for left and right:
1. 2 and 42
2. 3 and 42
3. 10 and 49
4. 77/78/79
5. 11 and 50
6. 12 and 51
7. 13 and 52
8. We don't have a single one for all of cingulate and it depends on which
parcellation you use. You should take the uniton of e.g. 1002 and such
(assuming you are using the aparc and not
Hi Amanda
it depends what you are doing. They will certainly distort thickness
estimates in those regions. It is really, really hard to get rid of dura
unless you acquire data for that purpose. If you have a highres FLAIR or T2
or a multi-echo mprage we have tools for automatically avoiding it
gical Sciences
Rush University Medical Center
Phone: (312) 563-3853
Fax: (312) 563-4660
Email: douglas_merki...@rush.edu
On Jan 6, 2015, at 7:39 AM, Bruce Fischl wrote:
Hi Anthony and Doug
have you tried control points? If you upload a subject dir I'll
take a look
again for the help!
Doug
Doug Merkitch
Neurological Sciences
Rush University Medical Center
Phone: (312) 563-3853
Fax: (312) 563-4660
Email: douglas_merki...@rush.edu
On Jan 6, 2015, at 7:39 AM, Bruce Fischl wrote:
Hi Anthony and Doug
have you tried control points? If you upload
ls -l and see if the 'x' bit is set. For example:
ls -l mris_register mris_register.c
-rwxrwxr-x 1 fischl fsdev 21563282 Jan 6 17:02 mris_register
-rw-rwxrw- 1 fischl fsdev37035 Jan 6 17:02 mris_register.c
mris_register.c is not and mris_register is executable
cheers
Bruce
On Wed, 7
Ja
Hi Raunak
I've messed around with this a bit, but never wrote anything that would be
usable by anyone else. The individual steps aren't that hard though if you
want to write it yourself using our outputs. We are happy to point you in
the right direction if so.
cheers
Bruce
On Thu, 8 Jan 20
Hi Mia
can you send us the recon-all.log? I don't think you included the error
message in your email so there isn't much for us to go on.
thanks
Bruce
On Thu, 8 Jan 2015, Borzello, Mia wrote:
Hi Freesurfers,
I'm wondering if you can help with the following error that occurred when
trying
rfer-boun...@nmr.mgh.harvard.edu
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl
> [fis...@nmr.mgh.harvard.edu]
> Sent: Thursday, January 08, 2015 2:34 PM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] recon-all error
>
> Hi Mia
>
> can yo
Hi Raunak
you can extract any label you want from files like aparc+aseg.mgz using
mri_extract_label or mri_binarize --match. Or you can just load the
label and intensity volumes into matlab and compute co-occurrence matrices
there easily using find and such.
cheers
Bruce
On Fri, 9 Jan 2015
Hi Krishnaprasad
what is your full recon-all command line? And how do you know it isn't
working? Have you tried running "top" during the mri_ca_register stage?
The upcoming (one of these months!) release will have much more in the
way of openmp optimization
cheers
Bruce
On Mon, 12 Jan 2015
. But from
this we cant compute the co-occurrence matrix right?
Please correct me if I am wrong anywhere.
Regards,
Raunak
-Original Message-----
From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu]
Sent: Friday, January 09, 2015 7:27 PM
To: Raunak Mundada
Cc: freesurfer@nmr.mgh.harvard.edu
S
Hi Sophie
what kind of modifications did you make? The 3 volumes are part of the
information in the gca, but not all of it (they don't contain the markov
information) so there is no way to recreate it from only them. mri_ca_train
is the only way to make a gca at the moment, although there is s
Hi Christina
I think this is something that is fixed in the new version. If you want a
patch we can send you new versions of recon-all and mris_make_surfaces
cheers
Bruce
On
Sat, 10 Jan 2015, Christina Chen wrote:
On Dec 24, 2014, at 10:44 PM, Christina Chen wrote:
> Hi!
>
> When looking
or
>>
>> Yea I didn't see it in /autofs/space/huygens_001/users/mia/subjects.
>> I attached the output error for recon-all.
>>
>> Thanks,
>> m
>>
>> From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-
>> boun.
--Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl
Sent: Montag, 12. Januar 2015 14:30
To: Freesurfer support list
Subject: Re: [Freesurfer] Openmp option does not work in Ubuntu 12.04
Hi Krishnaprasad
wh
Bruce Fischl
Sent: Montag, 12. Januar 2015 14:51
To: Freesurfer support list
Subject: Re: [Freesurfer] Openmp option does not work in Ubuntu 12.04
yes, in 5.3 there is only openmp support in a couple of binaries. Those stages
are reached maybe 15 minutes into recon-all depending on your hardware
Hi Gabriella
make_average_subject calls make_average_surface (and
make_average_volumes I believe). You probably want to use
make_average_subject and let it do what it wants to (that is, let it make
everything it knows how to, both surfaces and volumes)
cheers
Bruce
On Mon, 12 Jan 2015, Hirsc
reesurfer-boun...@nmr.mgh.harvard.edu
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl
> [fis...@nmr.mgh.harvard.edu]
> Sent: Monday, January 12, 2015 8:39 AM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] recon-all error
>
> does that dicom exist? Can you run
> From: freesurfer-boun...@nmr.mgh.harvard.edu
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl
> [fis...@nmr.mgh.harvard.edu]
> Sent: Monday, January 12, 2015 9:08 PM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] recon-all error
>
>
thoughts?
Many thanks,
Peter
Mehul Sampat mpsampat at gmail.com
Fri Aug 15 22:20:31 EDT 2014
Thank Bruce.
I have uploaded the case to transfer/incoming in surfer.nmr.mgh.harvard.edu
My file is missingRightParcLabels.tar.gz
Mehul
On Fri, Aug 15, 2014 at 3:17 PM, Bruce Fischl
wrote:
> Sure,
Hi Naveed
try
recon-all -s -make all
cheers
Bruce
On Fri, 16 Jan 2015, Muhammad Naveed
Iqbal Qureshi wrote:
Hi,
How can I execute recon-all on an incomplete preprocessed file in
freesurfer.
My Pc was accidently shut down during the process.
Thank you.
Best Regards
Naveed
Hi Kasper
yes, this should be doable in matlab. If you erased stuff in the
brainmask it should be set to 1 (not 0), so you can find all those
voxels, clone the value in from the brain.finalsurfs.mgz, then set them
all to 1 in brain.finalsurfs.manedit.mgz
cheers
Bruce
On Thu, 15 Jan 2015, Kas
Hi Mark
yes, that should work
cheers
Bruce
On Thu, 15 Jan 2015, Mark Fletcher wrote:
Dear FreeSurfer Community,
I am correcting a lot of brains and am wondering if I can combine two steps?
Currently, I first correct pial surfaces by manually deleting voxels (dura,
bad skull strip, etc). I th
Hi Bronwyn
the surface area at each vertex (I assume you mean vertex and not voxel) is
simply the average of the area of the triangles it is attached to.
cheers
Bruce
On Fri, 16 Jan 2015, Bronwyn Overs wrote:
> Dear Mailing List,
>
> I would like to understand how freesurfer calculates the sur
Hi Celine
hard to tell from the slices. Are there voxels labeled ventricle there?
If so, you need to correct the aseg. If not, it's probably a topological
defect that is fixed incorrectly. If you upload the subject we'll take a
look
Bruce
On Fri, 16 Jan 2015, Celine Louapre wrote:
> Sorry forg
Hi Meiling
to go from volume points to the surface you pretty much have to search.
We speed this up internally by compiling the surface into a spatial
lookup table then only searching through the vertices that are in each
bin, but there is no easy external interface to that code (although you
Hi Pradeep
pbsubmit is a wrapper script for submitting a job to a PBS cluster. If you
don't have a cluster you should just run the commands that it runs.
cheers
Bruce
On Mon, 19 Jan 2015, pradeep mahato wrote:
> Hello experts,
> I am using rebuild_gca_atlas.csh,v 1.22 2011/03/02 20:16:39. I
Hi Mia
If all you want to do is convert try
mri_convert ct.anat.nii ct.anat.mgz
Cheers
Bruce
> On Jan 19, 2015, at 10:33 PM, Borzello, Mia wrote:
>
> Hi Freesurfers,
>
> I'm looking at Freesurfer files from are from years ago trying to look at the
> ct.anat file. Unfortunately, i have the
> From: freesurfer-boun...@nmr.mgh.harvard.edu
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl
> [fis...@nmr.mgh.harvard.edu]
> Sent: Monday, January 19, 2015 10:38 PM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] converting .nii to .mgz
Hi Muhammad
can you really run 40 subjects at the same time? Usually that means you
have a processor farm and it has some mechanism for submitting jobs and
load balancing and such (like qsub).
cheers
Bruce
On Tue, 20 Jan 2015, Muhammad Naveed
Iqbal Qureshi wrote:
Can we apply recon-all on
Hi Amanda,
click the "truncate" button.
cheers
Bruce
On Tue, 20 Jan 2015, Worker, Amanda wrote:
> My command line was "tksurfer mean.lh.thick_age.thickness.10.mgh lh inflate"
> d- which is when I got the error.
