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Thank you! I have a gca for subcortical and two gcs (lh/rh) for cortical
structures.
I created an annot (rh/lh) and a mgz using mris_ca_label and mri_ca_label
for parcellation/segmentation stats.
For the PET analysis I have the following problem:
If
It gets the subcortical from apas+head.mgz which gets created along the
way by xcerebralseg. You can create your own with xcerebralseg by
specifying your volume as the mergevol. I think this will work, but I'm
not sure. I'm assuming you've used the GCA to create your own
subcortical seg for the
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I just realized that the above mentioned command (gtmseg --s XYZ --o
BN.gtmseg.mgz --ctx-annot BN_Atlas.annot --ctab
'/media/XYZ/BN_Atlas_freesurfer/BN_Atlas_246_LUT.txt' --no-xcerseg) gives
me only the cortical segmentation. Is there any way to also in
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Thanks alot lilla.
Nader
On Tue, 29 Oct 2019, 19:37 Lilla Zollei
> Our default setting to run mrri_cvs_register on our cluster is to use
> 35gb.
> Lilla
>
> On Tue, 29 Oct 2019, Nader Razmara wrote:
>
> >
> > Hi expertsI use freesurfer vm 5.3 on oracl
Our default setting to run mrri_cvs_register on our cluster is to use
35gb.
Lilla
On Tue, 29 Oct 2019, Nader Razmara wrote:
Hi expertsI use freesurfer vm 5.3 on oracle vb 6 with 8 GB ram.
When i use mri_cvs_register as:
mri_cvs_register --mov subjid --mni or
mri_cvs_register --mov subjid -
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Hi experts
I use freesurfer vm 5.3 on oracle vb 6 with 8 GB ram.
When i use mri_cvs_register as:
mri_cvs_register --mov subjid --mni or
mri_cvs_register --mov subjid --template subjid in both cases it stops in
step 2 by diffrent errors. I asked zollei t
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Hello,
I am trying to do a within-subject co-registration between b0 volumes and
T1's for my subjects. This is an old dataset that does not have anything
for correcting b0 inhomogeneities. The registration using --dti and normal
parameters for bbregist
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Alright, thanks!
On Tue, Aug 13, 2019 at 5:10 PM Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> wrote:
> There is no cut off for the minimum size. As it gets smaller, the PVC
> noise amplification will become bigger (it also depends on the shape as
There is no cut off for the minimum size. As it gets smaller, the PVC
noise amplification will become bigger (it also depends on the shape as
well).
I think the --no-xcerseg is the right way to go now
On 8/13/19 11:00 AM, Boris Rauchmann wrote:
>
> External Email - Use Caution
>
> Thank
External Email - Use Caution
Thank you for your prompt answer - the command worked. This is the atlas
mentioned: http://atlas.brainnetome.org/brainnetome.html
What is approximately the smallest possible segment when using PVC?
Also, does the exclusion of extracerebral structures ha
I don't know what the Brainnetome is, but it looks like you have it in
annotation form. I think that command should work. Why are you using
--no-xcerseg? This will cause it to not include extracerebral
structures. Also note that you cannot use arbitrarily small segments
when doing PVC.
On 8/13
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Dear all,
my intention is to use the Brainnetome Atlas parcellation/segmentation in
PETSurfer to obtain PVC corrected SUVRs for the atlas ROIs. I used:
gtmseg --s XYZ --o BN.gtmseg.mgz --ctx-annot BN_Atlas.annot --ctab
'/media/XYZ/BN_Atlas_freesurfer/
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Hello Sebastian,
Please download the zip archive from the following link,
https://drive.google.com/file/d/1w0vZyWTY0HrbcDiP1jWsmGl_GMUSh7tR/view?usp=sharing
Then expand and read the README.patch file and follow the instructions.
When you are done, you
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I understand.
Thanks for your response, Feifei!
Bruce Fischl 于2019年7月16日周二 下午10:09写道：
> Hi Feifei
>
> we don't compute thickness using the method introudced by (MacDonald et
> al.2000). For that you can look at either our 1999 NeuroImage pair of
>
Hi Feifei
we don't compute thickness using the method introudced by (MacDonald et
al.2000). For that you can look at either our 1999 NeuroImage pair of
papers or the 2000 PNAS paper.
