date:20140612

[Freesurfer] How to extract significant result for each subject

2014-06-12 Thread kangchengwang0...@gmail.com

Dear freesurfers,
   I contrast depression and control and find that patients have a lower 
thickness in region of inferior frontal gyrus. Now, I want to extract the data 
of thickness for each subject. Could you tell which command could do this?
Thank you


Wang Kangcheng ( New learner of freesurfer )

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[Freesurfer] volume-based controls

2014-06-12 Thread kristen yoo

I am attempting to do volume-based analysis using a data from normals as my 
control. Does fsaverage provide volume-based data for this purpose? Where can I 
find these values? Are they found anywhere outside of the freesurfer suite? 
Thanks in advance!
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Re: [Freesurfer] ?Sequence for Hippo_subfields

2014-06-12 Thread Eugenio Iglesias

Yes! If Im not mistaken, ADNI  is acquiring this type of data on 3T platforms.
Cheers
Eugenio

Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu

Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer


- Original Message -
From: Kev 
To: Freesurfer support list 
Sent: Thu, 12 Jun 2014 18:51:03 +0200 (CEST)
Subject: Re: [Freesurfer] ?Sequence for Hippo_subfields

Much appreciated Eugenio.

I had read a paper where authors report using a ultra high field scanner (7T - 
Cho Z-H, et al. J Psychiatr Res 2010; 44: 881–886), and I notice the reference 
you kindly provided uses a 4T scanner...

I presume using a 3T might be stretching things a bit, and I wonder whether 
future FS releases using T2-weighted images will "accept" 3T scans?

Best regards and thanks again for great support you guys provide,

Kev


On Jun 12, 2014, at 3:49 AM, Eugenio Iglesias wrote:

> Dear Kev,
> for the subfields, people have been acquiring T2 scans with high in-plane 
> (coronal) resolution like the ones in this paper:
> http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1820772/
> The subfield atlas in FreeSurfer cannot handle such scans, but we will 
> (hopefully soon) release a version that can.
> Kind regards,
> /Eugenio
> 
> Juan Eugenio Iglesias
> Postdoctoral researcher BCBL
> www.jeiglesias.com
> www.bcbl.eu
> 
> Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer
> 
> 
> - Original Message -
> From: "Kev" 
> To: "Freesurfer support list" 
> Sent: Wednesday, June 11, 2014 8:32:33 PM
> Subject: [Freesurfer] ?Sequence for Hippo_subfields
> 
> Dear FS experts,
> 
> I'm in the designing stage of a neuroimaging project on a 3T scanner, and I'm 
> interested in looking at structural information on hippocampus (including 
> subfields).
> 
> In addition to the MPRAGE or IR-SPGR, is it worth running a specific 
> acquisition sequence geared to get the most out of all the hippocampus 
> structural measures? 
> 
> Thanks and regards,
> 
> Kev
> ___
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> 
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> at
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> but does not contain patient information, please contact the sender and 
> properly
> dispose of the e-mail.
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[Freesurfer] Messages not appearing on Mail Archive

2014-06-12 Thread Sherryse Corrow

Hi,

The messages I am sending to free sur...@nmr.mgh.harvard.edu are not showing up 
on the site here: 
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/maillist.html.  But 
they are showing up on the digest emails that I am receiving.  Is that normal?

For example, the message pasted below is this morning’s digest.  And my message 
is listed there, however, my previous two messages are not listed on the new 
mail archive from the website linked above.  Am I doing something wrong?

