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 Colin, I'm not familiar with CARET, and I don't think that any of the
other FS developers are either. Maybe contact the wash u guys?
doug
On 12/27/13 12:54 PM, Colin Reveley wrote:
Hi - I actually sent this a couple of weeks back, but only just
noticed it was bounced back because I use
what is your command line and terminal output?
On 12/30/13 10:22 AM, Caspar M. Schwiedrzik wrote:
Hi Freesurfer Experts,
I am trying to apply a mask that I made with FSL's bet to a NIFTI file
that I got from someone else.
The mask looks fine, the NIFTI file is in float format, does not
conta
macaque_stripped_mask.nii.gz
macaque_stripped_final2.nii
this is the terminal output:
DoAbs = 0
Found 14652800 voxels in mask
Writing masked volume to macaque_stripped_final2.nii...done.
The same thing happens when I use nii.gz or mgz files.
Caspar
2013/12/30 Douglas Greve <mailto:gr...@nmr.mgh.harvard.
very
narrow range of values, between 43.7308 and 43.8476, to cover the
whole range of tissues in the image.
It is an average over several subjects, and before skull stripping,
there are hardly any zeros in the image.
Is there a way to rescale the file?
Thanks, Caspar
2013/12/30 Douglas
No, sorry. Why are you using such an old version?
doug
On 1/9/14 5:26 PM, Caspar M. Schwiedrzik wrote:
Hi Doug,
do you have a version of spatialsmooth-sess with the option to set
mask file name?
Thanks, Caspar
___
Freesurfer mailing list
Free
it is necessary to do the aparc.a2009s. It should not be needed for
wmparc (unless other files are not there)
On 1/10/14 8:08 PM, sujith vijayan wrote:
Hi Doug,
These were not done by me. What I have are the electrodes on top of MR
images as well as their RAS coordinates (I sent you a scre
HiAmirhossein, don't use the DOSS feature in QDEC because there is a bug such
that
it does not always do the right thing. Sorry, I sent out an email
about 8mo ago on this, but it is not easy to let people know about a bug
once the bug is out there. If you want to use DOSS, use mri_glmfit direc
, "Douglas Greve" <mailto:gr...@nmr.mgh.harvard.edu>> wrote:
HiAmirhossein, don't use the DOSS feature in QDEC because there is a bug
such that
it does not always do the right thing. Sorry, I sent out an email
about 8mo ago on this, but it is not easy to let
Sounds like it is some problem with the display libraries. I think
someone else was having the same problem recently (ie, hemisphere
displayed upside down in tksurfer). Does anyone remember? Zeke?
doug
On 1/12/14 5:03 AM, Schweren, LJS (med) wrote:
No, in Freeview I encountered no such p
Hi Matteo, I don't think it can be done in tksurfer.
doug
On 1/12/14 9:32 AM, matteo.di...@unito.it wrote:
> Dear Freesurfer experts,
> I would like to change the colour of the surface in tksurfer (e.g. from
> "grey" brain to "blue" brain). How can i obtain it? Thank you very much
> in advance
volume is ?h.volume, which is the "volume" at a vertex (basically vertex
thickness * vertex area, where vertex area is the mean of the areas of
the triangle that belong to that vertex)
sulc is ?h.sulc, which is the sulcal depth of each vertex
curv is ?h.curv, which is the gaussian curvature at
sorry, ?h.curv is the mean curvature, not gaussian
On 1/12/14 5:54 PM, Douglas Greve wrote:
volume is ?h.volume, which is the "volume" at a vertex (basically
vertex thickness * vertex area, where vertex area is the mean of the
areas of the triangle that belong to that vertex
ug and how can check if the slopes are different?
On Jan 12, 2014 12:33 AM, "Douglas Greve" <mailto:gr...@nmr.mgh.harvard.edu>> wrote:
Use DODS to test whether the slopes differ between the three
groups. If they do not, then use DOSS.
doug
On 1/11/14 5:03 P
Use mri_surf2vol on thicknessess that have been mapped to fsaverage.