Essentially surface area is just the average area of the triangles that the
vertex is attached to, and then v
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Dear Freesurfer experts,
I want to know how Freesufer to compute the volume and area at each vertex.
Are there any references? I just found the reference which introduces the
measure of thickness(MacDonald et al.2000).
Any help with this would be
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Hello John,
You might be able to tell from the log what directory recon-all was cd'd
into when the creation of the soft link failed. You could try to cd
there as your userid (which I assume you used to run recon-all), and see
if you can manually
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Post-doc position for MRI-research on dementia and normal aging available
at Karolinska institute.
We are looking for a Post-doc researcher for a 1-year scholarship (with a
possibility for an extension to 2-year) at our section at the
NVS-department at
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Alright, thanks I confused that. I already found a better way for my purposes.
Im just running mri_gtmpvc using the flags —psf=0 and —no-tfe to get the non
PVC subcortical SUVs.
> Am 17.05.2019 um 17:28 schrieb Greve, Douglas N.,Ph.D.
> :
>
> In mr
In mri_segstats, use --seg $SUBJECTS_DIR/xyz/mri/aparc+aseg.mgz --ctab-default
...
when you use --annot, you are saying that the input is on the surface.
On 5/17/2019 9:07 AM, Boris Rauchmann wrote:
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Dear Freesurfer community,
I am trying to extract SUV valu
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Dear Freesurfer community,
I am trying to extract SUV values from sub-cortical segmentation or gtmseg
I don t want to use any PVC.
I used the following commands:
gtmseg --s xyz
then
mri_coreg --s xyz --mov abetapet.nii.gz --reg abetapet.reg.lta
fol
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Yes, the theshold was the solution. Thanks again for your precious help!
On Fri, Mar 29, 2019 at 3:50 PM Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> wrote:
> What threshold are you using in tksurfer? It should be the same as
> -log10(cwp), where
What threshold are you using in tksurfer? It should be the same as -log10(cwp),
where cwp is the --cwp threshold you used in mri_glmfit-sim. If it is
different, then it might not show all the cluster
On 3/29/19 6:48 AM, Giuliana Klencklen wrote:
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Hi FS exper
External Email - Use Caution
Hi FS experts,
I use tksurfer (e.g., tksurfer fsaverage/ lh inflated -gray) to open the
overlays (i.e., something.sig.cluster.mgh) I generated with the permutation
simulation correction. It goes perfectly well for most of them expect for
some, where t
do you mean the section in the left hemi temporal lobe (the lower right
portion of your image)? That does not look like real white matter to me as
it is adjacent to csf. Did you accidentally put some control points in gray
matter (or csf)?
On Mon, 25 Mar 2019, Erika Portera wrote:
E
Hello - I'm wondering how to generate a label in FreeSurfer from peak
activation in a cluster? Is there a specific command?
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_
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Bruce
Fischl
Sent: Monday, February 4, 2019 12:27:48 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] (no subject)
Hi Jorgan
do you have read permission for
list
Subject: Re: [Freesurfer] (no subject)
Hi Jorgan
do you have read permission for that file/directory? It looks like not
cheers
Bruce
On Mon, 4 Feb 2019, Jordan Fowler wrote:
>
> External Email - Use Caution
>
> Here is the message displayed:
>
>
> Setti
Hi Jorgan
do you have read permission for that file/directory? It looks like not
cheers
Bruce
On Mon, 4 Feb 2019, Jordan Fowler wrote:
External Email - Use Caution
Here is the message displayed:
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME /A
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Here is the message displayed:
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME /Applications/freesurfer
FSFAST_HOME /Applications/freesurfer/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR /Applications/freesurfer/sub
om: "Larissa Bechtle"
> Subject: Re: [Freesurfer] (no subject)
> To: "Freesurfer support list"
> Message-ID:
>
> >
>
> Content-Type: text/plain; charset="utf-8"
>
> External Email - Use Caution
>
> Hi Ruopeng,
>
> Thank
External Email - Use Caution
Hi Ruopeng,
Thank you very much for your quick answer and advice. So I am going to update
freeview!
Thanks!
