[Freesurfer] Fwd: Segmentation of hippocampal subfilelds

[mohan boddu]

-- Forwarded message --
From: mohan boddu 
Date: Tue, Aug 9, 2011 at 6:17 AM
Subject: Re: [Freesurfer] Segmentation of hippocampal subfilelds
To: Koen Van Leemput 


Hello,

I would like to thank you for the information, but the problem is, I am a CS
student working on this and I dont have much idea about it. Basically my
task is to convert those images into ROI mask. For this I have to follow the
instructions in the website stated below:

http://brainybehavior.com/neuroimaging/2010/06/saving-individual-labels-from-freesurfers-aseg/

But the process stated in the above website works for label maps, and if the
images generated in the "*segmentation of hippocampal subfields*" (
http://www.freesurfer.net/fswiki/HippocampalSubfieldSegmentation) (8 images
are generated for each side) stage are probability maps then what should be
given as upper threshold(-uthr) and lower threshold(-thr) values. And as the
last step says to divide it by its label number to normalize it. Is it
necessary for the probability maps, if it is, then what would be the number
that we have to divide?

Sorry, if I am not clear and thank you very much for helping me out.








On Tue, Aug 9, 2011 at 10:41 AM, Koen Van Leemput
wrote:

> Hi Mohan,
>
> The segmentation results are given as probability maps: a (unsigned
> 8-bit) value of 0 means probability 0 , 255 means probability 1, and
> everything in between scales linearly.
>
> The proper way to obtain "crisp" label maps from these images is to
> assign each voxel to the label map that has the highest probability,
> so you'd need to read in all probabilty maps, visit each voxel and
> compare the probabilities in the voxel for all structures.
>
> Generating such "scrisp", winner-takes-all label maps is not
> recommended to calculate e.g., volumes etc, though...
>
> Hope this helps,
>
> Koen
>
>
> On Mon, Aug 8, 2011 at 2:26 PM, mohan boddu 
> wrote:
> > I have completed the segmentation of hippocampal subfileds, but now I
> would
> > like to know the generated images are in probability map or label map? If
> > they are in label map what would be the best upper and lower thresholds
> to
> > generate the ROI mask images. Could you please also tell me the way to do
> > so.
> >
> > --
> > --Mohan Boddu--
> > Research Assistant
> > Department of Radiology and Imaging
> > Research II Building
> > Indiana University School Of Medicine
> > Indiana University-Purdue University Indianapolis
> > Indianapolis, IN 46202
> >
> >
> > ___
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> > 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
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> > error
> > but does not contain patient information, please contact the sender and
> > properly
> > dispose of the e-mail.
> >
> >
>



-- 
--Mohan Boddu--
Research Assistant
Department of Radiology and Imaging
Research II Building
Indiana University School Of Medicine
Indiana University-Purdue University Indianapolis
Indianapolis, IN 46202




-- 
--Mohan Boddu--
Research Assistant
Department of Radiology and Imaging
Research II Building
Indiana University School Of Medicine
Indiana University-Purdue University Indianapolis
Indianapolis, IN 46202
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Re: [Freesurfer] tksurfer & rtview

[Douglas N Greve]

Hi Michelle, I don't think you are looking at the angle. The eccen angle 
should go from 0-2pi. The polar angle should go from -pi to +pi. What is 
you visualization command-line? You can change the color scale from the 
View->Configure->Overlay window.
doug

Michelle Umali wrote:
> Dear Freesurfers,
>
> In an effort to figure out why my field sign data is a bunch of   
> blue/red speckles, I looked at the polar and eccentricity maps  
> separately on the surface.
>
> In both maps, I found that the values range from 0 to approximately  
> 65. Does that seem to be OK, and if so, what do these numbers  
> represent in terms of polar angle or eccentricity? Also, it seems that  
> the color ranges in the overlay cannot show any values above 4; is  
> there a way to visualize larger ranges (such as 0 to 65)?
>
> Thank you very much.
> Michelle
>
>
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>
>   

-- 
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
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Re: [Freesurfer] repeated measures ANOVA

[Douglas N Greve]

Hi Sandra, it is usually just a matter of setting up a design matrix and 
contrast matrices to test what you are interested in then using any glm 
software. If you just have two time points, then you can just subtract 
them and do a one-sample group mean (design matrix a column of all ones; 
contrast matrix = [1]).

doug

swood...@nmr.mgh.harvard.edu wrote:
> Hello all,
>
> We would like to analyise our repeated measures DTI data using an ANOVA. 
> We are wondering if someone might have experience running AVOVA's on 3D
> data?  Is there a particular tool used or did you use MATLAB for this type
> of analysis?
>
>
> Thank you,
>
> Sandra
>
>
> Sandra Woodman
> Mood and Motor Control Laboratory
> Athinoula Martinos Center for Biomedical Imaging
> Massachusetts General Hospital
>
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>
>
>   

-- 
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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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Re: [Freesurfer] : Memory and CPU Allocation?

[Douglas N Greve]

Hi Tapsya, it looks like your data are going to require about 12G of memory due 
to an inefficient use of memory by selxavg when there are so many time points 
across a run (I've never tested it with 6570 total time points!). If you want 
to run this on launchpad, then you'll need to request that much memory when you 
launch the job.

doug



tap...@nmr.mgh.harvard.edu wrote:
> Dear FSFAST,
>
> I am using the program selxavg3-sess on 3D data for a single session (i.e.
> selxavg3-sess -s avml07 -analysis $ana_vol -force) and it errors out with
> the following message:
>
> OLS Residual Pass
>   run 1t= 0.0
> ??? Error using ==> unknown
> Out of memory. Type HELP MEMORY for your options.
>
> Error in ==> fast_selxavg3 at 469
>   rho1run = sum(rrun(1:end-1,:).*rrun(2:end,:))./rsserun;
>
>
> I am using FSFAST v 5.1. My analysis uses FIR design, 6 runs in each
> session with 18 contrasts. I executed the program on clusters 'launchpad'
> (@ Martino's center) and allocated 49GB to it.
>
> My question is how much CPU and memory you recommend I should
> allocate? I have also attached the log file in this email.
>
> Any help is greatly appreciated!
>
> Thanks.
>
> Wishes,
> Tapsya
>
>
>
>
>
>   
> 
>
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-- 
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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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Re: [Freesurfer] mri_glmfit & .nii files

[Douglas N Greve]

What's your command line? Looks like you might be putting a slash (/) as 
the first character to your glmdir. You will not have permissions to 
create this directory.

doug

Chindhuri Selvadurai wrote:
> I am actually getting an error message when I type my mri_glmfit command:
>
> ERROR: fio_pushd: /group_analysis/volume/m1/mstmct_v_base/type_v_rest
> ERROR: must specify input y file
>
>
> I did specify a y file and I do not know what fio_pushd is.
>
>
>   
>> This is controlled by the $FSF_OUTPUT_FORMAT. By default this is
>> compressed nifti (nii.gz). Both nii and nii.gz store the same
>> information. The nii.gz is compressed, so you save some space.
>>
>> doug
>>
>> Chindhuri Selvadurai wrote:
>> 
>>> Hi freesurfers,
>>>
>>> I am trying to run an analysis right now, however, after using
>>> isxconcat,
>>> I am only finding ces.nii.gz files in the output directory and no .nii
>>> files.
>>>
>>> output dir: /cluster/manoach/milton/subjects/group_analysis/volume/m1
>>> subjects_dir: /cluster/manoach/milton/subjects
>>>
>>> command: mri_glmfit --y
>>> /group_analysis/volume/m1/mstmct_v_base/type_v_rest/ces.nii.gz --glmdir
>>> group_analysis/volume/m1/ --osgm
>>>
>>> Not sure why this is the case.. any help would be appreciated! Thanks!
>>> ___
>>> 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
>> gr...@nmr.mgh.harvard.edu
>> Phone Number: 617-724-2358
>> Fax: 617-726-7422
>>
>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>>
>>
>>
>> 
>
>
> Best,
>
> Chindhuri Selvadurai
>
>  Psychiatric Neuroimaging, Manoach Lab
>  Martinos Center for Biomedical Imaging, MGH
>  Phone: (617)726-0307
>
>
>   

-- 
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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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[Freesurfer] (no subject)

[Antonella Kis]

Dear Freesurfers,

I am ready to run the make_average_subject and I need to specify  
-xform  for the talairach transform: talairach.lta , talairach.m3z or 
talairach.xfm. What is the difference between
this and what should I use for the make_average_subject in order to prepare my 
data for the GLM analysis?


