h will hopefully will show what we
are trying to do.
Thanks,
Shyam
On 5/31/16, 4:20 PM, "Bruce Fischl" wrote:
Hi Shyam
it's hard to give you an answer unless I understand what the source of
your inaccuracy is. Perhaps you can point an image that is zoomed in on a
region with arrows
Hi Maryam
why don't you want to use tracula? That is what it is designed for
cheers
Bruce
On Tue,
31 May 2016, Syeda Wajiha Maryam wrote:
> Hello Freesurfer experts,
>
> I am looking to extract certain white matter pathways (for instance, the
> superior longitudinal fasciculus, uncinate fascic
Hi Marja
yes, if you want to compare measures averaged over our predefined ROIs that
is all you need to do. Note that for volumes you probably want to include
ICT/eTIV as a regressor
cheers
Bruce
On Wed, 1 Jun 2016, Marja
Caverlé wrote:
Hi guys,
I just wanted to make sure I am underst
only want to look at cortical
>> thickness for now.
>>
>> Best,
>>
>> Marja
>>
>>> On Wed, Jun 1, 2016 at 11:11 PM, Bruce Fischl
>>> wrote:
>>> Hi Marja
>>>
>>> yes, if you want to compare measures averaged over
On Thu, Jun 2, 2016 at 9:29 PM, Bruce Fischl
wrote:
Sorry, ICV (intracranial volume)
On Jun 2, 2016, at 4:40 AM, John Epiktitos
wrote:
Hello,
What is ICT ?
Thanx
On Jun 1, 2016 4:21 PM, "Marja Caverlé"
wrote:
Hi Bruce,
Thanks for
Hi Kari
the average thickness in some ROIs is 5mm??? Like which ones? That
certainly seems like something is wrong. Do the surfaces look accurate?
What were the parameters/resolution/sequence of the data you gave to
recon-all?
cheers
Bruce
On Fri, 3 Jun 2016, Kari Parsons wrote:
> Hi,
>
>
Hi Mahtab
we do all the analysis in native space and don't transform the data to a
template (although we do compute mappings to various templates).
As for your other question, there are too many variables to control for
(age, gender, scanner type, sequence) for us to distribute a normative
d
Hi Lawrence
you can you the
make_average_subject
script, but as Doug implies you probably don't need to. Our warp is
high-enough dimensional that you rarely need to build average subjects from
your own population
cheers
Bruce
On Fri, 3 Jun 2016, shi yao wang wrote:
>
> Hello !
>
> I work
hmmm, that suggests that the aseg failed badly. What does it look like?
cheers
Bruce
On
Fri, 3 Jun 2016, Jaiashre Sridhar wrote:
Bruce,
The lh.inflated.nofix shows the brainstem and cerebellum are attached to the
cortical surface. Also, the ventricles are not filled in the filled.mgz.
Could
does it segment the cerebellum ok? If so, it should be removed during
recon-all
On Fri, 3 Jun 2016, Jaiashre Sridhar wrote:
Bruce,
The aseg looks fine to me. Is there anything in specific that I should be
looking for in aseg?
Thanks,
Jaiashre.
__
Hmmm, that sounds like a bug. If you upload the subject we will take a look
Cheers
Bruce
> On Jun 3, 2016, at 6:54 PM, maryam koochaki wrote:
>
> Dear freesurfer experts,
> I have a subject ending up with this error after recon-all.
> I tried to edit the aseg and run it, but it stuck at topologi
Hi Gonzalo
we seek to minimize these explicitly, but given the difference in T1s at
different field strength it's pretty hard to get rid of them completely.
Xiao Han wrote a paper on this, and I think Jorge Jovicich did as well
cheers
Bruce
On Mon, 6 Jun 2016, Gonzalo Rojas Costa
wrote:
Hi John
I'm not exactly sure what you mean, but you can use mri_extract to pull
out rectangular subvolumes.
cheers
Bruce
On Wed, 8 Jun 2016, John Anderson wrote:
Dear FS Experts,
Are there any tools in Freesurfer or Matlab scripts that can help to break
down a 3D volume ( created using mri_v
t; and the command is mri_extract x0 y0
z0 dx dy dz how can I use the command properly?
: is this where my file is located?
x0 y0 z0 dx dy dz: What I should use here?
