[Freesurfer] Cerebellar Vermis

[Sarosh, Cyrus]

We are interested in using the Cerebellar vermis for an analysis with our PET 
data. Is the cerebellar vermis segmented during the FreeSurfer pipeline 
analysis? If it is, which file is it located in or how can I export a nifti 
file containing this segmentation?

Thanks,

Cyrus Sarosh
[Description: Description: Description: Description: Description: Description: 
Description: cid:image002.png@01CC3BB7.F8D9A990]
Research Technician Senior
Department of Radiology
Functional Neuroimaging, Cognitive and Mobility Laboratory


**
Electronic Mail is not secure, may not be read every day, and should not be 
used for urgent or sensitive issues 
___
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.

Re: [Freesurfer] (no subject)

[Z K]

The XQuartz upgrade from v2.7.5 to v2.7.6 broke some of the FreeSurfer 
GUIs. Please reinstall XQuartz v2.7.5. It can be downloaded from this 
page (http://xquartz.macosforge.org/trac/wiki/Releases).

On 07/14/2014 04:41 AM, Hugh Pemberton wrote:
> Hi everyone, I'm getting the follow error and it's jus started happening
> after updating Xquartz.. any ideas what I can do? Also, i dont have a
> .debug_tkmedit file, when tkmedit was running normally the first line
> would say could not create debug file.
>
> Many thanks,
> Hugh
>
> ERROR: A segfault has occurred. This is not your fault,
>: but is most likely an unrecoverable error and has
>: made the program unstable.
>:
>: Please send the contents of the file .xdebug_tkmedit
>: that should be in this directory to freesurfer@nmr.mgh.harvard.edu
> 
>:
>: Now exiting...
>
>
> ___
> 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


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.

Re: [Freesurfer] Cerebellar Vermis

[Alan Francis]

Hi there:

As of now, FreeSurfer does not parcellate the cerebellar vermis. It gives
you 4 measurements of the cerebellum (Left total, left WM, Right total and
right WM).

There is a toolbox called SUIT that works within SPM 8 that can accomplish
this for you. See details at the website below:

http://www.icn.ucl.ac.uk/motorcontrol/imaging/suit.htm

best,

Alan Francis


On Tue, Jul 15, 2014 at 8:53 AM, Sarosh, Cyrus 
wrote:

>  We are interested in using the Cerebellar vermis for an analysis with
> our PET data. Is the cerebellar vermis segmented during the FreeSurfer
> pipeline analysis? If it is, which file is it located in or how can I
> export a nifti file containing this segmentation?
>
>
>
> Thanks,
>
>
>
> Cyrus Sarosh
>
> [image: Description: Description: Description: Description: Description:
> Description: Description: cid:image002.png@01CC3BB7.F8D9A990]
>
> Research Technician Senior
>
> Department of Radiology
>
> Functional Neuroimaging, Cognitive and Mobility Laboratory
>
>
>
>
>
> **
> Electronic Mail is not secure, may not be read every day, and should not
> be used for urgent or sensitive issues
>
> ___
> 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


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] Making Substancia Nigra label

[Shantanu Ghosh]

Dear Freesurfer experts,

I have a set of T2w Dicoms from Parkinson's patients and Control subjects.

I want to extract and visualize the Substancia Nigra regions of each of
these brains.

Can you please suggest a way to do this (command line instructions would
be great)?

Thanks in advance.
Shantanu


-- 
Shantanu Ghosh, Ph.D.
Harvard Medical School & Massachusetts General Hospital
Martinos Center for Biomedical Imaging
--
Not only is the universe stranger than we think, it is stranger than we
can think. -Werner Heisenberg

___
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] Updated process v. files excel sheet?

[Makaretz, Sara Johanna]

Hi all,

I like the excel presentation of the recon-all process/files table for 
Freesurfer 3.0.5 found here: 
https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllFilesVsSteps
Is there an updated document for a more recent version? (I am using 5.3.0)

Also, are 5.2 and 5.3 similar enough to reference the 5.2 stable table for file 
order/rerunning steps? 
(https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllTableStableV5.2)

Thank you!

Sara


___
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] bad freesurfer segmentation

[Doety Prins]

Hi Bruce,

Thanks for your reply. Yes I realize now that this is causing me the
troubles. But since fsl is able to do a good segmentation, I think
Freesurfer should also be able to do this?