Thank you very much for your help.
Antonella
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Re: [Freesurfer] (no subject)

[Bruce Fischl]

Hi Antonella

talairach.lta and .xfm are linear transforms to a Talairach coordinate 
system. The .m3z is a nonlinear morph and will give you much higher 
anatomical resolution.


cheers
Bruce

On Thu, 11 Aug 2011, Antonella Kis wrote:


Dear Freesurfers,


I am ready to run the make_average_subject and I need to specify   -xform  for 
the talairach transform: talairach.lta , talairach.m3z or talairach.xfm. What 
is the
difference between this and what should I use for the make_average_subject in 
order to prepare my data for the GLM analysis?

Thank you very much for your help.
Antonella


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[Freesurfer] make_average_subject

[Antonella Kis]

Hi Bruce,

Many thanks again for your help. So just to make sure that I understood corect: 
is better to use the talairach.m3z win my make_average_subject?
I was reading that the  talairach coordinate is based on talairach.xfm (unless 
changed with --xform) so your suggestion was to change it to talairach.m3z?

Many thanks.
Antonella




From: Bruce Fischl 
To: Antonella Kis 
Cc: "freesurfer@nmr.mgh.harvard.edu" 
Sent: Thursday, August 11, 2011 12:52 PM
Subject: Re: [Freesurfer] (no subject)

Hi Antonella

talairach.lta and .xfm are linear transforms to a Talairach coordinate 
system. The .m3z is a nonlinear morph and will give you much higher 
anatomical resolution.

cheers
Bruce

On Thu, 11 Aug 2011, Antonella Kis wrote:

> Dear Freesurfers,
> 
> 
> I am ready to run the make_average_subject and I need to specify   -xform  
> for the talairach transform: talairach.lta , talairach.m3z or talairach.xfm. 
> What is the
> difference between this and what should I use for the make_average_subject in 
> order to prepare my data for the GLM analysis?
> 
> Thank you very much for your help.
> Antonella
> 
> 
>
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Re: [Freesurfer] make_average_subject

[Bruce Fischl]

it depends whether you want things in a coordinate system that is more 
anatomically accurate (.m3z) or more of a true "Talairach" one 
(talaraich.xfm)


On 
Thu, 11 Aug 2011, Antonella Kis wrote:



Hi Bruce,

Many thanks again for your help. So just to make sure that I understood corect: 
is better to use the talairach.m3z win my make_average_subject?
I was reading that the  talairach coordinate is based on talairach.xfm (unless 
changed with --xform) so your suggestion was to change it to talairach.m3z?

Many thanks.
Antonella

___
From: Bruce Fischl 
To: Antonella Kis 
Cc: "freesurfer@nmr.mgh.harvard.edu" 
Sent: Thursday, August 11, 2011 12:52 PM
Subject: Re: [Freesurfer] (no subject)

Hi Antonella

talairach.lta and .xfm are linear transforms to a Talairach coordinate
system. The .m3z is a nonlinear morph and will give you much higher
anatomical resolution.

cheers
Bruce

On Thu, 11 Aug 2011, Antonella Kis wrote:

> Dear Freesurfers,
>
>
> I am ready to run the make_average_subject and I need to specify   -xform  
for the talairach transform: talairach.lta , talairach.m3z or talairach.xfm. What 
is the
> difference between this and what should I use for the make_average_subject in 
order to prepare my data for the GLM analysis?
>
> Thank you very much for your help.
> Antonella
>
>
>
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Re: [Freesurfer] Fwd: Segmentation of hippocampal subfilelds

[Koen Van Leemput]

Hi Mohan,

The short answer is that you can not use the instructions you mention
for the hippocampal subfields.

The long answer is that the instructions only work for segmentations
that are already crisp, such as the ones contained in the aseg.mgz
file: each intensity level in aseg.mgz corresponds to a certain
structure, and voxels having that intensity are assigned exclusively
to the structure. The hippocampal subfield segmentation results are
stored in a different way that tells you something about the
uncertainty with which such assigned can be made, so you'll need to
make those exclusive assignments to a single structure manually...

Hope this helps,

Koen




On Thu, Aug 11, 2011 at 10:06 AM, mohan boddu  wrote:
>
>
> -- Forwarded message --
> From: mohan boddu 
> Date: Tue, Aug 9, 2011 at 6:17 AM
> Subject: Re: [Freesurfer] Segmentation of hippocampal subfilelds
> To: Koen Van Leemput 
>
>
> Hello,
>
> I would like to thank you for the information, but the problem is, I am a CS
> student working on this and I dont have much idea about it. Basically my
> task is to convert those images into ROI mask. For this I have to follow the
> instructions in the website stated below:
>
> http://brainybehavior.com/neuroimaging/2010/06/saving-individual-labels-from-freesurfers-aseg/
>
> But the process stated in the above website works for label maps, and if the
> images generated in the "segmentation of hippocampal subfields"
> (http://www.freesurfer.net/fswiki/HippocampalSubfieldSegmentation) (8 images
> are generated for each side) stage are probability maps then what should be
> given as upper threshold(-uthr) and lower threshold(-thr) values. And as the
> last step says to divide it by its label number to normalize it. Is it
> necessary for the probability maps, if it is, then what would be the number
> that we have to divide?
>
> Sorry, if I am not clear and thank you very much for helping me out.
>
>
>
>
>
>
>
> On Tue, Aug 9, 2011 at 10:41 AM, Koen Van Leemput 
> wrote:
>>
>> Hi Mohan,
>>
>> The segmentation results are given as probability maps: a (unsigned
>> 8-bit) value of 0 means probability 0 , 255 means probability 1, and
>> everything in between scales linearly.
>>
>> The proper way to obtain "crisp" label maps from these images is to
>> assign each voxel to the label map that has the highest probability,
>> so you'd need to read in all probabilty maps, visit each voxel and
>> compare the probabilities in the voxel for all structures.
>>
>> Generating such "scrisp", winner-takes-all label maps is not
>> recommended to calculate e.g., volumes etc, though...
>>
>> Hope this helps,
>>
>> Koen
>>
>>
>> On Mon, Aug 8, 2011 at 2:26 PM, mohan boddu 
>> wrote:
>> > I have completed the segmentation of hippocampal subfileds, but now I
>> > would
>> > like to know the generated images are in probability map or label map?
>> > If
>> > they are in label map what would be the best upper and lower thresholds
>> > to
>> > generate the ROI mask images. Could you please also tell me the way to
>> > do
>> > so.
>> >
>> > --
>> > --Mohan Boddu--
>> > Research Assistant
>> > Department of Radiology and Imaging
>> > Research II Building
>> > Indiana University School Of Medicine
>> > Indiana University-Purdue University Indianapolis
>> > Indianapolis, IN 46202
>> >
>> >
>> > ___
>> > 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.
>> >
>> >
>
>
>
> --
> --Mohan Boddu--
> Research Assistant
> Department of Radiology and Imaging
> Research II Building
> Indiana University School Of Medicine
> Indiana University-Purdue University Indianapolis
> Indianapolis, IN 46202
>
>
>
>
> --
> --Mohan Boddu--
> Research Assistant
> Department of Radiology and Imaging
> Research II Building
> Indiana University School Of Medicine
> Indiana University-Purdue University Indianapolis
> Indianapolis, IN 46202
>
>
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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 n

[Freesurfer] Volumetric analysis of thalamus in freesurfer

[Knut J Bjuland]

I am working to do a volumetric analysis in Freesurfer using Thalamus. I
do not know if this is the correct way to go. Should I first register
thalamus to a surface using tkregister? There was also another post on
this list, which suggested using tkregister2?  I am also search to find
a tutorial on how to create a volmask and the use it to calculate
statistic  in Freesurfer for Thalamus.