Appreciated,

Sherryse

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Today's Topics:

   1. Re: aparc manual correction (Bruce Fischl)
   2. Fwd: Extracting mean diffusivity values from diffusion data
  in freesurfer 5.3 (Rotem Saar)
   3. ?Sequence for Hippo_subfields (Kev)
   4. Displaying subset of labels on template (nmw)
   5. Re: Displaying subset of labels on template (dgw)
   6. Re: From NIfTI T1 to its volume cortical thickness map in
  MNI152 space. (Fred Sampedro)
   7. Re: Displaying subset of labels on template (Bruce Fischl)
   8. Re: From NIfTI T1 to its volume cortical thickness map in
  MNI152 space. (Bruce Fischl)
   9. FW: Registration of Functional Data to the Inflated Brain
  (Sherryse Corrow)
--
Sherryse Corrow, Ph.D. / Postdoctoral Fellow
Human Vision and Eye Movement Lab
Department of Ophthalmology & Visual Sciences
UBC/VGH Eye Care Centre
360A-2550 Willow Street
Vancouver, BC, V5Z 3N9
Tel: 604-875-4111 ext 67672
Cell: 604-315-6717
sherryse.cor...@eyecarecentre.org
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Re: [Freesurfer] ?Sequence for Hippo_subfields

2014-06-12 Thread Kev

Much appreciated Eugenio.

I had read a paper where authors report using a ultra high field scanner (7T - 
Cho Z-H, et al. J Psychiatr Res 2010; 44: 881–886), and I notice the reference 
you kindly provided uses a 4T scanner...

I presume using a 3T might be stretching things a bit, and I wonder whether 
future FS releases using T2-weighted images will "accept" 3T scans?

Best regards and thanks again for great support you guys provide,

Kev

On Jun 12, 2014, at 3:49 AM, Eugenio Iglesias wrote:

> Dear Kev,
> for the subfields, people have been acquiring T2 scans with high in-plane 
> (coronal) resolution like the ones in this paper:
> http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1820772/
> The subfield atlas in FreeSurfer cannot handle such scans, but we will 
> (hopefully soon) release a version that can.
> Kind regards,
> /Eugenio
> 
> Juan Eugenio Iglesias
> Postdoctoral researcher BCBL
> www.jeiglesias.com
> www.bcbl.eu
> 
> Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer
> 
> 
> - Original Message -
> From: "Kev" 
> To: "Freesurfer support list" 
> Sent: Wednesday, June 11, 2014 8:32:33 PM
> Subject: [Freesurfer] ?Sequence for Hippo_subfields
> 
> Dear FS experts,
> 
> I'm in the designing stage of a neuroimaging project on a 3T scanner, and I'm 
> interested in looking at structural information on hippocampus (including 
> subfields).
> 
> In addition to the MPRAGE or IR-SPGR, is it worth running a specific 
> acquisition sequence geared to get the most out of all the hippocampus 
> structural measures? 
> 
> Thanks and regards,
> 
> Kev
> ___
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> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> 
> 
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> addressed. If you believe this e-mail was sent to you in error and the e-mail
> contains patient information, please contact the Partners Compliance HelpLine 
> at
> http://www.partners.org/complianceline . If the e-mail was sent to you in 
> error
> but does not contain patient information, please contact the sender and 
> properly
> dispose of the e-mail.
> 
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Re: [Freesurfer] tumor mask & extreme hydrocephalus- white matter is not recognized

2014-06-12 Thread Bruce Fischl


Hi Andrea

did you try running it with -bigventricles?

cheers
Bruce
On Thu, 12 Jun 2014, Andrea 
Horváth wrote:



Dear Freesurfer Experts,

I have two questions:

1. How can I add a previously created a tumor mask along with the mprage to
improve segmentation?

2. I ran recon-all on a subject with extreme hydrocephalus. Registration to
Talairach space and skull stripping were OK. However, a part of occipital
white matter was not recognized as white matter even after adding control
points and running recon-all -autorecon2-cp -autorecon3  due to the large
ventricle as you can see in the attachment. What can you recommend to  fix
this problem?

Thank you for your help!

Cheers,

Andrea


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Re: [Freesurfer] Segfault errors in tkmedit and tksurfer

2014-06-12 Thread Joonkoo Park, Ph.D.

Hi Zeki

I'm using OSX 10.7.5. And, yes I have installed XQuartz as instructed by
the freesurfer installation website.

Thanks!