I am now using MRI_segment, in which I want to set new limits for the white
matter, but it doesn't seem to work yet. I use wm.mgz as input volume and
output volume something like wm.new.mgz, and -wm_low and -wm_hi with
different values as optional arguments. But what file should be included as
'classifier file'? I couldn't find that anywhere in the description.

Thanks in advance for your help again!

Doety


Op vrijdag 11 juli 2014 heeft Bruce Fischl  het
volgende geschreven:
> the 2mm slice thickness is going to be problematic and is probably why you
> lose so much cortical constrast. Typically we don't recommend using
> anything more than 1.5 and really no reason these days not to get closer
to
> 1mm (for example, you can get a very nice 1.25mmx1.25x1mm mprage in a bit
> over 2 minutes)
>
> cheers
> Bruce
>
>
> On
> Fri, 11 Jul 2014, Doety Prins wrote:
>
>> slice thickness: 2 mm
>> Repetition time: 25 ms (I think this might have caused the low contrast)
>> flip angle: 30 degrees
>> I'm sorry, can't find any data on acceleration
>>
>> Doety
>>
>> On 11 jul. 2014, at 15:10, Bruce Fischl 
wrote:
>>
>>> Hi Doety
>>>
>>> that is a very low contrast-to-noise image. Can you give us more details
>>> on the acquisition? The matrix was 256x256, what is the slice thickness?
>>> And the other parameter (sequence name? TR/TR/flip angle? acceleration?)
>>>
>>> cheers
>>> Bruce
>>>
>>>
>>> On
>>> Thu, 10 Jul 2014, Doety Prins wrote:
>>>
 Hi Bruce,

 Thanks for your reply. In my previous e-mail I already tried to attach
>>> one of my subjects, but got the response that the message was too big,
and
>>> therefore it was rejected. So how should I upload the image? The images
are
>>> T1-weighted, 3D, acquired with a 3T scanner, resolution 256 256.

 I discovered that FSL does a proper segmentation on this subjects, so
I was looking for a way to import these segments from FSL into the
Freesurfer pipeline, but I didn't succeed so far. I used the white matter
segment from FSL as wm.mgz (in a subject in which I already ran recon-all),
I used mri_vol2vol to get this segment in the right space, and normalized
with mri_normalize. Then I rerun recon-all with -autorecon2-wm. But it
gives me the error message: 'ERROR: mri_segment-MRIcheckVolDims: volume1
depth=160 != volume2 depth=256.' So apparently, the wm.mgz still doesn't
have the right size. Do you have any experience with this? Or any ideas
about this?

 Best regards,

 Doety

 On 9 jul. 2014, at 15:00, Bruce Fischl 
wrote:

> Hi Doety
>
> yes, that looks pretty bad. Can you tell us about the acquisition?
What
> resolution/field strength/scan type was it?
>
> If you upload the subject we will take a look
>
> cheers
> Bruce
> On Wed, 9 Jul 2014, Doety
> Prins
> wrote:
>
>>> Dear freesurfer experts,
>>>
>>> I experienced some problems with the segmentation of my T1 scans,
as both the white surface and the pial surface are placed incorrectly (see
attached images). This seems to me to be a too big difference with what it
should look like, that I think could not be fixed with the standard
troubleshooting strategies.
>>>
>>> Do you have any solutions for this? Is it for instance possible to
make changes to the recon-all script to shift the surfaces?
>>>
>>> Thanks in advance,
>>>
>>> Doety
>>
>>
> ___
> 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



>>> ___
>>> 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
>>
>>
>>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu

Re: [Freesurfer] bad freesurfer segmentation

[Bruce Fischl]

Hi Doety

our segmentation assumes we can resolve cortex as it used an adaptive 
filtering that estimates the orientation of the gray/white boundary in 
spatial neighborhoods. It may be more sensitive to low resolution than FSL. 
Not sure if anyone has a script for importing FSL segmentations into our 
processing pipeline, but someone might.

cheers
Bruce



On Tue, 15 Jul 2014, Doety Prins wrote:

