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Today's Topics:
1. Re: mritotal failed - help with manual registration (Bruce Fischl)
2. recon -all errors (Jasmin Alves)
3. Re: Processing .mnc files (Ankita Chatterjee)
4. Re: Processing .mnc files (Bruce Fischl)
5. Re: mri_binarize --i sig.cluster.mgh --min 1.3 --o
thresholded.mgh 1.3 = -log10(.05) (Erik Lindberg)
6. hippocampal subfields - multispectral segmentation with FLAIR
(Luigi Antelmi)
7. Re: hippocampal subfields - multispectral segmentation with
FLAIR (Eugenio Iglesias)
8. Re: recon -all errors (Bruce Fischl)
9. Re: mri_binarize --i sig.cluster.mgh --min 1.3 --o
thresholded.mgh 1.3 = -log10(.05) (Bruce Fischl)
10. Re: mri_binarize --i sig.cluster.mgh --min 1.3 --o
thresholded.mgh 1.3 = -log10(.05) (Erik Lindberg)
11. Re: mri_binarize --i sig.cluster.mgh --min 1.3 --o
thresholded.mgh 1.3 = -log10(.05) (Bruce Fischl)
12. FDR map: hide very little cluster (stdp82@virgilio.it)
13. [All] position available immediately (Bruce Fischl)
14. Re: mri_binarize --i sig.cluster.mgh --min 1.3 --o
thresholded.mgh 1.3 = -log10(.05) (Douglas Greve)
15. Re: FDR map: hide very little cluster (Douglas Greve)
16. R: Re: FDR map: hide very little cluster (stdp82@virgilio.it)
17. R: Re: FDR map: hide very little cluster (stdp82@virgilio.it)
18. Re: R: Re: FDR map: hide very little cluster (Douglas N Greve)
19. R: R: Re: FDR map: hide very little cluster (stdp82@virgilio.it)
20. Re: R: R: Re: FDR map: hide very little cluster (Douglas N Greve)
21. R: Re: R: Re: FDR map: hide very little cluster
(stdp82@virgilio.it)
----------------------------------------------------------------------
Message: 1
Date: Sun, 24 Jan 2016 18:58:54 -0500 (EST)
From: Bruce Fischl <fischl@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] mritotal failed - help with manual
registration
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<alpine.LRH.2.20.1601241858240.29174@door.nmr.mgh.harvard.edu>
Content-Type: text/plain; charset=US-ASCII; format=flowed
Hi Will
can you take the same images with freeview and send them along? Also:
tell us a bit about your images. What format did they start in? Were they
dicoms?
Bruce
On Mon, 25 Jan 2016, will brown wrote:
> Hi all,
> After attempting recon-all I received the error "mritotal failed, see
> transforms/talairach.log" etc which I understand may have something to do
> with bad output from registration. I've checked orig.mgz which does look out
> of line - the orientation is off so that it appears the subject has their
> head tilted off to one side (see Image1.jpg).
>
> I have tried to fix this manually with the help of this tutorial:
>
> http://freesurfer.net/fswiki/FsTutorial/Talairach_freeview
>
> Hovever, the "movable" blurry image that I'm trying to line up with my
> subjects image does not match the coronal, sagittal or horizontal views,
> e.g. when I click "coronal" my subject is displayed correctly but the
> movable image is displayed horizontally (see Image2.jpg and Image3.jpg).
>
> Am I missing something obvious? (and am I even on the right track given this
> error?)
>
> Thanks in advance for any help.
>
> Cheers,
> Will
>
>
------------------------------
Message: 2
Date: Sun, 24 Jan 2016 18:36:11 -0800
From: Jasmin Alves <jalves@usc.edu>
Subject: [Freesurfer] recon -all errors
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<CACuamQ5whG9jjQLPvD5Hq4BAF+=C4ZvrACb3PrF2+KAx=aLN=Q@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"
Hello Freesurfer,
I am trying to learn freesurfer and ran into the following issues below
running the recon -all command.
FREESURFER_HOME: /Applications/freesurfer
Build stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0
Kernel info: Darwin 14.5.0 x86_64
1)
joya
2)
Jasmins-MacBook-Pro:subjects jasminalves$ recon-all -i
T1_original_joya.nii -subject joya -all &
3)
[1] 12300
Jasmins-MacBook-Pro:subjects jasminalves$ mkdir:
/Applications/freesurfer/subjects/joya: Permission denied
mkdir: /Applications/freesurfer/subjects/joya/scripts: Permission denied
mkdir: /Applications/freesurfer/subjects/joya/scripts: Permission denied
cp: /Applications/freesurfer/subjects/joya/scripts/build-stamp.txt: No such
file or directory
cat: /Applications/freesurfer/subjects/joya/scripts/build-stamp.txt: No
such file or directory
INFO: FreeSurfer build stamps do not match
Subject Stamp:
Current Stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0
INFO: SUBJECTS_DIR is /Applications/freesurfer/subjects
Actual FREESURFER_HOME /Applications/freesurfer
/Applications/freesurfer/subjects/joya: No such file or directory.
