Dear all,
I want to design a group t-test analysis and correlation analysis for pial
thickness. I have read the PPT of freesurfer.groupanalysis, and I wrote a
specific design matrix and contrast for my data. However it is the first time
that I design matrix in fsgdf by freesurfer. I didnot confi
Hi Doug,
Thanks Doug.
I tried the "-run 15" option, it generate a "015" folder. However unpacksdcmdir
code echo ERROR message:
"ERROR:mri_convert
child killed: segmentation violation ",
and the script terminated.
All the best.
2013-12-17
Rujing Zha
发件人：Douglas N Greve
发送时间：2013-12-17
look at the CWP column
doug
On 12/16/2013 05:14 PM, Jon Wieser wrote:
> Hi Doug
>
> I ran :
> mri_glmfit-sim --glmdir MTA_ADHD_MJ --cache 2.0 abs --cwp .9
>
> I have attached three of the output summary files
>
> Can you please confirm how to assess the cluster-wise p-value?
>
> Jon
>
> -
Pablo,
I need the recon-all.log file located in the $SUBJECTS_DIR/scripts
directory. Sorry for the confusion.
-Zeke
On 12/13/2013 04:48 PM, pablo najt wrote:
> Dear Zeke,
> Thank you so much. As I am not sure which is the log file that we use I
> am attaching mri_nu (in mri directory) and talai
Hi Doug
I ran :
mri_glmfit-sim --glmdir MTA_ADHD_MJ --cache 2.0 abs --cwp .9
I have attached three of the output summary files
Can you please confirm how to assess the cluster-wise p-value?
Jon
- Original Message -
From: "Douglas N Greve"
To: "Jon Wieser" , Freesurfer@nmr.mgh
Hello Emad,
Considering your output when you run this from the source command
generates only the first subject in your list, I would check to see if
there is a looping issue. Because you are no longer within the same
directory as when you ran it from the terminal, the script may not be
returning t
Hi Markus
for example, this is what is in the one we use:
mris_info $FREESURFER_HOME/average/lh.destrieux.simple.2009-07-29.gcs
reading color table from GCSA file
average std = 3.9 0.2 using min determinant for regularization = 0.000
0 singular and 1066 ill-conditioned covariance matrices
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
problem here:
http://stackoverflow.com/q/20617206/2769441
All the best,
Emad
___
Freesurfer maili
Dear Bruce or someone else,
would you mind answering a little more in detail, please? I am stuck. There
is hardly any thread about the command mris_sample_parc, but I need this
function.
1) This file called "cma_parcellation_colors.txt", is an option for
mris_sample_parc. Where does that file com
If you passed "-run 015" it should have generated a 015 folder and not a
013 folder. The only thing I can think may have gone wrong is that it
expected 15 instead of 015.
doug
On 12/16/2013 09:24 AM, Bruce Fischl wrote:
> sorry, I don't know that code very well. Doug is probably the right
> on
yes, no problem
On 12/16/2013 10:13 AM, r...@nmr.mgh.harvard.edu wrote:
> Yes. Sorry, I should mention this: the data is DTI (FA maps) from FSL. Can
> I still use the same methods?
>
>
>> Hi Jacky, have you looked at the group analysis tutorial? It includes
>> instructions on how to include age a
Hi Rujing
you can use either our FTP site or our file drop. Info for this is at
http://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange
and
https://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
cheers
Bruce
On Mon, 16 Dec
2013, Rujing Zha wrote:
Hi Bruce,
Maybe 163 email has some
Hi Bruce,
Maybe 163 email has some problems. I will try my gmail to send you and Louis my
data. But I donot know whether your email can get attachment size 289M?
Thanks.
All the best.
2013-12-16
Rujing Zha
发件人：Bruce Fischl
发送时间：2013-12-16 22:37
主题：Re: [Freesurfer] unpacksdcmdir: specifies
Yes. Sorry, I should mention this: the data is DTI (FA maps) from FSL. Can
I still use the same methods?
> Hi Jacky, have you looked at the group analysis tutorial? It includes
> instructions on how to include age as a continuous covariate.
> doug
>
>
> On 12/12/2013 06:28 PM, r...@nmr.mgh.harvar
no, I didn't get it
On Mon, 16 Dec 2013, Rujing Zha wrote:
Dear Bruce,
Thanks Bruce. That's all right.
I want to know if I e-mail to you my subject's data successfully. The
subject's image had a incorrect segmentation in surfs after recon-all.
Thanks in advance.
All the best.
2013-12-16
_
Dear Bruce,
Thanks Bruce. That's all right.
I want to know if I e-mail to you my subject's data successfully. The subject's
image had a incorrect segmentation in surfs after recon-all.
Thanks in advance.
All the best.
2013-12-16
Rujing Zha
发件人：Bruce Fischl
发送时间：2013-12-16 22:24
主题：Re: [Fre
sorry, I don't know that code very well. Doug is probably the right one to
help you
Bruce
On Mon, 16 Dec 2013, Rujing Zha wrote:
Dear Bruce,
I did setup the "-run 015" not "013" in unpacksdcmdir as I told in previous
message. But it generated the "013" folder automatically after running
unpac
Dear Bruce,
I did setup the "-run 015" not "013" in unpacksdcmdir as I told in previous
message. But it generated the "013" folder automatically after running
unpacksdcdir, which made me so confused.
As it created the "013" folder, I guess unpacksdcmdir didnot recognized
structure image correctl
but why are you giving recon-all the path to run 013 instead of 015? I
don't know the fsfast file structure, but your scan.info says that 013 is
an EPI fun and 015 is the mprage
On Sat,
14 Dec 2013, Rujing Zha wrote:
Hi Bruce,
It generated a 013 subfolder in after running this code "unpacks
Hi Bruce,
I saw the scan.info, and the 13 line is functional image which has a "6"
number. I guess this is why recon-all report the multiple frames. Would you
please tell me how I can deal with this problem which unpacksdcmdir recognize
the number "13" not "15"?
Thanks.
All the best.
2013-12-16
Hi Rujing
why does the input volume have multiple frames? Is it a multi-echo
dataset?
cheers
Bruce
On Sat, 14 Dec 2013, Rujing Zha wrote:
Hi Bruce,
It generated a 013 subfolder in after running this code "unpacksdcmdir
-src ../data/liujunhao -targ ../work/liujunhao -fsfast -run 015 3danat m
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