> Hi Bruce,
> 
> Thanks for your reply. Yes I realize now that this is causing me the
> troubles. But since fsl is able to do a good segmentation, I think
> Freesurfer should also be able to do this?
> 
> I am now using MRI_segment, in which I want to set new limits for the white
> matter, but it doesn't seem to work yet. I use wm.mgz as input volume and
> output volume something like wm.new.mgz, and -wm_low and -wm_hi with
> different values as optional arguments. But what file should be included as
> 'classifier file'? I couldn't find that anywhere in the description.
> 
> Thanks in advance for your help again!
> 
> Doety
> 
> 
> Op vrijdag 11 juli 2014 heeft Bruce Fischl  het
> volgende geschreven:
> > the 2mm slice thickness is going to be problematic and is probably why you
> > lose so much cortical constrast. Typically we don't recommend using
> > anything more than 1.5 and really no reason these days not to get closer
> to
> > 1mm (for example, you can get a very nice 1.25mmx1.25x1mm mprage in a bit
> > over 2 minutes)
> >
> > cheers
> > Bruce
> >
> >
> > On
> > Fri, 11 Jul 2014, Doety Prins wrote:
> >
> >> slice thickness: 2 mm
> >> Repetition time: 25 ms (I think this might have caused the low contrast)
> >> flip angle: 30 degrees
> >> I'm sorry, can't find any data on acceleration
> >>
> >> Doety
> >>
> >> On 11 jul. 2014, at 15:10, Bruce Fischl 
> wrote:
> >>
> >>> Hi Doety
> >>>
> >>> that is a very low contrast-to-noise image. Can you give us more details
> >>> on the acquisition? The matrix was 256x256, what is the slice thickness?
> >>> And the other parameter (sequence name? TR/TR/flip angle? acceleration?)
> >>>
> >>> cheers
> >>> Bruce
> >>>
> >>>
> >>> On
> >>> Thu, 10 Jul 2014, Doety Prins wrote:
> >>>
>  Hi Bruce,
> 
>  Thanks for your reply. In my previous e-mail I already tried to attach
> >>> one of my subjects, but got the response that the message was too big,
> and
> >>> therefore it was rejected. So how should I upload the image? The images
> are
> >>> T1-weighted, 3D, acquired with a 3T scanner, resolution 256 256.
> 
>  I discovered that FSL does a proper segmentation on this subjects, so I
> was looking for a way to import these segments from FSL into the Freesurfer
> pipeline, but I didn't succeed so far. I used the white matter segment from
> FSL as wm.mgz (in a subject in which I already ran recon-all), I used
> mri_vol2vol to get this segment in the right space, and normalized with
> mri_normalize. Then I rerun recon-all with -autorecon2-wm. But it gives me
> the error message: 'ERROR: mri_segment-MRIcheckVolDims: volume1 depth=160 !=
> volume2 depth=256.' So apparently, the wm.mgz still doesn't have the right
> size. Do you have any experience with this? Or any ideas about this?
> 
>  Best regards,
> 
>  Doety
> 
>  On 9 jul. 2014, at 15:00, Bruce Fischl 
> wrote:
> 
> > Hi Doety
> >
> > yes, that looks pretty bad. Can you tell us about the acquisition?
> What
> > resolution/field strength/scan type was it?
> >
> > If you upload the subject we will take a look
> >
> > cheers
> > Bruce
> > On Wed, 9 Jul 2014, Doety
> > Prins
> > wrote:
> >
> >>> Dear freesurfer experts,
> >>>
> >>> I experienced some problems with the segmentation of my T1 scans, as
> both the white surface and the pial surface are placed incorrectly (see
> attached images). This seems to me to be a too big difference with what it
> should look like, that I think could not be fixed with the standard
> troubleshooting strategies.
> >>>
> >>> Do you have any solutions for this? Is it for instance possible to
> make changes to the recon-all script to shift the surfaces?
> >>>
> >>> Thanks in advance,
> >>>
> >>> Doety
> >>
> >>
> > ___
> > 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.
> >
> 
> 
>  

Re: [Freesurfer] Temporal lobe reconstruction problem

[james pardon]

Hi Bruce,

I was wondering whether you have seen my email below?

