Dear Kiyotaka,
It is okay to distribute the buckner_data we post on our website for tutorial
purposes.
Allison
On Jan 8, 2018, at 6:35 AM, Kiyotaka Nemoto wrote:
> Dear FreeSurfer experts,
>
> We are planning to have a one-day neuroimaging workshop in Japan. One topic
> of the workshop is "F
the waiting list every time we held a
course so don't be dismayed if you end up on the waiting list.
Allison Stevens
Lab Manager/Course Organizer
FreeSurfer Development Team
Laboratory for Computational Neuroimaging
Massachusetts General Hospital
Athinoula A. Martinos Center for Biome
and will be notified if a spot becomes available. *Do not submit a payment
or make travel arrangements until you have received an email confirmation that
you successfully secured a seat in the course.
Allison Stevens
> Lab Manager
> FreeSurfer Development Team
> Laboratory for Comp
Hi everyone,
There is just a week and a half left before the deadline to sign up for
the FreeSurfer course being held in Copenhagen, Denmark on August 10th
through the 12th. The deadline is June 1st.
We still have a few places left! You can sign up for one here:
https://fscph.nru.dk/regis
course, please visit:
http://fscph2016.nru.dk/
Please feel free to contact my friends at NRU (cc'd) with any questions.
Allison Stevens
Lab Manager/Course Organizer
Laboratory for Computational Neuroimaging
FreeSurfer Development Team
___
Frees
Postdoc position at Martinos Center for Biomedical Imaging - Massachusetts
General Hospital / Harvard Medical School
The Laboratory for Computational Neuroimaging at the Martinos Center for
Biomedical Imaging has a job opening for a post-doctoral fellow to work on
modeling cortical layers and
Hi everyone,
There will be a FreeSurfer course held in Sao Paulo, Brazil on March 9th.
It will be taught by 4 of our FreeSurfer team members. Please see the Sao
Paulo section of our website for links to more information, who to
contact with questions, and how to register:
https://surfer.nmr.mgh
You could also add a lot more voxels to the wm.mgz (beyond what is wm) and
depending on the source of the problem, that could fix it.
On Mon, 3 Nov 2014, Bruce Fischl wrote:
Hi Christina
it's tough to tell from just a single image, but it looks to me like you are
missing a bunch of white mat
Hello everyone,
We have 8 spots remaining in our upcoming FreeSurfer course happening on
October 27-29. We will accept late registrations up to the course date;
however, since the payment deadline has passed, payment is due immediately
upon registration.
Details on the course and a link to the
n
On Mon, 29 Sep 2014, Allison Stevens wrote:
> Hello everyone,
> The next FreeSurfer Course will be held October 27th-29th at the Martinos
> Center in Charlestown, Massachusetts. Registration for the course is now
> open:
> https://surfer.nmr.mgh.harvard.edu/fswiki/CourseDescription
arrangements until you have received an *email confirmation* that you
successfully registered for the course.
Allison Stevens
Lab Manager
FreeSurfer Development Team
Laboratory for Computational Neuroimaging
Massachusetts General Hospital
Athinoula A. Martinos Center for Biomedical Imaging
Bldg. 149
; From: freesurfer-boun...@nmr.mgh.harvard.edu
> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Allison Stevens
> Sent: Friday, April 18, 2014 3:16 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: [Freesurfer] 2 available spots in Boston FreeSurfer course
>
> We have had some
We have had some last minute drop outs and there are now 2 spots available
in the upcoming Boston FreeSurfer course (May 5-7th). If you would like to
sign up for these spots, please register here:
https://surfer.nmr.mgh.harvard.edu/cgi-bin/fsurfer/register.8263.cgi
Note that credit card cannot b
FreeSurfer Course Copenhagen 2014
We are pleased to announce a European FreeSurfer Course that will be held from
August 11th to 13th 2014 in Copenhagen, Denmark. The course will be organized
by the Neurobiology Research Unit, Copenhagen University Hospital and the
Department for Computer Scienc
Please see the job descriptions at the following links:
https://surfer.nmr.mgh.harvard.edu/fswiki/ResearchAssistant
https://surfer.nmr.mgh.harvard.edu/fswiki/ResearchTechnologist
Allison
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://
Hi Saurabh,
That information is automatically calculated for you by FreeSurfer. You
can find more information about it here:
https://surfer.nmr.mgh.harvard.edu/fswiki/MorphometryStats
Allison
On Wed, 26 Feb 2014, Saurabh Thakur wrote:
Hi Freesurfer expert,
I am looking for just volumetric q
Hi Rujing,
If you are looking for the cortical thickness measures of a subject, you
can find it in that subject's freesurfer directory in the 'stats' folder.
