Dear Freesurfer community,
we are doing cortical thickness analyses with Freesurfer version 5.3.0 in a
Linux environment. In order to do the autorecon-1 and autorecon-2 steps, we
need to download the new version of mri_segstats.
Unfortunately, the link on the Freesurfer Release Notes Webpage do
Hi Freesurfer experts,
I am trying to perform whole brain tractography using FSL's Probtrackx2 with
Freesurfer white surfaces as seed and pial surfaces as targets. To obtain a
whole brain connectivity graph I need the streamlines between the hemispheres.
This means that I need to remove the par
hi,
an update on the files needed for a vanilla recon-all run (evaluation done
using cde: http://www.pgbovine.net/cde.html):
freesurfer files: https://www.dropbox.com/s/a56nzr3b7b8uqz6/fslist.txt
all files (fs + system+ output):
https://www.dropbox.com/s/1mhcuugb20cebod/allfiles.txt
size of fs co
Hi Kim
what structure is it? Our definitions are different - for example I
believe we include lateral thalamic nuclei in the thalamus and they do
not. Have you visually inspected both sets of segmentations?
cheers
Bruce
On Mon, 4 Nov
2013, jh kim wrote:
Dear Doug and experts
I've analyz
I have put patches for mri_segstats here:
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0-patch/
this should fix the problem
doug
On 11/3/13 12:09 PM, jana dinges wrote:
Dear freesurfer community,
unfortunately there was a mistake in the previous mail.
Please find attached the c
I've put new versions here:
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0-patch/
doug
On 11/4/13 7:09 AM, Matura, Silke wrote:
Dear Freesurfer community,
we are doing cortical thickness analyses with Freesurfer version 5.3.0
in a Linux environment. In order to do the autorecon
hi doug,
could you please highlight the changes - especially if there are any
critical bug fixes? and should we rerun the new mri_segstats on our current
5.3 processed data?
cheers,
satra
On Mon, Nov 4, 2013 at 9:26 AM, Douglas Greve wrote:
> I've put new versions here:
> ftp://surfer.nmr.mgh
Hello Freesurfers,
I am trying to use mri_surf2vol to convert my thickness files into
analyze/nifty format to use with a custom code. Is there a way I can write all
output files from mri_surf2vol in axial format? Also, is there a way in
FreeSurfer to combine these thickness files fro
The Hospital of the University of Munich, Germany, is one of the largest and
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Hi Jon,
The limit numbers correspond to voxel intensities in the brainmask.mgz. I
believe you will want a lower number for the -wlo/-wm_low flag to make the
wm surf extend further out, assuming that the wm voxels that are not being
captured by the surface is hypo-intense (<< 110).
-Louis
On
Hello all,
Is there a way to expand a GM label into the white matter by n voxels?
Corinna
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There is not a single command to do it, but you could do something like
mri_binarize --i aparc+aseg.mgz --wm --o wmmask.mgz # mask of white matter
mri_binarize --i seg.mgz --match 17 --o mask17.mgz # mask of seg 17
mri_binarize --i seg.mgz --match 17 --dilate 2 --o mask17.dil2.mgz #
mask of seg
Hi Linda
try using the expert options to specify the gray and white matter
intensity ranges
cheers
Bruce
On Mon, 4 Nov 2013, Linda Zhang wrote:
> Dear all,
>
> A few of my subjects end up with surfaces where the white matter
> surface is actually the pial surface, probably due to less than idea
Hi Corinna
I think this what Doug's WM parcellation tool does
cheers
Bruce
On Mon, 4 Nov 2013,
Corinna Bauer wrote:
> Hello all,
> Is there a way to expand a GM label into the white matter by n voxels?
>
> Corinna
>
>
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Fre
Hey Louis,
thanks for your response. It’s actually a bit different, in my case an entire
sulcus, including the empty space within it has been segmented and surfaced as
white matter. I’m trying to reduce the WM surface such that the empty space is
not included. I’ve tried removing segmentation
ok thanks, I'll give that a try. I would have to do that for each of the
segmentations of interest and I get the number from the LUT?
On Mon, Nov 4, 2013 at 11:47 AM, Douglas N Greve
wrote:
>
> There is not a single command to do it, but you could do something like
>
> mri_binarize --i aparc+ase
Hi Jon
this is almost certainly due to a topological defect. Improving the
segmentation quality can frequently reduce the # of defects and get rid of
big ones, so if you find that the wm segmentation isn't as visually
accurate as is usually the case, using expert opts to improve its quality
ma
Bruce,
If I understand you correctly, you’re saying I should tweak my expert options?