Larissa
Gesendet mit der WEB.DE Mail App
Am 07.01.19 um 17:35 schrieb Ruopeng Wang
> Hi Larissa,
>
> The latest development version of fr
Hi Larissa,
The latest development version of freeview supports drawing labels on
surface. You can take a look here on how to update freeview:
https://surfer.nmr.mgh.harvard.edu/fswiki/UpdateFreeview
In the latest version, you can draw paths on surface and use custom fill
to create/edit labels
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Hi everybody,
after finishing my group analysis I am currently trying to run a ROI analysis.
However I have some problems/general questions.
I am trying to draw a ROI on fsaverage in order to use the mri_label2label
command afterwards.
I opened Freev
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Can? you send the full terminal output?
On 12/05/2018 01:25 AM, Sara Jafakesh wrote:
>
> External Email - Use Caution
>
>
>
>
>
>
> Dear freesurfer experts,
> I want to calculate corrolation between two seeds with
> free
External Email - Use Caution
Dear freesurfer experts,
I want to calculate functional connectivity between two seeds with
freesurfer-linux-centos6_x86_64_stable_pub-v6 . after using fcseed-config
and fseed-sess commands, I use fcseedcor command. the command that I trying
to run i
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Dear freesurfer,
I have some question about GE date (have 2 run) to run TRACULAR. How
can I get some answers?
Sent from Mail for Windows 10
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The information in this e-mail is intended only for the person to whom
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confirm 185a0e2daad6a81d7f3f1a9403d86009db538c35___
Freesurfer mailing list
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The information in this e-mail is inten
Hi Maedeh
in your command line you need a space between the 'n' and the '2', so it
should be:
-n 2
not
-n2
cheers
Bruce
On Mon, 23 Jul 2018, Maedeh Khalilian wrote:
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Dear FreeSurfer experts,
I would like to use the FreeSurfer package to do a
External Email - Use Caution
Dear FreeSurfer experts,
I would like to use the FreeSurfer package to do a parcellation.Just for
testing, I am using "buckner_data" and there is a step I have been stuck
in.I have problem using "mris_ca_train" command.This is the whole code I
run
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Hi everybody,
I was wondering if you could help me.
I run a hyppocampal segmentation in a subject and it seemed to work. Now when
I'm trying to extract the infos and run "quantifyHippocampalSubfields.sh" I
just get this message:
Gathering results
Hi Sudeshna
according to our local neuranatomical expert:
it is probably ventral claustrum (ventral claustrum stretches in to
the temporal lobe ,especially at the anteriorly (slightly anterior to
amygdala).
so this region is not cortex and you shouldn't worry about the surfaces
there.
As
help unsubscribe
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addressed. If you believe this e-mail w
Hi vidhu
use recon-all to process the dataset, then mri_extract_labels or
mri_binarize can be used to extract just the hippocampus
cheers
Bruce
On Wed, 1 Nov 2017,
Vidhu Agrawal wrote:
Respected Sir,
How can i scoop out or separate only hippocampus from a 3D MRI of whole brain?
With reg
Hi Vidhu,
After your standard recon-all, do:
mri_binarize --i yoursubjectname/mri/aseg.mgz --match 17 --o left_hip.nii
mri_binarize --i yoursubjectname/mri/aseg.mgz--match 53 --o right_hip.nii
Hope that helps.
Best Wishes,
Elijah
On Wed, Nov 1, 2017 at 5:57 AM, Vidhu Agrawal
wrote:
> Respec
Respected Sir,
How can i scoop out or separate only hippocampus from a 3D MRI of whole
brain?
With regards
vidhu agarwal
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The infor
El El mar, 12 sept 2017 a las 20:19, José Gómez-Feria Ferreiro <
josegomezfe...@gmail.com> escribió:
> Dear Freesurfer,
>
> Is it possible to keep on the supporting list but without receiving emails
> from other people? My email account is getting stuck with so many emails.
>
> Thanks,
>
> Jose
>
Dear Freesurfer,
Is it possible to keep on the supporting list but without receiving emails
from other people? My email account is getting stuck with so many emails.
Thanks,
Jose
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Hi Yvonne
can you try using freeview instead? We don't really support tksurfer any
longer.
cheers
Bruce
On Tue, 12 Sep 2017, y...@nyu.edu wrote:
Hi all,
I have finished the command “recon -all” without error. But I get an error that
says:
“Received X error!
Error code :158
Hi all,
I have finished the command “recon -all” without error. But I get an error that
says:
“Received X error!