Knut J

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Re: [Freesurfer] Volumetric analysis of thalamus in freesurfer

[Bruce Fischl]

Hi Knut

you don't need to register it since the segmentation (aseg) is created 
from the same data as the surface. What kind of analysis are you thinking 
of doing?

cheers
Bruce


On Thu, 11 Aug 2011, Knut J Bjuland 
wrote:

> I am working to do a volumetric analysis in Freesurfer using Thalamus. I
> do not know if this is the correct way to go. Should I first register
> thalamus to a surface using tkregister? There was also another post on
> this list, which suggested using tkregister2?  I am also search to find
> a tutorial on how to create a volmask and the use it to calculate
> statistic  in Freesurfer for Thalamus.
>
> Knut J
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
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Re: [Freesurfer] tksurfer & rtview

[Michelle Umali]

Hi Doug,
You're right it was the wrong map, and now the angles make sense.

But when I look at the correct images, the eccen and polar maps are  
very, very speckled.  So, in the relevant visual areas, there are  
hardly any 0 values, so I would expect a more contiguous color pattern.

Is there any way to improve the visualization?

Here is the command I used:
tksurfer-sess -a rtopy.self.lh -s sj17 -map angle

Thanks.
Michelle

Quoting Douglas N Greve :

> Hi Michelle, I don't think you are looking at the angle. The eccen
> angle should go from 0-2pi. The polar angle should go from -pi to +pi.
> What is you visualization command-line? You can change the color scale
> from the View->Configure->Overlay window.
> doug
>
> Michelle Umali wrote:
>> Dear Freesurfers,
>>
>> In an effort to figure out why my field sign data is a bunch of 
>> blue/red speckles, I looked at the polar and eccentricity maps
>> separately on the surface.
>>
>> In both maps, I found that the values range from 0 to approximately  
>>   65. Does that seem to be OK, and if so, what do these numbers
>> represent in terms of polar angle or eccentricity? Also, it seems   
>> that the color ranges in the overlay cannot show any values above   
>> 4; is  there a way to visualize larger ranges (such as 0 to 65)?
>>
>> Thank you very much.
>> Michelle
>>
>>
>> ___
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>>
>>
>>
>
> -- 
> 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>
>
>
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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
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> in error
> but does not contain patient information, please contact the sender and
> properly
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Re: [Freesurfer] tksurfer & rtview

[Douglas N Greve]

Look at the significance maps to make sure they look reasonable. Just run

tksurfer-sess -a rtopy.self.lh -s sj17

doug

Michelle Umali wrote:
> Hi Doug,
> You're right it was the wrong map, and now the angles make sense.
>
> But when I look at the correct images, the eccen and polar maps are  
> very, very speckled.  So, in the relevant visual areas, there are  
> hardly any 0 values, so I would expect a more contiguous color pattern.
>
> Is there any way to improve the visualization?
>
> Here is the command I used:
> tksurfer-sess -a rtopy.self.lh -s sj17 -map angle
>
> Thanks.
> Michelle
>
> Quoting Douglas N Greve :
>
>   
>> Hi Michelle, I don't think you are looking at the angle. The eccen
>> angle should go from 0-2pi. The polar angle should go from -pi to +pi.
>> What is you visualization command-line? You can change the color scale
>> from the View->Configure->Overlay window.
>> doug
>>
>> Michelle Umali wrote:
>> 
>>> Dear Freesurfers,
>>>
>>> In an effort to figure out why my field sign data is a bunch of 
>>> blue/red speckles, I looked at the polar and eccentricity maps
>>> separately on the surface.
>>>
>>> In both maps, I found that the values range from 0 to approximately  
>>>   65. Does that seem to be OK, and if so, what do these numbers
>>> represent in terms of polar angle or eccentricity? Also, it seems   
>>> that the color ranges in the overlay cannot show any values above   
>>> 4; is  there a way to visualize larger ranges (such as 0 to 65)?
>>>
>>> Thank you very much.
>>> Michelle
>>>
>>>
>>> ___
>>> 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
>> gr...@nmr.mgh.harvard.edu
>> Phone Number: 617-724-2358 Fax: 617-726-7422
>>
>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>>
>>
>>
>> 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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>
>
>   

-- 
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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358 
Fax: 617-726-7422

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[Freesurfer] tksurfer & rtview

[Michelle Umali]

Hi Doug,
The z-values are consistently near or greater than 4. It just seems that the
visualization of the angles is somehow incorrect...

Is there be anything else that I need to check?

Thanks.
Michelle
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Re: [Freesurfer] tksurfer & rtview

[Douglas N Greve]

what does the activation look like? Does it look right? Can you send a pic?
doug

Michelle Umali wrote:
> Hi Doug,
> The z-values are consistently near or greater than 4. It just seems that the
> visualization of the angles is somehow incorrect...
>
> Is there be anything else that I need to check?
>
> Thanks.
> Michelle
> ___
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>
>
>   

-- 
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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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Re: [Freesurfer] Volumetric analysis of thalamus in freesurfer

[Knut J Bjuland]

Hi Bruce

I am now responding to the list as well. I have a group with different
subjects where I wish to correlate thalamus volume with gender
difference. Though I have extract the data using asegstats2table. I wish
to be sure that the group difference is correct. Due to this reason I
wish to use multiple comparsion within Freesurfer for instant FDR. I
have some trouble figuring out --iv volmeasfile or how to use an label
to include thalamus but exclude everything else?

Knut J


Knut J

On 08/11/2011 08:42 PM, Bruce Fischl wrote:
> Hi Knut
>
> you should respond onlist so Doug and Nick can answer! If all you want
> is thalamic volume then why do you have multiple comparisons? You only
> have one number/subject, no?
> Bruce
>
> On Thu, 11 Aug 2011, Knut J Bjuland wrote:
>
>> Hi Bruce
>>
>> I wish to use a group difference analysis using gender and correlate
>> thalamus volume with IQ, and then apply multiple comparisons using FDR
>> or Monte Carlo simulation. Do you have any links to a good tutorial? I
>> inted to use mris_preproc and mris_glm for voulmetirc analysis, but I
>> have some trouble figuring out --iv volmeasfile?
>>
>> Cheers
>> Knut J
>>
>>
>> Knut J
>>
>> On 08/11/2011 08:03 PM, Bruce Fischl wrote:
>>> Hi Knut
>>>
>>> you don't need to register it since the segmentation (aseg) is created
>>> from the same data as the surface. What kind of analysis are you
>>> thinking of doing?
>>>
>>> cheers
>>> Bruce
>>>
>>>
>>> On Thu, 11 Aug 2011, Knut J Bjuland wrote:
>>>
 I am working to do a volumetric analysis in Freesurfer using
 Thalamus. I
 do not know if this is the correct way to go. Should I first register
 thalamus to a surface using tkregister? There was also another post on
 this list, which suggested using tkregister2?  I am also search to
 find
 a tutorial on how to create a volmask and the use it to calculate
 statistic  in Freesurfer for Thalamus.