Thank you very much for your help
John
Sent: Wednesday, June 08, 2016 at 9:13 AM
From: "Bruce Fischl"
To: &quo
Hi Jonathan
as far as we know, FreeSurfer is the most reliable and robust
longitudinal brain morphometry tool that is publicly available. We are
working to improve it (always!), but the answer to your question is yes,
certainly 5.3 and the upcoming 6.0 are both excellent longitudinal tools
Bruc
1. This is based on Randy Buckner's paper showing that the tal xform gives
you a pretty accurate estimate of the TIV (which is hard to compute
directly from a T1 image since you can't distinguish bone from CSF).
2. I think including it as a covariate is a better approach, but perhaps
others
Hi Marja
we do whole cerebellum white matter and gray matter, but things like
lobules aren't released yet.
cheers
Bruce
On Fri, 10 Jun 2016, Marja Caverlé wrote:
Hi all,
I am hoping to find some cerebellar volumes, but I don't know how to get
them.
I already did recon -all on all my subject
es, I assume I also need
to use the eTIV as regressor right? (just like for the cerebral volumes?
And maybe a stupid question, but can I use the eTIV as regressor by just
dividing the structure volume by the eTIV?
Best,
Marja
On Fri, Jun 10, 2016 at 10:56 PM, Bruce Fischl
wrote:
Hi Marja
11:14 PM, Bruce Fischl
wrote:
Hi Marja
yes, you can just use those volumes, and no, including it as a
regressor isn't the same as dividing by eTIV (although you can
do that instead).
cheers
Bruce
On Fri, 10 Jun 2016, Marja Caverlé wrote:
. This seemed to me the way to do that, but of
course I am not an expert.
Best,
Marja
On Fri, Jun 10, 2016 at 11:23 PM, Bruce Fischl
wrote:
if you expect cerebellar volume to vary in an uninteresting way
with head size (which I think you probably do)
On Fri, 10 Jun 2016, Marja
Hi Marja
how did you swap them? And more importantly, how did you check that
the orientations were correct after conversion?
cheers
Bruce
On Mon, 13 Jun 2016, Marja Caverlé wrote:
Hi guys,
Just a quick question; I have converted my original DICOMs into niftis.
After the conversion I manu
, and then visually compared them (since the heads are not very
symmetrical that was not too hard).
Best,
Marja
On Tue, Jun 14, 2016 at 12:35 AM, Bruce Fischl
wrote:
Hi Marja
how did you swap them? And more importantly, how did you check
that the orientations were correct after
Hi Navena
hmmm, sounds like that subject didn't finish processing for some reason.
You could try rerunning just that step with:
recon-all -s N1 -sd /Users/navenalingum/Applications/freesurfer/subjects
-cortparc -cortparc2 -cortparc3
and see if that completes (it should only take a couple o
there they seemed to match.
So my question is; is there a possibility that dimensions are swapped during
the recon -all? If not, then I am sure R=R and L=L.
Thanks!
On Tue, Jun 14, 2016 at 12:55 AM, Bruce Fischl
wrote:
Hi Marja
what did you visualize it in? I would suggest freeview
ing during the recon-all. If not, than I can safely
assume that the results are correct.
Best,
Marja
On Tue, Jun 14, 2016 at 1:29 AM, Bruce Fischl
wrote:
so you convert from dicom to nifti, then view in freeview and
you think that the anatomical orientations are incorrect? That
les called eg
1254890234, so I have no clue how to get the right files.
Thanks!
On Tue, Jun 14, 2016 at 5:36 AM, Bruce Fischl
wrote:
Hi Marja
why are you converting at all? Why not just give one
of the dicom files in the correct series to
recon-all directl
Hi Kojima
tkmedit has been deprecated. Can you try using freeview instead?
cheers
Bruce
On Tue, 14
Jun 2016, kojima_masaki_m...@yahoo.co.jp wrote:
Hi.
I have this error, when I was doing tkmedit
PSY1001fs/Users/MRI/Desktop/fsurfer_test_kojima/Surf_data_main/PSY1001fs/mri/brainma
sk.mgz -a
tkmedit?
Regards,
Kojima
- Original Message -
From: Bruce Fischl
To: kojima_masaki_m...@yahoo.co.jp; Freesurfer support list
Date: 2016/6/14, Tue 21:50
Subject: Re: [Freesurfer] tkmedit
Hi Kojima
tkmedit has been deprecated. Can you try using
Hmmm, I'm not sure I understand your question. SIENAX is indeed from the
FSL group and different than what we do. What are you trying to accomplish?