Thanks so much

Cheers,
James


On Sat, Jul 12, 2014 at 9:18 AM, james pardon 
wrote:

> Hi Bruce,
>
> I have sent the link for a problem subject via a private message. Please
> note since MS causes hypointense lesions in white matter I have used an
> algorithm that fills hypointense lesions in WM with median intensity of
> normal appearing WM.
>
> Thanks
> James
>
>
> On Fri, Jul 11, 2014 at 11:19 PM, Bruce Fischl  > wrote:
>
>> Hi James
>>
>> if you upload a problem subject we will take a look (the whole subject
>> dir please)
>> cheers
>> Bruce
>>
>> On Fri, 11 Jul 2014, james pardon wrote:
>>
>>  Hi all,
>>> On a few subjects with a specific pathology (MS) I cannot easily
>>> reconstruct temporal lobes.
>>> I think this issue comes up quite regularly on the mailing list, and I
>>> have tried to trouble
>>> shoot using control points, WM edits, even getting back to orig/001.mgz
>>> to correct areas that
>>> may seem the culprit for breaking surface reconstruction. Some subjects
>>> have gone through 7-8
>>> runs of recon-all with different edits but still the problem persists in
>>> a few subjects in my
>>> study.
>>>
>>> I have also tried to use -mprage and -3T flags along the way to allow
>>> more liberal control
>>> point growing, despite an improvement in my results some of subjects
>>> still have very bad
>>> surface constructions. I have attached two snapshots to this email and I
>>> am happy to upload
>>> the complete subject folder if you need to take a look at them.
>>>
>>> As far as the SNR is concerned, I have designed my study based on
>>> recommended Freesurfer
>>> parameters a couple of years ago on 3T Siemens Trio with 32-channel
>>> receiver coil.
>>>
>>> A huge thank you for your previous helps, and thanks in advance for
>>> helping me with this new
>>> issue.
>>>
>>> James
>>>
>>>
>> ___
>> 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


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.

Re: [Freesurfer] mri_cor2label revisited

[Douglas N Greve]

Are you trying to view it in the volume or the surface? When I run 
freeview viewing the surface and load the label using the "Load Label" 
button (not File->LoadLabel), it works  for me.

Can you try the tksurfer command below? It runs for me. You can ignore 
the warning about 0 nonzero vertices since they are all set to 1.


tksurfer fsaverage lh inflated -label ~/tmp/lh_binarymap_area_covar8.label
subject is fsaverage
hemiis lh
surface is inflated
surfer: current subjects dir: 
/autofs/cluster/con_009/users/greve/ixi-subjects
surfer: not in "scripts" dir ==> using cwd for session root
surfer: session root data dir ($session) set to:
surfer: /autofs/cluster/con_009/users/greve/ixi-subjects/ixi320/mri
checking for nofix files in 'inflated'
Reading image info 
(/autofs/cluster/con_009/users/greve/ixi-subjects/fsaverage)
Reading 
/autofs/cluster/con_009/users/greve/ixi-subjects/fsaverage/mri/orig.mgz
surfer: Reading header info from 
/autofs/cluster/con_009/users/greve/ixi-subjects/fsaverage/mri/orig.mgz
surfer: vertices=163842, faces=327680
surfer: curvature read: min=-0.673989 max=0.540227
surfer: single buffered window
surfer: tkoInitWindow(fsaverage)
setting percentile thresholds (-1.00, 0.00, 0.00)
loading label /homes/4/greve/tmp/lh_binarymap_area_covar8.label
reading white matter vertex locations...
  0 nonzero vertices found 
label stat field identically zero - setting to 1
surfer: using interface 
/autofs/space/tanha_002/users/greve/fsdev.build/tktools/tksurfer.tcl
Reading 
/autofs/space/tanha_002/users/greve/fsdev.build/tktools/tkm_common.tcl
Reading 
/autofs/space/tanha_002/users/greve/fsdev.build/tktools/tkm_wrappers.tcl
Reading 
/autofs/space/tanha_002/users/greve/fsdev.build/lib/tcl/fsgdfPlot.tcl
Reading /autofs/space/tanha_002/users/greve/fsdev.build/tktools/tkUtils.tcl
Successfully parsed tksurfer.tcl
reading white matter vertex locations...