 Knut J

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 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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[Freesurfer] full flat patch issue

[francesca strappini]

Hi, I'm trying to create a full flat map. The process of flattening seems
has finished without any errors, but I got this error message when I tried
to show up the full flat patch:

lh.full.flat.patch.3d: face[0] = 0, but face 0 not in vertex 0 face list

Thanks a lot

Francesca
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Re: [Freesurfer] full flat patch issue

[Bruce Fischl]

Hi Francesca

how are you trying to visualize it? Try:

tksurfer  lh inflated -patch  lh.full.flat.patch.3d

cheers
Bruce

On 
Thu, 11 Aug 2011, francesca strappini wrote:

> Hi, I'm trying to create a full flat map. The process of flattening seems has 
> finished without any errors, but I got this error message when I tried to 
> show up the full
> flat patch:
> 
> lh.full.flat.patch.3d: face[0] = 0, but face 0 not in vertex 0 face list
> 
> Thanks a lot
> 
> Francesca
> 
> 
>
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Re: [Freesurfer] Volumetric analysis of thalamus in freesurfer

[Douglas N Greve]

use --segno 10 --segno 49
These codes are from $FREESURFER_HOME/FreeSurferColorLUT.txt and 
correspond to left and right thalamus. Use -m volume to get the volume 
of thalamus (this is the default). If you're only looking at one 
measure, then no correction for multiple comparisons is necessary. You 
can test the effect of gender by loading this output into a stats 
program or using mri_glmfit with the --table option.
doug

Knut J Bjuland wrote:
> Hi Bruce
>
> I am now responding to the list as well. I have a group with different
> subjects where I wish to correlate thalamus volume with gender
> difference. Though I have extract the data using asegstats2table. I wish
> to be sure that the group difference is correct. Due to this reason I
> wish to use multiple comparsion within Freesurfer for instant FDR. I
> have some trouble figuring out --iv volmeasfile or how to use an label
> to include thalamus but exclude everything else?
>
> Knut J
>
>
> Knut J
>
> On 08/11/2011 08:42 PM, Bruce Fischl wrote:
>   
>> Hi Knut
>>
>> you should respond onlist so Doug and Nick can answer! If all you want
>> is thalamic volume then why do you have multiple comparisons? You only
>> have one number/subject, no?
>> Bruce
>>
>> On Thu, 11 Aug 2011, Knut J Bjuland wrote:
>>
>> 
>>> Hi Bruce
>>>
>>> I wish to use a group difference analysis using gender and correlate
>>> thalamus volume with IQ, and then apply multiple comparisons using FDR
>>> or Monte Carlo simulation. Do you have any links to a good tutorial? I
>>> inted to use mris_preproc and mris_glm for voulmetirc analysis, but I
>>> have some trouble figuring out --iv volmeasfile?
>>>
>>> Cheers
>>> Knut J
>>>
>>>
>>> Knut J
>>>
>>> On 08/11/2011 08:03 PM, Bruce Fischl wrote:
>>>   
 Hi Knut

 you don't need to register it since the segmentation (aseg) is created
 from the same data as the surface. What kind of analysis are you
 thinking of doing?

 cheers
 Bruce


 On Thu, 11 Aug 2011, Knut J Bjuland wrote:

 
> I am working to do a volumetric analysis in Freesurfer using
> Thalamus. I
> do not know if this is the correct way to go. Should I first register
> thalamus to a surface using tkregister? There was also another post on
> this list, which suggested using tkregister2?  I am also search to
> find
> a tutorial on how to create a volmask and the use it to calculate
> statistic  in Freesurfer for Thalamus.
>
> Knut J
>
> ___
> 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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>
>
>   

-- 
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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
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[Freesurfer] recon-all and corrected hemispheres

[Ayaz, Muhammad]

Dear All,

I acquired the images using Phillips scanner. I converted the images from par 
into analyze using MRIcro. I noticed that images were flipped when I view them 
in the axial plane, i.e. when I look at the images on the computer screen the 
Right hemisphere (where we tapped the fish oil tablet) is on the right side of 
the image.

Should I flip the images before running through the recon-all?

Thanks
Ayaz


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Re: [Freesurfer] recon-all and corrected hemispheres

[Bruce Fischl]

Hi Ayaz

you are *much* better off avoiding analyze as a format entirely. Can't 
you give the dicoms right off the scanner to recon-all?


cheers
Bruce
On Thu, 11 Aug 2011, 
Ayaz, Muhammad wrote:




Dear All,

 

I acquired the images using Phillips scanner. I converted the images from
par into analyze using MRIcro. I noticed that images were flipped when I
view them in the axial plane, i.e. when I look at the images on the computer
screen the Right hemisphere (where we tapped the fish oil tablet) is on the
right side of the image.

 

Should I flip the images before running through the recon-all?

 

Thanks

Ayaz


The information contained in this message and any attachments is intended
only for the use of the individual or entity to which it is addressed, and
may contain information that is PRIVILEGED, CONFIDENTIAL, and exempt from
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Re: [Freesurfer] recon-all and corrected hemispheres

[Ayaz, Muhammad]

Dear Bruce

If I use analyze would it effect the results?

Dicoms are preferable because?

I have processed about 30 subjects using analyze. I have noticed some cases 
where surfaces were not done correctly in few regions other than that no major 
problems.

If it makes big difference to use dicom. Should I use par images to transform 
them into dicom on scanner or is there any other way to do it?. 

Thanks
Ayaz 

-Original Message-
From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu] 
Sent: Thursday, August 11, 2011 2:10 PM
To: Ayaz, Muhammad
Cc: 'freesurfer@nmr.mgh.harvard.edu'
Subject: Re: [Freesurfer] recon-all and corrected hemispheres

Hi Ayaz

you are *much* better off avoiding analyze as a format entirely. Can't 
you give the dicoms right off the scanner to recon-all?

cheers
Bruce
On Thu, 11 Aug 2011, 
Ayaz, Muhammad wrote:

> 
> Dear All,
> 
>  
> 
> I acquired the images using Phillips scanner. I converted the images from
> par into analyze using MRIcro. I noticed that images were flipped when I
> view them in the axial plane, i.e. when I look at the images on the computer
> screen the Right hemisphere (where we tapped the fish oil tablet) is on the
> right side of the image.
> 
>  
> 
> Should I flip the images before running through the recon-all?
> 
>  
> 
> Thanks
> 
> Ayaz
> 
> 
> The information contained in this message and any attachments is intended
> only for the use of the individual or entity to which it is addressed, and
> may contain information that is PRIVILEGED, CONFIDENTIAL, and exempt from
> disclosure under applicable law. If you are not the intended recipient, you
> are prohibited from copying, distributing, or using the information. Please
> contact the sender immediately by return e-mail and delete the original
> message from your system.
>


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for the use of the individual or entity to which it is addressed, and may 
contain information that is PRIVILEGED, CONFIDENTIAL, and exempt from 
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Re: [Freesurfer] recon-all and corrected hemispheres

[Bruce Fischl]

Hi Ayaz

the big difference is that once you convert to analyze you will never be 
sure which side of the image is anatomically on the left and which is on 
the right, as analyze doesn't store this info.


cheers
Bruce


On Thu, 11 Aug 2011, Ayaz, Muhammad wrote:


Dear Bruce

If I use analyze would it effect the results?

Dicoms are preferable because?

I have processed about 30 subjects using analyze. I have noticed some cases 
where surfaces were not done correctly in few regions other than that no major 
problems.

If it makes big difference to use dicom. Should I use par images to transform 
them into dicom on scanner or is there any other way to do it?.

Thanks
Ayaz

-Original Message-
From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu]
Sent: Thursday, August 11, 2011 2:10 PM
To: Ayaz, Muhammad
Cc: 'freesurfer@nmr.mgh.harvard.edu'
Subject: Re: [Freesurfer] recon-all and corrected hemispheres

Hi Ayaz

you are *much* better off avoiding analyze as a format entirely. Can't
you give the dicoms right off the scanner to recon-all?

cheers
Bruce
On Thu, 11 Aug 2011,
Ayaz, Muhammad wrote:



Dear All,

 

I acquired the images using Phillips scanner. I converted the images from
par into analyze using MRIcro. I noticed that images were flipped when I
view them in the axial plane, i.e. when I look at the images on the computer
screen the Right hemisphere (where we tapped the fish oil tablet) is on the
right side of the image.

 

Should I flip the images before running through the recon-all?

 

Thanks

Ayaz


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Re: [Freesurfer] registration issues with lesioned brains and kids' brains

[Bruce Fischl]

Hi Catherine

when you say "left" do you mean the left side of the image or the left side 
of the brain? In tkmedit the left side of the image will always represent 
the right side of the brain (as indicated by the little green "R" and 
arrow).


As for the goodness of the surface fit to talairach, that just is a 
function of the blurriness of the talairach coordinate system.


cheers
Bruce

 On Thu, 11 Aug 2011, Catherine Wan wrote:


Dear Freesurfer-list,

I have 2 questions: one regarding lesioned brains and another regarding kids? 
brains.

