Hello Freesurfer experts,
I would like to display stats images that are in MNI space on an MNI surface
volume.
I found this thread on the mailing list that explains how to use mri_vol2surf
to convert volumetric images to a surface:
https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2014-Ap
HI expert !
My name is Areum. I have some question to you.
1. Does FreeSurfer offer a effect size? if that offer, how can i use effect
size?
2. I was wondering about the stats.dat file in stats_table (in Qdec folder).
Stats.dat file’s value mean that each area’s average (include whole vertex)
Hi Janosch - That's strange. Can you send me one of those mean path files?
Thanks,
a.y
On Sun, 9 Aug 2015, Janosch Linkersdörfer wrote:
Hi Anastasia,
yes, I am. But it looks similar in the distributed version :(
Thanks,
Janosch
Am 08.08.2015 um 00:48 schrieb Anastasia Yendiki :
Hi Jano
Hi Daniel - That "hack" is not as bad as it may sound. The structural
images that TRACULA uses from the time points have already been mapped to
the within-subject base template space, so at that point using one of
those images or their median (the base template itself) for inter-subject
regis
yes, it should
Bruce
On Mon, 10 Aug 2015, Nate Vack wrote:
On Fri, Aug 7, 2015 at 2:45 PM Douglas N Greve
wrote:
On 08/07/2015 03:11 PM, Nate Vack wrote:
> Thanks. Any other file types I should look for tags in?
I think the surfaces have the subject name imbedded in them.
Hi Emma
can you clarify? Did you process one subject in a directory then overwrite
it with a second? If so you probably can't recover it without rerunning
recon-all.
cheers
Bruce
On Mon, 10 Aug 2015, Emma Thompson wrote:
> Hi,
> I'm re-posting my query in case it got buried on the listserve
Hi Emma,
You should be able to just copy the subject folders in question to a new
location. When you want to work with them just set your SUBJECTS_DIR
variable to whatever that new path is. Could you explain why you think
you will have to recreate surface reconstructions? That should not be
t
Thanks Christopher for your response. I have read the tutorials/wiki page.
My subject directory is set up somewhat similarly (See below). The problem
is I would like to create and move the "PP*" patients to an entirely new
and different FS 'subjects' directory while keeping the "MM*" patients in
th
On Fri, Aug 7, 2015 at 2:45 PM Douglas N Greve
wrote:
> On 08/07/2015 03:11 PM, Nate Vack wrote:
> > Thanks. Any other file types I should look for tags in?
> I think the surfaces have the subject name imbedded in them.
>
Would there be a way to take it out?
> > Out of curiosity, how do .mgz
I think it's a bit unclear what you're asking for. Have you followed the
tutorials on the wiki? Can you post your directory structure?
What I do on my system is keep studies separate from one another. Each study
directory has its own FS directory, and I keep the raw images separate. So
somethin
Hi,
I'm re-posting my query in case it got buried on the listserve:
Dear Freesurfers,
I created a single subject directory and then imported sdata from two
separate studies, in the end I realized I should have created two subject
directories and would like to now rectify the situation. My questio
Hi there,
The command I submitted is:
mri_volcluster --in merged_encode_Young_NEUT_hit_V_miss_n41.nii.gz --thmin 1.3
--minsizevox 5 --sign neg --sum adebayo_young_neut_p.05 —fsaverage
How would I:
1) Specify the voxel size
2) Have the results output in MNI?
Thanks,
Keji
> On Aug 10, 2015,
Thanks Doug,I downloaded and rerun and changed the permissions but it still
says: /Applications/freesurfer/bin/mri_probedicom: Permission denied.Any
idea?Thanks,EIraqn
On Monday, August 10, 2015 6:18 PM, Douglas N Greve
wrote:
Hi Eiran, can you download the following two binaries
Dear all,
In an earlier post, I was asking for help implementing dilated ROIs.