Should I further change the limits, how so? You previously advised that I not
adjust the -p threshold, is this still the case?
Basically, I’m still confused after your response.
Sorry to bother,
Jon
On Nov
Bruce,
If I understand you correctly, you’re saying I should tweak my expert options?
Should I further change the limits, how so? You previously advised that I not
adjust the -p threshold, is this still the case?
Basically, I’m still confused after your response.
Sorry to bother,
Jon
On Nov
Hi Jon
maybe you should upload your data and we'll take a look
cheers
Bruce
On Mon, 4 Nov 2013,
Jonathan Holt wrote:
> Bruce,
>
> If I understand you correctly, you?re saying I should tweak my expert
> options? Should I further change the limits, how so? You previously advised
> that I not ad
OK,
been uploaded as JONbrain.tar
Please let me know!
On Nov 4, 2013, at 1:15 PM, Bruce Fischl wrote:
> Hi Jon
>
> maybe you should upload your data and we'll take a look
>
> cheers
> Bruce
> On Mon, 4 Nov 2013,
> Jonathan Holt wrote:
>
>> Bruce,
>>
>> If I understand you correctly, you
Got it, I'll take a look.
On Mon, 4 Nov 2013, Jonathan Holt wrote:
> OK,
>
> been uploaded as JONbrain.tar
>
> Please let me know!
>
>
> On Nov 4, 2013, at 1:15 PM, Bruce Fischl wrote:
>
>> Hi Jon
>>
>> maybe you should upload your data and we'll take a look
>>
>> cheers
>> Bruce
>> On Mon, 4 No
I am obviously using mri_vol2vol incorrectly but I'm stumped.
Goal is to get the $SUBJECTS/fsaverage/mri/aseg.mgz file into the FSL MNI152
space to do some fslmaths.
>From looking around it seemed the command to accomplish this is (inside
>$SUBJECTS/fsaverage/mri)
mri_vol2vol --targ $FSLDIR/da
Hi Roddy
can you check whether fslview shows the directions as correct even if it
displays it upside down? That is, do they still know which direction is
superior, anterior, etc...?
cheers
Bruce
On Mon, 4 Nov 2013, Roderick McColl wrote:
> I am obviously using mri_vol2vol incorrectly but I
Hi guys,
When running mri_cvs_register on linux (5.3.0), I get into problem with
mris_resample, which cannot find libboost_programs_options.so.5. I installed
the latest version of boost-1.52.0 for my system, but there are unresolved
symbols.
Which version is suitable for mris_resample?
Thanks
It gives the same results as the 5.3 version. The difference is that it
does not require the ribbon.mgz file to be there in order to run. If you
run recon-all from start to finish, then there is not a problem. If you
run recon-all partially, then it may fail because it runs mri_segstats
before
Yes. As Bruce mentioned you can also use the program that creates the
wmparc (mri_aparc2aseg). You can look in the recon-all.log file for the
command line (there will be two in there, one to create aparc+aseg and
one to create wmparc). You can run this command with --wmparc-dmax to
set the maxi
thanks doug.
cheers,
satra
On Mon, Nov 4, 2013 at 5:33 PM, Douglas N Greve
wrote:
> It gives the same results as the 5.3 version. The difference is that it
> does not require the ribbon.mgz file to be there in order to run. If you
> run recon-all from start to finish, then there is not a proble
try this command instead
mri_vol2vol --mov $FSLDIR/data/standard/MNI152_T1_1mm.nii.gz \
--targ aseg.mgz --inv --reg transforms/reg.mni152.1mm.dat --o
asegmni152.nii.gz
On 11/04/2013 04:37 PM, Roderick McColl wrote:
> I am obviously using mri_vol2vol incorrectly but I'm stumped.
>
> Goal i
To get them both in one file, run mri_surf2vol to get the left
hemisphere. When you run it a 2nd time for the right hemisphere add
"--merge vol.lh.nii". I think FSL has software to swap dimensions
doug
On 11/04/2013 09:53 AM, Govindarajan, Koushik Athreya wrote:
>
> Hello Freesurfers,
>
>
*
try running this command
mri_label2vol --label lh.words10_10.label --temp rawavg.mgz --reg
rawreg.dat --fillthresh .5 --o lh.words10_10.nii
*
On 11/04/2013 07:55 AM, Zhao Jingjing wrote:
> Hi Doug,
>
> I asked a question a couple days ago for how to convert .label files
> into .nii files in fr
Hmmm,
Actually using aseg.mgz works just fine (just tried this now),
displays correctly on fslview.
