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
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
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 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
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
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://
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
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
; 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
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
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
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
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
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
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
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
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
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
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
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
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 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
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 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
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
It would be pbsubmit and would only work if you are logged into
seychelles.
On Thu, 2 Oct 2008, Jared Price wrote:
Hi everybody, this is Jared over at the Brigham. Quick question for anyone
who knows. I am trying to rebuild a subcortical atlas using the script
rebuild_gca_atlas.csh. When
It's the volume created after the first normalization and skull stripping.
Allison
On Wed, 12 Nov 2008, Alexa Nardelli wrote:
Hey, I was just wondering if the brainmask.mgz file is the image after
normalization?
Thanks
Alexa
___
Freesurfer mailing
recon-all will copy the brainmask.auto.mgz to the brainmask.mgz so they
should be the same.
Allison
On Tue, 2 Dec 2008, Barkay, Gavriel wrote:
Hi,
I ran recon-all -all crashed for reasons unrelated to FreeSurfer. I re-ran the
analysis without -clean.
Is the new skull stripped volume stored in
Kelly,
The aseg looks good to me (as far as just those two slices go - of course
you would need to check every slice). I'm not sure I understand your
question about separating them. As far as FreeSurfer's goal, this looks
like a good result.
Allison
--
On Tue, 13 Jan 2009, Kelly Silva wrote:
You do not need to manually separate the cerebellum from the cortex if the
pial surface is accurately following the cortex (as it's doing in the
pictures you sent). In fact, deleting too much cerebellum might cause
other problems. Do you have any other reason why you want to separate
them?
All
The mean curvature for that particular parcellation.
There is a slide demonstrating curvature here:
https://surfer.nmr.mgh.harvard.edu/fswiki/ArticlesSlidesAndPosters
Under the Slides section, the one called "Anatomical Analysis with
FreeSurfer". It's slide #14.
--
On Tue, 27 Jan 2009, Vina
Kelly,
For your first question, how are you erasing it? The only way to change
the label of a voxel in the segmentation is to call it another label -
there is no real "erase" option as there are with white matter edits.
If you want to change the label of the voxel, you will need to choose
anot
I will edit the wiki page - I believe it is wrong. You cannot erase a
segmentation by using the 3rd mouse button. In order to erase, you
actually have to re-draw what the underlying segmentation was originally.
If you are working on the aseg.mgz and plan to save your edits as
aseg.mgz, to "era
Zhen Zonglei wrote:
The log files from both version 4.03 and version 4.30 report this error(
t4_read: talsrcimg_to_711-2C_as_mni_average_305_t4 read error ). It occurs
in imgreg_4dfp.
attachment is my logfile,please check it.
2009/4/17 Allison Stevens
What version of FreeSurfer are you usin
recon-all -all will take approximately 30 hours. It depends on the quality
of your data and how many errors need to be fixed.
Allison
--
On Wed, 29 Apr 2009, Elina Pitri wrote:
Hello Freesurfer Creators,
I am wondering how much time should Volume and Surface processing (using
recon-all comm
ly erasing
some voxels, so I think I will stick with it.
Thanks in advance,
Regards,
Falk
-Original Message-
From: Allison Stevens [mailto:astev...@nmr.mgh.harvard.edu]
Sent: Tuesday, May 19, 2009 5:38 PM
To: Nick Schmansky
Cc: Falk Lüsebrink
Subject: RE: [Freesurfer] mri_fill
Falk,
I c
Iwo,
If you do
ls $FREESURFER_HOME/bin
Do you see mri_nu_correct.mni there?
If you do, this message might help you:
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg06793.html
Essentially, you have to make sure the nu_correct uses perl so you need to
make sure it knows where it's
You can find this information in:
/stats/?h.aparc.stats
Allison
--
On Fri, 29 May 2009, Zhangyuanchao wrote:
Dear Mr or Ms
Is there any way that we can obtain curvature value of the pial surface? I am
not sure whether lh.curv is the curvature file that I want. How can I calculate
the me
Dana,
I believe you can achieve this by running recon-all on the subjects with
the -norandomness flag. Unless you are using a version of FreeSurfer that
is older than v3.0.4 - let me know if you are.
--
On Mon, 15 Jun 2009, Dana W. Moore wrote:
Hi all,
I have run the same image twice with
Hi,
This is a bug in an older version of FreeSurfer. What version are you
using? Can you upgrade to a newer version?
Allison
--
On Tue, 16 Jun 2009, Sharmili 57 wrote:
hey,
Loading aparc.a2005s.thickness i get the attached error message.
