> I'm testing the total processing time of recon-all -all using -openmp
> 4,6,8,12 .
> The runs with 4 and 6 threads took almost the same amount of time.
> The runs with 8 and 12 threads took almost the same amount of time.
>
> (1)Is the work divided evenly between the threads (mri_ca_register,
Hi Clara
did you upload the dataset to our ftp site?
Bruce
On Thu, 30 Apr 2015,
silve...@gmx.com wrote:
Hi,
Following up on this thread, has there been any updates regarding the
crossing medial surfaces problem?
Thanks.
Dear Bruce, where could I upload the base of a child participant?
I don't know what you mean. can you elaborate?
On 04/30/2015 06:41 PM, Ghazal Kiani wrote:
> Hi,
>
> We were wondering when viewing group data on the inflated brain using
> FreeSurfer, if FreeSurfer applies any correction and how we c an
> control the correction value?
>
> Thanks,
> Ghazal
>
>
>
I'm testing the total processing time of recon-all -all using -openmp 4,6,8,12 .
The runs with 4 and 6 threads took almost the same amount of time.
The runs with 8 and 12 threads took almost the same amount of time.
(1)Is the work divided evenly between the threads (mri_ca_register,
mri_en_re
Hi,
We were wondering when viewing group data on the inflated brain using
FreeSurfer, if FreeSurfer applies any correction and how we c an control
the correction value?
Thanks,
Ghazal
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Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://ma
malshikh@icepuff2 scripts]$ which mri_glmfit
/usr/local/freesurfer/dev/bin/mri_glmfit
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve
[gr...@nmr.mgh.harvard.edu]
Sent: Thursday, April 30, 2
hmmm, I just tried it in dev and it worked. Type "which mri_glmfit"
while you're in dev and send me the result
On 04/30/2015 06:12 PM, Alshikho, Mohamad J. wrote:
> I know what is the story.
>
> I am sourcing /usr/local/freesurfer/dev
>
> I tried
>
> /usr/local/freesurfer/stable5_3_0
>
> and it w
I know what is the story.
I am sourcing /usr/local/freesurfer/dev
I tried
/usr/local/freesurfer/stable5_3_0
and it worked
___
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Alshikho, Mohamad J.
Sent: T
Hi Doug,
I still receive the same error :bellow is the input and output:
[malshikh@icepuff2 L_Precentralgyrus]$ mri_glmfit --y ces.nii.gz --wls
cesvar.nii.gz --fsgd fsgd --surface fsaverage lh --glmdir my-glm.wls --nii.gz
--C Contrast1group.diff.mtx --C Contrast2group1.mtx --C Contrast3group2.mt
I just ran the following command
mri_glmfit --y ces.nii.gz --wls cesvar.nii.gz --fsgd fsgd --surface
fsaverage lh --glmdir my-glm.wls --nii.gz --C Contrast1group.diff.mtx
--C Contrast2group1.mtx --C Contrast3group2.mtx --C
Contrast4g1g2.intercept.mtx
and did not receive an error. Can you try
I used the following link https://gate.nmr.mgh.harvard.edu/filedrop2/ to send
the files and I included your email address
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas Greve
[gr...@nmr.mgh.harva
To the filedrop, url at the end of this email
On 4/30/15 4:58 PM, Alshikho, Mohamad J. wrote:
> Hi Doug,
> To this email address freesurfer@nmr.mgh.harvard.edu or to your email?
>
>
> Mohamad
>
> From: freesurfer-boun...@nmr.mgh.harvard.edu
> [freesurfer-b
Hi,
Following up on this thread, has there been any updates regarding the crossing medial surfaces problem?
Thanks.
Dear Bruce, where could I upload the base of a child participant? Is there a freesurfer specific platform or something?
Cheers, Clara
- Ursprüngliche Mail -
V
Hi Doug,
To this email address freesurfer@nmr.mgh.harvard.edu or to your email?
Mohamad
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas Greve
[gr...@nmr.mgh.harvard.edu]
Sent: Thursday, April 30,
Can you tar or zip the following files and post them to me on our file
drop (see below): ces.nii.gz cesvar.nii.gz fsgd C1.mtx C2.mtx C3.mtx C4.mtx
doug
On 4/30/15 2:06 PM, Alshikho, Mohamad J. wrote:
> Hi Doug,
> I finished recently running FSFAST on fmri data set.
> I want to run group GLM for
Francesca,
How was lh.EKppa.annot created? Is it a custom list of annotations?
Does it include an embedded colortable appropriate for those
annotations?
Can you send me the files 'lh.EKppa.annot' and 'lh.white'? I can try to
replicate the problem.
Also, can you run this:
mris_info lh.EKppa.an
Hi Doug,
I finished recently running FSFAST on fmri data set.
I want to run group GLM for the following analysis:
OSGM, FSGD( no covariates)
For OSGM I ran the following command line like in Wiki:
mri_glmfit --y ces.nii.gz --wls cesvar.nii.gz --osgm --surface fsaverage lh
--glmdir my-glm.wls
Hi Freesurfers,
I've just completed recon-all -all and pulled up the brain in Freesurfer V5.0
on my Linux machine, and realized I needed to run the following command
"recon-all -skullstrip -wsthresh 30 -clean-bm -no-wsgcaatlas -s sub122.fs" to
pick up cerebellum that was missing. After the co
Hi Alan,
Do you have the image processing toolbox installed in matlab? If not, I guess
this is the source of the error.
