [Freesurfer] tcsh in groupanalysis
收件人："freesurfer"
抄送：
You do not, but you will need to source the proper env file (
SetUpFreeSurfer.sh instead of SetUpFreeSurfer.csh)
dou
It looks reasonable to me, although you can't tell for sure from just one slice
Bruce
> On Dec 18, 2013, at 5:38 PM, sujith vijayan wrote:
>
> Hi All,
>
> I am wondering whether the talairach registration for one of my subjects
> needs to be fixed. It looks a little off to me, but I am not su
Hi Doug and others,
Thanks Doug.
I modifiled my number of class in the fsgd which can be got in the attachment.
And I am confused with 3 problems:
1st: Is what I modified proper?
2nd: How can I deal with my high correlation between age and edu?
3rd: Is it necessary to tell mri_glmfit to distinguish
On 12/18/13 10:26 PM, Rujing Zha wrote:
Hi Doug and others,
Thanks Doug.
I modifiled my number of class in the fsgd which can be got in the
attachment.
And I am confused with 3 problems:
1st: Is what I modified proper?
Yes
2nd: How can I deal with my high correlation between age and edu?
If
I would just treat them as separate runs and analyze them as "normal"
(ie, with -per-run alignment). bbregister should be able to do the
registration properly. Do you foresee problems with that?
doug
On 12/18/13 6:17 PM, Rosa Lafer-Sousa wrote:
Hi Doug,
I collected all the runs in the sam
Hi Doug and others,
Thanks Doug.
For the 2nd problem: I understand orthogonalization between nuisance variables.
I just want to test the difference between two group mean pial thickness
controling the age and edu (if it is necessary to control the age and sex). So
I guess I have two option: one:
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