In there, you will find a file called ?h.aparc.stats - one for each
hemisphere. Within the stats file, you'll see the Average thickness f
The entire hippocampus is currently labeled by default in the recon-all
stream. You can see it in the aseg.mgz (in the mri directory) and
find volume information in stats/aseg.stats.
To get the hippocampal subfields you have to run recon-all with an
additional flag. This is documented here:
Hi Rashmi,
You can find an explanation of the various measures we offer here:
https://surfer.nmr.mgh.harvard.edu/fswiki/MorphometryStats
Allison
On Fri, 13 Sep 2013, Rashmi Singh wrote:
> I am doing volumetric studies where instead of using ICV, I use total brain
> volume as a co-variate. This
ore the recon-all process exits with errors.
On Jul 8, 2013, at 1:37 PM, Allison Stevens Player wrote:
In short, the answer is yes. The 2nd and 3rd steps will take the subject ID and
find the relevant files. But I would expect the first step to take nifti just
fine. Can you send the command yo
In short, the answer is yes. The 2nd and 3rd steps will take the subject
ID and find the relevant files. But I would expect the first step to take
nifti just fine. Can you send the command you are running?
On Mon, 8 Jul 2013, Jonathan Holt wrote:
> As I'm having trouble importing nifti files in
That's correct.
On Thu, 14 Mar 2013, Mehul Sampat wrote:
Hi Folks,I was looking at the autorecon2-cp, autorecon-pial and autorecon-wm
flags in recon-all help and also here
http://surfer.nmr.mgh.harvard.edu/fswiki/OtherUsefulFlags
My interpretation is when I use autorecon-pial, I only need the
Hi Kev,
For the two scenarios you mentioned, here are my best estimates. I assume
a healthy, adult population scanned with our recommended sequences. Any
other type of dataset (pediatric, one with some type of pathology, one
acquired long ago using a less than optimal sequence or coil, etc.) wo
dicoms, and make that my last resort since it
> takes a day to complete.
> Thanks,
> m
> ________
> From: Allison Stevens Player [astev...@nmr.mgh.harvard.edu]
> Sent: Monday, May 14, 2012 3:16 PM
> To: Borzello, Mia
> Cc: freesurfer@nmr.m
n't open rh.orig.nofix and lh.orig.nofix. On the popup
> image, it doesn't look like the skull is present, but it does look like the
> cerebellum is.
> ____________
> From: Allison Stevens Player [astev...@nmr.mgh.harvard.edu]
> Sent: Monday, May 14,
freesurfer-boun...@nmr.mgh.harvard.edu
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Borzello, Mia
> Sent: Monday, May 14, 2012 1:37 PM
> To: Allison Stevens Player
> Cc: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] "cannot allocate memory" issue
>
> I
coms then?
>
> thanks,
> Mia
> ________
> From: Allison Stevens Player [astev...@nmr.mgh.harvard.edu]
> Sent: Monday, May 14, 2012 1:02 PM
> To: Borzello, Mia
> Cc: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] "cannot alloc
Hi Cat,
You'll need to rerun those subjects with 5.1 to be able to use the
longitudinal analysis in 5.1.
You can also find a detailed explanation on how to go about edits here:
https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalEdits
Allison
On Wed, 18 Apr 2012, Cat Chong wrote:
Dear F
Hi Jordan,
I'm not sure I understand your question. If you run -make all, it will run
recon-all again starting at the earliest step in which there are files that
were changed that affect that step. It will run all the way through to the end
as each step affects the next one. This will change you
Anthony,
Depending on what version of FreeSurfer you are running, you would have to
run the command it would normally run to create the aseg but substitute in
your atlas.