[1]+ Exit 1 recon-all -i T1_original_joya.nii -subject
joya -a
Thank you,
Jasmin
Jasmin Alves
Predoctoral Student
Medical Biology Graduate Program
University of Southern California
jalves@usc.edu
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Message: 3
Date: Mon, 25 Jan 2016 03:55:01 +0000
From: Ankita Chatterjee <achat04@gmail.com>
Subject: Re: [Freesurfer] Processing .mnc files
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<CAGG19OQ=36Q5O9QfCoTmkx1T4hMdWT6-0HTNU+ihvOrY0LHuTg@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"
Thank you for your help! The process took 22 hours, but it completed
without errors! Now I will start looking at the output to analyze.
I was wondering if it is possible to run 3-4 of the freesurfer processes
like recon-all simultaneously? I will be running these on a Mac with 8 Ghz
of Memory and a 2.66 GHz processor - is that sufficient hardware capability
to run several simultaneous processes?
Thanks again!
Ankita
On Sun, Jan 24, 2016 at 6:41 AM Bruce Fischl <fischl@nmr.mgh.harvard.edu>
wrote:
> nope, keep waiting. Depending on your hardware and how different the
> anatomy is from normal it can take up to a day.
>
> as for LGI, check recon-all -help
> cheers
> Bruce
> On Sun, 24 Jan 2016, Ankita
> Chatterjee wrote:
>
> > I ran the command recon-all -all -s t2 -i t1xxxxx.mnc as Bruce suggested
> and
> > the process took off but has been running for more than 6 hours and
> seems to
> > be not doing anything after the step which reads MRISunfold() max_passes
> = 1
> > -----------it has a few steps after that, but doesn't say that it
> completed.
> > The last line reads -
> > randomSeed 1234. Is it hung? Should I exit the program?
> >
> > Thank you for your help!
> > Ankita
> >
> >_______________________________________________
> 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
> 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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Message: 4
Date: Sun, 24 Jan 2016 23:11:54 -0500
From: Bruce Fischl <fischl@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Processing .mnc files
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <764A39E9-F19D-4C04-A94E-7EFAE6F101BA@nmr.mgh.harvard.edu>
Content-Type: text/plain; charset="us-ascii"
Hi Ankita
Glad it worked :) How many cores do you have? If only 1 there is nothing to be gained by running them in parallel. If more than 1 I think you should be able to fit at least two in that much ram, but perhaps someone else can comment? Maybe 3?
Cheers
Bruce
> On Jan 24, 2016, at 10:55 PM, Ankita Chatterjee <achat04@gmail.com> wrote:
>
> Thank you for your help! The process took 22 hours, but it completed without errors! Now I will start looking at the output to analyze.
>
> I was wondering if it is possible to run 3-4 of the freesurfer processes like recon-all simultaneously? I will be running these on a Mac with 8 Ghz of Memory and a 2.66 GHz processor - is that sufficient hardware capability to run several simultaneous processes?
>
> Thanks again!
> Ankita
>
>> On Sun, Jan 24, 2016 at 6:41 AM Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:
>> nope, keep waiting. Depending on your hardware and how different the
>> anatomy is from normal it can take up to a day.
>>
>> as for LGI, check recon-all -help
>> cheers
>> Bruce
>> On Sun, 24 Jan 2016, Ankita
>> Chatterjee wrote:
>>
>> > I ran the command recon-all -all -s t2 -i t1xxxxx.mnc as Bruce suggested and
>> > the process took off but has been running for more than 6 hours and seems to
>> > be not doing anything after the step which reads MRISunfold() max_passes = 1
>> > -----------it has a few steps after that, but doesn't say that it completed.
>> > The last line reads -
>> > randomSeed 1234. Is it hung? Should I exit the program?
>> >
>> > Thank you for your help!
>> > Ankita
>> >
>> >_______________________________________________
>> 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.
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Message: 5
Date: Mon, 25 Jan 2016 09:39:53 +0100
From: Erik Lindberg <erikoloflindberg@gmail.com>
Subject: Re: [Freesurfer] mri_binarize --i sig.cluster.mgh --min 1.3
--o thresholded.mgh 1.3 = -log10(.05)
To: freesurfer@nmr.mgh.harvard.edu
Message-ID:
<CA+71YOir4vkPNSoESQXSd7SnscBKrTBS7w0WsVD+iMnbwAvSkQ@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"
Dear Douglas and Freesufers,
You suggested:
mri_binarize --i sig.cluster.mgh --min 1.3 --o thresholded.mgh 1.3 =
-log10(.05)
I tried this and was expecting that I would get a three-dimensional mask in
which the statistical significant part would be white and the rest black.