Best,
Marie
On Apr 30, 2015, at 7:51 AM, Alan Francis
mailto:alandarkene...@gmail.com>> wrote:
Hi Marie:
I am trying to run the LGI post processing step on 60 ASD subject
Hi Cecilio
you need more computers, or run it on the amazon cloud. Pedro Paulo has
some utilities for this
cheers
Bruce
On Fri, 1 May 2015,
Cecilio C Baro Perez wrote:
Oh thank you, that makes things much more clear! So prefessor, that means
that there is any way possible to speed up the
Oh thank you, that makes things much more clear! So prefessor, that means
that there is any way possible to speed up the freesurfer processing? I
have 30 patients and for each of the it takes like 25 h.
Best regards; Cecilio.
2015-04-30 23:33 GMT+08:00 Bruce Fischl :
> no, you need to run each su
no, you need to run each subject separately. What I was saying is that
you don't need to separate out the importing into two steps. You can run:
recon-all -s Pat1 \
-i /9-2-1.dcm \
-all
for each subject
cheers
Bruce
On
Thu, 30 Apr 2015, Cecilio C Baro Perez wrote:
H
Hi!
Thank you for quick response! Yes, Pat1 and Pat2, etc are already imported
into the freesurfer directory. So what I want to do do the further
processing. Sorry, but I'm kind of confuse, I following the online
tutorials:
(1)
recon-all -s Pat1 \
-i /9-2-1.dcm
recon-all -s Pat2 \
-i /9
The minmax options are for thresholding. 1.3 means 10^-1.3 = 0.05 which
means that clusters with p<.05 will be displayed. The max just sets the
maximum color scale. For CWP=.0009, -log10(CWP) = 3.0458, so any min
threshold less than that will show that cluster.
doug
On 04/30/2015 10:26 AM, Als
Sadly, no.
On 04/30/2015 04:05 AM, Alain Imaging wrote:
> Hi Douglas,
> indeed reading more carefully the documentation page of mri_mcsim I
> figured it out. But thank for confirming it!
> Is there any rule (or also rule of thumb) for choosing the
> cluster-forming threshold ?
>
> A.
>
> > Date:
Hi Volker,
You need to set the QA_TOOLS environmental variable. You can do this with
one of the following line (fill in the correct path to where you have
QAtools saved):
In bash:
export QA_TOOLS=
QAtools needs the QA_TOOLS and SUBJECTS_DIR environmental variables set in
order to work. Hope
Hi Marie:
I am trying to run the LGI post processing step on 60 ASD subjects. I am
using FreeSurfer 5.3. The recons went well and the processed brains look
great. However when I run the LGI step, I am getting the following error
which is as follows: Could you please help me?
[alanf@micc FreeSurfe
Dear FreeSurfers,
I would like to run the reconstruction process starting from segmentations
(grey, white and deep grey matter) obtained with a different software. The
ultimate goal is to measure the cortical thickness in correspondence of the
regions in the Desikan-Killiany atlas.
I searched
Hi Cecilio
are Pat1 and Pat2 etc... different patients? If so, they need to be run
separately. e.g.
recon-all -s Pat1 -i p.s. for the tcsh bug you should just get your sysadmin to update the
version of tcsh you are using.
On Thu, 30 Apr 2015, Cecilio C Baro Perez wrote:
Dear professor Br
Hi Mohamad
the minmax flags allows you to set the min and max thresholds for the
colorscale in tksurfer. It doesn't change any pvalues - just how they are
displayed. Since you are displaying -log10(p), a min of 2 will only show
pvalues that are <.01 and a max of 3 will saturate the color scale
Hi Doug,
After running FSFAST tool and correcting the results for multiple comparisons.
I want t visualize the results using the command line (AS IN WIWKI):
tksurfer fsaverage lh inflated -overlay
my-glm.wls/osgm/cache.th30.pos.sig.cluster.nii.gz -annot
./my-glm.wls/osgm/cache.th30.pos.sig.o
Dear professor Bruce!
Sorry for bothering again, well I did exatly as you told before in order to
process different subject at the same time:
recon-all -s Pat1 -i Pat2 -i Pat3 -i Pat5 -all
there Pat 1 (and the rest) are subjid. thought I got this error message:
ARNING: tcsh v6.17.06 has an exit
Dear experts,
we have a problem with installation of QA-Tools. It seems that it is not
because of ImageMagick and Gawk not being properly installed, but rather there
seems to be some problems with environmental variables. For example, when
changing into QA-Tools directory in the terminal and sta
Hi, sorry to bother, I'm re-posting this question just in case it got lost.
Thanks.
Hi,
I have a question about mris_convert. I've created some regions on the
surface and now I would like to make them directly readable into SUMA. I
ran this command but it ended with an error message.
mris_conver
Hi Douglas,
indeed reading more carefully the documentation page of mri_mcsim I figured it
out. But thank for confirming it!
Is there any rule (or also rule of thumb) for choosing the cluster-forming
threshold ?
A.
> Date: Wed, 29 Apr 2015 11:38:00 -0400
> From: gr...@nmr.mgh.harvard.edu
> To:
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