Joon

--
Joonkoo Park, Ph.D.
Postdoctoral Associate
Center for Cognitive Neuroscience
Duke University
http://www.joonkoo.org/


On Thu, Jun 12, 2014 at 11:51 AM, Z K  wrote:

> Hi Joon,
>
> What version of OSX are you on and have you installed XQuartz (
> http://xquartz.macosforge.org/landing/)? XQuartz is required for proper
> tkmedit/tksurfer functionality.
>
> -Zeke
>
>
> On 06/11/2014 11:48 PM, Joonkoo Park, Ph.D. wrote:
>
>> Hello,
>>
>> I've used FreeSurfer previously on a linux machine (from a previous
>> lab). Now, I have just installed it on a Mac OSX, using the
>> "freesurfer-Darwin-lion-stable-pub-v5.3.0.dmg" version. I followed all
>> the instructions on the installation page. However, there were segfault
>> errors when running both tkmedit and tksurfer as follows:
>>
>> dyn-152-3-184-222:freesurfer joonkoopark$ more .xdebug_tkmedit
>> tkmedit started: Wed Jun 11 23:28:05 2014
>>
>>  /Applications/freesurfer/tktools/tkmedit.bin bert orig.mgz
>>
>> $Id: tkmedit.c,v 1.343 2011/03/01 01:41:22 nicks Exp $ $Name: stable5
>> $
>> Set user home dir to /Applications/freesurfer
>> Set subject home dir to /Applications/freesurfer/subjects/bert
>> Using interface file /Applications/freesurfer/tktools/tkmedit.tcl
>>
>> Segfault
>> Setting global interpreter
>> xDebug stack (length: 2)
>>  01: main()
>>  01: Setting global interpreter
>>00:
>>00:
>> dyn-152-3-184-222:freesurfer joonkoopark$ more .xdebug_tksurfer
>>
>> Segfault
>> Initializing glut
>> xDebug stack (length: 1)
>>00:
>>00: Initializing glut
>>
>> Segfault
>> Initializing glut
>> dyn-152-3-184-222:freesurfer joonkoopark$
>>
>>
>> Any idea what went wrong and how to fix it?
>>
>> Thank you!
>>
>> Joon
>>
>>
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>>
>>
>
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> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
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> properly
> dispose of the e-mail.
>
>
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Re: [Freesurfer] Segfault errors in tkmedit and tksurfer

2014-06-12 Thread Z K

Hi Joon,

What version of OSX are you on and have you installed XQuartz 
(http://xquartz.macosforge.org/landing/)? XQuartz is required for proper 
tkmedit/tksurfer functionality.

-Zeke

On 06/11/2014 11:48 PM, Joonkoo Park, Ph.D. wrote:
> Hello,
>
> I've used FreeSurfer previously on a linux machine (from a previous
> lab). Now, I have just installed it on a Mac OSX, using the
> "freesurfer-Darwin-lion-stable-pub-v5.3.0.dmg" version. I followed all
> the instructions on the installation page. However, there were segfault
> errors when running both tkmedit and tksurfer as follows:
>
> dyn-152-3-184-222:freesurfer joonkoopark$ more .xdebug_tkmedit
> tkmedit started: Wed Jun 11 23:28:05 2014
>
>  /Applications/freesurfer/tktools/tkmedit.bin bert orig.mgz
>
> $Id: tkmedit.c,v 1.343 2011/03/01 01:41:22 nicks Exp $ $Name: stable5 $
> Set user home dir to /Applications/freesurfer
> Set subject home dir to /Applications/freesurfer/subjects/bert
> Using interface file /Applications/freesurfer/tktools/tkmedit.tcl
>
> Segfault
> Setting global interpreter
> xDebug stack (length: 2)
>  01: main()
>  01: Setting global interpreter
>00:
>00:
> dyn-152-3-184-222:freesurfer joonkoopark$ more .xdebug_tksurfer
>
> Segfault
> Initializing glut
> xDebug stack (length: 1)
>00:
>00: Initializing glut
>
> Segfault
> Initializing glut
> dyn-152-3-184-222:freesurfer joonkoopark$
>
>
> Any idea what went wrong and how to fix it?
>
> Thank you!
>
> Joon
>
>
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Re: [Freesurfer] freeurfer manual edits

2014-06-12 Thread Harms, Michael


FWIW: In FS 5.3, -autorecon2-cp and -autorecon2-wm invoke the exact same
set of flags.  (This wasn't the case in earlier versions).

cheers,
-MH

--
Michael Harms, Ph.D.

