Sorry, I'm still having a problem following what you are trying to do.
You have a 3x3 functional design (3 levels of reward, 3 levels of risk),
and you want to look for an interaction between reward and risk?
On 02/24/2016 12:10 PM, Afzal, Afsana wrote:
> Hi Doug,
>
> Upon reviewing the repeat
No, not yet, though I recently had a need to do the same thing. It is
pretty easy to do though. If you run mri_gtmpvc with --save-input, it
will create a file called input.rescaled.nii.gz. Then you can run
mri_segstats --i input.rescaled.nii.gz --seg aux/seg.nii.gz --ctab
aux/seg.ctab --avgwfvol
On 02/29/2016 02:38 AM, Bittner, Nora wrote:
>
> Dear FreeSurfer Experts,
>
> Sorry for reposting this massage again, but I still have two
> questions, which you can hopefully answer to:
>
> 1)
>
> I calculated several analyses with LGI as my dependent variable,
> resulting in several significa
I would recon the mni152 (or whatever space the AAL atlas is in), map
the AAL ROIs onto the surface (vol2surf), then use mri_surf2surf to
transfer them to the individual.
On 02/29/2016 06:37 PM, pfot...@nmr.mgh.harvard.edu wrote:
> Hi FS community,
>
> I have recon-ed a set of subjects and I was
I cannot replicate the error. What version of FS are you using? What
happens if you run
mri_glmfit --fsgd RPA-acc.fsgd
or
mri_glmfit --fsgd RPA-accGT.fsgd
On 02/29/2016 09:38 PM, Joseph Dien wrote:
> Hi,
> I’m having an fsgd error that has totally stumped me. I’m trying to run
> the fol
Create a contrast between the two conditions
On 03/01/2016 01:27 AM, Silas wrote:
>
> Dear FreeSurfer team,
>
>
> Thank you for all your help so far!
>
>
> I would like to visualize the difference between two fMRI data sets.
>
> Data set1: Cortical activation during movement of a finger.
>
> Data
Dear. freesurfer experts.
Hi. I'm using freesurfer version 5.3.0.
I tried mc-sess onto runs that have different number of slices.
However, due to this different number of slices in different runs, mc-sess
gives an error.
I expected that running mc-sess in freesurfer version 5.3.0 would handle
t
Can you send me rh_time_spval.mgh?
On 03/01/2016 04:42 PM, Jennifer Legault wrote:
> Hi Doug,
>
> Thank you for responding. I actually realized what was the matter (I
> had specified the path for fsaverage which led to the error; this is
> no longer an issue so long as I use "--subject fsaverag
The command I used is:
mktemplate-sess -s $SUBJECT -df sessdirfile -fsd bold_retino
mc-sess -s $SUBJECT -df sessdirfile -fsd bold_retino -per-session
Thank you.
Best,
Ji Won
2016-03-03 12:22 GMT-05:00 Ji Won Bang :
> Dear. freesurfer experts.
>
> Hi. I'm using freesurfer version 5.3.0.
>
>
Do you have write permission to that folder? Is the disk full?
On 03/02/2016 11:12 AM, Óscar Soto Angona wrote:
> Hello,
>
> We are medicine students who are using freesurfer for research. We had
> been using freesurfer in Ubuntu 12.02 without encountering any
> trouble; recently we updated to 1
Dear FS experts,
I am using Qdec to study the differnce in cortical thicnkess between two groups.
Qdec is running a GLM analysis. This will output a statistical map (sig.mgh) for the differnce between the groups in cortical thicnkess.
How can I extract the numbers of cortical thickness for every
In the first command you only used 5 samples in your simulation. If you
read the "Notes" section below the command, you'll see that this should
be something like 5000. Only 5 was used because it would take very long
to run. In general, you don't need to run the simulation because it has
already
you have to use -per-run not -per-session
On 03/03/2016 12:27 PM, Ji Won Bang wrote:
> The command I used is:
>
> mktemplate-sess -s $SUBJECT -df sessdirfile -fsd bold_retino
>
> mc-sess -s $SUBJECT -df sessdirfile -fsd bold_retino -per-session
>
> Thank you.
>
> Best,
> Ji Won
>
>
>
> 2016-03-03
not sure what you mean. the statistical map will have a single value,
not a value for each subject
On 03/03/2016 12:31 PM, John Anderson wrote:
> Dear FS experts,
> I am using Qdec to study the differnce in cortical thicnkess between
> two groups.
> Qdec is running a GLM analysis. This will outp
All the values are between 0 and 1, so I suspect this is a map of
p-values, not a map of -log10(p). Is that right? If so, convert it to
-log10(p) and rerun. You can do this in matlab with
p = MRIread('rh_time.mgh');
sig = p;
sig.vol = -log10(abs(p.vol));
MRIwrite(sig,'sig.mgh');
On 03/03/2016
what is your command line? You have to use -per-run and not -per-session
On 03/03/2016 12:22 PM, Ji Won Bang wrote:
> Dear. freesurfer experts.
>
> Hi. I'm using freesurfer version 5.3.0.
>
> I tried mc-sess onto runs that have different number of slices.