For example, in v5.1:
https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllTableStableV5.1
You can see the step next to -cala
You can make a copy of the LUT and remove all regions from it you don't want to
see. Then when you load you volume, specify you want to use this new LUT and
you will only see the ROIs in it.
Allison
On Apr 12, 2012, at 11:40 PM, Adil Javed wrote:
> Hi,
> is there any way to overlay only certai
Julia, could you send a snapshot of the area in question?
On Apr 2, 2012, at 5:33 AM, "Richter, Julia"
wrote:
> Dear freesurfer experts,
>
> I have several subjects whose cortical grey matter isn't included in the pial
> surface. Is there any possibility to correct the pial surface? I added
Hi Darshan,
There are instructions on how to do this here:
https://surfer.nmr.mgh.harvard.edu/fswiki/UserContributions/FAQ#Q.Ihavealreadyskull-strippeddata.CanIsubmitittorecon-all.3F
Allison
On Tue, 27 Mar 2012, Darshan P wrote:
I have an MRI volume dataset, which is deskulled beforehand .
Is
Hi everyone,
We had a last minute drop-out from our Boston FreeSurfer course which
takes place April 2nd through the 4th. If anyone is interested in taking
this spot, please let me know.
Details about the course content, the registration fee, and other
logistics can be found here:
http://surfer
Hi everyone,
The Department of Radiology at VU University Medical Center in Amsterdam,
Netherlands is hosting a FreeSurfer Course on June 27th through June 29th.
Registration is now open. You can find details about course as well as the
registration form on the following website:
http://www.free
Although the white surface finds its place based on intensity, it's starting
point is the wm.mgz. So if there are no voxels in the wm.mgz in the area you
mention, drawing in some voxels combined with the intensity changes that come
from the control points may help.
Allison
On Mar 12, 2012, at 6
> recon-all -s P102_corr exited with ERRORS at Fri Mar 2 14:23:15 CET 2012
>
> For more details, see the log file
> To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>
> Best,
> Martijn
>
> On Fri, Mar 2, 2012 at 2:15 PM, Allison Stevens P
Hi Martijn,
autorecon-cp is correct, we start the process a bit earlier now. But even
better, regardless of what edits you make, you can rerun with "recon-all -make
all" and it will start at the earliest needed step. (Although running from
autorecon2 after the skullstrip fix is correct as well).
g volume to the MNI305 atlas, so the spatial
> normalization in FreeSurfer is still done in volume space but not in surface
> space, right?
>
> Best,
> Xiangyu
>
> On Fri, Feb 24, 2012 at 5:20 AM, Allison Stevens Player
> wrote:
> Maybe you can apply the tran
Maybe you can apply the transform using mri_convert or mri_vol2vol created
during autorecon1. Is that what you are looking for?
http://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllDevTable
On Feb 22, 2012, at 11:26 AM, Long wrote:
> Dear all,
>
> I had EPI images and T1 image and the EPI images
Vincent,
Some may look like holes but as you mention are just sulci being cut through by
that plane.
A way to check if it is the above is to put the cursor on the surface that
creates this hole and then toggle to the other views (sagittal, axial,
coronal). It will become clearer whether it is
I don't think there is any other way. Is the talairach really that bad in all
of your data? It won't recon without fixing it?
On Feb 22, 2012, at 6:17 PM, cloud.c...@me.com wrote:
> After reading the tutorial at
> http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach, I understand
> th
Okay, I'll take a look.
Allison
On Mon, 17 Oct 2011, Jordan Pierce wrote:
We've uploaded the file as 30193retry.tar.gz
Jordan Pierce
___
___
Freesurfer mailing list
Freesurfe
Hi Heather,
The cerebellum is not included in 5.1's total subcortical gm or total gm
volumes. Let me double check on what is included in the subcortical gray
matter total volume.
Allison
On Mon, 3 Oct 2011, Lugar, Heather wrote:
> Can you please tell me if the cerebellum is included in Freesurf
Hi Torsten,
I believe we have this on our to do list for tkmedit fixes.