This seems not to be the case. While the program is telling me that it is
creating a mask in which x-number of voxels are included I cannot see
anything when I open the thresholded.mgh (in Freeview) Further when I look
at the dimensions of the generated image it seems to have 27307 ?slices? in
one direction but only one and 6 slices in the other directions.
Is this the wrong approach for creating a 3-dimensional mask for the region
with the significant clusters?
Best
Eric
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Message: 6
Date: Mon, 25 Jan 2016 09:43:29 +0100
From: Luigi Antelmi <luigi.antelmi@gmail.com>
Subject: [Freesurfer] hippocampal subfields - multispectral
segmentation with FLAIR
To: freesurfer@nmr.mgh.harvard.edu
Message-ID:
<CA+erP2_y34F-C5r7Uq3=qi7gBVWBttx6Xw2RG4sx2FKfyZ0jnQ@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"
Dear members,
in our center we are evaluating whether to introduce a T2 into a protocol
that, among others, already includes a T1 and a FLAIR sequences.
Our main concern is to to maximize the information-to-duration ratio of the
entire protocol.
In order to improve the subfields' segmentation we read that it is better
to add a T2 or "other" sequences.
Will the FLAIR alone (+T1) can work well as the T2?
If instead the T2 is preferable, what is the coarsest-but-still-informative
resolution you suggest?
Thank you for sharing your experience!
Have a nice day,
Luigi.
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------------------------------
Message: 7
Date: Mon, 25 Jan 2016 10:02:11 +0100 (CET)
From: Eugenio Iglesias <e.iglesias@bcbl.eu>
Subject: Re: [Freesurfer] hippocampal subfields - multispectral
segmentation with FLAIR
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <2126229362.814626.1453712531163.JavaMail.zimbra@bcbl.eu>
Content-Type: text/plain; charset="utf-8"
Ciao Luigi,
I haven't tried FLAIR for images the subfields, but if you sent me a high-res FLAIR acquisition of the hippocampus, I could take a look.
If you are doing T2, you could implement the procotol used in ADNI: coronal slices with 0.4x0.4 in plane resolution, with 2mm slice separation (ideally, you would position the box in an slightly oblique positions such that the coronal slices cut the hippocampus perpendicularly to it major axis).
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
From: "Luigi Antelmi" <luigi.antelmi@gmail.com>
To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu>
Sent: Monday, January 25, 2016 9:43:29 AM
Subject: [Freesurfer] hippocampal subfields - multispectral segmentation with FLAIR
Dear members,
in our center we are evaluating whether to introduce a T2 into a protocol that, among others, already includes a T1 and a FLAIR sequences.
Our main concern is to to maximize the information-to-duration ratio of the entire protocol.
In order to improve the subfields' segmentation we read that it is better to add a T2 or "other" sequences.
Will the FLAIR alone (+T1) can work well as the T2?
If instead the T2 is preferable, what is the coarsest-but-still-informative resolution you suggest?
Thank you for sharing your experience!
Have a nice day,
Luigi.
_______________________________________________
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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Message: 8
Date: Mon, 25 Jan 2016 09:33:52 -0500 (EST)
From: Bruce Fischl <fischl@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] recon -all errors
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<alpine.LRH.2.20.1601250932260.8444@door.nmr.mgh.harvard.edu>
Content-Type: text/plain; charset="utf-8"
Hi Jasmin
you need to create a directory where you have write permission and room
for the subject reconstruction to be written to, then set the SUBJECTS_DIR
environment variable to point to it. At the moment you are trying to use
the subject directory we distribute, which is in some system (and
read-only) location. You can do this on the command line of recon-all via:
recon-all -sd <path to directory> ...
cheers
Bruce
On Sun, 24 Jan 2016, Jasmin Alves
wrote:
> Hello Freesurfer,
>
> I am trying to learn freesurfer and ran into the following issues below
> running the recon -all command.?
>
> FREESURFER_HOME: /Applications/freesurfer
>
> Build stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0
>
> Kernel info: Darwin 14.5.0 x86_64
>
> ??1)?
>
> joya
>
> ?2)?
>
> ?Jasmins-MacBook-Pro:subjects jasminalves$ recon-all -i T1_original_joya.nii
> -subject joya -all &
>
>
> 3)
>
> [1] 12300?
>
> Jasmins-MacBook-Pro:subjects jasminalves$ mkdir:
> /Applications/freesurfer/subjects/joya: Permission denied
>
> mkdir: /Applications/freesurfer/subjects/joya/scripts: Permission denied
>
> mkdir: /Applications/freesurfer/subjects/joya/scripts: Permission denied
>
> cp: /Applications/freesurfer/subjects/joya/scripts/build-stamp.txt: No such
> file or directory
>
> cat: /Applications/freesurfer/subjects/joya/scripts/build-stamp.txt: No such
> file or directory
>
> INFO: FreeSurfer build stamps do not match
>
> Subject Stamp:?