---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave.   Tel: 314-747-6173
St. Louis, MO  63110Email: mha...@wustl.edu




On 6/12/14 10:15 AM, "Bruce Fischl"  wrote:

>Hi Jidan
>
>for your first point, if you make both wm edits and add control points
>you
>can run -autorecon2-cp -autorecon3 as it is a superset of -autorecon2-wm.
>
>For the second one, it's hard to diagnose from the single slice. Is there
>white matter through-plane that is not included in the white surface or
>the
>wm.mgz?
>
>cheers
>Bruce
>
>On Thu, 12 Jun 2014, Jidan Zhong wrote:
>
>> Dear FreeSurfer Experts,
>>
>> I have two questions about freesurfer troubleshoot.
>>
>> My subjects are people with multiple sclerosis, so for most of them I
>>need
>> to add control points as well as edit white matter due to lesions. As
>>far as
>> I know, I should add control points and do recon-all -autorecon2-cp
>> -autorecon3  to my subject and then edit white matter, do recon-all
>> -autorecon2-wm -autorecon3.
>>
>> My question is, it seems there are some repeated steps for those two
>>recon
>> steps, and it takes so long to run them. Is there anyway that I can save
>> some process steps and leave it to the last recon? To be specific, can
>>I do
>> recon-all -autorecon2-cp only after I added control points, then do
>> recon-all -autorecon2-wm -autorecon3 after wm edits? I think it is
>> reasonable as after -autorecon2-cp the new white matter surface is
>>already
>> generated and can help to detect wm failure. But I am not sure whether
>>this
>> makes sense to you guys.
>>
>> Another question is, some of my subjects they have degenerated white
>>matter
>> and grey matter, so some parts get so dark that freesurfer would not
>>include
>> it even in the pial surface. I attached one figure for your referece. If
>> there is no white matter detected in that unlabled part (at the top of
>>the
>> figure), what should I do? should I leave it or just add some white
>>matter
>> and control points myself to get a better segmentation and surface?
>>[The
>> case I show in the attachment is much better than some other cases,
>>whose
>> brain has some parts so dark that even I can not tell which is grey
>>matter
>> or white matter from my experience..]
>>
>> Thanks!
>>
>>
>> --
>> Regards,
>>
>> Jidan
>>



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Re: [Freesurfer] freeurfer manual edits

2014-06-12 Thread Bruce Fischl


Hi Jidan

for your first point, if you make both wm edits and add control points you 
can run -autorecon2-cp -autorecon3 as it is a superset of -autorecon2-wm.


For the second one, it's hard to diagnose from the single slice. Is there 
white matter through-plane that is not included in the white surface or the 
wm.mgz?


cheers
Bruce

On Thu, 12 Jun 2014, Jidan Zhong wrote:


Dear FreeSurfer Experts,

I have two questions about freesurfer troubleshoot.

My subjects are people with multiple sclerosis, so for most of them I need
to add control points as well as edit white matter due to lesions. As far as
I know, I should add control points and do recon-all -autorecon2-cp
-autorecon3  to my subject and then edit white matter, do recon-all
-autorecon2-wm -autorecon3.

My question is, it seems there are some repeated steps for those two recon
steps, and it takes so long to run them. Is there anyway that I can save
some process steps and leave it to the last recon? To be specific, can I do
recon-all -autorecon2-cp only after I added control points, then do
recon-all -autorecon2-wm -autorecon3 after wm edits? I think it is
reasonable as after -autorecon2-cp the new white matter surface is already
generated and can help to detect wm failure. But I am not sure whether this
makes sense to you guys.