Error code :158
Request code : 148
Minor code: 2
Error text :’GLXBadLargeRequest’”
I am using the command “tksurfer sub lh inflated”.
Then clic
Hello,
I try to map the surface to the native space, using the following command
adjusted for my data:
mri_surf2surf --sval-xyz pial --reg register.native.dat rawavg.mgz
--tval lh.pial.native --tval-xyz --hemi lh --s subjectname
the output is:
ERROR: --tval-xyz flag needs 1 argument
FYI: --tval-x
rvard.edu] on behalf of Bruce Fischl
> [fis...@nmr.mgh.harvard.edu]
> Sent: Wednesday, June 07, 2017 1:47 PM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] (no subject)
>
> that should work if th erest of the slices are in your current directory.
> Mike is suggestion you coul
the help.
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl
[fis...@nmr.mgh.harvard.edu]
Sent: Wednesday, June 07, 2017 1:47 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] (no subject
[mha...@wustl.edu]
> Sent: Wednesday, June 07, 2017 11:57 AM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] (no subject)
>
> This email contains a suspicious URL
>
> dcm2niix with the -s flag will allow you to convert a single DICOM that is
> pa
e?
Thanks,
Emily
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Harms, Michael
[mha...@wustl.edu]
Sent: Wednesday, June 07, 2017 11:57 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] (no subj
freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] (no subject)
>
> I did not mean for you to send them to me. You should use one of them
> (any one of them) as input to recon-all
>
>
> On 06/06/2017 05:14 PM, Emily Rogers wrote:
>> Yes I have the original
M
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] (no subject)
I did not mean for you to send them to me. You should use one of them
(any one of them) as input to recon-all
On 06/06/2017 05:14 PM, Emily Rogers wrote:
> Yes I have the original 160 files, attac
arvard.edu] On Behalf Of Douglas N Greve
Sent: Tuesday, June 06, 2017 5:48 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] (no subject)
I did not mean for you to send them to me. You should use one of them (any
one of them) as input to recon-all
On
...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve
Sent: Tuesday, June 06, 2017 5:48 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] (no subject)
I did not mean for you to send them to me. You should use one of them (any one
of them) as input
__
> 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: Tuesday, June 06, 2017 5:11 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] (no subject)
>
arvard.edu]
> Sent: Tuesday, June 06, 2017 4:43 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] (no subject)
>
> mri_convert is having a problem reading 1400composite.dcm. It is not
> even recognizing it as a dicom. Where did it come from and what is in it?
&g
-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve
[gr...@nmr.mgh.harvard.edu]
Sent: Tuesday, June 06, 2017 4:43 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] (no subject)
mri_convert is having a problem reading 1400composite.dcm. It is not
mri_convert is having a problem reading 1400composite.dcm. It is not
even recognizing it as a dicom. Where did it come from and what is in it?
On 06/06/2017 04:35 PM, Emily Rogers wrote:
> Apologies-- This email contains attachment. Thank you.
>
>
Apologies-- This email contains attachment. Thank you.
Hello,
I am trying to implement using Freesurfer segmentation in my analysis for MEG
data. I am trying to segment this structural MRI (1400composite.dcm) and I keep
getting errors. I hav
I could not follow what they did in the abstract. I don't think it is a
tool that we offer in FS. Try contacting them directly
On 05/25/2017 05:09 PM, Huang, Caleb (NIH/NINDS) [F] wrote:
> Hi all,
>
> I'm trying to figure out a way to do create seed-based structural
> covariance networks throug
Hi all,
I'm trying to figure out a way to do create seed-based structural covariance
networks through Freesurfer like the one shown in the link below. From the
images, it looks like it's done through QDEC. Any tips how to get started?
https://ww5.aievolution.com/hbm1601/index.cfm?do=abs.viewAbs
just erode it once using mri_morphology, then subtract it from the
un-eroded volume
On Tue, 16 May 2017, Gamaliz wrote:
Bruce,
I tried mris_fill, but it gives me a filled white matter volume (I already
have that in the mri directory. I need the contour only.
Douglas, Looking into the --help
Bruce,
I tried mris_fill, but it gives me a filled white matter volume (I already
have that in the mri directory. I need the contour only.