On 07/15/2014 09:04 AM, Lars M. Rimol wrote:
> Hi,
>
> I go to File -> Label -> load label  and there I pick 
> lh_binarymap_area_covar8.label and then I get the error message:
>
>
> %   0 nonzero vertices found 
> label stat field identically zero - setting to 1
>
>
> That's it!
>
> I don't know, but it seems to be saying that all vertices are zero, 
> doesn't it?
>
> When I cat the file, I see this:
>
> 163839  -34.195  -22.897  -24.093 0.00
>
> 163840  -34.295  -23.062  -23.449 0.00
>
> 163841  -35.093  -23.358  -22.788 0.00
>
> The leftmost column surely is vertex number, I don't know what the 
> next two are (if this were a volume, I'd say x,y,z coordinates) and if 
> the final column is the value of each vertex, I would have to agree 
> with tksurfer that there are no nonzero vertices.
>
> When I load the mgh file, thogh, it has some zero vertices and 98877 
> that are 100, that is they are larger than 99.992.
>
> >> size(find(gt(testing,99.992)))
>
> ans =
>
>98877   1
>
>
> Here's the code I used to make the binary map and save it as an mgh file:
>
> log10pID = significance threshold
>
> binaryVLBWlhcovar8(find(gt(binaryVLBWlhcovar8,log10pID))) = 100; 
> binaryVLBWlhcovar8(find(lt(binaryVLBWlhcovar8,log10pID))) = 0;
>
> fs_save_mgh(binaryVLBWlhcovar8,'lh_binarymap_area_covar8.mgh',mri);
>
>
> So mri_cor2label must be changing some of these vertices from 
> 99.9etc. to 0, right?
>
>
> LMR
>
>
>
> On Mon, Jul 14, 2014 at 7:33 PM, Douglas N Greve 
> mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>
>
> It loads ok for me both in 5.1 and 5.3. Can you give more info on
> what is going wrong with tksurfer?
>
>
> On 07/13/2014 05:35 AM, Lars M. Rimol wrote:
>
> Hi Doug,
>
> I'm having some problems with the label creation again. When I
> run mri_cor2label, it seems OK (please see below), but when I
> try to open it in tksurfer, it gives me an error message (bottom).
>
> Would you mind taking a look at this label to see what's wrong
> with it? I'm attaching the binary mgh file and the label. NB!
> The binary .mgh file is from matlab, where I have set all
> suprathreshold vertices to 100 and all others to 0. Of course,
> Matlab doesn't really do this, it sets them to somewhere close
> to 99.992. I don't suppose I could use "greater
> than 99" in mri_cor2label?
>
> #
> creating label:
>
> [LMR in ~ ] mri_cor2label --i
> 
> /home/lmr/ANALYSIS/STUDIER/VMI_Kam_103/OUTDIR/binary_pmaps/lh_binarymap_area_covar8.mgh
> --id 100 --l
> 
> /home/lmr/ANALYSIS/STUDIER/VMI_Kam_103/OUTDIR/binary_pmaps/lh_binarymap_area_covar8
> --surf fsaverage lh
> $Id: mri_cor2label.c,v 1.12 2011/03/02 00:04:14 nicks Exp $
> Loading mri
> 
> /home/lmr/ANALYSIS/STUDIER/VMI_Kam_103/OUTDIR/binary_pmaps/lh_binarymap_area_covar8.mgh
>  

Re: [Freesurfer] Fw: Re: Problem with uploading Cluster Simulation data

[Douglas N Greve]

You have to load a surface and then load the overlay on top of that. See 
the freeview tutorial
doug

ps. Please post to the list!

