date:20130919

Re: [Freesurfer] recon-all-hippo-subfeilds

2013-09-19 Thread Koen Van Leemput

Hi,

I believe "recon-all -s NC -hippo-subfields" should do that.

Please let us know if it doesn't.

Koen
 On Sep 19, 2013 9:00 AM, "Anupa AV"  wrote:

> Dear FS experts,
>
> I've a query regarding the recon-all analysis.
>
> I ran recon-all using the following command
> eg.
> recon-all -i location/nc.nii -s NC -all
>
> I got the analysis done.
> Now I'm interested to calculate the hippocampal structures.
>
> I knw the command line for that also
>
> recon-all -i location/nc.nii -s NC -all -hippo-subfields
>
>
> Problem for me is that I've 45 subjects. I ran recon-all without
> hippo-subfields commands.
> i.e. from  motion correction to Ex-vivo Entorhinal Cortex Label rh. (log
> file)
>
> Is there any way to do hippo-sufields alone than running the whole steps
> again (which is very time consuming).
>
> Thanks in advance.
>
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>
>
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Re: [Freesurfer] Mappin lesions labels to Talairach space

2013-09-19 Thread Lisa Prilop

I created the label with tkmedit using an MPRage of the patient (1mm isovoxel).

Gesendet: Montag, 16. September 2013 um 17:11 Uhr
Von: "Douglas Greve"
An: freesurfer@nmr.mgh.harvard.edu
Betreff: Re: [Freesurfer] Mappin lesions labels to Talairach space

The problem is probably that each label represents a finite amount of space. If the space between your label points is much more than 1mm, then you will get the pattern you show. How did you create the label in the first place?

doug

On 9/16/13 4:43 PM, Lisa Prilop wrote:

Hi Bruce!

The command line I used was: mri_label2label --srcsubject pat3 --srclabel /home/lisap/CIMT/fscal/pat3/label/testsept9 --trgsubject fsaverage --trglabel /home/lisap/CIMT/fscal/pat3/label/talairach --regmethod volume . The testsept9 -label looks perfectly normal (but corresponds to the original patient - on fsaverage it is wrongly placed), the new talairach-label is the grid i attached as an jpg-file - the location on fsaverage is correct (but not anymore so on the individual patient).

Lisa

Gesendet: Montag, 16. September 2013 um 14:52 Uhr
Von: "Bruce Fischl"
An: "Lisa Prilop"
Cc: freesurfer@nmr.mgh.harvard.edu
Betreff: Re: [Freesurfer] Mappin lesions labels to Talairach space

Hi Lisa what you are seeing is probably the effects of resampling. What did the labels look like before mapping? And you need to send us your full mri_label2label command line so that we (Doug?) can help. cheers Bruce On Mon, 16 Sep 2013, Lisa Prilop wrote: > Hi, > I have the following problem: I'm trying to map lesions from different > patients into talairach space. I hand-drew the lesions and saved them as > labels, then opened them on fsaverage. I didn't get an error-message, but in > the direct comparison between the native label (of the individual patient) > to the transformed label on fsaverage I could see that the lesions were > wrongly placed. I tried that with different flags on mri_label2label. Once > the place was roughly correct but then the label itself looked different (it > was a grid). What can I do to put that right? I attached a jpg-file > demonstrating what i mean. > > Thanks for your help! > > Lisa Prilop > > 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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[Freesurfer] ACFFWHM for surface-based analyses in FSFAST?

2013-09-19 Thread Caspar M. Schwiedrzik

Hi Freesurfer Experts,
mkanalysis-sess seems to default to a FWHM of 20 for the smooting of the
ACF (in version 5.1). I was wondering whether it makes sense to use the
same FWHM for volume and surface based analyses of functional data in
FSFAST? I seem to remember that the autocorrelations differ between, e.g.,
grey and white matter, which might be a reason to use a different FWHM on
the surface?

Thank you very much,
Caspar
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[Freesurfer] Qdec analysis with one group and two covariates (1 dichotomic, 1 continuous)

2013-09-19 Thread E. Scariati

Dear Freesurfer experts,

I would like to study the relationship between cortical thickness and one
clinical variable with qdec, but correcting for age and gender.

Given that I have only one group and 2 covariates (one continuous, one
dichotomic) I don't know how I should set the design of my analysis in
qdec, especially for the gender variable.

I have tried two different ways (both DOSS design):

1) selecting Discrete = gender; Continuous = clinical measure; Nuisance
factor = age
and looking at the contrast called : "Does the correlation between
thickness and clinical measure accounting for gender differ from 0?
nuisance factor : age"

2) selecting : continuous = clinical measure; Nuisance Factor = age, gender
(coded as 1 and 2)
 and looking at the contrast called : "Does the correlation between
thickness and clinical measure differ from 0, nuisance factor : age, gender"

But the two contrasts give very different results, which I find very
surprising. I exported cortical thickness at the peak significance of the
clusters and tried to run a GLM myself in SPSS and it seems that coding
gender as a continuous variable with two values (1 and 2) provides the most
realistic results. However, I saw many times on the mailing list that you
recommend to use gender as a discrete variable, so I am very confused.
Could you explain me the difference between these contrasts and help me to
identify which one will accurately identify the correlation between
cortical thickness and my clinical variable correcting for the effect of
age and gender.

Thank you in advance for your answer,
Best regards
Elisa
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[Freesurfer] mri_glmfit without --cortex?