1) All of our patients have large lesions on the left side. After the recon-all 
step, I used tkmedit brainmask.mgz and found that for some patients,  the 
lesion location
had been flipped from left to right (see attached). Any suggestions on how to 
solve this issue, prior to running a group level analysis?

2) We have preprocessed some images of typically-developing children (9-11yo). 
After recon-all, I checked the registration using tkregister2 --mgz ?s--fstal 
--surf orig and
found that the green line didn?t cover the surfaces well in most cases (see 
attached) . I?ve read in previous postings that Freesurfer should be fine with 
kids? brains, so
perhaps we don't need to modify them manually?  Is there any other way to check 
for registration? Any other suggestions?

Many thanks in advance for your help!

Regards,
Catherine

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Re: [Freesurfer] long_mris_slopes error

[Martin Reuter]

Hi Hyojeong,

on the wiki release notes is a fixed mris_calc binary.

Best, Martin

On Aug 11, 2011, at 8:00 AM, Administrator wrote:

> Dear Martin,
> 
> I've received the same error as below which discussed previously.
> Would you tell me if you managed build a fixed file, please?
> 
> Hyojeong Lee
> Hallym University College of Medicine, Anyang, Korea
> 
> 
> long_mris_slopes --qdec ./qdec/long.qdec.tem_VNL01_KCY.dat --meas thickness 
> --hemi lh --do-avg --do-rate --do-pc1 --do-spc --do-stack --do-label --time 
> weeks --qcache fsaverage
> ..
> ===
> SUBJECT VN1 fwhm 0  computing SPC
> 
> mris_calc -o 
> /Volumes/data/freesurfer_analysis/VN_longitudinal/VN1/surf/lh.long.thickness-spc.fwhm0.mgh
>  ./tmp-VN1_lh_thickness_OLudiD/beta1.mgh div 
> ./tmp-VN1_lh_thickness_OLudiD/beta0.mgh
> 
> ERROR -10 : mris_calc compute sym. pct. change (spc) problem?
> 
> 
> 


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Re: [Freesurfer] registration issues with lesioned brains and kids' brains

[Bruce Fischl]

p.s. note that the image you show of the surface over the tal volume has 
a caption saying "surface registration", but in fact what you are showing 
is the talairach (volume) registration applied to the surface, *not* the 
surface registration. The easiest way to check the surface registration is 
to look at the accuracy of the ?h.aparc.annot. If it looks good then the 
surface registration worked.


On Thu, 11 Aug 
2011, Catherine Wan wrote:



Dear Freesurfer-list,

I have 2 questions: one regarding lesioned brains and another regarding kids? 
brains.

1) All of our patients have large lesions on the left side. After the recon-all 
step, I used tkmedit brainmask.mgz and found that for some patients,  the 
lesion location
had been flipped from left to right (see attached). Any suggestions on how to 
solve this issue, prior to running a group level analysis?

2) We have preprocessed some images of typically-developing children (9-11yo). 
After recon-all, I checked the registration using tkregister2 --mgz ?s--fstal 
--surf orig and
found that the green line didn?t cover the surfaces well in most cases (see 
attached) . I?ve read in previous postings that Freesurfer should be fine with 
kids? brains, so
perhaps we don't need to modify them manually?  Is there any other way to check 
for registration? Any other suggestions?

Many thanks in advance for your help!

Regards,
Catherine

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Re: [Freesurfer] recon-all and corrected hemispheres

[Ayaz, Muhammad]

We tap tablet on the right side of the head wouldn't that help to identify the 
anatomical left?

Or is it preferable to use dicom for many other reasons? 

Thanks for the quick reply.

Ayaz

-Original Message-
From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu] 
Sent: Thursday, August 11, 2011 2:23 PM
To: Ayaz, Muhammad
Cc: 'freesurfer@nmr.mgh.harvard.edu'
Subject: RE: [Freesurfer] recon-all and corrected hemispheres

Hi Ayaz

the big difference is that once you convert to analyze you will never be 
sure which side of the image is anatomically on the left and which is on 
the right, as analyze doesn't store this info.

cheers
Bruce


On Thu, 11 Aug 2011, Ayaz, Muhammad wrote:

> Dear Bruce
>
> If I use analyze would it effect the results?
>
> Dicoms are preferable because?
>
> I have processed about 30 subjects using analyze. I have noticed some cases 
> where surfaces were not done correctly in few regions other than that no 
> major problems.
>
> If it makes big difference to use dicom. Should I use par images to transform 
> them into dicom on scanner or is there any other way to do it?.
>
> Thanks
> Ayaz
>
> -Original Message-
> From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu]
> Sent: Thursday, August 11, 2011 2:10 PM
> To: Ayaz, Muhammad
> Cc: 'freesurfer@nmr.mgh.harvard.edu'
> Subject: Re: [Freesurfer] recon-all and corrected hemispheres
>
> Hi Ayaz
>
> you are *much* better off avoiding analyze as a format entirely. Can't
> you give the dicoms right off the scanner to recon-all?
>
> cheers
> Bruce
> On Thu, 11 Aug 2011,
> Ayaz, Muhammad wrote:
>
>>
>> Dear All,
>>
>>  
>>
>> I acquired the images using Phillips scanner. I converted the images from
>> par into analyze using MRIcro. I noticed that images were flipped when I
>> view them in the axial plane, i.e. when I look at the images on the computer
>> screen the Right hemisphere (where we tapped the fish oil tablet) is on the
>> right side of the image.
>>
>>  
>>
>> Should I flip the images before running through the recon-all?
>>
>>  
>>
>> Thanks
>>
>> Ayaz
>>
>>
>> The information contained in this message and any attachments is intended
>> only for the use of the individual or entity to which it is addressed, and
>> may contain information that is PRIVILEGED, CONFIDENTIAL, and exempt from
>> disclosure under applicable law. If you are not the intended recipient, you
>> are prohibited from copying, distributing, or using the information. Please
>> contact the sender immediately by return e-mail and delete the original
>> message from your system.
>>
>
>
> 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.
>
>
> The information contained in this message and any attachments is intended 
> only for the use of the individual or entity to which it is addressed, and 
> may contain information that is PRIVILEGED, CONFIDENTIAL, and exempt from 
> disclosure under applicable law.  If you are not the intended recipient, you 
> are prohibited from copying, distributing, or using the information.  Please 
> contact the sender immediately by return e-mail and delete the original 
> message from your system.
>
>
>


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Re: [Freesurfer] recon-all and corrected hemispheres

[Bruce Fischl]

yes, that will help, but life will be easier if you avoid analyze. There's 
really no reason to use it instead of nifti these days, and *many* reasons 
not to. You can get other flips (e.g. front/back) that will completley mess 
things up, and you really don't want to process things with a left/right 
flip as this may induce subtle hemispheric-asymmetry biases in our 
processing.


On Thu, 11 Aug 2011, Ayaz, Muhammad wrote:


We tap tablet on the right side of the head wouldn't that help to identify the 
anatomical left?

Or is it preferable to use dicom for many other reasons?

Thanks for the quick reply.

Ayaz

-Original Message-
From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu]
Sent: Thursday, August 11, 2011 2:23 PM
To: Ayaz, Muhammad
Cc: 'freesurfer@nmr.mgh.harvard.edu'
Subject: RE: [Freesurfer] recon-all and corrected hemispheres

Hi Ayaz

the big difference is that once you convert to analyze you will never be
sure which side of the image is anatomically on the left and which is on
the right, as analyze doesn't store this info.

cheers
Bruce


On Thu, 11 Aug 2011, Ayaz, Muhammad wrote:


Dear Bruce

If I use analyze would it effect the results?

Dicoms are preferable because?

I have processed about 30 subjects using analyze. I have noticed some cases 
where surfaces were not done correctly in few regions other than that no major 
problems.

If it makes big difference to use dicom. Should I use par images to transform 
them into dicom on scanner or is there any other way to do it?.