On 07/15/2014 09:03 AM, car...@van-vlodrop.de wrote:
> I have opened freeview with the commands 'freesurfer' and 'freeview'.
> I thought that I could upload the data directly in freeview. Or which 
> command do I need?
> *Gesendet:* Montag, 14. Juli 2014 um 19:38 Uhr
> *Von:* "Douglas N Greve" 
> *An:* "car...@van-vlodrop.de" , 
> "Freesurfer@nmr.mgh.harvard.edu" 
> *Betreff:* Re: Fw: Aw: Re: [Freesurfer] Problem with uploading Cluster 
> Simulation data
>
> what is your command line? Or otherwise, how are you visualizing it?
>
>
>
> On 07/14/2014 08:09 AM, car...@van-vlodrop.de wrote:
> > *Gesendet:* Sonntag, 06. Juli 2014 um 22:48 Uhr
> > *Von:* "car...@van-vlodrop.de" 
> > *An:* "Freesurfer support list" 
> > *Betreff:* Aw: Re: [Freesurfer] Fw: Problem with uploading Cluster
> > Simulation data
> > Hi Doug,
> > I have already uploaded a text file of my corrected results from the
> > Monte Carlo Cluster Simulation which reports 15 Clusters (attached
> > picture).
> > There is another file ending with .mgh and the tutorial identifies it
> > to be the overlay (clusterwise corrected map) which I can upload in
> > freeview.
> > In freeview there are the alternatives of uploading a surface or a
> > volume. If I upload the file ending with .mgh as a volume I just
> > recieve a black image with a few numbers on the coordinate plane
> > (attached picture). There is no brain visible.
> > Is it correct to upload the overlay (file ending with .mgh) as a
> > volume or how should I proceed? Do I have to upload a template first
> > and which is the right template?
> > Thank you so much.
> > Yours sincerely,
> > Carina
> > *Gesendet:* Montag, 16. Juni 2014 um 12:45 Uhr
> > *Von:* "Douglas Greve" 
> > *An:* "car...@van-vlodrop.de" , "free surfer"
> > 
> > *Betreff:* Re: [Freesurfer] Fw: Problem with uploading Cluster
> > Simulation data
> >
> > You should be able to view the map results in freeview just as you
> > would any other map.
> > doug
> >
> >
> >
> >
> >
> > On 6/12/14 12:19 PM, car...@van-vlodrop.de wrote:
> >
> > *Gesendet:* Dienstag, 10. Juni 2014 um 11:18 Uhr
> > *Von:* "car...@van-vlodrop.de" 
> > *An:* freesurfer@nmr.mgh.harvard.edu
> > *Betreff:* Problem with uploading Cluster Simulation data
> > Dear freesurfer experts,
> > we are conducting cortical-thickness analysis using
> > freesurfer-4.4.0 and the final analysis with qdec. I have a
> > question concerning the Clusterwise Correction for Multiple
> > Comparison.
> > Is it correct that I have to visualize the results of the Monte
> > Carlo Simulation in freeview?
> > Do I have to upload a special model in freeview before uploading
> > the Cluster Simulation data?
> > Yours sincerely,
> > Carina
> >
> >
> > ___ 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.
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@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/

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@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

Re: [Freesurfer] Is there any saving a brain from this type of error?

[Bruce Fischl]

Hi Jon

maybe, depending on the quality of the image. Did the intensity 
normalization fail? Looks like it might have eaten into the gray matter. 
Compare the brain.mgz and the orig.mgz. If cortex is intensity-normalized 
to look like wm try using the -gentle flag, otherwise try setting some of 
the mri_segment intensity thresholds with xopts


Bruce


On Tue, 15 Jul 2014, Jonathan Holt wrote:


Attached is an image of wm.mgz after a routine recon-all... 


___
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] sulcal depth

[Aleksandar Ristic]

Hi Freesurfer experts,



I did thickness group analysis in pts and healthy subject groups in qdec
(age corrected( and got thicker cortex in left insula and thinner precentral
gyrus bilaterally that survived FDR 0.01

Surface area and curvature analysis found no difference. However, sulcal
depth analysis reveled striking difference (positive) in bilateral insula
(survived FDR 0.001). As this finding can attribute significantly to
understanding of the background of investgated disorder, I kindly ask for
representative references covering sulcal depth method (as the variability
of the folding patterns is still largely not understood, and different
methods have been employed already to best of my knowledge). Second, do I
have to correct sulcal depth for age?

thanks,

Alex



Aleksandar J. Ristić, MD, PhD

Epilepsy Center

Neurology Clinic, Clinical Center of Serbia

University of Belgrade, Belgrade - Serbia





---
avast! antivirus zaštita je aktivna stoga ova e-pošta nema virusa i 
zlonamjernih programa.
http://www.avast.com
___
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] recon-all exits after mri_nu_correct

[ISAAC PEDISICH]

Hi All,
I'm trying to reconstruct surfaces using recon-all. Though many of the
subjects have succeeded, a few are failing at the mri_nu_correct stage. The
error file (posted below) provides little detail as to why the error is
occurring.

Even if it is not fixable, it would be nice to know what caused this error.
I can provide data if requested.

Thank you for your help,
Isaac

The following is the contents of the reocn-all.error file:
--
SUBJECT UP044
DATE Thu Jun 26 11:19:36 EDT 2014
USER analy
HOST rhino.psych.upenn.edu
PROCESSOR x86_64
OS Linux
Linux rhino.psych.upenn.edu 2.6.18-371.4.1.el5 #1 SMP Thu Jan 30 06:08:24
EST 2014 x86_64 x86_64 x86_64 GNU/Linux
$Id: recon-all,v 1.379.2.73 2013/05/12 23:15:37 nicks Exp $
/usr/global/freesurfer/bin/recon-all
PWD /data3/eeg/freesurfer/subjects/UP044/mri
CMD mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale
--i orig.mgz --o orig_nu.mgz
___
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.