>
> However, due to this different number
Hi Freesurfer team,
*Short question: *Will (accidentally) using the fsaverage v5.3 subject in
our v5.1 directory influence our reconstructions?
*Long question:* Our server has 2 different freesurfer environments. A
recon was accidentally run on a single v5.1 subject in the v5.1 directory
with fr
Hi Doug,
How can I use this statistical map ( e.g. as a mask) to calculate the mean cortical thickness only in the areas of significant differnce between the groups for every subject?
Bests,
John
Sent: Thursday, March 03, 2016 at 12:37 PM
From: "Douglas N Greve"
To: freesurfer@nmr.mgh.h
Hi Don, there is not an easy way to get this information. You can use
mri_binarize to create a surface of each ROI, something like
mri_binarize --i wmparc.mgz --match 3013 --surf lh.wm.lingual
Use this version of mri_binarize
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_bina
You will have to extract clusters (mri_surfcluster) to create an
annotation, then use mri_segstats with the --annot option and specifying
the y.mgh file as input and the output using something like --avgwf
output.txt (also add --exludeid 0). The output will have a row for each
frame in y.mgh (i
If it affects anything, it would only affect the BA labels. If the BA
labels did not change between 5.1 and 5.3, I don't think it would affect
anything.
On 03/03/2016 12:41 PM, Adam Martersteck wrote:
> Hi Freesurfer team,
>
> *Short question: *Will (accidentally) using the fsaverage v5.3 subj
Thanks very much, Doug.
I could always hope.
> -Original Message-
> From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-
> boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve
> Sent: Thursday, March 03, 2016 12:45 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Fr
This si Great!!! Thanks Doug. One more question:
What is the correct input in the command mri_surfcluster. Is it the image "sig.mgh" ?
Bests,
John
Sent: Thursday, March 03, 2016 at 12:47 PM
From: "Douglas N Greve"
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Qdec-sta
yes
On 03/03/2016 01:06 PM, John Anderson wrote:
> This si Great!!! Thanks Doug. One more question:
> What is the correct input in the command mri_surfcluster. Is it the
> image "sig.mgh" ?
>
> Bests,
> John
> *Sent:* Thursday, March 03, 2016 at 12:47 PM
> *From:* "Douglas N Greve"
> *To:* frees
Hi,
I have been working on speeding up the the hippocampal segmentation in
freesurfer 6 beta and I have been playing around with both -openmp and
-use-gpu flags. I noticed that freesurfer does seem to make use of all the
threads in freesurfer 6 irrespective of passing the -openmp flag or not. Is
t
Hi Doug,
Thanks for your response!
Panos
> I would recon the mni152 (or whatever space the AAL atlas is in), map
> the AAL ROIs onto the surface (vol2surf), then use mri_surf2surf to
> transfer them to the individual.
>
> On 02/29/2016 06:37 PM, pfot...@nmr.mgh.harvard.edu wrote:
>> Hi FS commun
Dear Doug, Thank you for your clarification. It sounds the right way for
correction is:mri_glmfit-sim \ --glmdir lh.gender_age.glmdir \ --cache 4
neg \ --cwp 0.05\ --2spaces
One last question: Is the resulting "cache.th40.neg.sig.cluster.summary"
the right file to look for post-correction cluste
Thanks for your reply. It works.
I have 1 more general question.
When running: mktemplate-sess -s $SUBJECT -df sessdirfile -fsd bold_day1
I get 2 files (template.log & template.nii.gz) under the functional
subdirectory(bold_day1) and under each run(001, 002 etc).
When I run: mc-sess -s $SUBJECT
On 03/03/2016 02:46 PM, Ji Won Bang wrote:
> Thanks for your reply. It works.
>
> I have 1 more general question.
>
> When running: mktemplate-sess -s $SUBJECT -df sessdirfile -fsd bold_day1
>
> I get 2 files (template.log & template.nii.gz) under the functional
> subdirectory(bold_day1) and und
yes, that is the right file
On 03/03/2016 02:20 PM, Karl Liu wrote:
> Dear Doug,
> Thank you for your clarification. It sounds the right way for
> correction is:
>
> mri_glmfit-sim \ --glmdir lh.gender_age.glmdir \ --cache 4 neg \
> --cwp 0.05\ --2spaces
>
>
>
> One last question: Is the result
On 3 March 2016 at 13:22, Francis Tyson Thomas
wrote:
> Also, it looks like development for GPU usage has been halted for now and so
> I was trying to use the CUDA 5 for getting it working under ubuntu 14.04. I
> have been not successful that as the cuda device isn't getting selected. Do
> you ha
Hi,
Thank you so much for assistant me in the process. I could do that. It
worked. Thanks
Faezeh Vedaei
On Wed, Mar 2, 2016 at 6:15 PM, Faeze Vedaei wrote:
> Hi
>
> Thank you so much for your help. I just got your meaning. I created new
> LUT file by just changing randomly the RBG values for e
Hello,
I ran several recon-all processes on raw T1 MRI data. I was trying to run
recon-all -lgi as per the instructions from this paper -
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3369773/ but it fails with an
error that Matlab is required. So, my question is if local GI is already
computed by ru
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