On Wed, 15 Jun 2016, Hassan bakhshi
wrote:
Hi,
I lately heard about SIENAX and when I looked into it it seems like
Freesurfer,
using the same
Hi Trisanna,
perhaps check with the BrainVisa people? We don't know the specs of that
format. Maybe you could read it into matlab, then write it out in our
format with write_surf.m?
cheers
Bruce
On Wed, 15 Jun 2016, Trisanna Sprung-Much wrote:
>
>
> Hi there
>
> is there a way to convert .
Hi Trisanna
you don't need to inflate the overlays. They can just use the existing
surface-based (sphere.reg) registration.
cheers
Bruce
On Wed, 15 Jun 2016,
Trisanna Sprung-Much wrote:
Hi there
So I have sulcal labels from another software (.mnc format) from which I am
trying to generate
itself?
best
Trisanna
--
Ph.D. CandidateMcGill University
Integrated Program in Neuroscience
Psychology
On Wed, Jun 15, 2016 at 11:11 AM, Bruce Fischl
wrote:
Hi Trisanna
you don't need to inflate the overlays. They can just use the existing
surface-based (sphere.reg) registr
maybe you want to check with the FSL group? It really depends on what
measures you want to obtain
On Wed, 15 Jun 2016, Hassan
bakhshi wrote:
> We have some cases which we want to process , I searched about SIENAX and as
> you are more expert in this area, I wanted to know
> Freesurfer preferen
Hi David
we don't have anything that does this by default, sorry. If you don't
care about the location of the white surface you could try setting all
the voxels in the wm.mgz that are left or right hippo/amygdala in the aseg
to 255 then running from autorecon2-wm forward.
cheers
Bruce
On W
Hi Nora
you need to send us the complete command line you ran and also the error
message and the complete terminal outpu
cheers
Bruce
On Thu, 16 Jun 2016, Bittner, Nora wrote:
Dear freesurfer experts,
I constructed an annotation file using mris_label2annot. I did this several
times and
Hi Alexandre
try mri_label2label using the ?h.sphere.left_right
cheers
Bruce
On Thu, 16 Jun 2016, Alexandre Routier wrote:
Hello everyone,
I have a label for the left hemisphere for my subject but I don't understand
the syntax to apply mris_apply_reg on this label to obtain the right
hemispher
wow, 4.4, that's pretty old. Not sure, I guess try it
Bruce
On Thu, 16 Jun 2016,
Alexopoulos, Dimitrios wrote:
I have successfully processed data with FS v5.3 (linux/CentOS) using
recon-all -all.
Is it possible to make modifications to the 5.3-generated brainmask.mgz
(primarily dura remov
Hi Nazanin
no, sorry, that isn't possible. Our accuracy is improved by the fact that
we model all subcortical structures simultaneously.
As for your second question you need to be more specific. Are you finding
some inaccuracies that you want to correct?
cheers
Bruce
On Sun, 19 Jun 2016,
> Saving target data
> > Saving to test.mgz
> >
> > best
> >
> > Trisanna
> >
> > --
> > Ph.D. Candidate
> > McGill University
> >
anks and have a lovely Sunday!
Trisanna
--
Ph.D. CandidateMcGill University
Integrated Program in Neuroscience
Psychology
On Sun, Jun 19, 2016 at 11:22 AM, Bruce Fischl
wrote:
Hi Trisanna
Doug is on vacation and his response time is likely to be pretty
slow. If any emails go
hm (N Saf)
4. Re: change the algorithm (Bruce Fischl)
5. Re: registering to fsaverage (Trisanna Sprung-Much)
6. Re: registering to fsaverage (Bruce Fischl)
--
Message: 1
Date: Sat, 1
/fsaverage/DISPLAY_overlays_fsaverage_l
eft/aalf_lh/test.mgz, -1): could not open file
mri_average: MRIread(test.mgz) failed
--
Ph.D. CandidateMcGill University
Integrated Program in Neuroscience
Psychology
On Sun, Jun 19, 2016 at 12:46 PM, Bruce Fischl
wrote:
no problem.
Bruce
On Sun, 1
hology
On Sun, Jun 19, 2016 at 12:46 PM, Bruce Fischl
wrote:
no problem.