Another question is, some of my subjects they have degenerated white matter
and grey matter, so some parts get so dark that freesurfer would not include
it even in the pial surface. I attached one figure for your referece. If
there is no white matter detected in that unlabled part (at the top of the
figure), what should I do? should I leave it or just add some white matter
and control points myself to get a better segmentation and surface?  [The
case I show in the attachment is much better than some other cases, whose
brain has some parts so dark that even I can not tell which is grey matter
or white matter from my experience..]

Thanks!


--
Regards,

Jidan

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Re: [Freesurfer] Corpus Callosum segmentation reliability

2014-06-12 Thread Bruce Fischl


Hi Alessia

I did, and unfortunately I'm not sure there is much I can do. One of the 
(long) list of engineering thing we would like to fix is how we deal with 
the initial nromalization of subject positioning. At the moment, the scans 
you sent me will be resliced differently, and it is that interpolation that 
causes the 5% or so differences in CC compartment volumes.


sorry,
Bruce


On Thu, 12 Jun 2014, Alessia Giuliano wrote:


Dear Bruce,
did you see the images that I have sent you?

Thanks,

Alessia Giuliano


From: alessia_giuli...@hotmail.it
To: freesurfer@nmr.mgh.harvard.edu
Date: Fri, 6 Jun 2014 06:46:29 +
Subject: Re: [Freesurfer] Corpus Callosum segmentation reliability

Dear Bruce,
the two subject dirs are here
https://www.dropbox.com/sh/k1z5o0e6sq90qq0/AABx38QxKvxDhUe2lV9imaa9a.
The original subject is s50 and the rotated one is rs50.

Thank you very much for your help.

Alessia Giuliano

Date: Thu, 5 Jun 2014 16:27:58 -0400
From: fis...@nmr.mgh.harvard.edu
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Corpus Callosum segmentation reliability

hmmm, that is puzzling. Can you upload the two subject dirs with the 
rotated direction cosines and I'll take a look?


thanks
Bruce
On Thu, 5 Jun 2014, Alessia 
Giuliano wrote:


> Dear Bruce,
> when I say "the image was rotated" in 2 I mean that I have changed the ima
ge header to reflect a new orientation,
> instead in 3 there was an additional image interpolation, therefore a blur
ring.
> As you said, I can understand that in the latter case things change, but h
ow can be explained so considerable change
> in CC subregions volumes and in CC total volume between case 2 and 1?
> 
> Moreover, we have noticed that the rostrum is sometimes included in the an

terior part but othertimes not, is there a
> way to correct this segmentation manually?
> 
> Can you give me any advices to improve the CC segmentation in order to con

sider the volumes of its subregions to be
> reliable?
> 
> Thank you,
> 
> Alessia Giuliano
> 
> Date: Thu, 5 Jun 2014 08:30:10 -0400

> From: fis...@nmr.mgh.harvard.edu
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Corpus Callosum segmentation reliability
> 
> Hi  Alessia
> 
> when you say "the image was rotated" do you mean you actually transformed 
> the  image, or you simply changed the image header to reflect a new 
> orientation? I wouldn't think the latter would have a big effect, but the 
> former will involve an additional image interpolation (blurring) and will 
> definitely change things. Same question for 3. Did you include an extra 
> interpolation?
> 
> cheers

> Bruce
>
>
>
>
> 
> On Thu, 5 Jun 2014, Alessia 
> Giuliano wrote:
> 
> > Dear FreeSurefer team,

> > in order to verify the reliability of the volumes of Corpus Callosum (CC
) subregions estimated by FreeSurfer
> > I have applied the recon-all on the same subject but in three different 
situations:

> >  
> > 1. when the image was not preliminarly rotated;
> > 2. when an initial soft rotation was manually performed with SPM;
> > 3. when an initial rigid coregistration in MNI space was performed with 
SPM.
> > 
> > Although the differences in image orientation between 1, 2 and 3 before 
the implementation of FreeSurfer