Douglas, Looking into the --help gave me a few ideas. I think the help page
(https://surfer.nmr.mgh.harvard.edu/fswiki/mri_surf2vol ) should include
this infor
96
Normal
0
false
false
false
EN-US
X-NONE
X-NONE
Dear all,
I am carefully starting up with the basics for analysis of 3T mri images.
After having done the recon all I am about to begin the review and editting
process where needed. However, I am now a bit overwhelmed. Is there any
logical or recommended order to proceed with the several potential
Also, what is this "old FreeSurfer 6". Are you referring to a beta?
On 02/07/2017 03:24 PM, Iglesias Gonzalez, Eugenio wrote:
> Dear Stephen,
> I would definitely rerun, for the sake of reproducibility. The results
> are sensitive not only to changes in the subfield module (which I
> believe I did
Dear Stephen,
I would definitely rerun, for the sake of reproducibility. The results are
sensitive not only to changes in the subfield module (which I believe I didn’t
modify in between your release and the final 6.0), but also to changes in the
main FreeSurfer stream. So, your results are diffe
Dear Dr. Iglesias,
Using the originally released version 6 (the one that was "unreleased") I ran
the recon -all -all and the subfield segmentations on a sample. I noticed that
the program was taken down then put back online after some updates.
Do you recommend we re-run these segmentations with
Hello:
I am using QATool in Freesurfer, and the script requires FS 5.1 and also works
for 5.3 which i am using, but when i run it, it always gives me error about
license:
ERROR: FreeSurfer license file /Applications/freesurfer/.license not found.
But FS 5.3 works fine with the license file lic
Hello FreeSurfer Developers,
I’m attempting to make some performances evaluation on recon-all using GPUs
on a node with 4 nVidia K80.
Submitting different instances of recon-all on 8 different subjects, every
instance run on the same device (#0), compromising the efficiency of the
test.
Is there a
Hi Sadhana, this has been answered several times. Are you not getting
the replies from the list?
On 12/16/16 6:13 PM, Sadhana Singh wrote:
Hello FreeSurfer Developers,
I'm running the recon-all on my subjects data as described in freesurfer tutorial (https://surfer.nmr.mgh.harvard.edu/fswiki/
Hello FreeSurfer Developers,
I'm running the recon-all on my subjects data as described in
freesurfer tutorial
(https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial), but it shows
the following error when I run the recon-all command:
ERROR: cannot find CON_101.nii
recon-all -s exited with ERRO
Hi Sadhana
did you not get the responses that Doug and I sent? Ceck to make sure you
are giving the actual full file name, with path and with .gz extension
(if it has that). Or just give it *one* file in the dicom series directly
and don't bother converting to nifti
cheers
Bruce
On Fri, 16 D
Try typing the full path to the CON_101.nii file
On 12/16/2016 02:05 PM, Sadhana Singh wrote:
> Hello FreeSurfer Developers,
>
> I'm running the recon-all on my subjects data as described in freesurfer
> tutorial (https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial), but it shows
> the followin
Hello FreeSurfer Developers,
I'm running the recon-all on my subjects data as described in
freesurfer tutorial
(https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial), but it shows
the following error when I run the recon-all command:
ERROR: cannot find CON_101.nii
recon-all -s exited with ERRO
Hi Sadhana
is the file CON_101.nii or CON_101.nii.gz? If the latter, you should give
that to recon-all. There is also no need to convert to nifti - you can
give recon-all a *single* file in the correct dicom series and it will
happily to its thing
cheers
Bruce
On Thu, 15 Dec 2016, Sadhana S
Is CON_101.nii in the/home/kumarlab/Downloads/Freesurfer_VBM folder? If
not, you must specify the full path to the the file
On 12/15/2016 06:26 PM, Sadhana Singh wrote:
> Hi
>
> I am using freesurfer for calculation cortical thickness in my subjects.
>
> Firstly, I have converted all the T1 weig
Hi
I am using freesurfer for calculation cortical thickness in my subjects.
Firstly, I have converted all the T1 weighted images from dcm into nii.gz
format.