Allison
On Tue, 4 Oct 2011, Torsten Ruest wrote:
> Hi there,
>
> I was wondering whether there is better option to resize the tkmedit
> window: when I drag it bigger, it appears that the same change in aspect
> ratio is app
Hi Torsten,
If you run:
recon-all -all -clean-bm -s subjid
This should trask all the edits you made to the brainmask volume and make
a new one to replace that. It will keep all your other edits.
Allison
On Tue, 4 Oct 2011, Torsten Ruest wrote:
> to correct the pial surface for incorrect assignm
There is some white matter there being excluded as well. If you include that,
the pial surface will likely grow out and include that gm.
On Aug 1, 2011, at 7:37 AM, _andre...@sapo.pt wrote:
> Dear FS experts,
>
> I'm correcting the pial surface when it includes more than it is supposed,
> but
Hi Antonella,
When you load the files that those buttons are associated with, then they
become active. When you loaded the orig surfaces, the orig surface button
still was not active?
If you choose any button besides the Navigate button, when you left click,
that will move the cursor (red cro
If it is, you can try running the skullstrip step a second time.
On Jul 20, 2011, at 7:14 PM, Bruce Fischl wrote:
> Hi Michael,
>
> if cerebellar gray matter is not something you are terribly interested in
> quantifying then you are fine.
>
> cheers
> Bruce
>
> On Wed, 20 Jul 2011, Murray, M
Hi Brian,
Meet Andre who I believe can help you.
Allison
On Wed, 20 Jul 2011, Brian C. Schweinsburg, Ph.D. wrote:
> Hi Folks,
> I noticed in the multiecho portion of the freesurfer wiki that it says
> custom multiecho sequences are available from Martinos for use.
> I was wondering who I might c
Fatima,
I can't really say anything on this topic but I did want to point you to
some information on FreeSurfer vs. VBM:
http://surfer.nmr.mgh.harvard.edu/fswiki/UserContributions/FAQ#Q.WhataretheadvantagesofFreeSurferoverVBM.3F
Allison
On Fri, 8 Jul 2011, Ahmed, F, Me wrote:
> Hello,
>
> I'm
Hi Antonella,
I found similar problems in the FreeSurfer mailing list archives:
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg07366.html
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg03433.html
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg07130.html
Hi Joel,
Can you send Khoa (cc'd) the case and we'll look at what might be going on
and then give you pointers on editing strategy?
Directions are here:
https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange
Allison
On Fri, 3 Jun 2011, Joel Bruss wrote:
> I have a subject run through recon-
Registration is not open yet and that date is tentative. Once the date is
confirmed and registration open, an email will be sent out to the Course
mailing list which has a link on the top of the Course Description wiki.
Allison
On Fri, 27 May 2011, Eisenstein, Sarah wrote:
> Does anyone know ho
Which version of FreeSurfer are you using? In the more recent versions, they
are the same. Cortical White Matter is all the white matter contained within
the white surface minus the subcortical gray matter and ventricles, etc.
On May 20, 2011, at 7:37 AM, "Righart, Ruthger Dr."
wrote:
> Dear
You can unsubscribe here:
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
On Thu, 12 May 2011, Krista Kelly wrote:
> How do I stop receiving emails from everyone asking and responding to
> questions about FreeSurfer?
>
___
Freesurfer mailin
When you look at the case in tkmedit, in that same area, do you see an error?
Looking at your snapshot, it looks like it could be normal.
On Apr 26, 2011, at 8:45 AM, Tetiana Dadakova wrote:
> Dear FreeSurfer list,
>
> When I look at inflated surface of my subjects (healthy males and
> females
yep that's a typo. sorry!
On Apr 25, 2011, at 9:22 PM, Bruce Fischl wrote:
> yes, I think that's a typo and should be autorecon2. Perhaps Nick can
> confirm?
>
> On Mon, 25 Apr 2011,
> Xiaoying Tang wrote:
>
>> Hi All,I find the following content on the wikipage of freesurfer:
>>
>> Q. I ha
Hi Sarah,
Nick will be out of the office until next week. I would suggest just
trying to run the default gcut and if you find you need to tweak it a bit,
doing mri_gcut --help will describe the parameter (-T) that you can adjust
for a cleaner skullstrip. You could also run -skullstrip a second t
Hi Sean,
Yes, we can help. Best would be to upload the subject and Khoa can take a
look. She can give you additional instructions if needed.