> > were really small, the differences in the volumes of the CC subregions b
etween 1, 2 and 3 are notable.
> > 
> > How can I base on this evident variability my volumetric analysis of CC 
subregions?
> > 
> > Do you have any suggestions to improve my approach to the CC segmentatio

n?
> > 
> > In order to make my results clear, I attach you a recapitulatory page an

d I send you a link to the
> > FreeSurfer output in 1, 2 and 3 (https://www.dropbox.com/sh/k1z5o0e6sq90
qq0/AABx38QxKvxDhUe2lV9imaa9a).
> > 
> > Thank you,
> > 
> > Alessia Giuliano
> > 
> >
> 
> ___ Freesurfer mailing list Fr

eesur...@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The informati
on in this e-mail is intended only for the
> person to whom it is addressed. If you believe this e-mail was sent to you
 in error and the e-mail contains patient
> information, please contact the Partners Compliance HelpLine at http://www
.partners.org/complianceline . If the
> e-mail was sent to you in error but does not contain patient information, 
please contact the sender and properly

> dispose of the e-mail.
> 
>


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error but d

[Freesurfer] Tracula preprocessing error ( set dob0 = 1 )

2014-06-12 Thread Elia S.

Dear Freesurfer community,
Whenever i try to launch the tracula preprocessing, using  "set dob0 = 1 " and 
the following command line:
trac-all -prep -no-isrunning -c 
'/home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/tracula.config
It stops, giving me errors like these:
niiRead(): error opening file 
/home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/T13D/timePoint1/dmri/dwi.nii.gz
ERROR: reading 
/home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/T13D/timePoint1/dmri/dwi_frame0.nii.gz
While setting "dob0 = 0" everything runs smoothly.
Can you help me please?  I'll attach the log + dmrirc (tracula.config)
Best,Elia.
--
Freesurfer version: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0
Linux Distribution: Ubuntu 12.04 precise - Ubuntu 12.04.4 LTS
Environment/Version: Linux king-ubuntu 3.2.0-56-generic #86-Ubuntu SMP Wed Oct 
23 09:20:45 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux 
   INFO: SUBJECTS_DIR is /home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/T13D
INFO: Diffusion root is /home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/T13D
Actual FREESURFER_HOME /home/alberto/Desktop/freesurfer
trac-preproc -c 
/home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/T13D/timePoint1/scripts/dmrirc.local
 -log 
/home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/T13D/timePoint1/scripts/trac-all.log
 -cmd 
/home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/T13D/timePoint1/scripts/trac-all.cmd
 -no-isrunning
#-
/home/alberto/Desktop/freesurfer/bin/trac-preproc 
#-
#@# Image corrections Thu Jun 12 12:07:07 CEST 2014
mri_convert 
/home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/DTI/timePoint1/1.3.12.2.1107.5.2.7.20118.301112231117586560353.dcm
 
/home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/T13D/timePoint1/dmri/dwi_orig.nii.gz
mri_convert 
/home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/DTI/timePoint1/1.3.12.2.1107.5.2.7.20118.301112231117586560353.dcm
 
/home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/T13D/timePoint1/dmri/dwi_orig.nii.gz
 
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from 
/home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/DTI/timePoint1/1.3.12.2.1107.5.2.7.20118.301112231117586560353.dcm...
Getting Series No 
INFO: Found 2245 files in 
/home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/DTI/timePoint1
INFO: Scanning for Series Number 6
Scanning Directory 
INFO: found 2240 files in series
INFO: loading series header info.