What I was really trying to do was convert aparc+aseg.mgz which does not
provide the expected orientation in fslview.
Does this mean aparc+aseg.mgz and aseg.mgz are in different spaces somehow?
F
Hi Kim, the answer is both easy and difficult. The easy answer is that
they are completely different methods and will often give inconsistent
results. I'm not sure what answer the reviewer will accept, and you
might need to post the same question to the VBM and DARTEL crews. In
your VBM analys
Caspar, is this resolved yet? What version of FS is your base
installation and for what platform?
doug
On 11/01/2013 01:29 PM, Caspar M. Schwiedrzik wrote:
> Hi again,
> I keep getting segmentation fault errors (this time with the centOS4
> version).
> After 1153 iterations, I get 78.91 0 ./c
Hi Suzanne, there is probably an easier way to do this. If you create
contrasts of each condition vs baseline then run isxconcat-sess on each,
you can then run something like
mri_segstats --seg mc-z.pos.23.lh.sig.ocn.mgh --i condition1.nii.gz
--avgwf condition1.table.dat --excludeid 0
where c
Hi Jonathan, see my email from earlier about the new permanent location
for mri_segstats
doug
On 10/30/2013 12:26 PM, Jonathan Harlap wrote:
> The version of mri_segstats that fixes the issue where mri_segstats
> fails unless -autorecon3 is run returns a file not found at the url
> ftp://surfer
Yes, true for all models. I'm not sure what I'm looking at in this
scatter plot. The scatter plot does not have the nuisance effects
removed, so it might be that when you remove the nuisance effect, then
HC>SAD
doug
On 10/30/2013 01:32 PM, Ashley Shurick wrote:
>
> Great - and this would be
That vol2surf command might miss the values you want to sample. Try
adding --projdist-max -2 0 .1
This will sample from 2mm into the hippo out to the surface in .1mm
increments and then take the maximum value it finds
doug
On 10/30/2013 03:08 PM, Marcos Martins da Silva wrote:
> Hi, Doug.
> Tha
Yes, that looks correct, though I could be more confident if you send
the command lines used and your fsgd file(s).
doug
On 10/31/2013 07:32 AM, Vivian R. Steiger wrote:
> Dear FS-Experts,
>
> I would like to compare 2 Groups (Responder (N=19) vs. Non-Responder (N=11))
> with longitudinal dat
Thanks Doug, I did see that.
Cheers,
Jonathan
> On Nov 4, 2013, at 6:23 PM, Douglas N Greve wrote:
>
> Hi Jonathan, see my email from earlier about the new permanent location
> for mri_segstats
> doug
>
>> On 10/30/2013 12:26 PM, Jonathan Harlap wrote:
>> The version of mri_segstats that fixes t
Hi Roddy, aparc+aseg.mgz and aseg.mgz are in the exact same space and
the same command line should generate the same result. Does it display
properly in tkmedit? If so and if you're having problems visualizing
with fslview, contact the FSL crew.
doug
On 11/04/2013 05:52 PM, Roderick McColl
Hi Doug,
I'm running into a strange seg fault when trying to use mri_segstats (it's
actually ocurring within mri_glmfit-sim, but I can reproduce it manually)
This is the line that fails (stripping the leading paths for readability):
mri_segstats --seg cache.th20.pos.sig.ocn.mgh --exclude 0 --i
Hi all,
We have ROIs (defined in mrVista) that we converted to label files and
would like to now make an average ROI. Does a pipeline exist that will help
us create an average ROI composed of these label files. We were thinking of
using mri_label2label to register the ROIs to a common surface but
Hi Miggy
Are the ROIs on different subjects? Do you have surfaces reconstructed for
each of them?
cheers
Bruce
On Mon, 4 Nov 2013, Miggy Chuapoco
wrote:
Hi all,
We have ROIs (defined in mrVista) that we converted to label files and would
like to
now make an average ROI. Does a pipeline
I would convert them to a binary mask (0,1) then average the masks
together. Each vertex would then be the "probability" that a given
vertex was in the ROI. You can convert the label to a binary mask with a
second call to mri_label2label (--outmask option)
doug
On 11/4/13 8:47 PM, Miggy Ch
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