>
> I have now tried loading fsaverage first with "tksurfer fsaverage lh
> inflated"
Hi Mohammad,
the thickness can be displayed as a map on any surface we create. We do
create ?h.sphere files by default, so you can use those if you want. If
you'd rather a planar representation you need to make cuts in the inflated
surface and use mris_flatten.
cheers
Bruce
On Wed, 21 Jan
Hi Jacek
if you give us an example of what the desired output would be for you it
would just be a couple of minutes to put it in the code. Or maybe someone
can post some sed code (or some easy alternative) to parse the CNR out of
the output.
Bruce
On Wed,
21 Jan 2015, Jacek Manko wrote:
1.666
Thanks in advance.
Cheers,
Jacek
Dnia 21-01-2015 o godz. 20:34 Bruce Fischl napisał(a):
Hi Jacek
if you give us an example of what the desired output would be for you it
would just be a couple of minutes to put it in the code. Or maybe someone
can post some sed code (or some easy alternativ
Hi Lars
you have to give recon-all some directive telling it what to do (-all,
-autorecon1, -autorecon2, -autorecon3).
cheers
Bruce
On Thu, 22 Jan 2015, Lars M. Rimol
wrote:
Hi,
I keep getting this error message when running, or trying to run, recon-all. I
suspect
there is a file somewher
Hi Ray
this should do the trick:
mri_convert -nth 10 all_frames.mgz frame10.mgz
or
mri_convert all_frames.mgz#10 frame10.mgz
note that the second syntax should be accepted by most of our tools
cheers
Bruce
On Thu, 22 Jan 2015, Ray Razlighi wrote:
Dear FreeSurfer Experts,
I have a .mgh
only, for example:
bruce 1.602
bert 1.555
john_doe 1.666
Thanks in advance.
Cheers,
Jacek
Dnia 21-01-2015 o godz. 20:34 Bruce Fischl napisał(a):
Hi Jacek
if you give us an example of what the desired output would be for you it
would just be a couple of minutes to put it in the code. Or mayb
Hi Maria
it's really hard to say - you'll need to try it out. There aren't strong
prior constraints on skull shape, but if the shape of the brain is too
different, things may degrade
Bruce
On Fri, 23 Jan 2015, Maria Holland wrote:
Hi all,
I am starting a project analyzing patients with cr
have you tried dcmdjpeg or dcmdjpls to uncompress them, then used some
other unpacker/converter (mri_convert etc...)
cheers
Bruce
On Tue, 27 Jan 2015, pradeep mahato wrote:
>
> Please tell how to use dcmunpack. Any help converting dicom to nii.
>
> On Jan 27, 2015 9:03 PM, "Douglas Greve" wr
p.s. sorry, I missed the multiframe part. I guess dcmunpack and
mri_convert won't work, but maybe decompressing and using something else
afterwards will do the trick?
On Tue, 27 Jan 2015, Douglas Greve wrote:
> If you run it with --help there will be lots of documentation and examples.
> It will
Hi Steano
a) You could do this but then you are testing a somewhat different
hypothesis - that the change in a specific structure is more than the
overall change in gray matter. Thus for example, widespread atrophy would
be regressed out. If that's what you are interested in, then this approac
Hi Sneha
can you send us some snapshots? Or upload the entire subject and we will
take a look. You can always erase cerebellum from brain.finalsurfs and
rerun recon3
cheers
Bruce
On Wed, 28 Jan 2015, Sneha Pandya wrote:
> Hi Team,
>
> Can anyone please share if they have been successful in
Hi Yawu
Can you upload those two volumes so we can take a look?
Cheers
Bruce
> On Jan 28, 2015, at 4:33 PM, Liu Y wrote:
>
> Dear experts,
> Recently I run freesurfer longitudinal analysis
> (freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0), during the creation of
> the BASE, I get the fo
.nii.gz
via FTP File Exchange.