This will put everything in fsaverage space. I don't know if that is
what you mean by the standard template
doug
On 1/16/14 9:19 PM, Muhammad Naveed Iqbal Qureshi wrote:
Dear Experts,
I need to know how can I convert the
Try using mri_label2vol instead of mri_convert. mri_convert just does a
mapping whereas mri_label2vol knows that this is a segmentation
doug
On 1/17/14 8:23 AM, Bruce Fischl wrote:
> Hi Gabor
>
> the volumes must change with reslicing. As to why they get consistently
> bigger in the hippocampus
yes
doug
On 1/23/14 4:21 PM, Alexopoulos, Dimitrios wrote:
Hi,
We'd like to map the cortical GM ribbon on our original single volume
native space anatomical T1.
The dataset has been run through recon-all -all.
The 'rawavg.mgz' or '001.mgz' is the native space T1 and 'ribbon.mgz'
is the cor
Have you tried running the defect-seg script? It creates annotations of
the defects. Look at the --help
doug
On 1/24/14 1:03 AM, Chris Adamson wrote:
Is there a way of making a volume like aparc+aseg with the defect
labels so that cortical region where the defects are show up red?
*Dr **C
Hi Dusan, find out where matlab is and add it to your path. Eg, on my
mac matlab is here
/Applications/MATLAB_R2011b.app/bin/matlab
In my .cshrc file, I have
set path = ($path /Applications/MATLAB_R2011b.app/bin/matlab)
doug
On 1/26/14 9:28 AM, Dusan Hirjak wrote:
Hi Sebastian,
I typed
On 1/28/14 7:03 AM, KimMJ wrote:
Dear Doug and experts
My question is about the choice of DODS or DOSS.
I want to compare cortical thickness between 2 groups (disease group
and control group), while controlling for the effect of age (nuisance
covariate).
I've already read through the mailing
The problem is that your input has multiple frames. What is the nature
of the input? Is it a multi-echo MPRAGE?
On 2/4/14 12:18 AM, Saurabh Thakur wrote:
Hello Everyone,
I am getting error
/===///
saurabh@saurabh-Dell-System-XPS-L502X:/
Hi Douglas, it looks like there is something wrong with those dicom
files because they are missing some key information. Where did they come
from? Did you anonymize them?
doug
On 2/5/14 10:05 AM, Douglas Wojcik wrote:
>
> Good morning;
>
> I am new to freesurfer, and I am having issues ge
look in the QDEC output folder. in each contrast subfolder you'll see a
"summary" file. This has most of the info you request.
doug
On 2/5/14 7:59 PM, Natasha Haris wrote:
Hello Freesurfers,
Is there any way to get a list of all the clusters (with information
on their location, x/y/z verti
Use mri_surf2vol
doug
On 2/5/14 11:31 PM, Muhammad Naveed Iqbal Qureshi wrote:
Hi,
How can I convert freesurfer .thickness files into .nii volume data to
analyze in SPM
I have already converted the .thickness files into .nii format by
using mri_convert command but the converted files ca
Mehul, I'm not sure what you are trying to do? Just get a version of the
aparc+aseg into mni152 space? If so, what is the application? In most
applications (eg, linear intersubject registration), this is not very
useful because the cortical labels are quite small (tailored to
surface-based an
If you know the acquisition parameters, you can enter them by hand into
the mri_convert cmd line. You could also specify a 9DOF registration to
have the registration program attempt to estimate the scale.
doug
ps. Please post all responses to the list and not to us personally.
On 2/7/14 9:59
No I don't, I just used read_surf. Can mris_convert do it?
On 2/9/14 3:15 PM, Bruce Fischl wrote:
> really? I didn't realize that as I don't use them much. Doug: do you have
> something like MRISread?
>
> On Sun, 9 Feb 2014, Lilla Zollei wrote:
>
>> Those .m files only give me a set of coordinat
what do you mean by "dots"? Eg, a mask surface overlay with 1s in some
vertices and 0s in others? Or a label?
doug
On 2/12/14 9:52 AM, peng wrote:
Dear Freesurfers,
I have run recon-all and got a set of surfaces for the subjects. I
wish to distribute N dots about evenly on the surface
sorry, you cannot have three levels in qdec (two max). You will need to
use the "command line" stream (ie, create a FSGD file and consrast
files, run mris_preproc, mri_surf2surf to smooth, mri_glmfit, and
mri_glmfit-sim). See the wiki for more details.
doug
On 2/16/14 4:53 PM, Yang, Daniel
Yes, you should see cyan. Note that you would see cyan if group1 slope
is 0 and group 2 slope is positive. Probably not a problem with age, but
it is just something to think about.
doug
On 2/17/14 1:38 AM, Yang, Daniel wrote:
Dear FreeSurfer developers and experts,
If I have a binary fac
e cortical thickening effect of Age is stronger in controls (vs.
patients)
Thanks, Doug!