Allison
On Mon, 18 Apr 2011, Seán Froudist Walsh wrote:
Dear FreeSurfer gurus,
I have T1 scans of a patient at three different time-points (one run at
Sorry, I meant not in 5.0.
On Fri, Apr 15, 2011 at 19:29, Allison Stevens
wrote:
John,
Tracula is available in the soon to be released 5.1 but not in 5.1.
Allison
On Fri, 15 Apr 2011, John Fredy wrote:
Hello all
I am doing the tutorial about tracula (
http://surfer.nmr.mgh.harvard.edu
John,
Tracula is available in the soon to be released 5.1 but not in 5.1.
Allison
On Fri, 15 Apr 2011, John Fredy wrote:
Hello all
I am doing the tutorial about tracula (
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula), but I can`t
find the trac-all command in my system. I was run
Hi Michael,
With 5.0, gcut is run by default I believe. If you look at the
recon-all.log for that subject and search for gcut, you should be able to
see if it ran.
Allison
On Thu, 7 Apr 2011, Dougherty, Michael wrote:
> Hello all,
> I would like to take advantage of the gcut feature to remove d
Hi Saad,
Since there is no message indicating it stopped due to error, I would try
running it again as it most likely stopped due to the machine it was running
on. You can pick up where it left off by doing:
recon-all -make all -s mysubject
On Apr 7, 2011, at 12:25 AM, Saad Ramadan wrote:
> De
Hi Jose,
I believe we just got rid of redundant information. The subcortical
structures are in the aseg.stats and don't need to be in the wmparc.stats.
On Wed, 6 Apr 2011, Jose Soares wrote:
> Hi all,
>
> I am working with FS 4.5 and 5.0 and I have noticed that in wmparc.stats in
> 5.0 there ar
al surface failed to include the
> added wm voxels in. Pls see the attachment. Does anyone encounter the same
> thing before? Thank you for advice!
>
> Min
>
> On Thu, Mar 31, 2011 at 1:11 PM, Allison Stevens <
> astev...@nmr.mgh.harvard.edu> wrote:
>
>> Hi Min,
Hi Min,
We've learned that -autorecon2-cp might not be doing what was intended.
Try runing -autorecon2 and see if it fixes everything.
Allison
On Thu, 31 Mar 2011, Min Liu wrote:
> Dear Freesurfer users,
>
> My first run of recon1&2 left some white and grey matter at temporal pole
> region exclu
You can just rerun autorecon2 and autorecon3. If you save it as aseg.mgz, it
will recognize edits were made when you rerun.
On Mar 30, 2011, at 7:51 AM, Tetiana Dadakova wrote:
> Dear FreeSurfer list,
>
> I am making some manual correction to subcortical structures using
> Edit Segmentation To
You can run the old command and then start the processing from that step on I
think.
On Mar 30, 2011, at 4:23 AM, Nikolas Borrel-Jensen
wrote:
> Hello!
>
> I have found a solution for the problem causing the bad registration.
>
> In Freesurfer 5.0, the function mri_robust_template is used
Amir,
We now have SupraTentorial which is the volume of Cortex +
Cortical White Matter + Subcortical Gray Matter. I don't think there is an
exact equivalent for BrainSegVol.
Allison
On Fri, 18 Mar 2011, Amir Tahmasebi wrote:
>
> Hi,
>
> BrainSegVol and BrainSegNVoxare removed from the newest ve
Hi Allison,
Can you send me the link to the wiki page that says that?
To my knowledge, you can only undo the very last edit you made in tkmedit
and that is by going to Edit > undo.
With freeview, you can select undo as many times as you'd like.
Allison
On Wed, 16 Mar 2011, Nugent, Allison C. (N
Hi Nadia,
You can follow instructions on how to check data using our tutorials:
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/OutputData
and
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TroubleshootingData
Allison
On Tue, 15 Mar 2011, nadia merhoum wrote:
> Hello
>
> I have just
Tibor,
We are working to put some exvivo wm segmentation methods into the next
FreeSurfer release although I'm not sure where that stands. We do process
our exvivo scans with FreeSurfer but we use scripts that use different
parameters than recon-all since the contrast is different and as you sai
Allie,
It's hard to tell from that one slice but the pial surface grows out from
the wm surface so most likely, in order to fix that error, you will have
to find where the white surface is inaccurate and add or remove voxels on
the wm.mgz.