RunNo = 5
INFO: sorting.
INFO: (128 128  64), nframes = 35, ismosaic=0
PE Dir COL COL
AutoAlign matrix detected 
AutoAlign Matrix - 
 1.000   0.000   0.000   0.000;
 0.000   1.000   0.000   0.000;
 0.000   0.000   1.000   0.000;
 0.000   0.000   0.000   1.000;

This looks like an MGH DTI volume
DTI is in non-moasic form, so cannot extract bvals/bvects
FileName
/home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/DTI/timePoint1/1.3.12.2.1107.5.2.7.20118.301112231117586560385.dcm
Identification
NumarisVersyngo MR 2004A 4VA25A 
ScannerModel  Allegra 
PatientName   5-001-11-MRDTI-PT-001-T00-000 
Date and time
StudyDate 20111223
StudyTime 120731.359000 
SeriesTime124439.515000 
AcqTime   123906.902499 
Acquisition parameters
PulseSeq  ep_b0#0 
Protocol  DTI 2x2x2 b700 5b0
PhEncDir  COL
EchoNo0
FlipAngle 90
EchoTime  87
InversionTime -1
RepetitionTime9300
PhEncFOV  256
ReadoutFOV256
Image information
RunNo 5
SeriesNo  6
ImageNo   1
NImageRows128
NImageCols128
NFrames   35
SliceArraylSize   64
IsMosaic  0
ImgPos128.3131 134.4756 -57.2379 
VolRes  2.   2.   2. 
VolDim128  128   64 
Vc -1.  -0.   0. 
Vr -0.  -1.  -0.0087 
Vs -0.  -0.0087   1. 
VolCenter   0.3131   5.9220   5.6427 
TransferSyntaxUID 1.2.840.10008.1.2
UseSliceScaleFactor 0 (slice 0: 1)
INFO: no Siemens slice order reversal detected (good!). 
TR=9300.00, TE=87.00, TI=-1.00, flip angle=90.00
i_ras = (-1, -0, 8.67362e-19)
j_ras = (-0, -0.62, -0.00872654)
k_ras = (-0, -0.00872654, 0.62)
writing to 
/home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/T13D/timePoint1/dmri/dwi_orig.nii.gz...
mri_probedicom --i 
/home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/DTI/timePoint1/1.3.12.2.1107.5.2.7.20118.301112231117

Re: [Freesurfer] ?Sequence for Hippo_subfields

2014-06-12 Thread Eugenio Iglesias

Dear Kev,
for the subfields, people have been acquiring T2 scans with high in-plane 
(coronal) resolution like the ones in this paper:
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1820772/
The subfield atlas in FreeSurfer cannot handle such scans, but we will 
(hopefully soon) release a version that can.
Kind regards,
/Eugenio

Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu

Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer


- Original Message -
From: "Kev" 
To: "Freesurfer support list" 
Sent: Wednesday, June 11, 2014 8:32:33 PM
Subject: [Freesurfer] ?Sequence for Hippo_subfields

Dear FS experts,

I'm in the designing stage of a neuroimaging project on a 3T scanner, and I'm 
interested in looking at structural information on hippocampus (including 
subfields).

In addition to the MPRAGE or IR-SPGR, is it worth running a specific 
acquisition sequence geared to get the most out of all the hippocampus 
structural measures? 

Thanks and regards,

Kev
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Re: [Freesurfer] Corpus Callosum segmentation reliability

2014-06-12 Thread Alessia Giuliano

Dear Bruce,
did you see the images that I have sent you?
Thanks,
Alessia Giuliano

From: alessia_giuli...@hotmail.it
To: freesurfer@nmr.mgh.harvard.edu
Date: Fri, 6 Jun 2014 06:46:29 +
Subject: Re: [Freesurfer] Corpus Callosum segmentation reliability




Dear Bruce,
the two subject dirs are here 
https://www.dropbox.com/sh/k1z5o0e6sq90qq0/AABx38QxKvxDhUe2lV9imaa9a.The 
original subject is s50 and the rotated one is rs50.
Thank you very much for your help.
Alessia Giuliano

Date: Thu, 5 Jun 2014 16:27:58 -0400
From: fis...@nmr.mgh.harvard.edu
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Corpus Callosum segmentation reliability

hmmm, that is puzzling. Can you upload the two subject dirs with the 
rotated direction cosines and I'll take a look?
 
thanks
Bruce
On Thu, 5 Jun 2014, Alessia 
Giuliano wrote:
 