>
> Current Stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0
>
> INFO: SUBJECTS_DIR is /Applications/freesurfer/subjects
>
> Actual FREESURFER_HOME /Applications/freesurfer
>
> /Applications/freesurfer/subjects/joya: No such file or directory.
>
>
> [1]+? Exit 1? ? ? ? ? ? ? ? ? recon-all -i T1_original_joya.nii -subject
> joya -a
>
> Thank you,Jasmin
>
> Jasmin AlvesPredoctoral Student?
> Medical Biology Graduate Program?
> University of Southern California
> jalves@usc.edu?
>
>
>
------------------------------
Message: 9
Date: Mon, 25 Jan 2016 09:35:11 -0500 (EST)
From: Bruce Fischl <fischl@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] mri_binarize --i sig.cluster.mgh --min 1.3
--o thresholded.mgh 1.3 = -log10(.05)
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<alpine.LRH.2.20.1601250934290.8444@door.nmr.mgh.harvard.edu>
Content-Type: text/plain; charset="utf-8"
Hi Erik
what is the dimensionality of sig.cluster.mgh? You can tell this with
mri_info. It is problaby a surface overlay (so nvertices in one dimension),
and can't be viewed in the volume but only on the surface.
cheers
Bruce
On Mon, 25 Jan 2016, Erik Lindberg wrote:
>
> Dear Douglas and Freesufers,
>
> ?
>
> You suggested:
>
> mri_binarize --i sig.cluster.mgh --min 1.3 --o thresholded.mgh 1.3 =
> -log10(.05)
>
> ?
>
> I tried this and was expecting that I would get a three-dimensional mask in
> which the statistical significant part would be white and the rest black.
>
> This seems not to be the case. While the program is telling me that it is
> creating a mask in which x-number of voxels are included I cannot see
> anything when I open the thresholded.mgh (in Freeview) Further when I look
> at the dimensions of the generated image it seems?to have 27307 ?slices? in
> one direction but only one and 6 slices in the other directions.
>
>
>
> ?
>
> Is this the wrong approach for creating a 3-dimensional mask for the region
> with the significant clusters?
>
> ?
>
> Best
>
> Eric
>
>
>
------------------------------
Message: 10
Date: Mon, 25 Jan 2016 16:22:28 +0100
From: Erik Lindberg <erikoloflindberg@gmail.com>
Subject: Re: [Freesurfer] mri_binarize --i sig.cluster.mgh --min 1.3
--o thresholded.mgh 1.3 = -log10(.05)
To: freesurfer@nmr.mgh.harvard.edu
Message-ID:
<CA+71YOg=553F5VKCPLP5Ghmh5-8Z6DCJDssM5qu9E8DiPG-NWw@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"
Dear Bruce and Freesurfers,
I probably then go about this in the wrong way. My aim is to create a
binary mask for regions that I found differences in - in a
group-comparison. I then want to export the mask so I can use it as
seed area in an fMRI analysis.
Can this be done
Thanks
Eric
Hi Erik
what is the dimensionality of sig.cluster.mgh? You can tell this with mri_info.
It is problaby a surface overlay (so nvertices in one dimension), and can't
be viewed in the volume but only on the surface.
cheers
Bruce
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Message: 11
Date: Mon, 25 Jan 2016 10:27:26 -0500 (EST)
From: Bruce Fischl <fischl@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] mri_binarize --i sig.cluster.mgh --min 1.3
--o thresholded.mgh 1.3 = -log10(.05)
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<alpine.LRH.2.20.1601251026280.8444@door.nmr.mgh.harvard.edu>
Content-Type: text/plain; charset="utf-8"
yes, but do you want to do the fMRI analysis on the surface or in the
volume? There are lots of advantages to doing it on the surface. If your
sig.cluster.mgh was a surface overlay then the threholded.mgh might be
exactly what you want. Load it on an inflated surface and take a look
cheers
Bruce
On Mon, 25 Jan 2016, Erik Lindberg wrote:
>
> Dear Bruce and Freesurfers,
>
> I probably then go about this in the wrong way. My aim is to create a binary
> mask for regions that I found differences in - in a group-comparison. I the
> n want to export the mask so I can use it as seed area in an fMRI analysis.
>
> Can this be done
>
> Thanks
> Eric
>
> Hi Erik
>
> what is the dimensionality of sig.cluster.mgh? You can tell this
> with?mri_info. It is problaby a surface overlay (so nvertices in one
> dimension),?and can't be viewed in the volume but only on the surface.