Allison
On Fri, 11 Mar 2011, Allie Rosen wrote:
> Hi,
That flag is needed if your input is larger than the required size by
FreeSurfer 256x256x256. You would not use it on input that did not require it
(ie it is smaller than 256x256x256).
On Mar 10, 2011, at 4:53 AM, Kenichiro Tanaka wrote:
> Hello All,
>
> I have a question about recon-all co
Sorry, Pom - the course is full. You can sign up for the course mailing
list to hear about upcoming courses:
http://surfer.nmr.mgh.harvard.edu/cgi-bin/fsurfer/interest.cgi
Allison
On Fri, 25 Feb 2011, Pom Sailasuta wrote:
> Hello,
>
> Is it too late to register for the April tutorial course at
Hi Fabrizio,
You can use mri_extract_label for this. You need to specify the index
number of the structure which you can find here:
$FREESURFER_HOME/FreeSurferColorLUT.txt
On Tue, 15 Feb 2011, fabrizio piras wrote:
> Dear FS experts,
> I run recon all on several patients, manual edited all the o
'save main volume as' as directed in the recommended recon workflow.
>
> Thanks,
>
> Cheryl
>
>
> On 1/31/11 7:05 PM, "Allison Stevens" wrote:
>
>> Hi Cheryl,
>> 1) Yes, just use save not save as
>> 2) this information is already genera
Hi Cheryl,
1) Yes, just use save not save as
2) this information is already generated and can be found in the
aseg.stats in each subject's stats dir. Some of the information is at the
top of that file.
On Mon, 31 Jan 2011, Cheryl McCreary wrote:
> Hi,
>
> I'm new to Freesurfer and am trying to
Rong,
You should wait until 5.1 comes out and use that to rerun your
cross-sectionals (which will have to be rerun to match a newer version)
and use that longitudinal stream which will be the most reliable.
Allison
On Thu, 23 Dec 2010, rong chen wrote:
> Hi,
> I want to use FreeSurfer to analyz
undary of this mask?
>
> Thanks for the help.
> Luke
>
> On 12/22/2010 04:35 PM, Allison Stevens wrote:
>> Hi Luke,
>> For subcortical structures, you would want to use the volume information
>> provided by the aseg.mgz and not information from the surfaces (which
Hi Luke,
For subcortical structures, you would want to use the volume information
provided by the aseg.mgz and not information from the surfaces (which are
intended for cortical measures).
Allison
On Wed, 22 Dec 2010, Luke Bloy wrote:
> Hello,
>
> I'm new to freeSurfer and just starting to look
Would the wmparc.mgz work for this? It should be in the mri dir.
--
On Fri, 10 Dec 2010, Ingalhalikar, Madhura wrote:
> Hi,
>
> Is there a way to get the cortical parcellations projected onto the WM
> boundary? I need to seed the boundary of the cortical ROI ( in WM) for fiber
> tracking.
> P
Could you let me know what version you are running and the full
asegstats2table command?
To put it in Excel, I open Excel first then go to File > Open, select the
.txt file created by using asegstats2table (I've never used the -delimiter
flag) and from there a box pops up where you can choose s
What version are you using?
--
On Thu, 9 Dec 2010, Jennifer Addicks wrote:
> Hello,
> I manually edited the aseg.mgz file for one of my participants, I was
> wondering if someone could tell me how to rerun the recon-all to
> ensure that these changes are incorporated in future steps and
> stati
You want to make sure you are placing the control points only on wm voxels
that are < 110 and wm voxels that are at least 1 voxel away from a gm
voxel in all directions.
If you'd like, you could send me a snapshot of where you placed the
control points and I can give you feedback on that. You a
Andreas,
Could you send us one of these subjects so we can take a look?