Daniel
--
Daniel (Yung-Jui) Yang, Ph.D.
Postdoctoral Researcher
Yale Child Study Center
New Haven, CT
Tel: (203) 737-5454
E-mail: _yung-jui.yang@yale.edu_
On 2/17/14 9:55 AM, "Douglas Gr
we have TR of 1, and 2?
Thanks for your advice!
Regards
Goi khia
On Tue, Nov 12, 2013 at 11:50 AM, Douglas Greve
mailto:gr...@nmr.mgh.harvard.edu>> wrote:
are you running "optseq" or "optseq2"? It should be optseq2. You
may need to make it executable (loo
Hi Greg, use the defect-seg script to create segmentations and labels.
See the help for more info.
doug
On 2/17/14 1:42 PM, Bruce Fischl wrote:
> Hi Greg
>
> there is a ?h.defect_labels file that gets created in curvature format I
> believe that you can overlay (the overlay is the defect numbe
Sorry, no. You can use mri_mask from the command-line though
doug
On 2/14/14 11:19 AM, Joerg Pfannmoeller wrote:
> Hello,
>
> I am using tkmedit to display functional data as an overlay on anatomical
> data. I am asking myself if there is a feature in tkmedit which allows to
> apply a mask to t
I've never used BV, so I can't help you. You might want to contact
the BV folks as they may have more experience in this.
best
doug
On 2/17/14 5:41 PM, Dave Frank wrote:
Hello,
I'm try
btw, if I had to guess, I'd say it is an "endianness" problem.
On 2/17/14 5:41 PM, Dave Frank wrote:
Hello,
I'm trying to use anatomical regions of a subject labeled by
freesurfer as an fMRI mask in brainvoy
oops, sorry! That command looks like it is correct. Can you say more
about what is going wrong? How are you determining that something is
going wrong?
doug
On 2/17/14 9:30 PM, Celine Louapre wrote:
> Hi Doug
> I don't know if you had the chance to read my email below to resample a
> lesion m
what does it look like if you run
tkmedit -f lowb.nii.gz -ov lesion_WM_vol2vol.nii.gz -fminmax .5 1
On 2/17/14 10:00 PM, Celine Louapre wrote:
> No problem, sorry!
> So when I am loading my lesion mask on freeview on brainmask.mgz and on
> DTI_fit_FA.nii, the lesions are correctly registered
When you loaded the lowb into freeview and it looked registered with the
anatomical, did you load the lowb with the registration file? If not,
then the registration may be wrong. Things may look almost right when
you don't specify a registration file because you probably collected the
dti and
Let's say you have four groups with 10 20 30 40 (100 total). The first
group would get a weight of .25 where it only had 10% of the total. I
don't think there is any way around this.
On 2/18/14 4:07 PM, Yang, Daniel wrote:
Doug, sorry, I am not sure I can fully understand.
Do you mean the
Are those dicom files ones that we distribute? If not, where do they
come from? They are missing a lot of important information. Were they
anonymized?
doug
On 2/19/14 2:01 AM, Saurabh Thakur wrote:
command i m using is
:mri_convert -i
/home/saurabh/Desktop/saurabh_freesurfer/bert/sam/I
I'm not sure I understand. Your contrasts below are fine. What are you
unsure about?
doug
On 2/20/14 7:48 PM, charujing123 wrote:
Hidoug and others,
Thanks doug.
I see.If I want to implement multiple regression, i.e. two EVs(score1
and score2) explain pial thickness, what contrast I shoul
Do you mean you want to create your own atlas? If so, then you need to
create a whole-brain segmentation for each subject, then run
mri_ca_train to create the atlas, then mri_ca_label to label a new subject
doug
On 2/21/14 4:54 AM, Saurabh Thakur wrote:
Hi Freesurfer expert,
Thanks for
yes, or do post hoc tests
doug
On 2/21/14 6:35 AM, Yang, Daniel wrote:
Thanks, Doug! I guess in order to interpret the interaction correctly,
I would need to extract the thickness value and plot the interaction.