I was using Doug's suggestion
mri_aparc2aseg --subject 01 --a2009s --labelwm --wmparc-dmax 2 --o
aparc.a2009s+aseg_liberal.mgz
followed by
mri_label2vol --seg aparc.a2009s+aseg_liberal.mgz --regheader orig.mgz --o
roi
Thanks for the response. When looking at pathstats.overall.txt, I did a
similar rh-lh name flip. But is this ok for pathstats.byvoxel.txt, where
the tracts are moved from the subjects' diffusion space to MNI space? The
stat log file shows it uses the reference volume from
.../dlabel/anatorig/aparc+
On 08/10/2015 10:47 AM, Morenikeji Adebayo wrote:
> Hi there,
>
> I have a a couple of question related to the output generated by the
> ‘mri_volcluster' command.
>
> 1) It seems that the command automatically assumes that my voxels are
> 8 mm^3. Is there a way to specify my voxel size when I
Hi Eiran, can you download the following two binaries and rerun? First
make a backup copy of the ones that are there. Then copy the two below
into $FREESURFER_HOME/bin (remove the .mac).
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_convert.mac
ftp://surfer.nmr.mgh.harvard.e
It is the same thing, but the permutation output will have the name you
gave the csdbase when you ran the simulation (ie, the 4th arg to --sim)
On 08/10/2015 05:54 AM, pablo najt wrote:
> Thank you Doug.
> I run permutations with mdi_glmfit-sim --sim perm. Would you be able
> to advice on the ou
Hi there,
I have a a couple of question related to the output generated by the
‘mri_volcluster' command.
1) It seems that the command automatically assumes that my voxels are 8 mm^3.
Is there a way to specify my voxel size when I run the command?
2) The output is given in Talairach coordinat
Hi Andre
you shouldn't need all the flags to mri_convert. Just cd into the
directory that contains the file and do:
mri_conver .mgz .nii.gz
cheers
Bruce
On Sun, 9 Aug 2015, Son, Andre wrote:
> Thank you Bruce.
> You're alway so helpful, even on the weekend!
>
> I'm also trying to convert mgz
I would be interested in details on a 7T stream also!
Thank you,
Andrea
-
Andrea Grant
Visual Neuroimaging Technologist
Center for Magnetic Resonance Research, University of Minnesota
2021 6th St. SE, Minneapolis, MN 55455, 612-626-4948
gran0...@umn.edu
umn.edu/~gran0260
On Sun, Aug 9, 2015
The license format has changed, so downloading a new license from the
freesurfer registration should solve that:
https://surfer.nmr.mgh.harvard.edu/registration.html
If not please contact me directly.
-Zeke
> On Aug 9, 2015, at 8:14 AM, Caspar M. Schwiedrzik
> wrote:
>
> Hi Zeke, we are ge
Hi Eugenio,
I have about 128 GB of RAM memory in both machine. I got segmentation fault
error in the new machine and not in the older one. I ran the test data (bert)
and I get segmentation fault error. I think the only difference between the two
machine is Ubuntu version. The new machine uses U
Hi Freesurfer Experts,
For the purpose of defining nodes in a graph theory analysis, I would like
to generate a list of X Y Z coordinates in MNI space for all the labels in
the Destrieux atlas. I came across a previous post with the following steps:
Step 1:
mri_annotation2label --subject fsavera
Hello developer~
I have some questions to you.
1. Does FreeSurfer offer a effect size? if that offer, how can i use effect
size?
2. I was wondering about the stats.dat file in stats_table (in Qdec folder).
Stats.dat file’s value mean that each area’s average (include whole vertex)
or each
Hello Freesurfers,I am using
freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0.I tried unpacking mosaic
functional dicoms taken with siemens prisma scanner using:
dcmunpack -src /users/eiran/Desktop/BSMT/201_/Study20150415_184518_65000 -targ
/Applications/freesurfer/BSMT_PROJECT/bsmt201 -run
Thank you Doug.I run permutations with mdi_glmfit-sim --sim perm. Would you be
able to advice on the output and how to open the permutation outputs? The
tutorial instructs on how to open the *.summary file for the summary of
clusters and *.sig.cluster.mgh the cluster corrected map, but not the
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