Thanks
Ayaz

-Original Message-
From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu]
Sent: Thursday, August 11, 2011 2:10 PM
To: Ayaz, Muhammad
Cc: 'freesurfer@nmr.mgh.harvard.edu'
Subject: Re: [Freesurfer] recon-all and corrected hemispheres

Hi Ayaz

you are *much* better off avoiding analyze as a format entirely. Can't
you give the dicoms right off the scanner to recon-all?

cheers
Bruce
On Thu, 11 Aug 2011,
Ayaz, Muhammad wrote:



Dear All,

 

I acquired the images using Phillips scanner. I converted the images from
par into analyze using MRIcro. I noticed that images were flipped when I
view them in the axial plane, i.e. when I look at the images on the computer
screen the Right hemisphere (where we tapped the fish oil tablet) is on the
right side of the image.

 

Should I flip the images before running through the recon-all?

 

Thanks

Ayaz


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only for the use of the individual or entity to which it is addressed, and
may contain information that is PRIVILEGED, CONFIDENTIAL, and exempt from
disclosure under applicable law. If you are not the intended recipient, you
are prohibited from copying, distributing, or using the information. Please
contact the sender immediately by return e-mail and delete the original
message from your system.




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Re: [Freesurfer] registration issues with lesioned brains and kids' brains

[Bruce Fischl]

what format are you using? Is it analyze?

And yes, Doug can confirm but I think that's as good as you are going to 
get for registering a subject's surfaces to a talairach average volume with 
a linear xform


On Thu, 11 Aug 2011, Catherine Wan wrote:


Hi Bruce,

Thanks for your prompt response.
I meant all lesions should be on the left side of the brain. So as you can see 
from the revised image (attached), the lesion of patient 1 has been flipped to 
the right
side of the brain when viewed in tkmedit. Any suggestions?

Just to clarify. Are you saying that we can disregard the tkregister2 step for 
these healthy kids' brains, and run the group level analysis after recon-all is 
done?

Many thanks!
Catherine


On Thu, Aug 11, 2011 at 3:25 PM, Bruce Fischl  
wrote:
  Hi Catherine

  when you say "left" do you mean the left side of the image or the left 
side of the brain? In tkmedit the left side of the image will always represent the right
  side of the brain (as indicated by the little green "R" and arrow).

  As for the goodness of the surface fit to talairach, that just is a 
function of the blurriness of the talairach coordinate system.

  cheers
  Bruce


 On Thu, 11 Aug 2011, Catherine Wan wrote:

  Dear Freesurfer-list,

  I have 2 questions: one regarding lesioned brains and another regarding 
kids? brains.

  1) All of our patients have large lesions on the left side. After the 
recon-all step, I used tkmedit brainmask.mgz and found that for some patients,  
the
  lesion location
  had been flipped from left to right (see attached). Any suggestions on 
how to solve this issue, prior to running a group level analysis?

  2) We have preprocessed some images of typically-developing children 
(9-11yo). After recon-all, I checked the registration using tkregister2 --mgz
  ?s--fstal --surf orig and
  found that the green line didn?t cover the surfaces well in most cases 
(see attached) . I?ve read in previous postings that Freesurfer should be fine
  with kids? brains, so
  perhaps we don't need to modify them manually?  Is there any other way to 
check for registration? Any other suggestions?

  Many thanks in advance for your help!

  Regards,
  Catherine




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[Freesurfer] Brodmann areas stats table

[_andreia_]

FreeSurfers,

Is there a way to get BA cortical thickness in a table to export from  
FS? As there is for aseg and aparc stats.

Thanks!
Andreia


-- 

Andreia Pereira, MSc student
Visual Neuroscience Laboratory
IBILI-Faculdade de Medicina
Azinhaga de Santa Comba
3000-354 Coimbra Portugal
Phone +(351) 239480220
Fax  +(351) 239480280
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Re: [Freesurfer] tksurfer & rtview

[Douglas N Greve]

The activation looks pretty reasonable. As you point out, the angles are 
a mess. How did you set the color scale for the angles? You should leave 
it as a heat scale (if you're using tksurfer-sess). How much did you smooth?

doug

Michelle Umali wrote:
> Hi Doug,
> Attached is a pic of the significance and angle maps for polar and eccen.
>
> What do you think?
>
> Thanks.
> Michelle
>
> Quoting Douglas N Greve :
>
>> what does the activation look like? Does it look right? Can you send 
>> a pic?
>> doug
>>
>> Michelle Umali wrote:
>>> Hi Doug,
>>> The z-values are consistently near or greater than 4. It just seems 
>>> that the
>>> visualization of the angles is somehow incorrect...
>>>
>>> Is there be anything else that I need to check?
>>>
>>> Thanks.
>>> Michelle
>>> ___
>>> 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
>> gr...@nmr.mgh.harvard.edu
>> Phone Number: 617-724-2358 Fax: 617-726-7422
>>
>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>>
>>
>>
>> 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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-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358 
Fax: 617-726-7422

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Re: [Freesurfer] Volumetric analysis of thalamus in freesurfer

[Douglas N Greve]

I'm not sure what you would visualize. These are just single numbers per 
subject.
doug

Knut J Bjuland wrote:
> Hi
>
> Is is possible to visualize this data on sub-cortical structure in wya
> similar to the aging tutorial?
>
> Knut J
>
> On 08/11/2011 09:03 PM, Douglas N Greve wrote:
>   
>> use --segno 10 --segno 49
>> These codes are from $FREESURFER_HOME/FreeSurferColorLUT.txt and
>> correspond to left and right thalamus. Use -m volume to get the volume
>> of thalamus (this is the default). If you're only looking at one
>> measure, then no correction for multiple comparisons is necessary. You
>> can test the effect of gender by loading this output into a stats
>> program or using mri_glmfit with the --table option.
>> doug
>>
>> Knut J Bjuland wrote:
>> 
>>> Hi Bruce
>>>
>>> I am now responding to the list as well. I have a group with different
>>> subjects where I wish to correlate thalamus volume with gender
>>> difference. Though I have extract the data using asegstats2table. I wish
>>> to be sure that the group difference is correct. Due to this reason I
>>> wish to use multiple comparsion within Freesurfer for instant FDR. I
>>> have some trouble figuring out --iv volmeasfile or how to use an label
>>> to include thalamus but exclude everything else?
>>>
>>> Knut J
>>>
>>>
>>> Knut J
>>>
>>> On 08/11/2011 08:42 PM, Bruce Fischl wrote:
>>>  
>>>   
 Hi Knut

 you should respond onlist so Doug and Nick can answer! If all you want
 is thalamic volume then why do you have multiple comparisons? You only
 have one number/subject, no?
 Bruce

 On Thu, 11 Aug 2011, Knut J Bjuland wrote:


 
> Hi Bruce
>
> I wish to use a group difference analysis using gender and correlate
> thalamus volume with IQ, and then apply multiple comparisons using FDR
> or Monte Carlo simulation. Do you have any links to a good tutorial? I
> inted to use mris_preproc and mris_glm for voulmetirc analysis, but I
> have some trouble figuring out --iv volmeasfile?
>
> Cheers
> Knut J
>
>
> Knut J
>
> On 08/11/2011 08:03 PM, Bruce Fischl wrote:
>  
>   
>> Hi Knut
>>
>> you don't need to register it since the segmentation (aseg) is
>> created
>> from the same data as the surface. What kind of analysis are you
>> thinking of doing?
>>
>> cheers
>> Bruce
>>
>>
>> On Thu, 11 Aug 2011, Knut J Bjuland wrote:
>>
>>
>> 
>>> I am working to do a volumetric analysis in Freesurfer using
>>> Thalamus. I
>>> do not know if this is the correct way to go. Should I first
>>> register
>>> thalamus to a surface using tkregister? There was also another
>>> post on
>>> this list, which suggested using tkregister2?  I am also search to
>>> find
>>> a tutorial on how to create a volmask and the use it to calculate
>>> statistic  in Freesurfer for Thalamus.
>>>
>>> Knut J
>>>
>>> ___
>>> 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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>>>   
>>>   
>
>
>   

-- 
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gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358 
Fax: 617-726-7422

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Re: [Freesurfer] Brodmann areas stats table

[Douglas N Greve]

you will have to run mris_anatomical_stats on each label to get a stats 
file. Look in recon-all for the command line. You can then run 
aparcstats2table on that.

doug

_andre...@sapo.pt wrote:
> FreeSurfers,
>
> Is there a way to get BA cortical thickness in a table to export from  
> FS? As there is for aseg and aparc stats.
>
> Thanks!
> Andreia
>
>
>   

-- 
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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358 
Fax: 617-726-7422

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Re: [Freesurfer] Longitudinal Subject/Base name errors

[Jeff Sadino]

Thank you all for your help.  Nick, I installed fs 5.1.0, and it is running
correctly now.  This brings up another question though.  We have about 200
subjects (600 scans) we are doing reconstruction on.  We are done with the
cross-sectional, and have completed 20 of the base templates, all in fs
5.0.0.  My fs 5.0 installation is running mri_robust_register 1.31.2.1 and
mri_robust_template 1.18.2.3, both dated 7/22/10.  Should I update those
binaries with the ones from fs 5.1.0, or would it be better to just do the
rest of the processing (180 templates and 600 long runs) in fs 5.1.0?