Best,
Daniel
--
Daniel (Yung-Jui) Yang, Ph.D.
Postdoctoral Researcher
Yale Child S
Yes.
doug
On 2/21/14 6:15 AM, Yang, Daniel wrote:
Dear FreeSurfer Experts,
In the example
here: http://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf1G2V, it describes
the testing of the main effects of two continuous variables.
In order to test the interaction effect, I think we can form an
int
On 2/21/14 10:04 AM, charujing123 wrote:
Hi all,
I finished the mri_glmfit-sim, and got some clusters in the cluster
summary.
1,I want to know how to extract mean thickness for each subject in
this cluster?
There should already be a file there called something like
something.y.ocn.dat. This
OCN = output cluster number. Each vertex gets a value, that value is the
integer number of the cluster number the vertex belongs to (or 0 if it
does not belong to a cluster). It is basically a segmentation. For
visualization, the .annot file is probably better. You might not have
seen anythi
When you actually run the simulation, it only runs it for the first
contrast. The simulation is the same for all contrasts, so you can just
copy the csd files from the first contrast to the others, then run
mri_glmfit-sim with the --no-sim option
doug
On 2/21/14 5:47 AM, charujing123 wrote
e I am wrong?
> Thanks.
> All the best.
> Rujing Zha.
> 2014-02-22
>
> charujing123
> ----
> *?? ?:*Douglas Greve
> *:*2014-02-2
Sorry, I don't know why tksurfer is failing to display the surface. I
suspect that it is a video driver problem, but that is just a
speculation, and I'm not qualified to debug video driver issues. Maybe
Zeke can chime in.
doug
On 2/24/14 9:56 PM, charujing123 wrote:
Sorry for this e-mail
You did not run it all the way through (you stopped at autorecon2)
doug
On 2/25/14 9:00 AM, sabin khadka wrote:
Thanks Doug. recon-all.log is attached herewith.
On Monday, February 24, 2014 5:07 PM, Douglas N Greve
wrote:
are you sure it did not fail? Can you post the recon-all.log file
On 2/25/14 10:09 AM, Rujing Zha wrote:
Hi FS experts and others,
I have done two group thickness difference analysis based on
whole brain. Now I want to do correlation analysis between specific
ROI thickness and behavior score. I searched roi in the FS website,
but I cannot distinguish
Please post questions to the list. Thanks! You need fsaverage. What are
you trying to do? Usually people point SUBJECTS_DIR to a folder in space
where they have write permission, then create a symlink from fsaverage
to that space. Can you not do this?
doug
On 2/25/14 10:04 AM, Boadu, Osei
That command definitely will not work. When you ran the command I sent,
did it at least show you something on the surface?
Ruopeng, is there a way to load a surface-based timecourse in freeview?
doug
On 2/26/14 9:11 PM, charujing123 wrote:
Hi doug,
Thanks doug.
I am sorry to describe my
this is a matlab problem, not a FreeSurfer problem, so I'm not sure. It
might be the MNE toolbox. I would try commenting out all the non-FS
stuff in your ~/matlab/startup.m file and see if the problem goes away.
On 3/1/14 8:50 AM, Borzello, Mia wrote:
> I haven't actually changed anything in th
That means that it was expecting to find 66 segmentations but only found
55. Sometimes there are some segmentations in one subject that are not
in another (usually hypointensities). But 11 is too many. Have you
looked at the aseg to see if it looks right? You can also compare the
aseg.stats f
On 3/4/14 7:18 PM, Xuelong Zhao wrote:
Dear Doug,
I've managed to get functional information onto the cortical surface
following your instructions.
But, there's a few issues that are still not resolved:
1/ wrt to registration I believe the supplied anatomical template (in
tailarach coords)
By default, the surface area is computed from the white surface (ie,
boundary between WM and GM). It is possible to compute it from the pial
surface (ie, boundary between GM and background)
doug
On 3/5/14 9:14 PM, ??? wrote:
Hi all,
I need to know how is the SurfArea in ?h.aparc.stats ca
On 3/5/14 5:25 PM, Tudor Popescu wrote:
Hello, I have some questions on doing group comparisons with
thickness, area and volume. Many thanks in advance for any help!