Thanks,
Yawu
On Thu, Jan 29, 2015 at 3:28 AM, Bruce Fischl
wrote:
Hi Yawu
Can you upload those two volumes so we can take a look?
Cheers
Bruce
On Jan 28, 2015, at 4:33 PM, Liu Y wrote:
Dear experts,
Recently I run
Hi Rujing
it is the mean intensity within the structure from the norm.mgz I believe
cheers
Bruce
On
Thu, 29 Jan 2015, Rujing Zha wrote:
HI all
What is mean of the subcortical intensity in the aseg.stats file?
Thanks.
rujing
___
Freesurf
Hi Juan
if you invert that matrix it will go the other direction
cheers
Bruce
On Thu, 29 Jan
2015, Diaz Rodriguez, Juan wrote:
I am trying to convert MNI305 coordinates to RAS. I have only been able to
find a way to find MNI305 from RAS but not the other way around:
MNI305RAS = TalXFM*Norig
__
> From: freesurfer-boun...@nmr.mgh.harvard.edu
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl
> [fis...@nmr.mgh.harvard.edu]
> Sent: Thursday, January 29, 2015 3:33 PM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] MNI305 coordinates to
the
longitudinal stream.
cheers
Bruce
On Fri, 30 Jan 2015, Liu Y wrote:
Hi Bruce,I run the command recon-all -base K_EL03_base -tp K_EL03_1 -tp
K_EL03_2 -all.I am to upload the recon_all.log to you.
Thanks,
Yawu
On Thu, Jan 29, 2015 at 6:07 PM, Bruce Fischl
wrote:
Hi Yawu
what
Hi Ernst
The new vertices are added o the end, so all the fsaverage5 vertex numbers
should be the same in fsaverage6
Cheers
Bruce
> On Feb 2, 2015, at 10:33 AM, Ernst Schwartz
> wrote:
>
> Hi!
>
> I have some data that's on a low-resolution mesh (fsaverage5) that I would
> like to upsampl
Hi David
this one is a good one to cite:
Satrajit S Ghosh, Sita Kakunoori, Jean Augustinack, Alfonso
Nieto-Castanon, Ioulia Kovelman, Nadine Gaab, Joanna A Christodoulou,
Christina Triantafyllou, John D E Gabrieli, Bruce Fischl (2010)
Evaluating the validity of volume-based and surface-based
sure, just draw an ROI in the volume (in e.g. freeview) and save it as a
.label file, then load it into tksurfer and it will get sampled onto the
surface (then save it)
On
Tue, 3 Feb 2015, rwlod...@uic.edu wrote:
> Hello!
> I was just wondering what the best way to find the cortical thickness
yes it does
cheers
Bruce
On Thu, 5 Feb 2015, jwa...@nmr.mgh.harvard.edu wrote:
> Hello Freesurfer,
> My MPRAGE dimensions are 1x1x1.33. The output of recon-all appears to
> be 1x1x1, judging by the fact that the aseg.stats columns for voxel
> number and volume in mm3 are identical. Should I conc
Hi Yawu
what was the full recon-all command line? What is your input format? If
all else fails you can mri_convert your input volume nifti or mgz and
override what is in the header (e.g. mri_convert -iks 1 ...)
cheers
Bruce
On Fri, 6 Feb
2015, Liu Y wrote:
> Dear Experts,
> When I run recon-a
Hi Silas
as far as I know there isn't a presma label. I'm also not sure how well
thresholding based on y will do either.
sorry
Bruce
On Fri, 6 Feb 2015, Silas wrote:
> Hi Freesurfer team,
>
> I'm currently investigating the volume of preSMA. Is there an existing label
> of preSMA?
>
> If
en complete the "recon-all -cw256 -s T8_1 -all", the orig.mgz was
re-scaled (stretched) in left-right direction, and could not see the left
and right boundaries of the brain.
Thanks,
Yawu
On Fri, Feb 6, 2015 at 3:18 PM, Bruce Fischl
wrote:
Hi Yawu
what was the full recon-
try --init-spm
On Fri, 6 Feb 2015, Anastasia Yendiki wrote:
>
> Hi Amanda - So it looks like --init-header didn't work, and neither does
> --init-fsl. I'll defer to the father of bbregister, Doug, for clues about
> how to proceed.