Does anybody know how to solve this proble
Antonio,
Can you describe what qdec is showing that's wrong or send a screenshot of
it?
Thanks,
Allison
--
On Thu, 18 Jun 2009, free_sur...@virgilio.it wrote:
Dear Freesurfer users,
We are experiencing a problem using Qdec (FS version
4.2.0; Qdec 1.0) for group data analysis.
Indeed, the qde
I looked at the revision history of the wiki and it shows a change to
"-tp" so I believe that is the correct one to use. However, I was able to
run both versions without error. When Nick returns, he can confirm but I
think you should be fine using -tp.
Allison
--
On Fri, 19 Jun 2009, Dabbs (
Sure. Since that release was on 11-25-06, I will send you the last edited
version of that page before that date (on 8-22-06) unless I find the
latest version without all the changes.
Allison
--
On Mon, 29 Jun 2009, Bruce Fischl wrote:
I'm not sure we have it so easily. Does anyone know?
On M
Rosa,
I'm not sure, but the last time someone wrote about this error message,
the problem was that they had more than 2 levels for one of their factors.
By any chance, did you have more than two for the factor you included in
these designs?
--
On Mon, 6 Jul 2009, Rosa Steimke wrote:
HI!
W
The newest version of FreeSurfer does not contain any changes to qdec I
believe.
Allison
--
On Thu, 9 Jul 2009, Prapti Gautam wrote:
Dear Freesurfers,
I just have some quick questions regarding qdec:
1. How many covariates does the latest version of qdec allow you to
select? I am
What areas are these where the pial is not extended enough?
In general, the pial surface might extend further if the white surface is
extended further but you would only want to do that if wm was also being
left out of the white surface.
On Tue, 14 Jul 2009, Devdutta W wrote:
Hi,I have been
Are you opening them from the same terminal window? If so, one is running
in the background and so you will not be able to use it.
Open each from a different terminal window.
--
On Wed, 15 Jul 2009 yzha...@artsci.wustl.edu wrote:
Whenever i try to open two windows(ie.' tkmedit bert orig.mgz
The parcellation is created using the surfaces and a cortical atlas so you
shouldn't have to worry about the subcortical segmentation overlabeling
like that. Take a look at the aparc+aseg.mgz in tkmedit.
--
On Fri, 4 Sep 2009, Kim, Miyoung wrote:
> Hi.
>
> Just a quick question - is cortical
You only need to use the flag -wmparc.
Allison
--
On Fri, 2 Oct 2009, Andrew Jahn wrote:
> Hello,
>
> I recently ran a batch file on several subjects, but set a time limit which
> prevented some of them from finishing all the steps of recon-all. In the
> recon-all-status.log for some of them, t
If they are gray, it means you have not made any edits to the main volume
yet (so there is nothing to be saved). The main volume is whichever volume
you loaded into tkmedit first. If you made edits to the second volume (the
aux volume), you have to save those changes by choosing "Save Aux Volume
It is difficult to tell from one slice and one view what is going on but
in general you can only get the pial boundary to extend more by extending
the wm boundary (but of course, only where there is actual wm). The pial
boundary grows out from the wm boundary so if the wm boundary is
incorrect,
It usually says that if your SUBJECTS_DIR is not set to the correct
location.
Try doing:
echo $SUBJECTS_DIR
and see if it is the path to where your data is located.
Allison
--
On Tue, 10 Nov 2009, nluc...@artsci.wustl.edu wrote:
> I have recently (in the past week) started receiving the fol
It's a little bumpier than usual but ultimately you would have to look at
the surfaces in tkmedit to determine whether these are errors.
Allison
--
On Fri, 4 Dec 2009, Jesse Bledsoe wrote:
> Hi experts,
>
> Should I be concerned about the number of white matter errors in the
> attached tif? I
Hello,
The Freesurfer group will be offering a two-day Freesurfer Tutorial and
Workshop on February 1st and 2nd at the Martinos Center in Charlestown,
MA.
A description of the February course and a list of the topics covered can
be found on the Course wiki page here:
http://surfer.nmr.mgh.har
Guang,
Without seeing the recon-all logs, I'm not exactly sure what happened but
running "recon-all -s" wouldn't have finished running the processing
stream so you would be comparing unfinished data to finished data.
--
On Tue, 8 Dec 2009, Guang Zeng wrote:
>
> Hi, there,
>
> I submit several
It looks like there might be some wm that is not labeled as wm. If you fix
this first (by adding wm to the wm.mgz or adding control points if it is
an intensity problem), that should fix the pial surface.