1) For a DOSS design with group and gender as categorical factors, I
see that an interaction contrast ("Is there a group-gender
ulate exterior surface of the cortical region ? The other
five surface (i.e. anterior, posterior, left, right, interior) are
excluded ?
Thanks!
Zhuangming
-原始邮件-
*发件人:* "Douglas Greve" mailto:gr...@nmr.mgh.harvard.edu>>
*发送时间:* 2014年3月6日 星期四
*收件人:* freesurfe
On 3/6/14 6:39 AM, Xuelong Zhao wrote:
Hi Doug,
A follow-up. I've gone back and re-done the registration using nifti
file with the ICA20 maps. I noticed in tkregister2 that when I press
on the TARGET tab there is extremely good alignment ( i think it is to
'orig.mgz' in the mri folder of my
The one from asegsats2table takes into account partial volume information
doug
On 3/6/14 7:13 AM, Saurabh Thakur wrote:
Hello Freesurfer Expert,
I am working on volumetric analysis of Hippocampus.
When i am find the no of voxel's for left Hippocampus (17) and Right
Hippocampus(53) using co
the exterior surface and the interior
surface are computed when FreeSurfer calculates the surface
area.
Thanks!
Zhuangming Shen
-原始邮件-
发件人: "Douglas
yes, that is the option. If you run it with --help, it will actually
give you an example.
doug
On 3/10/14 7:23 PM, Thomas Yeo wrote:
> Hi Jeff,
>
> I am a little unsure myself since I usually work with data mapped to
> fsaverage space. I think you might want to use mri_surf2surf, since
> there's
I don't know of anything that will do this (or what a single object
would mean in this case). If you have the overlay in a volume format
(eg, mgz), you can use MRIread.m. This gives you a value for each
vertex, not face, so you'd have to write something to assign the value
to a face.
doug
On 3/11/14 3:41 PM, pfot...@nmr.mgh.harvard.edu wrote:
> Hi Doug,
>
> Thanks for your reply. Just to be clear, I need to ask some trivial
> questions:
>
> 1) I need to do that subtraction in the fsgd file right? (In which case
> there will be negative numbers as well)
Correct.
>
> 2) I ran the ana
But what is in rh.ttest.thickness.10.mgh? Is it a stack of all your
subjects (the file you passed with --y to mri_glmfit)? If so, then add
"-t rh.ttest.thickness.10.mgh" to your tksurfer command line. Ruopeng
just added something to freeview to do it, but you'd have to get a new
version
dou
Use mri_surf2vol to do this. Soemthing like
mri_surf2vol --surfval rh.36...mgh --hemi rh --fillribbon --subject
fsaverage --template $SUBJECTS_DIR/fsaverage/mri/orig --o yourvolume.nii
doug
On 3/11/14 10:10 PM, charujing123 wrote:
Hi Bruce,
Thanks Bruce.
I knew that code, but I have no ide
It is just a standard multiple regression analysis where all regressors
are fit simultaneously. One weight does not include that of another weight.
doug
On 3/12/14 5:16 AM, L. Schweren wrote:
Dear FreeSurfer experts,
I am attempting to disentangle the effects of different features of
phar
Run it with --debug as the first option and send me the terminal output
doug
On 3/14/14 3:44 AM, Dusan Hirjak wrote:
I did type the same line es mentioned in your Email and I did not put
the 1.3 in quotes.
However, it is still not working:-( Any other ideas???
Thanks.
DH
> Subject: Re: [Fr
yes
On 3/18/14 9:14 AM, amirhossein manzouri wrote:
Tanks doug,
Is it ok like this: mri_glmfit-sim --glmdir qdec/Untitled --cache 1.3
neg ?