Bruce
On Sun, 19 Jun 2016, Trisanna Sprung-Much wrote:
thanks Dr. Fischl - I think sometimes my
emails don't get sent out on the
first try and so I resend
YOu could try increasing the density of the search (which will slow it
down considerably). Maybe -s 7? It's hard to diagnose without looking at
your data, so feel free to upload it if this fails and also send us the
exact command line you ran
On Mon, 20 Jun 2016, HONG Sujin wrote:
Hello,
on, Jun 20, 2016 at 9:27 AM, Bruce Fischl
wrote:
yes, your last file on the command line should be the output file (the
average)
cheers
Bruce
On Mon, 20 Jun 2016, Trisanna Sprung-Much wrote:
As a follow-up, here is the mri_info for one of my overlays in the folder
Universitätsklinikum Düsseldorf
40225 Düsseldorf
Tel.: 0211-8106109
Email: n.bitt...@fz-juelich.de
-Ursprüngliche Nachricht-
Von: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Im Auftrag von Bruce Fischl
Gesendet: Donnerstag, 16. Juni 2016
Hi Pradeep
Doug is on vacation and is the best one to answer your question. If you
don't get a response in a week or 10 days can you repost?
thanks
Bruce
On Tue, 21 Jun
2016, Pradeep wrote:
Hello Freesrufer Team,
I am trying to use the Partial volume correction procedure implemented in
t
Hi John
you can try mri_nlfilter if you like. It implement a nonlocal means/medians
algorithm that I wrote in 1995 or so:
Bruce Fischl and Eric L. Schwartz.
1999. Adaptive Nonlocal Filtering: A Fast Alternative to Anisotropic
Diffusion for Image Enhancement. IEEE Trans. Pattern Anal. Mach
Hi Greg
you could threshold then look at Hausdorff distance of the blobs. Or you
could smooth before computing correlation as that will take spatial stuff
into account.
Or if you have a patch that you want to cross-correlate against the rest of
the surface you could do it on the sphere, althou
when creating the overlay using mri_vol2surf?
thanks
Trisanna
--
Ph.D. CandidateMcGill University
Integrated Program in Neuroscience
Psychology
On Mon, Jun 20, 2016 at 12:11 PM, Bruce Fischl
wrote:
Hi Trisanna
the binaries that take mandatory command-line arguments (i.e
Hi Stephen
how did you create the patch? It looks like it is corrupted since that
vertex # is way too big. The total # of vertices in the patch is also
wrong.
cheers
Bruce
On Thu, 23 Jun 2016, S.V.Shepherd [work] wrote:
Hello all,
I'm trying to make a patch and have run into the 'bad vert
The UCSF Department of Radiology and Biomedical Imaging is looking for a
researcher with strong interests in neuroimaging interested in a Specialist
position at UCSF. We are a neurodevelopment and neuroimaging lab.
Specialists (research assistant) appointed at the junior rank must possess a
bac
hen v. shepherd phd
The Rockefeller University / 1230 York Avenue / New York NY 10065-6307 USA
// 212.327.7699
On Thu, Jun 23, 2016 at 9:58 AM, Bruce Fischl
wrote:
Hi Stephen
how did you create the patch? It looks like it is corrupted
since that vertex # is way too big. The total
k around it.
Thanks for thinking about the problem and sorry to report it was simply user
error!
stephen
stephen v. shepherd phd
The Rockefeller University / 1230 York Avenue / New York NY 10065-6307 USA
// 212.327.7699
On Thu, Jun 23, 2016 at 1:00 PM, Bruce Fischl
wrote:
hmmm, are you sure
you can load the overlay on the surface either by highlighting the
surface and doing it from the interface or on the command line via:
freeview -f surface:overlay=file_name
cheers
Bruce
On Fri,
24 Jun 2016, Lars M. Rimol wrote:
Hi,
Is it possible to overlay .mgh files with statistics (e
Hi Matthew
we typically ask people to get licenses from us so we can keep track of
them.
cheers
Bruce
On Fri, 24 Jun 2016, Matthew Brett wrote:
> Hi,
>
> Over at our nibabel Python package, we've got stuck trying to work out
> what license we should give to a file we got from Freesurfer version
yes, it's fine
Bruce
On Fri, 24 Jun 2016, Matthew Brett wrote:
> Hi,
>
> On Fri, Jun 24, 2016 at 2:44 PM, Bruce Fischl
> wrote:
>> Hi Matthew
>>
>> we typically ask people to get licenses from us so we can keep track of
>> them.