>
> a.y
>
> On Wed, 21 Jan 2015, Worker, Amanda wrote:
>
>> Hi Anas
Hi Phil
try running recon-all -make all on those subjects. Something was rebuilt
but not run to completion I suspect.
cheers
Bruce
On Sun, 8 Feb 2015, Kelly, Philip
wrote:
Dear FreeSurfer experts,
I am running Spherical Daemon on my reconstructed surfaces as part of the
Winkler et al
the original
information of voxel size. I omitted the first 3 dcm images then it worked
during freesurfer analysis.
Cheers
Yawu
On Fri, Feb 6, 2015 at 6:26 PM, Bruce Fischl
wrote:
and what was the recon-all -i command line? Does the rawavg.mgz
look correct? You can send us whatever
mri_extract should do the trick
Bruce
On Sun, 8 Feb 2015, SOURAV RANJAN KOLE
wrote:
> Dear Freesurfer community,
> Please let me know of an elegant way to reduce image size from 256x256x256
> to 256x256x160 and keeping the voxel size the same. The images are currently
> in analyze format but I ha
>
>
>
> From: freesurfer-boun...@nmr.mgh.harvard.edu
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl
> [fis...@nmr.mgh.harvard.edu]
> Sent: Sunday, February 08, 2015 4:12 PM
> To: Freesurfer support list
> Subject: Re: [Fr
gt; Regards,
>
> Sourav
>
>
> From: freesurfer-boun...@nmr.mgh.harvard.edu
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl
> [fis...@nmr.mgh.harvard.edu]
> Sent: Sunday, February 08, 2015 5:04 PM
> To: Freesurfer support
uide me to determine the starting coordinates for
extraction. Thank you.
Regards,
Sourav
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl
[fis...@nmr.mgh.harvard.edu]
Sent: Sunday, February 08, 2015 6:34 PM
To: Freesurfer support list
S
Hi Noam
it looks like the talairach alignment failed. You can usually find answers
on our wiki for what to do in this type of case. For example:
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach_tktools
cheers
Bruce
On Mon, 9 Feb 2015, Ben Eliezer, Noam wrote:
Hi Freesurfer su
Hi Salil
in the end of the look valid there's not much more you can do. It would be
on a case-by-case basis depending on the details of the lesion/surgery
cheers
Bruce
On Tue, 10 Feb 2015, Salil Soman wrote:
> Hi,
> Is there an official thought on using freesurfer on cases were there is
> volu
Hi Razib
yes, I think mri_label2label will do this if you have reconstructed the
surfaces.
cheers
Bruce
On Tue, 10 Feb 2015, Muhammad Razib wrote:
Hi,
I am wondering is there a way in freesurfer to map manually labeled IBSR MRI
.img/.hdr volume files to freesurfer surface file (e.g. lh.pial/
Hi Andre
sorry, there is no way to run only part of the steps as there is lots of
interdependancy. You need to run -all. That said, the new version that
should be coming out in a couple of months is significantly faster and has
a lot more openmp support.
cheers
Bruce
On Wed, 11 Feb 2015, An
Hi Don
are you running a single job on the 8G machine? What FS version? We haven't
seen any core dumps in mri_ca_register recently. If you run it without
openmp does it work? Kind of worrisome that it dies in a different place on
a different machine
Bruce
On Wed, 11 Feb 2015, Krieger, Donal
/Text
-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-
boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl
Sent: Wednesday, February 11, 2015 9:39 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] time critical problem: mri_ca_register failure d
Hi Konrad
you should be able to do this with mri_surf2surf, although the syntax
might be tricky.
cheers
Bruce
On Mon, 9 Feb 2015, Konrad Wagstyl wrote:
> Hi all,
>
> We're having some trouble using interhemispheric registration. It works fine
> for files that are automatically registered eg th
esurfer-requ...@nmr.mgh.harvard.edu
>
> You can reach the person managing the list at
>freesurfer-ow...@nmr.mgh.harvard.edu
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of Freesurfer digest..."
>
>
> Today's
Hi Silas
you should certainly try to avoid a group-by-processing parameters bias.
Is there a reason that one group would require different parameters than
another?
cheers
Bruce
On Mon, 16 Feb 2015, Silas wrote:
> Hi Freesurfer team,
> I'm currently making an structural analysis using freesurfe
Hi Melina
1. Can you send us a picture? I'm not sure given your description,
although the surfaces can be arbitrary in the hippocampus/amygdala and
should be ignored there.