Best regards,
Amirhossein Manzouri
On Mon, Mar 17, 2014 at 8:25 PM, Douglas N Greve
mailto:gr...@nmr.mgh.harvard.edu>> wrote:
you will have
It is constructing a GLM with design matrix with 2 columns and N rows
where each row is a subject. The row of your patient gets 1 0 and the
rows for the other subjects gets 0 1. When you set up a contrast with [1
-1], you are comparing the value of the subject against the mean of the
others
Can you verify that the label does actually have label points in it?
Just open it in a text editor or cat it to a terminal. If it does have
points, send it to me. Also let me know which version of FS you are running.
doug
On 3/17/14 5:35 PM, Rupa Sabbineni wrote:
muen223-105-dhcp:subjects
When you say they don't match, what do you mean? You have set the
cwpvalthresh to .99, so when you run tkmedit, you should set the
-fminmax to something like .01 3 otherwise you will not see all the
clusters you see in the summary table
doug
On 3/19/14 6:28 PM, Omar Singleton wrote:
> Hello
The ocn will have all clusters found in the summary file. Are you seeing
more than that? What you see in the sig.cluster file depends on what
threshold you set when you run tkmedit. Below, you have 1.3 = p < .05,
so it should only shows clusters in the summary file that have p < .05
doug
On
Try using the --paint option to mri_label2label
doug
On 3/24/14 10:53 AM, Karen Marie Sandø Ambrosen wrote:
Hi Bruce,
Thanks for your answer. I will like to do it automatically as I have a
lot of labels. However, I can't find an option called close in
mri_label2label. Can you give me anoth
In theory, it should be possible. I have not used Jorge's stream, so I
don't know that much about it. Does it save an estimate of the FWHM? If
so, then you can run mri_surfcluster passing it the p-value (ie,
-log10(p)) map, the FWHM, the mask, and a voxel-wise threshold. This is
what mri_glmfi
In that case, you can just do a paired analysis. Do a search for that on
the wiki and you'll find examples
doug
On 3/21/14 5:50 PM, Peggy Skelly wrote:
The actual time between tp1 & tp2 varies for subjects, *but* every
subject received the same "dose" of treatment between timepoints. To
ask
On 3/23/14 6:46 AM, Eileen Moore wrote:
> Hello FreeSurfer experts,
>
> I am using freesurfer v5.3 on a linux os. I have a few questions regarding
> individual aseg statistics (volume, intensity) for a subcortical region that
> is not automatically segmented by freesurfer. Using tkmedit I have m
On 3/23/14 2:47 PM, Tudor Popescu wrote:
Hi Doug,
> 3) In a group X gender X age DODS design, exactly which contrast
> (interaction) has to be examined in order to see if the analysis
> proceeds as DODS or as DOSS? And what would the course of action be
> assuming there are sign
How much of a difference is there? There should not be much, but there
will be some because the aparc does not cover the exact same vertices as
cortex.label
doug
On 3/24/14 8:04 AM, _andre...@sapo.pt wrote:
> Hello list,
>
> I have a question regarding what stats are more correct to use to ge
On 3/26/14 8:24 AM, Markus Gschwind wrote:
Dear Doug and Bruce,
I have three more questions concerning 'pctsurfcon'.
1) The inner sampling distance is set to 1mm by default, but the outer
sampling is done at a 30% of the cortical thickness. I saw that I
could easily change the parameters or
What is your vol2vol command line?
On 3/26/14 3:58 PM, Gabriel Gonzalez Escamilla wrote:
Dear FS experts,
I've been dealing with the conversion to MNI152 of some volumetric
labels of my subjects extracted with mris_extract_label in FS v.5.1
but, I've been unable to succeed.
I've tried b
Surface-based analysis is an alternative to talairach-based analysis. It
does not make sense to do both. Is the AFNI talairach space affine (ie,
12 dof)? If so, then it is possible to undo the resampling to talairach
space. You will need to know which space the afni results are in (ie,
MNI152
This is not something that was ever ready for use.