--
On Wed, 24 Feb 2010, Gonzalo Rojas wrote:
> Hi:
>
> How can I correct the pial surf
f Radiology
Las Condes Clinic
Lo Fontecilla 441, Las Condes, Santiago, Chile.
Tel: 56-2-2105170
Cel: 56-9-97771785
www.clc.cl
El 24-02-2010 14:55, Allison Stevens escribió:
It looks like there might be some wm that is not labeled as wm. If you
fix this first (by adding wm to the wm.mgz or adding co
Xiaoying,
You can find information about changing the skull strip thresholds on this
wiki:
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/SkullStripFix
The wmparc.mgz has the wm parcellated and labeled according to the closest
cortical (gm) region. The aparc+aseg.mgz will show you the gm r
Hi Helen,
That's a good question. You don't have to start at autorecon1, however.
When you run -autorecon2-wm or -autorecon2-pial one of the first steps is:
mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz
which is changing the brain.finalsurfs.mgz to take into account the
changes yo
Liang,
mri_annotation2label will separate all the ROIs in the
?h.aparc.a2009s.annot - is this what you need? I'm not sure what you mean
by "mask image based on this image using 1, 2". You can merge or split
labels as well.
To display aparc.a2009s+aseg.mgz in tkmedit, you can do:
tkmedit subjid
from BOLD fMRI scanned from the same
> subject. Can you give some advice how to accurately make it. Also, I am
> worried the registeration issues across different modality images.
>
> Best,
> Liang
>
> 2010/3/11 Allison Stevens
>
>> Liang,
>> mri_annotation2l
Xiaoying,
There are directions for how to do this located here:
https://surfer.nmr.mgh.harvard.edu/fswiki/UserContributions/FAQ?highlight=%28FAQ%29#SkullStrippingOptions
Allison
--
On Fri, 12 Mar 2010, Xiaoying Tang wrote:
> Hi all,
>
> When we do recon-all, we usually do autorecon1, autorecon2
Ed,
Usually a problem with the pial surface indicates a problem with the white
surface and fixing the wm.mgz will fix the pial. But you said the wm
segmentation is okay in the areas where the pial is a problem?
What area of the brain are you finding this problem?
Allison
--
On Fri, 12 Mar 201
Liang,
You can find instructions on how to do this here:
http://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat
Sometimes using mri_convert will cause the orientation to be off so you
may want to follow those instructions instead.
Allison
--
On Sat, 13 Mar 2010, Bruce Fischl wrote:
> H
I am
>> curious
>> why I can not directly find this website from the main interface
>> http://surfer.nmr.mgh.harvard.edu/fswiki. Is there a website listing all
>> the
>> great links. Thanks.
>>
>> Liang
>>
>> 2010/3/15 Allison Stevens
Guang,
You'll want to use aseg.stats over wmparc.stats for those values.
Allison
--
On Tue, 16 Mar 2010, Guang Zeng wrote:
>
> Hi, there,
>
> I have a question about wmparc.stats and aseg.stats,
>
> In aseg.stats, I read,
>
> # Measure BrainSegNotVent, BrainSegVolNotVent, Brain Segmentation Vol
Dave,
Yep, if it looks okay, just run with -notal-check.
Allison
--
On Wed, 17 Mar 2010, Dave Brohawn wrote:
> Hello,
>
> I am working on unpacking a subject scanned in Bay 8 on Thursday, 3/11/2010.
>
> I entered recon-all -autorecon-all -s FB0011090A
>
> and after unpacking for approximately 4
Try running this:
recon-all -skullstrip -no-wsgcaatlas -s
If that goes through without error, you can finish processing your data by
running:
recon-all -autorecon2 -autorecon3 -s
Allison
--
On Wed, 17 Mar 2010, Gabriel Go.Es. wrote:
I was trying to run a recon-all and I recibe an error
Lindsay,
I think this wiki page might help:
https://surfer.nmr.mgh.harvard.edu/fswiki/tksurfer_labeledit
Allison
--
On Tue, 16 Mar 2010, Lindsay Lewis wrote:
> hi,
>
> I am trying to manually draw a "grid" of many small ROIs/labels on an
> occipital flattened surface patch in tksurfer, and am h
Kelly,
I believe they are in Talairach space. Information on how to get them in
MNI space is located here:
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg10038.html
Allison
--
On Fri, 19 Mar 2010, Kelly Silva wrote:
Hello,
I would like to know if the output coordinates
Guang,
Working in tksurfer, be sure to first do to Edit > Deselect Label and
Edit > Unmark all Vertices just to make sure nothing else is chosen besides the
4 vertices you are interested in (unless you are sure that's all you have
clicked on). Then click on the 4 vertices you want to mark. After
Ronald,
This looks correct for now. I believe Martin is working on a way to make
this easier for the future.