Thank You!
Jeff Sadino

On Wed, Aug 10, 2011 at 10:27 AM, Nick Schmansky
wrote:

> stable 5.1 contains the fix, which is the addition of -w to the grep on
> line 5428.  that particular fix works for the example names given
> (11 as the basename, 11_S0 and 11_S1 in the base-tps file).
>
> can someone give me the basename and base-tps contents so that i can
> replicate the problem?
>
> n.
>
> On Wed, 2011-08-10 at 14:45 -0400, Martin Reuter wrote:
> > Hi Nick,
> > can you look into this? I think we fixed this bug in 5.0 or is it
> > something different? Is it still not fixed in 5.1?
> >
> > Thanks, Martin
> >
> > On Wed, 2011-08-10 at 11:19 -0700, Irwin, William wrote:
> > > Hi-
> > >
> > > Note, this bug still exists in 5.1. Below is my exchange with Martin
> and Nick a several months ago.
> > >
> > > -Wil
> > >
> > > ---
> > > |-Original Message-
> > > |From: Nick Schmansky [mailto:ni...@nmr.mgh.harvard.edu]
> > > |Sent: Wednesday, May 25, 2011 3:52 PM
> > > |To: Irwin, William; Martin Reuter
> > > |Subject: RE: 5.1.0 Longitudial syntax question
> > > |
> > > |Martin,
> > > |
> > > |attached is his log.  it seems like it will fail if the basename
> > > |partially matches a timepoint name.
> > > |
> > > |
> > > |
> > > |Wil, there are two possible workarounds:
> > > |
> > > |1) edit line 5421 of recon-all to change:
> > > |if ( ! $status) then
> > > |
> > > |to
> > > |
> > > |if ( 0 ) then
> > > |
> > > |
> > > |so that this block is never run
> > > |
> > > |or
> > > |
> > > |2) change the name of the basename so that its not a sub-match, for
> > > |instance change to xxx_base
> > > |
> > > |
> > > |we'll have to figure out how this happened.
> > > |
> > > |n.
> > > ---
> > > |-Original Message-
> > > |From: Martin Reuter [mailto:mreu...@nmr.mgh.harvard.edu]
> > > |Sent: Wednesday, August 10, 2011 10:10 AM
> > > |To: Jeff Sadino
> > > |Cc: freesurfer@nmr.mgh.harvard.edu
> > > |Subject: Re: [Freesurfer] Longitudinal Subject/Base name errors
> > > |
> > > |Hi Jeff,
> > > |
> > > |this was a known bug in 5.0 and there are fixes on the web (release
> notes),
> > > |just download the recon all from there (and did you grab the robust
> template
> > > |binary)?.
> > > |
> > > |http://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes
> > > |
> > > |Best, Martin
> > > |
> > > |On Mon, 2011-08-08 at 17:43 -1000, Jeff Sadino wrote:
> > > |> Hello Experts,
> > > |>
> > > |>
> > > |> I am using fs 5.0.0.  My naming convention is similar to 11_S01
> > > |> and 11_S02 for subject, and then 11 for the base.  Now when
> I
> > > |> process the runs longitudinally, I get: ERROR: longitudinal base ID
> > > |> cannot be the same as a timepoint.  I believe this is because of
> line
> > > |> 4845 in recon-all: grep $longbaseid
> > > |> ${longbasedir}/${BaseSubjsListFname} >& /dev/null.  I can just as
> > > |> easily cut out this part of the code, or I could manipulate the
> > > |> base-tps file, or rename the base folder.  But I do not know if
> there
> > > |> are other spots in the code that rely on the original naming
> > > |> conventions.  Can anyone recommend one approach over the other?
> > > |>
> > > |>
> > > |> Thank you very much,
> > > |> Jeff Sadino
> > > |> ___
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> > > |> 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
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[Freesurfer] Flipping analyze images

[Catherine Wan]

 Dear List,

I have a question regarding using .img in Freesurfer.

We only have analyze images, but we can tell the orientation of the images
through the patient's lesion location. Because freesurfer sometimes flips
these image after recon-all, I'm now flipping the "problematic" ones using
mri_convert  --out_orientation RAS  before running them
again.

Could someone please explain why if we use analyze images, some of them
would be flipped by Freesurfer but not others? Does that only apply to
lesioned/patient brains and not normal brains?

Many thanks!
Catherine
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Re: [Freesurfer] tksurfer & rtview

[Douglas N Greve]

Try smoothing (eg, -fwhm 5) when running fieldsign-sess. You can also 
try using the sphere instead of the occip patch.
doug

Michelle Umali wrote:
> Hi Doug,
>
> Thanks again for your advice, the heat maps look much better. However,
> they still do not visualize the continuous range of angles or
> eccentricities but rather divide it into two intervals such as red vs.
> blue. Is there any way to adjust the color range to make it more
> appropriate for this kind of data?
>
> The heat map for the field sign data still looks speckled. I attached
> an image showing the heat maps for polar angle, eccentricity, and
> field sign, with the corresponding overlay settings.
>
> I used 5mm smoothing.
>
> Thank you very much,
> Michelle
>
>
>
> Quoting Douglas N Greve :
>
>> The activation looks pretty reasonable. As you point out, the angles
>> are a mess. How did you set the color scale for the angles? You should
>> leave it as a heat scale (if you're using tksurfer-sess). How much did
>> you smooth?
>>
>> doug
>>
>> Michelle Umali wrote:
>>> Hi Doug,
>>> Attached is a pic of the significance and angle maps for polar and 
>>> eccen.
>>>
>>> What do you think?
>>>
>>> Thanks.
>>> Michelle
>>>
>>> Quoting Douglas N Greve :
>>>
 what does the activation look like? Does it look right? Can you 
 send a pic?
 doug

 Michelle Umali wrote:
> Hi Doug,
> The z-values are consistently near or greater than 4. It just   
> seems that the
> visualization of the angles is somehow incorrect...
>
> Is there be anything else that I need to check?
>
> Thanks.
> Michelle
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>
>

 -- 
 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html



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  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
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 and
 properly
 dispose of the e-mail.
>>>
>>>
>>>
>>>  
>>>
>>>
>>>  
>>>
>>>
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>>
>> -- 
>> 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>
>
>
>
> - End forwarded message -
>
>
> 
>
> 
>
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gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358 
Fax: 617-726-7422

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Re: [Freesurfer] Flipping analyze images

[Rouhollah Abdollahi]

Dear Catherine
I think freesurfer uses the voxel space not world space (hdr file). some
other programs use hdr file too which means world space like spm.
if you want to have same world space and voxel space you have to have
re-slice your img file in spm if you use spm. then everything would be same
in every program.