>
> So, what we wan
Hi Dan
that defect is too big, there must be something wrong. Check to see if the
surface is connected to dura or across the hemis or something. You can look
at the lh.inflated.nofix and/or the lh.orig.nofix to see where the defects
are. Then you'll need to correct something once you've figure
Hi Nabin
unless the areas are the same size, the mean of the areal means won't
equal the overall mean.
cheers
Bruce
On Sat, 25 Jun 2016, Nabin Koirala wrote:
Hi freesurfer team,
I extracted the cortical thickness values using aparcstats2table command and
I got the cortical thickness values
known' region, so you don't have to do it yourself.
Regards,
Nabin
On Sat, Jun 25, 2016 at 3:29 PM, Bruce Fischl
wrote:
Hi Nabin
unless the areas are the same size, the mean of the areal means
won't equal the overall mean.
cheers
Bruce
On Sat
Hi Lars
I'll leave this for Ruopeng.
cheers
Bruce
On Mon, 27 Jun 2016, Lars Morten Rimol wrote:
Hi Bruce,
Yes, now it works (my guess is I loaded a single subject surface as template
before…) but I don’t find an FDR correction button in the Configure Overlay
interface. The fdr threshold
importing probability maps formed as .mnc and
creating overlays from them? The percentages seem to be very odd for
min and max threshold.
Trisanna
--
Ph.D. CandidateMcGill University
Integrated Program in Neuroscience
Psychology
On Wed, Jun 22, 2016 at 9:32 PM, Bruce Fischl
wrote:
H
Hi Dorsa
what specific models do you need? The 10-20 hours is to process the data
from a single subject at a single timepoint. If you check out our wiki
(http://surfer.nmr.mgh.harvard.edu/fswiki) there are lots of tutorials and
sample datasets and such
cheers
Bruce
On Mon, 27 Jun 2016, Dorsa
Hi Abbie
what are you trying to create a mesh of? We supply meshes for the
gray/white interface and for the pial surface. We supply voxel
segmentations of lots of other things that you could mesh, but we don't
by default.
cheers
Bruce
On Mon, 27 Jun 2016, Abbie McNulty wrote:
> Hello,
> I am
of what Freesurfer
> can do and not quite a play-by-play interaction of Freeview, I am stuck.
>
> Thanks
>
> Abbie
>
> On Mon, Jun 27, 2016 at 3:30 PM, Bruce Fischl
> wrote:
> Hi Abbie
>
> what are you trying to create a mesh of? We supply meshes f
Hi Olivia and others
we are having major disk problems at Martinos and many of the links may
not work for a few days
sorry
Bruce
On Tue, 28 Jun 2016, Olivia Cheung wrote:
Hi Freesurfer team,
I would like to download a copy of the updated mri_convert but the link on
the Release Notes webpage
Hi Jessica
if we have T1/PD maps we typically run them through mri_synthesize to
create a strongly T1-weighted image that is then passed to recon-all. Can
you tell us more about what data you have?
cheers
Bruce
On Tue, 28 Jun 2016, Jessica Sevick wrote:
Hello,
I was wondering if it wa
d I put them in a folder in my
> subjects_dir. but I get errors when using recon-all on the folder containing
> the
> MRIs. Can you help me with that? I really appreciate your help
>
> Thank you
>
> Dorsa
>
> On Mon, Jun 27, 2016 at 3:13 PM, Bruce Fischl
> wrote
Hi Gabor,
it depends on what you are doing. What you describe is sufficient for
maps/structure volumes, but for example if you wanted to measure thickness
within parcels you would have to check the accuracy of the cortical
parcellation
cheers
Bruce
On Tue, 28 Jun 2016, Gabor Perlaki wrote:
following error:files are
not found to be different and cannot be sorted
Do you have any suggestions?
Thank you
Dorsa
On Tue, Jun 28, 2016 at 12:57 PM, Bruce Fischl
wrote:
just give recon-all a single slice from the series with -i
. It will figure out
the rest of them
e.
On Tue, Jun 28, 2016 at 4:06 PM, Bruce Fischl
wrote:
Hi Dorsa
you need to give us more information that that if you want us to
help you. Send us the full command line you ran and the full
screen output and log files for starters.
cheers
Bruce
On Tue
n-all -i LT7616_3TS_Copy_0001.dcm -subjid test6 -all
On Tue, Jun 28, 2016 at 4:23 PM, Bruce Fischl
wrote:
Hi Dorsa
can you just copy and paste the text into the email? It's much
easier than trying to look at images of text.