Allison
--
On Mon, 22 Nov 2010, Andreas Berger wrote:
> Hello Surfers,
>
> we just finished processing our subjects (recon-all -all) with freesurfer
> version 5.0. In 16 out of 240 subjects i found severe errors: in about
Looks like there is wm missing from the white surface as well. If you fix
that, it will fix the pial surface. You would want to edit the wm.mgz.
Allison
--
On Mon, 22 Nov 2010, xuemei lei wrote:
Hi
I have ran the recon-all using Freesurfer 5.0 version. And I found some GM
tissue exluded from
Suzanne,
You could try running different watershed thresholds to see if it fixes
the problem without having to clone it in:
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/SkullStripFix
Allison
--
On Fri, 19 Nov 2010, suzanne oosterwijk wrote:
> Hi,
>
> I have been running recon1 recently
Jeff,
Yes, you would only want to take it from the aseg.stats. I believe this is
fixed or on the list to be fixed for future versions.
Allison
--
On Fri, 12 Nov 2010, Jeff Sadino wrote:
> bump :)
>
> On Tue, Nov 9, 2010 at 11:38 AM, Jeff Sadino wrote:
>
>> Hello,
>>
>> When I look at the Brain
Hi Kristina,
You can find the answer to your question here:
http://surfer.nmr.mgh.harvard.edu/fswiki/UserContributions/FAQ#Q.IgetanerrormessagefromtheTalairachFailureDetection.Whatdoesthismean.3F
As a new user, you might find that FAQ helpful.
Allison
--
On Wed, 3 Nov 2010, Rapuano, Kristina (N
You can although we generally advise against it (it's best to try
automatic fixes first). What is not correct about the hippocampal
segmentation?
--
On Thu, 28 Oct 2010, antonio cerasa wrote:
> Dear FS experts,
>
> I 've question concerning the automatic subcortical labelling provided by FS.
>
r wm only cortical volumes are present. Is there no
> subcortical wm volume present or defined?
>
> Ed
>
> On 27 Oct 2010, at 15:58, Allison Stevens wrote:
>
>> Ed,
>> I would use the values in the aseg.stats. I'm not sure why there is
>> this
>>
Ed,
I would use the values in the aseg.stats. I'm not sure why there is this
difference (Doug might be able to elaborate on how the values in
aseg.stats are calculated) but for v5.0, we went over how all the stats
were being calculated and make sure the values in the aseg.stats were the
most ac
Alice,
You might find this tutorial helpful:
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultiModalFmriIndividual
and mri_volcluster or mri_surfcluster
Allison
--
On Tue, 26 Oct 2010, Alice Albrecht wrote:
> Hi Everyone,
>
> I'm new to freesurfer so I apologize if my question ha
What does it say in transforms/talairach_avi.log?
--
On Thu, 14 Oct 2010, Maria Luisa Mandelli wrote:
> Hi!
>
> I get this error running recon_all
>
>
> Applications/freesurfer/bin/talairach_avi --i nu.mgz --xfm
> transforms/talairach.auto.xfm
> ERROR: mpr2mni305 failed, see transforms/talairac
None should be the first label in the FreeSurferColorLUT.txt (it's labeled
as "Unknown" with an ID# of 0). But really you should be labeling it what
it truly is. Is this the gray matter you are labeling as CSF?
--
On Thu, 7 Oct 2010, Wang, Xin wrote:
> one more question: I replace the mislabe
Nathan,
You can find that info here:
https://surfer.nmr.mgh.harvard.edu/fswiki/SystemRequirements
--
On Thu, 7 Oct 2010, Nathan Dankner wrote:
> Hi all,
>
> I was curious as to approximately how much memory is required to run a
> surface through autorecon 1 and 2, and autorecon 2 and 3. I'm ru
You can try to add voxels to the wm.mgz in the area that you know is wm.
If that's already there or you tried that already, let us know.
Allison
--
On Wed, 6 Oct 2010, Soon Hock Wei wrote:
Dear All:
Just to follow up with my previous enquiry, is there any suggestion/advice over
this pial ed
Mustafa,
There are a couple of relevant pages with information on this.
These:
http://surfer.nmr.mgh.harvard.edu/fswiki/PALS_B12
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg13908.html
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg04901.html
Allison
--
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