After that, I have run the recon-all in one subject using this script
'recon-all
-i CON_101.nii -s CON_101 -all' , but it shows error
The
To get the t-score, compute the square root of the F, like
fscalc F.mgh sqrt -o t.mgh
You can then get the clusters with
mri_surfcluster --in t.mgh --thmin t-threshold --sign sign --no-adjust
--sum sumfile --ocn ocn.mgh
ocn (output cluster number) will be a map with the custer number as the
Hi Doug et al,
I would like to get a different cluster summary stat out of mri_glmfit-sim.
Rather than size, I'd like to use the "sum of t-scores" (after Maris &
Oostenwald 2007, for example). That is, set a cluster inclusion threshold,
and then for each cluster of adjacent vertices that clear the
Hello,
I made an analysis thanks to the QDEC tool :
I tested a correlation between an inhibition score and cortical thickness,
corrected for age
(continuous = inhibition score ; nuisance = age ; smoothing = 25 and FDR
corrected)
*** * ** *** * *** *** *** ** ***
Hi FreeSurfer experts,
I'm running a task-based analysis on mni305 space, running a regression of
load-dependent activation on RBC folate values, regressing out the effects of
age and gender.
The analysis runs fine, but when I visualize the sig.mgh map in tkmedit there
is a border of functiona
Hello,
As we know, Freesurfer generates separate surface models and associated
labels for each brain hemisphere, is there any way to merge two hemisphere
and come up with a single cortex surface?
My best,
Saeed
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Dear experts,
I would like to ask you for some advice about matrix.
I use FreeSurfer for automatic segmentation of infant brains and have a
problem with infants under 6 months. Could you give me advice what are the
optimal parameters of the matrix for automatic segmentation from newborns
to 6-month
Dear experts,
I would like to ask you for some advice about matrix.
I use FreeSurfer for automatic segmentation of infant brains and have a
problem with infants under 6 months. Could you give me advice what are the
optimal parameters of the matrix for automatic segmentation from newborns
to 6-month
Dear all,
I need to compute the geodesic distance (i.,e. the distance on the cortical
surface) between a series of vertices. Specifically, I want to compute the
distance between all the vertices in the right hemisphere (>10) and a
series of vertices of interest (around 2), always located
Hi Josh
the script recon-all will do everything you want. It is perfectly happy
with nii files as input and will generate surfaces and segmentations
including hippcampal labels. If you add one of:
recon-all --help | grep subfie
-hippocampal-subfields-T1 : segmentation of hippocampal subfiel
Hi, I’m new to freesurfer, I’m an undergraduate currently doing research
involving analyzing mri scans to produce volume measurements of the
hippocampus. I’ve been using FSL’s FIRST method to do this thus far, but from
what I’ve read online, freesurfer is much better for volumetric analysis of
It automatically performs highpass filtering using a 2nd order
polynomial. You can increase the order to make the cutoff higher. You
can also use cosine filtering to set up a bandpass filtering with -hpf
and -lpf as inputs to mkanalysis-sess
On 03/26/2016 06:11 AM, std...@virgilio.it wrote:
> H
Hi,I'm wondering whether the FS-FAST performed bandpass filtering.
Stefano
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The information in this e-mail is intended only for the pe
Thanks very much, I'll have a look!
On Fri, Feb 26, 2016 at 4:13 PM, Bruce Fischl
wrote:
> yes, they are documented pretty extensively on our wiki
> https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems
>
> On Fri, 26 Feb 2016, Maheen Siddiqui wrote:
>
> Hi,
>> Thanks for your reply. I hav
yes, they are documented pretty extensively on our wiki
https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems
On Fri, 26 Feb
2016,
Maheen Siddiqui wrote:
Hi,
Thanks for your reply. I have sought advice from someone who is experienced
in Homer2 atlas viewer.
Is it possible to find out
Hi,
Thanks for your reply. I have sought advice from someone who is experienced
in Homer2 atlas viewer.
Is it possible to find out the the coordinate system of the T1.mgz file and
the surface file created by FreeSurfer?
Thanks!
On Fri, Feb 26, 2016 at 3:36 PM, dgw wrote:
> Maheen,
>
> it soun
Maheen,
it sounds like a question that could be better answered by the Homer2 list.
hth
d
On Fri, Feb 26, 2016 at 8:13 AM, Maheen Siddiqui
wrote:
> Dear FreeSurfer Users,
>
> I have a head surface mesh and a pial surface mesh obtained after
> segmentation of a T1 MRI scan. I am going to importi
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