Best
Rouhi

On Thu, Aug 11, 2011 at 4:34 PM, Catherine Wan  wrote:

> Dear List,
>
> I have a question regarding using .img in Freesurfer.
>
> We only have analyze images, but we can tell the orientation of the images
> through the patient's lesion location. Because freesurfer sometimes flips
> these image after recon-all, I'm now flipping the "problematic" ones using
> mri_convert  --out_orientation RAS  before running them
> again.
>
> Could someone please explain why if we use analyze images, some of them
> would be flipped by Freesurfer but not others? Does that only apply to
> lesioned/patient brains and not normal brains?
>
> Many thanks!
> Catherine
>
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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
> 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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With Best Regards
   Rouhollah Abdollahi
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Re: [Freesurfer] Label2label on fsaverage

[Rouhollah Abdollahi]

Dear Bruce
I think I found the problem. The problem came from the original oriantation
of T1 image and I think mris_register could not find it itself during the
recon-all. I added to have initial alignment to inflated and the problem
solved.( mris_register -curve -inflated  ?h.sphere  
?h.sphere.reg ) I think it is very important to add it to recon-all because
if the user doesn't know the real oriantation it might make such a problem.

Thanks for your quick response.

On Thu, Aug 11, 2011 at 10:45 AM, Rouhollah Abdollahi wrote:

> Dear Bruce
>
> I am working on Freesurfer 2 caret meshes. I am using
>   FreeSurfer2CaretConvertAndRegisterClean.sh from Van Essen lab to create
> caret surfaces. when I look at my subjects' surfaces I can see in flat map
> in caret some of subjects sulci patterns are really distorted and I think it
> is related to sphere registration to fsaverage sphere.
> Beacsue the code is using sphere.reg to create all surfaces. for the
> subjects which I have less distortion on sulci pattern I have good data  (3
> subjects) but for the (9 subjects) rest it seems they have problem to
> register to fsaverage. Is there any way that I can be sure that
> sphere.reg properly created?
>
> Thank you very much
>
> Rouhi
>
>
>
> On Thu, Aug 11, 2011 at 4:37 AM, Bruce Fischl 
> wrote:
>
>> Try using fsaverage as the trgsubject
>> Cheers
>> Bruce
>>
>>
>>
>> On Aug 10, 2011, at 8:35 PM, Rouhollah Abdollahi 
>> wrote:
>>
>> > .V1_reg.label --regmethod surface --srcsurfreg sphere --trgsurfreg
>> sphere.reg --hemi rh and when I tried to load the output label file on
>> fsaverage surface like inflated one it shows a lot of point looks like it is
>> not deformed properly. Is it related to registration to fsaverage or
>> something esle? The question is how I can register the subjects surfaces to
>> fsaverage surfaces? -- With Best Regards Rouhi
>> --0015175120c69a3c6804aa2ffb81 Content-Type: text/html; charset=ISO-8859-1
>> Content-Transfer-Encoding: quoted-printable Dear freesurfer experts
>> >
>> > I've tried to export my label file from individual space to fsaverage
>> space by using this command:
>> >
>> > mri_label2label --srclabel rh.V1.label --srcsubject SUB1  --trgsubject
>> SUB1 --trglabel rh.V1_reg.
>> > like it is not deformed properly.
>> > Is it related to registration to fsaverage or something esle?
>> > The question is how I can register the subjects surfaces to fsaverage
>>
>>
>> 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.
>>
>>
>
>
> --
> With Best Regards
>Rouhollah Abdollahi
>
>
>
>


-- 
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   Rouhollah Abdollahi
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Re: [Freesurfer] Label2label on fsaverage

[Rouhollah Abdollahi]

Dear Bruce,

I have two questions.
I saw there are a lot of algorithms for mris_register. Which one are more
precise and has less distortion on sulci pattern?
In initial alignment if I want to rotate the surface with -rotate [ alpha is
(ear to ear) beta(Back to nose) ... ]. Am I right?. and if I want that
mris_register does not apply any rigid alignment after initial rotation what
I have to do?

Thanks
Rouhi


On Thu, Aug 11, 2011 at 9:25 PM, Bruce Fischl wrote:

> What format is the attachment in?
>
>
>
> On Aug 11, 2011, at 8:32 PM, Rouhollah Abdollahi 
> wrote:
>
> Dear Bruce
> I checked the parcellation and look quiet OK. I attached two subjects ,
> whcih subj_1 shows bad registration to fsaverage  and subj_2 shows the good
> registration.  I attached a file which compare two subjects according to
> sphere and sphere.reg. For the subj_1 , it has more figures to see how the
> parcellation is.
> Thanks in advance
>
> Best
> Rouhi
>
> On Thu, Aug 11, 2011 at 10:48 AM, Bruce Fischl <
> fis...@nmr.mgh.harvard.edu> wrote:
>
>> Hi Rouhi
>>
>> check the parcellations. If they are correct then the sphere.reg must be
>> pretty accurate.
>>
>> cheers
>> Bruce
>>
>> On Thu, 11 Aug 2011, Rouhollah Abdollahi wrote:
>>
>>  Dear Bruce
>>>
>>> I am working on Freesurfer 2 caret meshes. I am using   **
>>> FreeSurfer2CaretConvertAndRegi**sterClean.sh from Van Essen lab to
>>> create caret surfaces. when I look at my subjects'
>>> surfaces I can see in flat map in caret some of subjects sulci patterns
>>> are really distorted and I think it is related to sphere registration to
>>> fsaverage sphere. Beacsue
>>> the code is using sphere.reg to create all surfaces. for the subjects
>>> which I have less distortion on sulci pattern I have good data  (3 subjects)
>>> but for the (9 subjects)
>>> rest it seems they have problem to register to fsaverage. Is there any
>>> way that I can be sure that sphere.reg properly created?
>>>
>>> Thank you very much
>>>
>>> Rouhi
>>>
>>>
>>>
>>> On Thu, Aug 11, 2011 at 4:37 AM, Bruce Fischl <
>>> fis...@nmr.mgh.harvard.edu> wrote:
>>>  Try using fsaverage as the trgsubject
>>>  Cheers
>>>  Bruce
>>>
>>>
>>>
>>>  On Aug 10, 2011, at 8:35 PM, Rouhollah Abdollahi <
>>> roohy...@gmail.com> wrote:
>>>
>>>  > .V1_reg.label --regmethod surface --srcsurfreg sphere --trgsurfreg
>>> sphere.reg --hemi rh and when I tried to load the output label file on
>>> fsaverage surface
>>>  like inflated one it shows a lot of point looks like it is not
>>> deformed properly. Is it related to registration to fsaverage or something
>>> esle? The question is
>>>  how I can register the subjects surfaces to fsaverage surfaces? --
>>> With Best Regards Rouhi --0015175120c69a3c6804aa2ffb81 Content-Type:
>>> text/html;
>>>  charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear
>>> freesurfer experts
>>>  >
>>>  > I've tried to export my label file from individual space to
>>> fsaverage space by using this command:
>>>  >
>>>  > mri_label2label --srclabel rh.V1.label --srcsubject SUB1
>>>  --trgsubject SUB1 --trglabel rh.V1_reg.
>>> > like it is not deformed properly.
>>> > Is it related to registration to fsaverage or something esle?
>>> > The question is how I can register the subjects surfaces to fsaverage
>>>
>>>
>>> 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.
>>>
>>>
>>>
>>>
>>> --
>>> With Best Regards
>>>Rouhollah Abdollahi
>>>
>>>
>>>
>>>
>>>
>
>
> --
> With Best Regards
>Rouhollah Abdollahi
>
>
>
> 
>
>


-- 
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   Rouhollah Abdollahi
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[Freesurfer] Tracula and number of fibres per voxel

[Jürgen Hänggi]

Dear Tracula experts

Is it possible to change the number of fibres per voxel in bedpostx (from 2
to 3) within the trac-all command?

I did not see any option for that.

Thanks in advance
Cheers
Jürgen


Jürgen Hänggi, Ph.D.
Division Neuropsychology
Institute of Psychology
University of Zurich
Binzmuehlestrasse 14, PO Box 25
8050 Zurich, Switzerland
0041 44 635 73 97 (phone office)
0041 76 445 86 84 (phone mobile)
0041 44 635 74 09 (fax office)
BIN 4.D.04 (office room number)
j.haenggi[at]psychologie.uzh.ch (email)
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http://www.juergenhaenggi.ch (private website)

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