2. You should be able to use mri_label2vol for this. Note that you can load
the label itself directly into freeview if yo
I think that's ok. In the end you want the best models, you just need to
make sure that there is no significant group-by-parameters interaction. Not
intervening can also cause a bias. For example if there is atrophy in one
group that allows the surfaces to avoid dura but in the other group
sign
Hi Ajay
if it covers the whoe brain you might be ok, try it and see how it goes
Bruce
On
Wed, 18 Feb 2015, Ajay Kurani wrote:
Hello Freesurfer experts,
I have a question regarding the use of the -T2 and -FLAIR flags in
freesurfer. I have 2
scans: 1 whole brain MPRAGE and 1 partial brain
can you check mri_segmet and mris_make_surfaces and see if the
auto-detected intensity parameters are reasonable? Things like max gray
at csf border and such. If not, you can set them explicitly using the
expert opts - this usually works
Bruce
On Wed, 18 Feb 2015, Pedro Rosa - Gmail
wrote:
AT_CSF_BORDER to 44.4 (was 40)
On Wednesday, February 18, 2015 at 7:58 PM, Bruce Fischl wrote:
can you check mri_segmet and mris_make_surfaces and see if the
auto-detected intensity parameters are reasonable? Things like max gray
at csf border and such. If not, you can set them explicitly using t
Hi Daniel
no, tksurfer visualizes surfaces exclusively, and the subcortical
structures are volumetric by and large. You could tesselate their surface
and view it in tksurfer, or just use tkmediit or freeview.
cheers
Bruce
On Thu, 19 Feb
2015, Yang, Daniel wrote:
> Dear FreeSurfer experts,
>
his is still valid, right?
>
> Best,
> Daniel
>
> On 2/19/15, 5:59 PM, "Bruce Fischl" wrote:
>
>> Hi Daniel
>>
>> no, tksurfer visualizes surfaces exclusively, and the subcortical
>> structures are volumetric by and large. You could tessela
Hi Claudia
I think mris_anatomical_stats can take a label file, which would do the
trick
cheers
Bruce
On Fri, 20 Feb 2015, Claudia Dacquino wrote:
Dear all freesurfers,
I have manually drawn a region of interest and saved it as a label file in the
/label folder
and I now want to extract mean
Hi Mark
no, that can be tough as it breaks many of our laminar assumptions.
sorry
Bruce
On Tue,
17 Feb 2015, Mark Fletcher wrote:
Dear FreeSurfer Development Team,
An additional, but different question. One of my subjects has some sort of
hole (lesion) in the left temporal lobe (slides 3-
http://www.frontiersin.org/files/Articles/18483/fnhum-06-00021-HTML/
image_m/fnhum-06-00021-g003.jpg).
Is it okay to visualize such subcortical activation via tksurfer? If not,
could you please recommend a method to visualize subcortical activation?
Sincerely,
Daniel
On 2/20/15, 9:06 AM, "Br
I would very much hope that replacing the RAM wouldn't change anything
Bruce
On
Mon, 23 Feb 2015, Pedro Rosa - Gmail wrote:
> Dear all,
> I would like to know whether a RAM memory replacement in a Mac computer would
> change
> FreeSurfer 5.3 processing.
> I have a sample that was almost complete
gt; expected that it is not the same for the RAM. Am I correct?
> Thanks again,
> Pedro.
>
>> On Feb 23, 2015, at 21:50, Bruce Fischl wrote:
>>
>> I would very much hope that replacing the RAM wouldn't change anything
>> Bruce
>> On
>> Mon, 23 Feb 201
Hi Norman
perhaps you can take a step back and tell us what you want to use it for?
We might be able to suggest a better analysis strategy
Bruce
On Tue, 24 Feb 2015,
Norman Benbrahim wrote:
> Hi,
> I want to use the Desikan-Kilany atlas to run some analysis in some regions,
> however
> I am ve
2011), and create masks out of those.
On Tue, Feb 24, 2015 at 4:22 PM, Bruce Fischl
wrote:
Hi Norman
perhaps you can take a step back and tell us what you want to use it
for?