> Dear Bruce,
> when I say "the image was rotated" in 2 I mean that I have changed the image 
> header to reflect a new orientation,
> instead in 3 there was an additional image interpolation, therefore a 
> blurring.
> As you said, I can understand that in the latter case things change, but how 
> can be explained so considerable change
> in CC subregions volumes and in CC total volume between case 2 and 1?
> 
> Moreover, we have noticed that the rostrum is sometimes included in the 
> anterior part but othertimes not, is there a
> way to correct this segmentation manually?
> 
> Can you give me any advices to improve the CC segmentation in order to 
> consider the volumes of its subregions to be
> reliable?
> 
> Thank you,
> 
> Alessia Giuliano
> 
> Date: Thu, 5 Jun 2014 08:30:10 -0400
> From: fis...@nmr.mgh.harvard.edu
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Corpus Callosum segmentation reliability
> 
> Hi  Alessia
> 
> when you say "the image was rotated" do you mean you actually transformed 
> the  image, or you simply changed the image header to reflect a new 
> orientation? I wouldn't think the latter would have a big effect, but the 
> former will involve an additional image interpolation (blurring) and will 
> definitely change things. Same question for 3. Did you include an extra 
> interpolation?
> 
> cheers
> Bruce
>
>
>
>
> 
> On Thu, 5 Jun 2014, Alessia 
> Giuliano wrote:
> 
> > Dear FreeSurefer team,
> > in order to verify the reliability of the volumes of Corpus Callosum (CC) 
> > subregions estimated by FreeSurfer
> > I have applied the recon-all on the same subject but in three different 
> > situations:
> >  
> > 1. when the image was not preliminarly rotated;
> > 2. when an initial soft rotation was manually performed with SPM;
> > 3. when an initial rigid coregistration in MNI space was performed with SPM.
> > 
> > Although the differences in image orientation between 1, 2 and 3 before the 
> > implementation of FreeSurfer
> > were really small, the differences in the volumes of the CC subregions 
> > between 1, 2 and 3 are notable.
> > 
> > How can I base on this evident variability my volumetric analysis of CC 
> > subregions?
> > 
> > Do you have any suggestions to improve my approach to the CC segmentation?
> > 
> > In order to make my results clear, I attach you a recapitulatory page and I 
> > send you a link to the
> > FreeSurfer output in 1, 2 and 3 
> > (https://www.dropbox.com/sh/k1z5o0e6sq90qq0/AABx38QxKvxDhUe2lV9imaa9a).
> > 
> > Thank you,
> > 
> > Alessia Giuliano
> > 
> >
> 
> ___ Freesurfer mailing list 
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information 
> in this e-mail is intended only for the
> person to whom it is addressed. If you believe this e-mail was sent to you in 
> error and the e-mail contains patient
> information, please contact the Partners Compliance HelpLine at 
> http://www.partners.org/complianceline . If the
> e-mail was sent to you in error but does not contain patient information, 
> please contact the sender and properly
> dispose of the e-mail.
> 
>

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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
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addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient infor

[Freesurfer] How to extract significant result for each subject

[Freesurfer] volume-based controls

Re: [Freesurfer] ?Sequence for Hippo_subfields

[Freesurfer] Messages not appearing on Mail Archive

Re: [Freesurfer] ?Sequence for Hippo_subfields

Re: [Freesurfer] tumor mask & extreme hydrocephalus- white matter is not recognized

Re: [Freesurfer] Segfault errors in tkmedit and tksurfer

Re: [Freesurfer] Segfault errors in tkmedit and tksurfer

Re: [Freesurfer] freeurfer manual edits

Re: [Freesurfer] freeurfer manual edits

Re: [Freesurfer] Corpus Callosum segmentation reliability

[Freesurfer] Tracula preprocessing error ( set dob0 = 1 )

Re: [Freesurfer] ?Sequence for Hippo_subfields

Re: [Freesurfer] Corpus Callosum segmentation reliability

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