>
> cheers
> Bruce
>
>
>
------------------------------
Message: 12
Date: Mon, 25 Jan 2016 16:39:52 +0100 (CET)
From: <stdp82@virgilio.it>
Subject: [Freesurfer] FDR map: hide very little cluster
To: freesurfer@nmr.mgh.harvard.edu
Message-ID:
<1004043139.1736401453736392850.JavaMail.httpd@fep-webmail-18.iol.local>
Content-Type: text/plain; charset="utf-8"
Hi list,please, could you help me because from several days I'm trying to have a solution.I have performed a seed-based fcMRI analysis by FAST.After mri_glmfit, I have obtained a sig.nii.gz which contains uncorrected results.I have corrected by FDR using the graphical interface provided in tksurfur. The FDR corrected contains some very small areas (<5-10 voxels) which I would like to hide in order to present a more clear map. How is possible to do it?I have tried with mri_surfcluster. To have vwsig.nii.gz I should have a CSD file. But this file could be also produced when FDR correction is applied? I'm very confused.Thank you very much for your work.Kind regards.
Stefano
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Message: 13
Date: Mon, 25 Jan 2016 10:47:39 -0500 (EST)
From: Bruce Fischl <fischl@nmr.mgh.harvard.edu>
Subject: [Freesurfer] [All] position available immediately
To: freesurfer@nmr.mgh.harvard.edu
Cc: "Dara S. Manoach" <dara@nmr.mgh.harvard.edu>
Message-ID:
<alpine.LRH.2.20.1601251047230.8444@door.nmr.mgh.harvard.edu>
Content-Type: text/plain; charset="utf-8"
Research?Coordinator Position in Psychiatric Neuroimaging at the
MGH-Martinos Center:
?
We are looking to hire a college graduate?with at least one year of research
experience and strong organizational and?interpersonal skills as a full time
research?coordinator.??The position involves working on or several?projects
investigating the neural basis and nature of cognitive deficits in
schizophrenia?and autism spectrum?disorder. The techniques employed include
polysomnography?(sleep electroencephaolography), functional magnetic
resonance imaging (fMRI),?magneto- and?electroencephalography (MEG/EEG), and
diffusion tensor imaging?(DTI).??Responsibilities are varied and?will
include conducting overnight sleep studies at the MGH?Clinical
Research?Center. The coordinator will work closely with the Principal
Investigator, lab?mates, and collaborators on all aspects of the research
projects.?Training in?data acquisition and analysis will be
provided.??Responsibilities include managing patient studies, recruitment,
screening?and characterization of?participants, maintaining accurate
records, and?assisting with grant applications, human subject applications,
and?publications.??Knowledge of Mac and/or Linux/UNIX?operating systems as
well as some programming experience are an asset, as is a?high level of
comfort with novel computer applications and environments.??We use?Matlab
and/or unix scripting in many?of our analyses. A background in psychology,
statistics, and neuroscience is an?asset.??A mentored research project
is?encouraged.??The candidate must be mature?and responsible with excellent
organizational, interpersonal as well as oral?and written communication
skills.??S/He?must be?able to work independently in a fast-paced
environment, juggle and?prioritize multiple tasks, feel comfortable working
with clinical and?non-clinical study populations,?working as part of a team
and seek assistance?when appropriate.??This is an excellent?research
opportunity for someone bound for graduate school in psychology,?cognitive
neuroscience, or medicine.??Position is available immediately.??A two-year
commitment is required.??Please submit a resume, writing sample,
college?transcript (unofficial?is fine) and contact information for three
references to?Dara Manoach <dara@nmr.mgh.harvard.edu>
Dara S. Manoach, Ph.D.
Psychiatric Neuroimaging and
Athinoula A. Martinos Center for Biomedical Imaging
Massachusetts General Hospital
Charlestown Navy Yard
149 13th Street, Room 1.111
Charlestown, MA 02129
email:?dara@nmr.mgh.harvard.edu
phone: 617-724-6148
fax: 617-726-4078
http://nmr.mgh.harvard.edu/manoachlab
??? I am dictating emails. Please excuse typos, word substitutions and the
lack of appropriate capitalization and punctuation. ???
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All mailing list
All@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/all
------------------------------
Message: 14
Date: Mon, 25 Jan 2016 11:03:41 -0500
From: Douglas Greve <greve@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] mri_binarize --i sig.cluster.mgh --min 1.3
--o thresholded.mgh 1.3 = -log10(.05)
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <56A6475D.40301@nmr.mgh.harvard.edu>
Content-Type: text/plain; charset="windows-1252"
please remember to include previous correspondences. We can't remember
every post ...
On 1/25/16 3:39 AM, Erik Lindberg wrote:
>
> Dear Douglas and Freesufers,
>
> You suggested:
>
> mri_binarize --i sig.cluster.mgh --min 1.3 --o thresholded.mgh 1.3 =
> -log10(.05)
>
> I tried this and was expecting that I would get a three-dimensional
> mask in which the statistical significant part would be white and the
> rest black.