Allison
--
On Tue, 23 Mar 2010, Pierson, Ronald K wrote:
> I apologize if this has been covered before, but I wanted to make sure I
> understand the best way to edit at the appropriate
Something like that I would say you usually have to manually edit.
Allison
--
On Fri, 26 Mar 2010, Andreas Berger wrote:
> hello freesurfers,
>
> we are having a problem with insufficient skull stripping, in 66 out
> of 200 subjects this affects the pial surface, as can be seen in the
> attache
John,
Information on editing the aseg is here:
http://surfer.nmr.mgh.harvard.edu/fswiki/TkMeditGuide/TkMeditWorkingWithData/TkMeditSegmentations
We generally advise against it if possible - what areas need editing?
Allison
--
On Thu, 1 Apr 2010, John Fredy wrote:
> Hello all,
>
> I'm trying t
Janani,
For the Failure Detection error, please take a look here:
http://surfer.nmr.mgh.harvard.edu/fswiki/UserContributions/FAQ#Q.IgetanerrormessagefromtheTalairachFailureDetection.Whatdoesthismean.3F
and
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg07958.html
For your other ques
Sherri, It's better if you compress the entire subject's directory and
send that.
In general, you can erase things from the pial surface but you can't add
things to it. You can only get the pial surface to grow out more by
changing the white surface (either through control points or adding voxe
Krishna,
How have you processed this data? Have you used any of the suggested flags
and/or parameters for monkeys?
See:
https://surfer.nmr.mgh.harvard.edu/fswiki/MonkeyData
--
On Wed, 7 Apr 2010, Srihasam, Krishna wrote:
> Hi,
>
> I have a (0.35 mm)^3 resolution monkey brain which I am tryin
wsthresh" against not using it in a few
> subjects from both groups. as far as the "-clean" flags are concerned, there
> is no bug: they do change the result, so i assume the previous volume is
> overwritten as it should, however the results are no improvement (see
>
tings.
>
> EDIT: forgot to attach the screenshots, sorry once more...
>
>
> On Tue, 13 Apr 2010 08:20:40 -0400 (EDT)
> Allison Stevens wrote:
>
>> Thanks, Andreas. That clears it up.
>>
>> There was no attachment though. Can you send me the screenshots?
>>
Jordan,
The -subcortseg step is going to be looking for inputs that were created
before it, so you can't really skip the steps before it. I suppose you can
skip the surface steps afterwards as long as you understand that the
aseg.mgz will not give you accurate wm and gm volumes.
In order to get
Sasa,
Are you middle clicking to add a control point?
Allison
--
On Tue, 27 Apr 2010, Sasa Kivisaari wrote:
> Dear FreeSurfers,
>
> I'm a postgraduate student and recently started with FreeSurfer. I have
> problems adding control points to the volumes I have loaded into tkmedit. For
> some re
There are a few suggestions for this from a previous question on the same
matter. Please see here:
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg07155.html
Allison
--
On Tue, 27 Apr 2010, Antoine Leflon wrote:
> hi ,
>
> I was processing autorecon3 and it screened me this erro
Right, your command to see that file should be:
tkmedit bai_hong_jun orig/001.mgz
Also, it only did the first step because your command was:
recon-all -i input -s subjid
To run the entire processing stream, you'll want to do:
recon-all -all -i input -s subjid
Allison
--
On Tue, 27 Apr 2010, B
Xin,
You do not have to correct the pial surface for that area - these surfaces
do not affect the aseg.mgz. You will often see the surfaces in the
hippocampus/amygdala regions as inaccurate, however your aseg will look
fine.
Allison
On Fri, 13 Jul 2007, Wang, Xin wrote:
This is an example o
Thanks, Mike. I'll work on this.