We might be able to suggest a better analysis strategy
Bruce
On Tue, 24 Feb 2015,
t up to do this in matlab, so I would only
need the atlas in nifti format
so I can pick out which regions to use (using the
rich club paper, van den Heuvel et
al. 2011), and create masks out of those.
On Tue, Feb 24, 2015
Hi Pablo
the mat file is an extension to analyze the specifies the direction
cosines. Without it we are only guessing at the anatomical orientation of
the image. Unless these images have some marker such as a vitamin E capsule
how will you ever know if we got left/right correct?
cheers
Bruc
Hi Dorian,
no, sorry, you pretty much need to run everything to get it.
cheers
Bruce
On Wed, 25 Feb
2015, Dorian P. wrote:
Hi folks,
I am using the parcellation of Freesurfer for some other analyses. I see
that the parcellation if obtained rather late in the pipeline:
http://surfer.nmr.mgh.h
Is there any reason you need it to be nonlinear? I would think bbregister and
mri_vol2vol would do the trick
Cheers
Bruce
> On Feb 25, 2015, at 11:18 PM, David Grayson wrote:
>
> Hi freesurfers,
>
> I am hoping to warp an aparc+aseg.mgh file from a subject's
> freesurfer-processed image to
Hi Pablo
I really don't know the analyze conventions or whether this will work. If
you are sure of the orientation then convert it to mgz and check in
tkmedit whether we got the orientation right (that is that the left side
of the brain is properly identified as such in tkmedit/freeview)
che
gain
Andre
Von: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu]" im Auftrag von "Bruce
Fischl [fis...@nmr.mgh.harvard.edu]
Gesendet: Donnerstag, 26. Februar 2015 15:13
An: Freesurfer support list
Betreff: Re: [Freesurfer] recon-all and subcortic
Hi Andre
if you ran recon-all you will have created a volume file names aseg.mgz
that has the subcortical segmentation (and an aparc+aseg.mgz that has
both subcortical and cortical in it)
cheers
Bruce
On Thu, 26 Feb 2015, André Schmidt
wrote:
Dear experts,
I use recon-all for the parcella
linear. I was hoping there
> might be a way to get a warp field to go between the two images without
> running both images through the recon-all pipeline. Are there any other
> possible tools?
>
> Thanks!
> -David
>
> On Wed, Feb 25, 2015 at 8:29 PM, Bruce Fischl
> wrote
Hi Sarah
have you used mri_vol2surf to sample the data onto the surface? When you
say "extract specific regions of functional data from a flat " do you
want to average within the ROI?
cheers
Bruce
On Thu, 26 Feb 2015, Sarah Finnegan wrote:
I have a question about the equivalent of fslmaths
Hi Ruthger
sorry, I don't think we have anything to do exactly what you want. It
would be easy enough to do in matlab though
cheers
Bruce
On Fri, 27 Feb 2015, Righart,
Ruthger wrote:
> Dear Freesurfers,
>
> I am using mris_convert to obtain per vertex thickness values in an
> ascii file.
>
> W
it if's a T1-weighted flash that should work
cheers
Bruce
On Mon, 2 Mar 2015, Satrajit
Ghosh wrote:
hi bruce,
we are missing a T1 scan from a participant. is there any pathway in
freesurfer to reconstruct from the T2-flair/flash scan?
cheers,
satra
___
you can use the command:
set_current_threshold_from_percentile(min, mid,max)
which will compute the thresholds based on the histogram of values
On Tue, 3 Mar 2015, Douglas N Greve wrote:
>
> I'm not sure what you mean. optimal in what sense?
> doug
>
> On 03/03/2015 03:21 PM, Hirsch, Gabriella
Hi Hassan
you need to add some directives to recon-all to tell it what to do. For
example, if you add "-all" to your command line it will do everything it
knows how to (pretty much)
cheers
Bruce
On Wed, 4 Mar 2015, Hassan bakhshi wrote:
HI,
Im using freesurfer newly, i have a folder of a
Hi Fabrizio
the strange error message is a bug in our reporting (which I just fixed),
but it isn't the source of your problem.
Does the cortex.label file exist? Note that you are specifying the right
hemi label file for the left hemi stats, which is almost certainly wrong. I
also don't think y
...@nmr.mgh.harvard.edu
> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl
> Sent: Tuesday, March 03, 2015 7:05 PM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] tksurfer overlay threshold
>
> you can use the command:
>
> set_current_threshold_from_p
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