>
> This seems not to be the case. While the program is telling me that it
> is creating a mask in which x-number of voxels are included I cannot
> see anything when I open the thresholded.mgh (in Freeview) Further
> when I look at the dimensions of the generated image it seems to have
> 27307 ?slices? in one direction but only one and 6 slices in the other
> directions.
>
>
>
> Is this the wrong approach for creating a 3-dimensional mask for the
> region with the significant clusters?
>
> Best
>
> Eric
>
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Message: 15
Date: Mon, 25 Jan 2016 11:10:47 -0500
From: Douglas Greve <greve@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] FDR map: hide very little cluster
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <56A64907.6010105@nmr.mgh.harvard.edu>
Content-Type: text/plain; charset="windows-1252"
Use the --minarea option to mri_surfcluster (not the CSD).
On 1/25/16 10:39 AM, stdp82@virgilio.it wrote:
> Hi list,
> please, could you help me because from several days I'm trying to have a solution.
> I have performed a seed-based fcMRI analysis by FAST.
> After mri_glmfit, I have obtained a sig.nii.gz which contains uncorrected results.I have corrected by FDR using the graphical interface provided in tksurfur. The FDR corrected contains some very small areas (<5-10 voxels) which I would like to hide in order to present a more clear map. How is possible to do it?I have tried with mri_surfcluster. To have vwsig.nii.gz I should have a CSD file. But this file
> could be also produced when FDR correction is applied? I'm very confused.
> Thank you very much for your work.
> Kind regards.
> Stefano
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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------------------------------
Message: 16
Date: Mon, 25 Jan 2016 17:21:21 +0100 (CET)
From: <stdp82@virgilio.it>
Subject: [Freesurfer] R: Re: FDR map: hide very little cluster
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<991888114.1746961453738881317.JavaMail.httpd@fep-webmail-18.iol.local>
Content-Type: text/plain; charset="utf-8"
Thanks. But I do not know how I can obtain a corrected sig.nii.gz.In this way I have obtained only summary.txt.If I add --vwsig vwsig cds file is request.
Stefano
----Messaggio originale----
Da: Douglas Greve <greve@nmr.mgh.harvard.edu>
Data: 25-gen-2016 17.10
A: <freesurfer@nmr.mgh.harvard.edu>
Ogg: Re: [Freesurfer] FDR map: hide very little cluster
Use the --minarea option to mri_surfcluster (not the CSD).
On 1/25/16 10:39 AM, stdp82@virgilio.it
wrote:
Hi list,
please, could you help me because from several days I'm trying to have a solution.I have performed a seed-based fcMRI analysis by FAST.
After mri_glmfit, I have obtained a sig.nii.gz which contains uncorrected results.I have corrected by FDR using the graphical interface provided in tksurfur. The FDR corrected contains some very small areas (<5-10 voxels) which I would like to hide in order to present a more clear map. How is possible to do it?I have tried with mri_surfcluster. To have vwsig.nii.gz I should have a CSD file. But this file
could be also produced when FDR correction is applied? I'm very confused.
Thank you very much for your work.
Kind regards.
Stefano
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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------------------------------
Message: 17
Date: Mon, 25 Jan 2016 17:25:44 +0100 (CET)
From: <stdp82@virgilio.it>
Subject: [Freesurfer] R: Re: FDR map: hide very little cluster
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<922672514.1748331453739144229.JavaMail.httpd@fep-webmail-18.iol.local>
Content-Type: text/plain; charset="utf-8"
Please could you suggest me an example of command line.I'm trying from several day without results.Thank you very much.
Stefano
----Messaggio originale----
Da: Douglas Greve <greve@nmr.mgh.harvard.edu>
Data: 25-gen-2016 17.10
A: <freesurfer@nmr.mgh.harvard.edu>
Ogg: Re: [Freesurfer] FDR map: hide very little cluster
Use the --minarea option to mri_surfcluster (not the CSD).
On 1/25/16 10:39 AM, stdp82@virgilio.it
wrote:
Hi list,
please, could you help me because from several days I'm trying to have a solution.I have performed a seed-based fcMRI analysis by FAST.
After mri_glmfit, I have obtained a sig.nii.gz which contains uncorrected results.I have corrected by FDR using the graphical interface provided in tksurfur. The FDR corrected contains some very small areas (<5-10 voxels) which I would like to hide in order to present a more clear map. How is possible to do it?I have tried with mri_surfcluster. To have vwsig.nii.gz I should have a CSD file. But this file
could be also produced when FDR correction is applied? I'm very confused.
Thank you very much for your work.
Kind regards.