Allison
On Fri, 2 Nov 2007, Michael Harms wrote:
Hello,
Just a couple miscellaneous items/suggestions regarding the very helpful
ReconAllDevTable:
1) The entry for -inflate2 currently indicates that ?h.white is the
input file. This should be ?h.smoothwm inste
The tutorial is here (it's 2 pages, be sure to click 'next'):
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/OutputData
Allison
On Wed, 2 Jan 2008, Bruce Fischl wrote:
Hi,
we don't usually stop and check anymore as things fail pretty rarely. You can
look at the tutorial on the wiki for
Kristine,
You should be able to use -ccseg which occurs after the aseg is created in
-autorecon2. First, you will need to copy your aseg.mgz to aseg.auto.mgz
as this is the file that -ccseg will work on (in the dev version of FS, it
uses the aseg.mgz).
Allison
On Tue, 22 Jan 2008
[EMAIL P
That should be fine (-ccseg -cortribbon -cortparc -aparc2aseg -wmparc).
Allison
On Wed, 23 Jan 2008 [EMAIL PROTECTED] wrote:
Thanks, I'll try that. Will I then need to redo all steps fromm -ccseg
onwards if I want a correct wmparc at the end, or can I safely skip some?
For instance, I could do
You can do:
"recon-all -make all -s and it will run all the remaining steps
that have not been done or are out of date.
On Fri, 25 Jan 2008, Chris Watson wrote:
Hello,
While running recon-all on a subject, my machine logged me off for an
unrelated reason. It was stopped during -autorecon3
completed.
Allison
On Fri, 25 Jan 2008, Chris Watson wrote:
Hi Allison, this is the error message I received:
[EMAIL PROTECTED] subjects]$ recon-all -make all -s
ERROR: Flag -make unrecognized.
-make all -s
I'm running v3.0.4.
Allison Stevens wrote:
You can do:
"recon-all -make a
Jared,
You can do recon-all -segstats for each subject. This uses the
aseg.mgz to create the aseg.stats, however, if the new aseg.mgz you
generated with the script I sent you is named something other than
aseg.mgz, then you will want to change it to aseg.mgz for this to
work.
Allison
On We
Jared,
You can do:
*recon-all -i **invol1** -i **invol2** -all -subjid **your_subject_name**
Allison
On Tue, 5 Feb 2008, Jared Morton wrote:
When I run the first portion of the recon-all script according to the
instructions in RecommendedReconstruction, the command I am instructed to
use is:
You can do:
recon-all -cortparc -parcstats -s
which will create the cortical parcellations and the associated stats
file. (Note: -cortparc2 and -parcstats2 will use the alternative atlas).
Steps like these can be found on the wiki, here:
https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllStable
In the meantime, you can make a tcl script with your preferences. Next
time you load tkmedit, pass it the tcl flag followed by the path to your
tcl script, like this:
tkmedit -tcl /path/to/yourscript.tcl
The following wiki page shows all the options you can set:
https://surfer.nmr.mgh.harvar
Lindsay,
If you do
cd $FREESURFER_HOME
You'll find the FreeSurferColorLUT.txt there which has all the labels for
cortical and subcortical structures.
Allison
On Tue, 1 Apr 2008, Lindsay Casmaer wrote:
Does the website contain a list of structures labeled in both version
3 and version 4? I a
I know someone that uses something like what is below to avoid using
tkregister:
mri_convert $subject/mri/T1.mgz $subject/mri/T1.mnc
mritotal -protocol icbm $subject/mri/T1.mnc $subject/mri/T1.xfm
mv $subject/mri/transforms/talairach.xfm
$subject/mri/transforms/oldtalairach.xfm
cp $subject/mri/T
You would want to edit the wm.mgz to fill the ventricles in if the
surfaces are not accurate. So from your picture, I would say the surfaces
do not look accurate in the right hemisphere since they are being pulled
into the ventricle.
Allison
On Tue, 15 Jul 2008, Dorit Kliemann wrote:
Hi,
I
It really shouldn't be a problem to only use one. Using two can give you
better SNR but many people have used one successfully - it mostly depends
on the quality of your data. For poor quality data, having two might be
more necessary.
Allison
On Mon, 25 Aug 2008 [EMAIL PROTECTED] wrote:
Hi!
You'll find surface area measurements for each cortical parcellation area
in your ?h.aparc.stats file within the stats directory for each subject.
Allison
On Wed, 3 Sep 2008, Barkay, Gavriel wrote:
Can I do surface area measurement using freesurfer?
--
Gavriel Barkay M.D. M.Sc.
Psychopharmaco
Ed, do you want to send me the subject and I'll take a look?
--
On Mon, 10 May 2010, Ed Gronenschild wrote:
> Hi,
>
> I've mailed this once before and tried to solve a persistent problem.
> Reviewing the results of recon-all I noticed that the derived pial
> surface chopped away an unacceptable
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