doug
On 3/27/14 3:22 PM, SHAHIN NASR wrote:
Hi,
For a project in which subjects have repeated head movements, I
want to register every TR to anatomical scans separately to reduce the
effect of head movement as much as possible. When I
Use mri_surf2surf to map the annotation or change the annotation into
labels (mri_annotation2label) then run mri_label2label
On 3/30/14 11:34 AM, charujing123 wrote:
Hi FS experts
I have done the group thickness analysis(two group t-test), and get
the result(i.e. sig.mgh). I got one clust
I think aparcstats2table automatically includes these measures. Can you
check? And, yes, mean thickness can be computed as (lh+rh)/2
doug
On 3/30/14 12:58 PM, Yang, Daniel wrote:
Dear FreeSurfer Experts,
I would like to extract the mean thickness for each subject, and I can
see that in the
I don't know what you mean by represent as non-surface. To load in
tksurfer run
tksurfer fsaverage lh inflated -aparc -overlay sig.mgh
On 3/30/14 11:16 AM, charujing123 wrote:
Hi FS experts
I completed group analysis by this
method:http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAn
On 3/29/14 3:09 PM, Ashley Shurick wrote:
Hi,
I have some questions about using monte carlo sim in qdec:
First of all, I just want to verify it's ok to use the simulation with
a whole-brain analysis and not just an ROI analysis.
yes
Second, I'm a bit confused about how to calculate the p-t
How did you create the glmdir? mri_glmfit should set things up so that
all of those files are there
On 3/30/14 11:09 AM, yd li wrote:
Hello experts,
I'm working with FS 5.3.0. When I used 'mri_glmfit-sim --glmdir
/home/a/freesurfer/g2.lh/C1 --sim mc-z 5000 4 mc-z.abs --sim-sign abs
--cwp
FMHM, or if I would need to run the statistics
from the beggining using in the terminal, and not in MatLab.
Do you think Jorge could comment on this issue?
Regards,
Pedro Rosa.
On Mar 24, 2014, at 12:44 PM, Douglas Greve
mailto:gr...@nmr.mgh.harvard.edu>> wrote:
In theory, it should be pos
If you want to test for interactions among nuisance variables, then you
have to create a new regressor where you multiply them together.
doug
On 3/30/14 4:20 PM, Clint Johns wrote:
I have a clarifying question about fsgd file format.
We have 40 participants, and a large battery of individual
e obvious. I'm really just not sure
that we have formatted them.fsgd files correctly!
Thanks for your time and attention.
clint
On Sunday, March 30, 2014, Douglas Greve <mailto:gr...@nmr.mgh.harvard.edu>> wrote:
If you want to test for interactions among nuisance variables,
Native anatomical space of the individual subject.
doug
On 3/31/14 7:16 PM, Salil Soman wrote:
Hi,
I was wondering what the default freesurfer coordinate space is
called? (MNI, something else)?
Thanks,
Sal
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Hi Ye, have you looked at the mris_preproc help? You can access it with
mris_preproc --help. Let me know if that does not answer your questions
doug
On 4/6/14 6:09 PM, ye tian wrote:
Hello Freesurfers,
I understand that the output of "mris_preproc" can be the input of
"mris_glmfit". In mri
more confused after reading the summary. The
summary basically reaffirms my understanding that "mris_preproc" gives
"an average subject". How can this be an appropriate "data" for GLM,
which for sure needs multiple data points?
Thank you!
Sincerely,
Ye
On Sun
yep, exactly
On 4/8/14 6:00 PM, Corinna Bauer wrote:
Hi Doug,
After I have the labels then in each subject's T1 space, I will need
to then put them into diffusion and resting state space.
I already have scripts that put the parcellations into
subject-specific diffusion/resting state space (u
Try setting the age to be a nuisance variable.
doug
On 4/8/14 7:06 PM, Walton, Matt wrote:
Hello Freesurfer experts.
I am trying to run a QDEC analysis on some MRI data I have. I want to
see if thickness is correlated with language scores I have for each
subject, while accounting for differ
You can use --projfrac (which can perform an interpolation with --interp
trilinear)
On 4/9/14 2:44 AM, Joerg Pfannmoeller wrote:
> Sorry for this question, but now I am confused. Do you mean that I should not
> use projopt and just use the interpolation? If so why should I not use
> projfrac?
By irregular, I mean irregularly shaped (non-concave) such that the
centroid is actually not inside the cluster. Eg, a ring would have the
centroid in the center but technically it would not be in the ring
On 4/9/14 2:48 AM, Joerg Pfannmoeller wrote:
> On Mon, 07 Apr 2014 12:02:24 -0400
> Doug
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