Stefano
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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------------------------------
Message: 18
Date: Mon, 25 Jan 2016 11:30:17 -0500
From: Douglas N Greve <greve@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] R: Re: FDR map: hide very little cluster
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <56A64D99.8010506@nmr.mgh.harvard.edu>
Content-Type: text/plain; charset=windows-1252; format=flowed
just use the FDR thresholded input and set --thmin to 0.5
On 01/25/2016 11:21 AM, stdp82@virgilio.it wrote:
> Thanks. But I do not know how I can obtain a corrected sig.nii.gz.
> In this way I have obtained only summary.txt.
> If I add --vwsig vwsig cds file is request.
>
> Stefano
>
> ----Messaggio originale----
> Da: Douglas Greve <greve@nmr.mgh.harvard.edu>
> Data: 25-gen-2016 17.10
> A: <freesurfer@nmr.mgh.harvard.edu>
> Ogg: Re: [Freesurfer] FDR map: hide very little cluster
>
> Use the --minarea option to mri_surfcluster (not the CSD).
>
> On 1/25/16 10:39 AM, stdp82@virgilio.it wrote:
>> Hi list,
>> please, could you help me because from several days I'm trying to have a solution.
>> I have performed a seed-based fcMRI analysis by FAST.
>> After mri_glmfit, I have obtained a sig.nii.gz which contains uncorrected results.I have corrected by FDR using the graphical interface provided in tksurfur. The FDR corrected contains some very small areas (<5-10 voxels) which I would like to hide in order to present a more clear map. How is possible to do it?I have tried with mri_surfcluster. To have vwsig.nii.gz I should have a CSD file. But this file
>> could be also produced when FDR correction is applied? I'm very confused.
>> Thank you very much for your work.
>> Kind regards.
>> Stefano
>>
>>
>> _______________________________________________
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
------------------------------
Message: 19
Date: Mon, 25 Jan 2016 17:31:03 +0100 (CET)
From: <stdp82@virgilio.it>
Subject: [Freesurfer] R: R: Re: FDR map: hide very little cluster
To: freesurfer@nmr.mgh.harvard.edu
Message-ID:
<2070326566.1749871453739463057.JavaMail.httpd@fep-webmail-18.iol.local>
Content-Type: text/plain; charset="utf-8"
mri_surfcluster --in intercept/sig.nii.gz --hemi rh --sign abs --no-adjust --fdr 0.05 --minarea 5 --sum summaryfile --subject fsaverage --annot aparc
produces only summary.txt
mri_surfcluster --in intercept/sig.nii.gz --hemi rh --sign abs --no-adjust --fdr 0.05 --minarea 5 --sum summaryfile --subject fsaverage --annot aparc --vwsig vwsig.nii.gzERROR: need csd with --vwsig
How can I obtain/visualize the correspective map to summary.txt?
Thanks,
Stefano
----Messaggio originale----
Da: stdp82@virgilio.it
Data: 25-gen-2016 17.25
A: "Freesurfer support list"<freesurfer@nmr.mgh.harvard.edu>
Ogg: [Freesurfer] R: Re: FDR map: hide very little cluster
Please could you suggest me an example of command line.I'm trying from several day without results.Thank you very much.
Stefano
----Messaggio originale----
Da: Douglas Greve <greve@nmr.mgh.harvard.edu>
Data: 25-gen-2016 17.10
A: <freesurfer@nmr.mgh.harvard.edu>
Ogg: Re: [Freesurfer] FDR map: hide very little cluster
Use the --minarea option to mri_surfcluster (not the CSD).
On 1/25/16 10:39 AM, stdp82@virgilio.it
wrote:
Hi list,
please, could you help me because from several days I'm trying to have a solution.I have performed a seed-based fcMRI analysis by FAST.
After mri_glmfit, I have obtained a sig.nii.gz which contains uncorrected results.I have corrected by FDR using the graphical interface provided in tksurfur. The FDR corrected contains some very small areas (<5-10 voxels) which I would like to hide in order to present a more clear map. How is possible to do it?I have tried with mri_surfcluster. To have vwsig.nii.gz I should have a CSD file. But this file
could be also produced when FDR correction is applied? I'm very confused.
Thank you very much for your work.
Kind regards.
Stefano
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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------------------------------
Message: 20
Date: Mon, 25 Jan 2016 11:35:27 -0500
From: Douglas N Greve <greve@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] R: R: Re: FDR map: hide very little cluster
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <56A64ECF.7030509@nmr.mgh.harvard.edu>
Content-Type: text/plain; charset=windows-1252; format=flowed
use --o instead of --vwsig
On 01/25/2016 11:31 AM, stdp82@virgilio.it wrote:
>
> mri_surfcluster --in intercept/sig.nii.gz --hemi rh --sign abs
> --no-adjust --fdr 0.05 --minarea 5 --sum summaryfile --subject
> fsaverage --annot aparc
>
>
> produces only summary.txt
>
>
> mri_surfcluster --in intercept/sig.nii.gz --hemi rh --sign abs
> --no-adjust --fdr 0.05 --minarea 5 --sum summaryfile --subject
> fsaverage --annot aparc --vwsig vwsig.nii.gz
>
> ERROR: need csd with --vwsig
>
>
> How can I obtain/visualize the correspective map to summary.txt?