Your recon-all command finished su
Hi Minos
we are having major hardware issues that we hope to have resolved
tonight. Try again tomorrow
cheers
Bruce
On Wed, 29 Jun 2016, C. Minos Niu wrote:
> Hello,
>
> I tried to have my new students download and install Freesurfer from
> https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAnd
Hi Gabor
the only way is to look at the parcellation over the white surface I guess.
There are some not-very-well documented interventions, but maybe your best
bet would be just to exclude subjects (since it almost never fails)
cheers
Bruce
On Wed, 29 Jun 2016, Gabor Perlaki
wrote:
> Dear
Hi Reza
can you use freeview? We don't do any development on tksurfer and hardly
use it anymore. Not sure if this is possible in freeview, I'll leave that
for Ruopeng
cheers
Bruce
On Wed, 29 Jun 2016, Reza Rajimehr wrote:
Hi,
In Tksurfer, we want to show functional activity map and borders o
it should all be working now, no?
On Wed, 29 Jun 2016, Bennet Fauber wrote:
> Looks like all downloads are broken, as the same message appears when
> trying to download the binary distribution,
>
> ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0/freesurfer-Linux-centos6_x86_64-stable-pu
try again - hopefully the stale mounts of been fixed now
cheers
Bruce
On Wed, 29 Jun 2016, Bennet Fauber wrote:
> Looks like all downloads are broken, as the same message appears when
> trying to download the binary distribution,
>
> ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0/fre
Trisanna
--
Ph.D. CandidateMcGill University
Integrated Program in Neuroscience
Psychology
On Mon, Jun 27, 2016 at 10:28 AM, Bruce Fischl
wrote:
Hi Trisanna
we need more information if you want us to help you. What does
"very odd mean"? If you do it in .mgz do you get a
about 10-40%
(i.e. the max overlap). For some reason when I create an overlay from this
it displays the % from 1-255.
Trisanna
--
Ph.D. CandidateMcGill University
Integrated Program in Neuroscience
Psychology
On Wed, Jun 29, 2016 at 12:20 PM, Bruce Fischl
wrote:
Hi Trisanna
what
Hi Sabrina
what are you trying to accomplish? This is unlikely to work well (if at
all), as we depend on the normalization
cheers
Bruce
On Wed, 29 Jun 2016, Sabrina Yu
wrote:
Hello,
I have a question about taking out the intensity normalization commands in
recon-all. I want to eliminate
Hi Lin
you could look that point up in the subject's aparc+aseg.mgz. This will
give you an index into the file $FREESURFER_HOME/FreeSurferColorLUT.txt
cheers
Bruce
On
Wed, 29 Jun 2016, Yuan Lin wrote:
> Dear FreeSurfer experts,
>
> I am a beginner to learn to use FreeSurfer. Now I have a quest
command to read .mgz file in MATLAB? Or can I
convert the .mgz file to .vtk file? Thank you so much.
Best,
Lin
在 2016年6月29日，下午5:56，Bruce Fischl 写道：
Hi Lin
you could look that point up in the subject's aparc+aseg.mgz. This will
give you an index into the file $FREESURFER
Hi Tamara
1. Run each timepoint through the cross-sectional stream separately.
2. recon-all will figure out what files to use when you tell it to create
the base.
cheers
Bruce
On Thu, 30 Jun 2016, Tamara Tavares wrote:
Hello All,
I am planning to run the longitudinal stream on my data se
eek, that's pretty awful. If you upload the subject dir we will take a
look
cheers
Bruce
On Thu, 30 Jun 2016, Katherine Reiter wrote:
Dear FreeSurfer experts,
I am working on a data set and am having particular difficulty with one
subject. It appeared the skull strip was mistakenly removing occ
urfer/MNI_average_2009a_asymm/spam_for_label_id_4_bl
ur_overlay.mgz
Dim: 152257 1 1
--
Ph.D. CandidateMcGill University
Integrated Program in Neuroscience
Psychology
On Wed, Jun 29, 2016 at 8:10 PM, Bruce Fischl
wrote:
Can you send the full output of that command?
On Jun 29, 2016, at 2:54 PM, Tri
Hi Walid
Recon editing mode is in the upcoming v6. Our recent hardware woes slowed
things down a bit, but we are still hoping to get It out soon
What was the gyrification question?