2013-09-19 Thread Caspar M. Schwiedrzik

Hi FreeSurfer Experts,
I am trying to run a group analysis with a custom fsaverage for which I do
not have a cortex.label file. It seems that in version 5.1, --cortex is
called by default. I did not find a flag to turn this off in the
documentation or the help.
Is there a way to run mri_glmfit without --cortex or an alternative version
where this is turned off?
Thanks, Caspar
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Re: [Freesurfer] Editing WM

2013-09-19 Thread Mihaela Stefan

Hi Louis,

I've got the idea about the wm edits, but I have a related question. From
what I see, that's a coronal cut at the level of the amygdala & basal
ganglia. Isn't that the "gray area"? How relevant is to make edits in that
area?

Thanks!
Mihaela


On Thu, Sep 19, 2013 at 4:07 PM, Louis Nicholas Vinke <
vi...@nmr.mgh.harvard.edu> wrote:

> Hi Francesco,
> If it is the portion of the wm surface I have circled in red, then I'd
> suggest looking a couple slices anterior and posterior to the current slice
> and erase any other falsely labeled wm voxels on the wm.mgz, even if the wm
> surf (blue line) doesn't currently include them.
>
> FYI, I've cc'ed the freesurfer list so others can chime in.
>
> -Louis
>
> On Thu, 12 Sep 2013, Francesco Siciliano wrote:
>
>  Hi Louis,
>>
>> Thanks for the reply! I've attached a screen cap. Unfortunately, my
>> cursor gets removed from screen caps, but I had the area highlighted with
>> my cursor and the intensity was a value of 1, indicating that I had edited
>> the area prior to running recon-all again. The area in question is the
>> jagged portion of the WM surface in the lower center of the screen above
>> the right temporal lobe).
>>
>> -Francesco
>> __**__
>> From: Louis Nicholas Vinke [vi...@nmr.mgh.harvard.edu]
>> Sent: Tuesday, September 10, 2013 5:55 PM
>> To: Francesco Siciliano
>> Cc: freesurfer@nmr.mgh.harvard.edu
>> Subject: Re: [Freesurfer] Editing WM
>>
>>
>> Hi Francesco,
>> Could you maybe send a snapshot of the brainmask and wm volumes where you
>> are seeing this?
>>
>> If you deleted any voxels on the wm mask then they should be a value of 1.
>>
>> You might want to look at the ?h.orig.nofix surfaces to see if that area
>> in question looks better (or at least different).  Ultimately the position
>> of the wm surface is what is important, not the presence or absence of wm
>> voxels (in the wm.mgz) which basically just initialize the wm surfaces.
>> -Louis
>>
>> On Mon, 9 Sep 2013, Francesco Siciliano wrote:
>>
>>  Hi,
>>> I've noticed that occasionally when I manually edit recons, the white
>>> matter
>>> surface will be drawn to include a portion of the volume where no white
>>> matter
>>> pixels are present. Therefore, when I go to correct the incorrectly drawn
>>> surface, there are no pixels to delete under the white matter mask. It is
>>> almost as if I have deleted the pixels already yet I have not and the
>>> white
>>> matter surface is still drawn to include an area where there are no white
>>> matter pixels. Why could this be happening? Does it matter as long as
>>> there
>>> are no pixels in the incorrect area?
>>>
>>> Thank you,
>>>
>>> Francesco
>>>
>>> Francesco Siciliano, B.A. Research Assistant
>>> Department of Child and Adolescent Psychiatry
>>> The New York State Psychiatric Institute
>>> Columbia University
>>> 1051 Riverside Drive, Unit 74
>>> New York, NY 10032
>>> (212) 543-6155
>>>
>>>
>>>
>>
>> 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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Re: [Freesurfer] recon-all-hippo-subfeilds

2013-09-19 Thread Anupa AV

Dear Koen,

It worked...
Thanks a lot





 From: Koen Van Leemput 
To: Anupa AV  
Cc: Freesurfer Mailinglist ; Bruce Fischl 
 
Sent: Thursday, September 19, 2013 12:48 PM
Subject: Re: [Freesurfer] recon-all-hippo-subfeilds
 


Hi,
I believe "recon-all -s NC -hippo-subfields" should do that.
Please let us know if it doesn't.
Koen

On Sep 19, 2013 9:00 AM, "Anupa AV"  wrote:

Dear FS experts,
>
>
>I've a query regarding the recon-all analysis.
>
>
>I ran recon-all using the following command 
>
>eg.
>
>recon-all -i location/nc.nii -s NC -all
>
>
>I got the analysis done.
>Now I'm interested to calculate the hippocampal structures.
>
>
>I knw the command line for that also 
>
>
>
>recon-all -i location/nc.nii -s NC -all -hippo-subfields
>
>
>
>
>Problem for me is that I've 45 subjects. I ran recon-all without 
>hippo-subfields commands.
>i.e. from  motion correction to Ex-vivo Entorhinal Cortex Label rh. (log file)
>
>
>
>Is there any way to do hippo-sufields alone than running the whole steps again 
>(which is very time consuming).
>
>
>Thanks in advance.
>
>___
>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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Re: [Freesurfer] recon-all-hippo-subfeilds

Re: [Freesurfer] Mappin lesions labels to Talairach space

[Freesurfer] ACFFWHM for surface-based analyses in FSFAST?

[Freesurfer] Qdec analysis with one group and two covariates (1 dichotomic, 1 continuous)

[Freesurfer] mri_glmfit without --cortex?

Re: [Freesurfer] Editing WM

Re: [Freesurfer] recon-all-hippo-subfeilds

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