>
>
> Thanks,
>
>
>
> Stefano
>
>
>
> ----Messaggio originale----
> Da: stdp82@virgilio.it
> Data: 25-gen-2016 17.25
> A: "Freesurfer support list"<freesurfer@nmr.mgh.harvard.edu>
> Ogg: [Freesurfer] R: Re: FDR map: hide very little cluster
>
> Please could you suggest me an example of command line.
> I'm trying from several day without results.
> Thank you very much.
>
> Stefano
>
> ----Messaggio originale----
> Da: Douglas Greve <greve@nmr.mgh.harvard.edu>
> Data: 25-gen-2016 17.10
> A: <freesurfer@nmr.mgh.harvard.edu>
> Ogg: Re: [Freesurfer] FDR map: hide very little cluster
>
> Use the --minarea option to mri_surfcluster (not the CSD).
>
> On 1/25/16 10:39 AM, stdp82@virgilio.it wrote:
>> Hi list,
>> please, could you help me because from several days I'm trying to have a solution.
>> I have performed a seed-based fcMRI analysis by FAST.
>> After mri_glmfit, I have obtained a sig.nii.gz which contains uncorrected results.I have corrected by FDR using the graphical interface provided in tksurfur. The FDR corrected contains some very small areas (<5-10 voxels) which I would like to hide in order to present a more clear map. How is possible to do it?I have tried with mri_surfcluster. To have vwsig.nii.gz I should have a CSD file. But this file
>> could be also produced when FDR correction is applied? I'm very confused.
>> Thank you very much for your work.
>> Kind regards.
>> Stefano
>>
>>
>> _______________________________________________
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
>
>
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
------------------------------
Message: 21
Date: Mon, 25 Jan 2016 17:36:35 +0100 (CET)
From: <stdp82@virgilio.it>
Subject: [Freesurfer] R: Re: R: Re: FDR map: hide very little cluster
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<1961786632.1751471453739795152.JavaMail.httpd@fep-webmail-18.iol.local>
Content-Type: text/plain;charset="UTF-8"
Please give an example of the command line.
I have performed fdr correction by tksurfer. Should I save that map?
Thanks
Stefano
>----Messaggio originale----
>Da: Douglas N Greve <greve@nmr.mgh.harvard.edu>
>Data: 25-gen-2016 17.30
>A: <freesurfer@nmr.mgh.harvard.edu>
>Ogg: Re: [Freesurfer] R: Re: FDR map: hide very little cluster
>
>just use the FDR thresholded input and set --thmin to 0.5
>
>On 01/25/2016 11:21 AM, stdp82@virgilio.it wrote:
>> Thanks. But I do not know how I can obtain a corrected sig.nii.gz.
>> In this way I have obtained only summary.txt.
>> If I add --vwsig vwsig cds file is request.
>>
>> Stefano
>>
>> ----Messaggio originale----
>> Da: Douglas Greve <greve@nmr.mgh.harvard.edu>
>> Data: 25-gen-2016 17.10
>> A: <freesurfer@nmr.mgh.harvard.edu>
>> Ogg: Re: [Freesurfer] FDR map: hide very little cluster
>>
>> Use the --minarea option to mri_surfcluster (not the CSD).
>>
>> On 1/25/16 10:39 AM, stdp82@virgilio.it wrote:
>>> Hi list,
>>> please, could you help me because from several days I'm trying to have
a solution.
>>> I have performed a seed-based fcMRI analysis by FAST.
>>> After mri_glmfit, I have obtained a sig.nii.gz which contains
uncorrected results.I have corrected by FDR using the graphical interface
provided in tksurfur. The FDR corrected contains some very small areas (<5-10
voxels) which I would like to hide in order to present a more clear map. How
is possible to do it?I have tried with mri_surfcluster. To have vwsig.nii.gz I
should have a CSD file. But this file
>>> could be also produced when FDR correction is applied? I'm very
confused.
>>> Thank you very much for your work.
>>> Kind regards.
>>> Stefano
>>>
>>>
>>> _______________________________________________
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>>
>>
>>
>> _______________________________________________
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>--
>Douglas N. Greve, Ph.D.
>MGH-NMR Center
>greve@nmr.mgh.harvard.edu
>Phone Number: 617-724-2358
>Fax: 617-726-7422
>
>Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
>www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
>_______________________________________________
>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
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>but does not contain patient information, please contact the sender and
properly
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>
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End of Freesurfer Digest, Vol 143, Issue 39
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