Cheers
Bruce
> On Jun 30, 2016, at 10:39 PM, Walid Yassin wrote:
>
> Hello freesurfers,
>
> I downloaded freesur
Hi Élodie
if you upload your subject we will take a look
cheers
Bruce
On Fri, 1 Jul 2016, Elodie
Cauvet wrote:
Dear Freesurfer list,
Sorry to bother by posting again, but I am bit stuck by this issue and would
be really glad to get some help on that issue. Of course I can upload some
data i
Hi Hinke
we need more details if you want us to help you. Images, exact command
lines and outputs, etc
cheers
Bruce
On Fri, 1 Jul 2016, Halbertsma, HN (ohk) wrote:
I’m having issues with the conversion of labels drawn in fsaverage to
subject’s space (using mri_label2label).
I’ve manuall
Hi Clara
I would use the stats from the long as they are most stable, and yes I
believe you should control for total volume when looking at surface area.
cheers
Bruce
On Thu, 30 Jun 2016, Clara
Kühn wrote:
Dear FreeSurfer experts,
I would like to look at longitudinal thickness data and
how do you know it is the right hemi and not the left?
Also, we don't use or support tksurfer anymore. Try freeview instead
cheers
Bruce
On Sun,
3 Jul 2016,
李琬 wrote:
Dear all,
I've been trying to use "tksufer" to check the surface images according
to the instruction of "Inspectio
Hi Jasmin
the norm.mgz isn't a voxel labeling - it's an intensity volume. We
typically check the aseg.mgz display *over* the norm.mgz to see if the
labels make sense w.r.t. the intensities.
cheers
Bruce
On Sat, 2 Jul 2016, Jasmin Alves
wrote:
Dear Freesurfer support,
I noticed in previous
PM, Bruce Fischl
wrote:
Hi Jasmin
the norm.mgz isn't a voxel labeling - it's an intensity volume.
We typically check the aseg.mgz display *over* the norm.mgz to
see if the labels make sense w.r.t. the intensities.
cheers
Bruce
On Sat, 2 Jul 20
Hi Lee
that is the correct option, I just haven't gotten around to putting it in
the help text yet.
Bruce
On Mon, 4 Jul 2016, Lee Subin Kristine wrote:
>
> Dear FreeSurfers,
>
>
> Is it possible to get tissue probability maps (for the purpose of using them
> in spm DARTEL, PVElab, etc) out
sounds right to me
Bruce
On Mon, 4 Jul 2016, Clara Kühn wrote:
I have decided now to not control for ICV or total gray matter volume when
looking at cotrical thickness but to control for total gray matter volume when
looking at surface area. Does that sound about right?
Cheers, Clara
- U
ne.0148852
that controls for tGM only for area and not CT.
Cheers Clara
- Ursprüngliche Mail -----
Von: "Bruce Fischl"
An: "Freesurfer support list"
Gesendet: Montag, 4. Juli 2016 15:37:57
Betreff: Re: [Freesurfer] controlling for total gray matter volume
sounds right to me
B
yes, just note that they are somewhat different hypothoses that you are
testing as noted by Mike in the past. If you use average surface
area/thickness you are testing the hypothesis that part of the brain is not
changing/different relative to the average. If you control for TIV (or the
2/3 roo
at if you could answer in
explanation form:
How do people develop finite element models from brain MRI?
How do people learn and implement the software on an example data set?
Abbie
On Mon, Jun 27, 2016 at 6:37 PM, Bruce Fischl
wrote:
Hi Abbie
you just use the recon-all script from t
Hi Barbara
yes, this is intentional and shouldn't be a problem. The hippocampus has
lots of internal structure that we don't model with the surfaces (but we do
with the subfield stuff), but we exclude it from our analyses so you should
be fine
cheers
Bruce
On Wed, 6 Jul 2016, Barbara Kreilkam
Hi Mahtab
you should look them up in a differential geometry textbook. Essentially,
a 2D surface has two curvatures at each point, one in the direction of
maximum folding (k1) and one in the direction of minimum folding (k2). The
Gaussian curvature is then k1*k2 and the mean is (k1+k2)/2
che
Hi Rito
the control points you have look like they are in voxels that contain
some gray matter, which will probably make things worse. YOu need to
identify why you are missing that part of the surface. Is the dark stuff
there labeled as white? Maybe it's a topological defect that gets filled
i
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